CHPC Bibliography (as of 4/28/2015)

2015

Abbasi, R. U., et al. (2015). A Northern Sky Survey for Point-Like Sources of EeV Neutral Particles with the Telescope Array Experiment. submitted.

Abbasi, R. U., et al. (2015). Study of Ultra-High Energy Cosmic Ray composition using Telescope Array’s

Middle Drum detector and surface array in hybrid mode. Astroparticle Physics, 64, 49 - 62. Almishaal, A., Jennings, S.G. (2015). Effects of Carrier Intensity on Amplitude Modulation Detection using

High and Low-fluctuating Noises,. Paper presented at the Thirty-eighth Annual Midwinter Meeting of the Association for Research in Otolaryngology, Baltimore, MD.

Armentrout, P. B., Mookerherjee, A. (2015). Peptide Fragmentation: Energetics, Structures, and Mechanisms (pp. poster): 2015 Lake Arrowhead Ion Chemistry Conference, Lake Arrowhead, CA.

Beckvermit, J., Harman, T., Bezdijian, A., Wight, C. (2015). Modeling Deflagration in Energetic Materials using the Uintah Computational Framework. Paper presented at the International Conference on Computational Science, accepted.

Beckvermit, J., et al. (2015). Parallel Petascale Modeling of Transportation Accidents Involving High Explosives (pp. poster). SIAM Conference on Computational Science and Engineering, Salt Lake

City, March 2015.

Boles, G., Armentrout, P.B. (2015). Thermodynamics and Mechanisms of Protonated Asparaginyl-Glycine Decomposition (pp. poster): 2015 Lake Arrowhead Ion Chemistry Conference, Lake Arrowhead,

CA. Bonthuis, P., Huang, W., Horndli, CS., Ferris E., Cheng, T. and Gregg, C. (2015). Highly Tissue and Cell

specific genomic imprinting effects influence phenotypes in offspring. Cell, under revision. Brown, S., Thorne, M.S., Miyagi, L., Rost, S. (2015). A composition origin to ultralow-velocity zones.

Geophys. Res. Lett, 42. doi: 10.1002/2014GL062097

Cai, H., Zhdanov, M.S. (2015). Modeling and inversion of magnetic anomalies caused by sediment-basement interface using 3D Cauchy-type integrals. IEEE Geoscience and Remote Sensing Letters, 12(3), 477 - 481.

Cheatham III, T. E., Roe, D.R. (2015). The impact of heterogeneous computing on workflows for

biomolecular simulation and analysis. Computing in Science and Engineering, in press. Chen, J., Jennings, S.G. (2015). Improved Decrement Detection with Decrement Location may Result

from Efferent Processing. Paper presented at the Thirty-eighth Annual Midwinter Meeting of the

Association for Research in Otolaryngology, Baltimore, MD. Cherukuru, N., Calhoun, R., Lehner, M., Hoch, S.W., Whiteman, C.D. (2015). Instrument configuration for

dual Doppler lidar co-planar scans: METCRAX II. J. Appl. Remote Sensing, accepted.

Coates, R., McNary, C.P., Armentrout, P.B. (2015). IRMPD Spectroscopy Investigations of Multiply Charged Zn and Cd Cation Complexes with Amino Acids (pp. poster): 2015 Lake Arrowhead Ion

Chemistry Conference, Lake Arrowhead, CA. Edalatpour, S., Cuma, M., Trueax, T., Backman, R., Francoeur, M. (2015). Computational near-field

radiative heat transfer: Convergence analysis of the thermal discrete dipole approximation using the exact solution for two spheres. Paper presented at the ICHMT International Symposium on

Advances in Computational Heat Transfer, Rutgers University, Piscataway, NJ.

Edalatpour, S., Cuma, M., Trueax, T., Backman, R., Francoeur, M. (2015). Convergence analysis of the thermal discrete dipole approximation. Physical Review E, submitted.

Fatehi, S., Steele, R.P. (2015). Multiple-Timestep ab initio molecular dynamics based on two-electron integral screening J Chem Theor Comput, 11, 884 - 898.

Fernando, H. J. S., et al. (2015). The MATERHORN – Unraveling the intricacies of mountain weather. Bull. Amer. Meteor. Soc., submitted.

Fleming, A. M., Alshykhly, O., Orendt, A.M., Burrows, C.J. (2015). Computational studies of electronic

circular dichroism spectra predict absolute configuration assignments for the guanine oxidation

product 5-carboxamido-5-formamido-2-iminohydantoin. Tetrahedron Lett., submitted.

Galindo-Murillo, R., Roe, DR, Cheatham III, T.E. (2015). Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC). Biochem. Biophys. Acta., 1850(5), 1041-1058. doi: 10.1016/j.bbagen.2014.09.007

Good, S. P., Noone, D., Bowen, G.J. (2015). Ecohydrologic routing of continental precipitation. Science, in revision.

Good, S. P., Noone, D., Kurita, N., Benetti, M., Bowen, G.J. (2015). Isotope Ratios In the Global Hydrologic Cycle. Geophysical Research Letters.

Gorski, G., et al. (2015). Vapor hydrogen and oxygen isotopes reflect water of combustion in the urban atmosphere. Proceedings of the National Academy of Sciences, 112(11).

Hamian, S., Gaffreau, A., Walsh, T., Lee, J., Park, K. (2015). AC Electrothermal Characterization of Doped-Si Heated Microcantilevers Using Frequency-Domain Finite Element Analysis. Journal of Heat Transfer, under review.

Hamian, S., Yamada, T., Faghri, M., Park, K. (2015). Finite Element Analysis of Transient Ballistic-Diffusive Phonon Heat Transport in Two-Dimensional Domains. International Journal of Heat and Mass Transfer, 80, 781 - 788.

Hang, C., Pardyjak, E.R., Nadeay, D.F., Hensen, D., Hoch, S.W. (2015). Playa Soil Moisture and

Evaporation Dynamics During the MATERHORN Field Program. Boundary-Layer Meteorology, submitted.

Hennessy, J. (2015). Asymmetric synthesis: Catalysis exposed. Nat. Chem, 7, 270.

Jennings, S. G., Ahlstrom, J.B., Dubno, J.R. (2015). Effects of Age, Hearing Impairment and Efferent Feedback on Overshoot. J Acous Soc Am., submitted.

Jennings, S. G., Hirschmugal, K.J. (2015). The Effects of Masker Fluctuation on Overshoot Measured with Narrowband-Noise Maskers. Paper presented at the Thirty-eighth Annual Midwinter Meeting of

the Association for Research in Otolaryngology, Baltimore, MD.

Jensen, D., Nadeau, D.F., Hoch, S.W., Pardyjak, E.R. (2015). Flux-gradient relationships over contrasting surfaces during the evening transition. Boundary-Layer Meteorology, submitted.

Johnson, D. P., et al. (2015). HDAC1,2 inhibition impairs EZH2- and BBAP-mediated DNA repair to overcome chemoresistance in EZH2 gain-of-function mutant diffuse large B-cell lymphoma.

Oncotarget, 6(7), 4863 - 4887.

Johnson, W. P. (2015). Mechanistic Quantitative Prediction of Nano- and Micro-Particle Retention in Porous Media: Contaminant Removal during Hyporheic Exchange, Riverbank Filtration, and Other Contexts. Paper presented at the 1st International Conference on All Materials Fluxes in River-Ecosystem (AMFR2015), Peking University, Beijing, China.

Kim, J., Reicher, T. (2015). Quantifying the uncertainty of the annular mode time scale and the role of

the stratosphere. Clim. Dyn, under review. Kochanski, A. K., Pardyjak, E., Stoll, R., Gowardhan, A., Brown, M.J., Steenburgh, W.J. (2015). One-way

coupling of the WRF-QUIC Urban Dispersion Modeling System. J. Appl. Meteor. Clim., submitted. Lehner, M., Whiteman, C.D., Hoch, S.W., Jensen, D., Pardyjak, E.R., Leo, L.S., DiSabatino, S., Gernando,

H.J.S. (2015). A case study of the nocturnal boundary-layer evolution on a slope at the foot of a desert mountain. J. Appl. Meteor. Clim., accepted.

Lehner, M., et al. (2015). The METCRAX II field experiment—A study of downslope windstorm-type flows

in Arizona's Meteor Crater. Bull. Amer. Meteor. Soc., submitted. Liu, J., Lin, C., Miller, J.D. (2015). Significance of Particle Aggregation in Reverse Flotation of Kaolinite

from Bauxite Ore. Minerals Engineering, submitted. Liu, J., Lin, C., Miller, J.D. (2015). Simulation of Cluster Formation from Kaolinite Suspension.

International Journal of Mineral Processing,, submitted.

Lund, A., Pagola, G., Orendt, A., Ferraro, M., Facelli, J. (2015). Crystal structure prediction from first principles: The crystal structures of glycine. Chemical Physics Letters, 626, 20 - 24.

Lund, M., Jevremovic, T. (2015). GEANT4 Based Assessment of the Cosmic Radiation Transport in Space: Examples of International Space Station and Apollo Missions. Paper presented at the Nuclear and

Emerging Technologies for Space (NETS) 2015, Albuquerque, New Mexico. Malkin, T. L., Murray, B.J., Salzmann, C.G., Molinero, V., Pickering, S.J., Whale, T.F. (2015). Stacking

Disorder in Ice I. Phys. Chem. Chem. Phys, 17(invited).

McCammant, M. S., Sigman, M.S. (2015). Development and investigation of a site selective palladium-catalyzed 1,4-difunctionalization of isoprene using pyridine–oxazoline ligands. Chem. Sci., 1355 - 1361.

McMillen, J. D., Steenburgh, W.J. (2015). Capabilities and limitations of convection-permitting WRF

simulations of lake-effect systems over the Great Salt Lake. Wea. Forecasting, submitted.

McMillen, J. D., Steenburgh, W.J. (2015). Impact of microphysics parameterizations on simulations of the 27 October 2010 Great Salt Lake effect snowstorm. Wea. Forecasting, 30, 136 - 152.

McNary, C. P., Nei, Y.W., Maitre, P., Rodgers, M.T., Armentrout, P.B. (2015). Infrared Multiple Photon Dissociation Spectroscopy of Protonated Amino Acids (Gly, Lys, His, and Arg) with 18-Crown-6

Ether: Effects of Binding Sites on Gas-Phase Conformation (pp. poster): 2015 Lake Arrowhead Ion Chemistry Conference, Lake Arrowhead, CA.

Milo, A., Neel, A.J., Toste, F.D., Sigman, M.S. (2015). A data-intensive approach to mechanistic

elucidation applied to chiral anion catalysis. Science, 347(6223), 737 - 743. Nguyen, A. H., Molinero, V. (2015). Identification of clathrate hydrates, hexagonal ice, cubic ice, and

liquid water in simulations: the CHILL+ algorithm. J. Phys. Chem. B, 119(8), 4104-4117. doi: 10.1021/jp510289t

Nguyen, A. H., Koc, H., Shepherd, T.D., Molinero, V. (2015). Structure of the Ice-Clathrate Interface. J. Phys. Chem. C, 119, 4101 - 4117.

Nguyen, B. T., Furse, C., Simpson, J.J. (2015). A 3-D stochastic FDTD model of electromagnetic wave

propagation in magnetized ionosphere plasma. IEEE Transactions on Antennas and Propagation, 63(1), 304 - 313.

Nguyen, B. T., Samimi, A., Simpson, J.J. (2015). A polynomial chaos approach for modeling uncertainty propagation in 3D-FDTD magnetized cold plasma. Paper presented at the IEEE International

Symposium on Electromagnetic Compatibility and Signal Integrity, Santa Clara, CA.

Nguyen, B. T., Samimi, A., Simpson, J.J. (2015). Recent advances in FDTD modeling of electromagnetic wave propagation in the ionosphere. Applied Computational Electromagnetics Society Journal, 29(12), 1003 - 1012.

Price, M., Ovcharenko, A., Thangaraj, R., Raeymaekers, B. (2015). Deformation of ultra-thin diamond-like

carbon coatings under combined loading on a magnetic recording head. Tribology Letters, 57(3).

Rutz, J. J., Steenburgh, W.J., Ralph, F.M. (2015). The inland penetration of atmospheric rivers over western North America: A Lagrangian analysis. Mon. Wea. Rev.

Sapkota, N., Yoon, S., Rose, J., Jeong, E.K. (2015). Estimation of Intra-Axonal Fraction in Spinal Cord White Matter by using Monte Carlo Simulation of Water Diffusion and High b-value Diffusion Sensitized MRI. Paper presented at the 23rd annual ISMRM,, Toronto, Canada.

Sapkota, N., et al. (2015). Estimation of Intra-Axonal Fraction in Spinal Cord White Matter by using Monte Carlo Simulation of Water Diffusion and High b-value Diffusion-Sensitized MRI,. in preparation.

Shen, P. S., Park, J., Qin, Y., Li, X., Parsawar, K., Larson, M.H., Cox, J., Cheng, Y., Lambowitx, A.M., Weissman, J.S., Brandman, O., Frost, A. (2015). Rqc2p and 60S ribosomal subunits mediate

mRNA-independent elongation of nascent chains. Science, 347(6217), 75 - 78. Shu, Y., Bolton, A.S., et al. (2015). The Sloan Lens ACS Survey. XII. Extending Strong Lensing to Lower

Masses. The Astrophysical Journal, 8013, 71 - 88.

Simpson, J. J. (2015). A summary of the major global 3-D FDTD modeling capabilities to-date. Paper presented at the International Conference on Computational Electromagnetics, Hong Kong,

China. Veals, P. G., Steenburgh, W.J. (2015). Climatological characteristics and orographic enhancement of

lake-effect precipitation east of Lake Ontario and over the Tug Hill Plateau. Mon. Wea. Rev., submitted.

Velupillai, S., et al. (2015). BluLab: Temporal Information Extraction for the 2015 Clinical TempEval Challenge. Paper presented at the 9th International Workshop on Semantic Evaluations., Denver, CO.

Velupillai, S., et al. (2015). Toward a Generalizable Time Expression Model for Temporal Reasoning in Clinical Notes. Paper presented at the AMIA Annu Symp 2015, San Francisco, CA.

Wang, Y., Creegan, E., Gelton, M., Huynh, G., Hocut, C., Fernando, H.J.S., Hoch, S.W., Whiteman, C.D.

(2015). Triple Doppler wind lidar observations during the MATERHORN field project. J. Appl. Meteor. Clim., submitted.

Yoon, D., Zhdanov, M.S. (2015). Optimal synthetic aperture method for marine controlled source EM surveys. IEEE Geoscience and Remote Sensing Letters, 12, 414 - 418.

Young, J. S., Whiteman, C.D. (2015). Laser ceilometer investigation of persistent wintertime cold-air

pools in Utah's Salt Lake Valley. accepted. Zhu, Y., Free, M.L. (2015). Electrochemical characterization, modeling, and prediction of corrosion

inhibition of ternary mixtures of homologous surfactants, Presentation, TEG-094x forum “State-of-the-Art Research on Corrosion Inhibitors, including molecular modeling of activity and related inhibitor design and relative performance testing among classes of inhibitors―. Paper presented at the NACE Corrosion Conference, Dallas, TX.

Zhu, Y., Free, M.L., Yi, G. (2015). Electrochemical measurement, modeling, and prediction of corrosion

inhibition of ternary mixtures of homologous surfactants in electrolyte solution. Corrosion Science, accepted.

Zhu, Y. (2015). Modeling of partitioning and corrosion inhibition of mixed inhibitors in steel-water-oil system (pp. poster). NACE Corrosion Conference 2015, Dallas, TX.

Zhu, Y., Free, M.L. (2015). Modeling of Partitioning in Aqueous-Oil System and Corrosion Inhibition on Steel of Mixed Inhibitors, C2015-6343, Research in Progress (RIP) Symposium Session. Paper presented at the NACE Corrosion Conference, Dallas, TX.

2014

Aab, A., et al. (2014). Searches for Large-Scale Anisotropy in the Arrival Directions of Cosmic Rays

Detected above Energy of 10^19 eV at the Pierre Auger Observatory and the Telescope Array.

Astrophysics Journal, 794. doi: 10.1088/0004-637X/794/2/172 Armentrout, P. B., Austin, C.A., Rodgers, M. T. (2014). Alkali Metal Cation Interactions with 15-Crown-5

in the Gas Phase: Revisited. J. Phys. Chem. A., 118, 8088 - 8097. Armentrout, P. B. (2014). Energetic probes of structure and mechanisms by guided ion beam mass

spectrometry. Paper presented at the 247th National American Chemical Society Meeting, Field

and Franklin Award for Outstanding Contributions to Mass Spectrometry Honoring Evan R. Williams, Dallas, TX.

Armentrout, P. B. (2014). Energetics from Collision-Induced Dissociation. Paper presented at the 26th Sanibel Conference on Mass Spectrometry, Ion Activation: Fundamentals, Applications, and New

Frontiers, Clearwater Beach, FL.

Armentrout, P. B. (2014). Finding D0(Sm+-O): A Guided Ion Beam Study of Sm+ Reactivity. Paper presented at the Informal Meeting on Mass Spectrometry, Balantonszarszo, Hungary.

Armentrout, P. B. (2014). Guided ion beam tandem mass spectrometry and ion funnels. Paper presented at the American Chemical Society Meeting, San Francisco, CA.

Armentrout, P. B. (2014). Mass Spectrometric Methods for the Determination of Thermodynamic Data. In A. Yergey (Ed.), The Encyclopedia of Mass Spectrometry. Volume 9: The History of Mass Spectrometry: Elsevier.

Armentrout, P. B., Yang, B., Rodgers, M.T. (2014). Metal Cation Dependence of Interactions with Amino Acids: Bond Dissociation Energies of Rb+ and Cs+ to the Acidic Amino Acids and Their Amide

Derivatives. J. Phys. Chem. B, 118(16), 4300 - 4314. Armentrout, P. B. (2014). Peptide Fragmentation: Energetics, Structures, and Mechanisms. Paper

presented at the SCIX2014 Meeting, Reno, NV.

Armentrout, P. B. (2014). Peptide Fragmentation: Energetics, Structures, and Mechanisms (pp. poster): 62nd ASMS Conference on Mass Spectrometry and Allied Topics, Baltimore, MD.

Armentrout, P. B., McNary, C.P., Wheeler, O. (2014). Reactions of iron and iron oxide clusters with carbon monoxide using guided ion beam tandem mass spectrometry (pp. poster): 247th National

American Chemical Society Meeting, Dallas, TX. Armentrout, P. B. (2014). Spectroscopic and Thermochemical Studies of Hydrated Copper Hydroxide

Cations. Paper presented at the SCIX2014 Meeting, Reno, NV.

Armentrout, P. B. (2014). Thermochemistry of Reactions of Lanthanide and Actinide Cations. Paper presented at the American Chemical Society Meeting, San Francisco, CA.

Armentrout, P. B., Cox, R.M. (2014). Thermochemistry of reactions of thorium cations with methane and other small molecules (pp. poster): Isolated Biomolecules and Biomolecular Interactions,

Porquerolles Island, France.

Armentrout, P. B. S., E. M. S. (2014). Thermodynamics and Mechanism of Protonated Cysteine Decomposition: A Guided Ion Beam and Computational Study. J. Am. Soc. Mass Spectrom, submitted.

Bailey, B., Stoll, R., Pardyjak, E., Mahaffee, W. (2014). Effect of vegetative canopy architecture on

vertical transport of massless particles. Atmospheric Environment, 95, 480-489. Ball, J. S., Sheehan, A.F., Stachnik, J.C., Lin, F.C., Collins, J.A. (2014). A Joint Monte Carlo Analysis of

Seafloor Compliance, Rayleigh Wave Dispersion and Receiver Functions at Ocean Bottom Seismic

Stations offshore New Zealand. Geochem., Geophys., Geosys., 15(5051 - 5068). doi: 10.1002/2014GC005412

Beckvermit, J., Harman, T., Bezdijian, A., Wight, C. (2014). Computational Modeling of DDT in Large Arrays of Energetic Materials. Paper presented at the Gordon Research Seminar on Energetic

Materials.

Beckvermit, J. (2014). Macro-Scale Modeling of Deflagration to Detonation Transitions in Large Arrays of Explosives, Visualization Showcase. Paper presented at the XSEDE’14 Conference on

High-Performance Computing. Beckvermit, J., et al. (2014). Modeling Accidental Explosions and Detonations. Paper presented at the

SIAM Annual Meeting, Chicago, IL. Beckvermit, J., Harman, T., Wight, C. (2014). Modeling Accidental Explosions and Detonations in Large

Arrays of Explosives (pp. poster). Gordon Research Conference on Energetic Materials, June

2014. Beckvermit, J., et al. (2014). Parallel Multiscale Modeling of Transportation Accidents Involving

Explosives. Paper presented at the XSEDE’14 Conference on High-Performance Computing. Bedrov, D. (2014). Molecular dynamics simulations of carbonates based electrolytes at charged surfaces.

Paper presented at the 248th National American Chemical Society Meeting, San Francisco, CA.

Bedrov, D. (2014). Molecular modeling of interfaces in energy storage devices. Paper presented at the 18th Annual Photonics Center Symposium on Advanced Materials by Design, Boston, MA.

Bess, E. N., DeLuca, R.J., Tindall, D.J., Oderinde, M.S., Roizen, J.L., DuBois, J., Sigman, M.S. (2014). Analyzing Site Selectivity in Rh2(esp)2-Catalyzed Intermolecular C–H Amination Reactions. J. Am. Chem. Soc., 136, 5783 - 5789.

Bess, E. N., Bischoff, A.J., Sigman, M.S. (2014). Designer substrate library for quantitative, predictive modeling of reaction performance. Proc. Natl Acad Sci, 111, 14698 - 14703.

Borodin, O., Bedrov, D. (2014). Interfacial Structure and Dynamics of the Lithium Alkyl Dicarbonate SEI Components in Contact with the Lithium Battery Electrolyte. J. Phys. Chem. C, 118(32),

18362-18371. Bradford, W., Hurdle, J.F., LaSalle, B., Facelli, J.C. (2014). Development of a HIPAA-compliant

environment for translational research data and analytics. J Am Med Informatics, 21, 185 - 189.

Cai, H., Ziong, B., Han, M., Zhdanov, M.S. (2014). 3D controlled-source electromagnetic modeling in anisotropic medium using edge-based finite element method. Computers & Geosciences, 73, 164

- 176. Campbell, L. S., WJ. (2014). Fine-scale orographic precipitation variability and gap-filling radar potential

in Little Cottonwood Canyon, Utah. Wea. Forecasting, 29, 912 - 935.

Chappanda, K., Smith, Y.R., Rieth, L.W., Tathireddy, P., Misra, M., Mohanty, S.K. (2014). Effect of sputtering parameters on the morphology of TiO2 nanotubes synthesized from thin Ti film on Si

substrate. IEEE Transactions on Nanotechonolgy, September 15. Chappanda, K., Smith, Y.R., Rieth, L.W., Tathireddy, P., Misra, M., Mohanty, S.K. (2014). TiO2-WO3

Composite Nanotubes from Co-Sputtered Thin Films on Si Substrate for Enhanced Photoelectrochemical Water Splitting. J of Electrochemical Society, 161(9), H431 - H437.

Chen, X., Liu, Y., Gu, B.L., Duan, W., Liu, F. (2014). Giant room-temperature spin caloritronics in

spin-semiconducting graphene nanoribbons. Phys. Rev. B, 90. Cherukuru, N. W., Calhoun, R., Lehner, M., Hoch, S.W., Whiteman, C.D., Brown, W.O.J. (2014).

Instrument configuration for dual-Doppler LiDAR co-planar scans: METCRAX II. Paper presented at the 16th Conf. Mountain Meteor., San Diego, CA.

Cox, R., Armentrout, P.B. (2014). A Guided Ion Beam and Theoretical Study of the Activation of CH4 by

Th+ (pp. poster): 247th National American Chemical Society Meeting. Cuma, M., Zhdanov, M.S. (2014). Massively parallel regularized 3D inversion of potential fields on CPUs

and GPUs. Computers & Geosciences, 62, 80-87. Depci, T., Onal, Y., Prisbrey, K.A. (2014). “Apricot Stone Activated Carbon Adsorption of Cyanide as

Revealed from Computational Chemistry Analysis and Experimental Study. Journal of the Taiwan Institute of Chemical Engineers,, 45(5). doi:

10.1016/j.jtice.2014.05.015

DeTar, C., Lee, S.H. (2014). Variational method with staggered fermions. Phys Rev. D, submitted. Earl, C., Sutherland, J.C., Might, M. (2014). Nebo: A DSL for Numerical Solution of PDEs on Current and

Emerging Architectures. Paper presented at the SIAM Parallel Processing Conference, Portland, OR. http://www.siam.org/meetings/pp14/index.php

Edalatpour, S., Francoeur, M. (2014). The Thermal Discrete Dipole Approximation (T-DDA) with Surface interaction: Formulation and Preliminary Results. Paper presented at the NanoRad 2014, Shanghai, China.

Edalatpour, S., Francoeur, M. (2014). The thermal discrete dipole approximation for near-field radiative heat transfer modeling between arbitrarily-shaped objects and a surface. Paper presented at the

Thirteenth International Conference on Near-Field Optics, Nanophotonics, and Related Techniques, Salt Lake City, UT.

Edalatpour, S., Francoeur, M. (2014). The Thermal Discrete Dipole Approximation with surface interaction. Paper presented at the 2nd International Workshop on Nano-Micro Thermal Radiation: Energy, Manufacturing, Materials, and Sensing (NanoRad2014), Shanghai, China.

Eiring, A. M., et al. (2014). Combined STAT3 and BCR-ABL1 inhibition induces synthetic lethality in therapy-resistant chronic myeloid leukemia. Leukemia, 29(3), 587 - 597. doi:

10.1038/leu.2014.245

Factorovich, M., Molinero, V., Scherlis, D.A. (2014). A simple grand canonical approach to compute the vapor pressure of bulk and finite size systems. J. Chem. Phys, 140.

Factorovich, M., Gonzalez Solveyra, E., Molinero, V., Scherlis, D.A. (2014). Sorption isotherms of water in nanopores: on the relation between hydropohobicity, adsorption pressure, and hysteresis. J. Phys. Chem. C, 118, 16290–16300.

Factorovich, M., Molinero, V., Scherlis, D.A. (2014). Vapor pressure of water nanodroplets. J. Am. Chem. Soc., 136, 4508 - 4514.

Farber, S., Neutens, T., Carrasco, J.A., C. Rojas. (2014). Social interaction potential and the spatial distribution of face-to-face social interactions. Environment and Planning B, 41(6), 960 - 976.

Fernando, H. J. S., et al. (2014). Mixing induced by slope and valley flow collisions in complex terrain. Paper presented at the AGU Fall Meeting 2014, San Francisco, CA.

Galindo-Murillo, R., Cheatham III, T.E. (2014). DNA-binding dynamics and energetics of Co, Ni, and Cu

metallopeptides. Chem. Med. Chem., 9, 1252 - 1259. Galindo-Murillo, R., Bergonzo, C., Cheatham III, T.E. (2014). Molecular modeling of nucleic acid

structure: Setup and analysis. Current Protocols Nucleic Acid Chemistry, 56, 7.10.11 - 17.10.21. Galindo-Murillo, R., Roe, D.R., Cheatham III, T.E. (2014). On the absence of intrahelical DNA dynamics

on the μs to ms timescale. Nature Commun, 5, 5152. doi: 10.1038/ncomms6152

Ghodrati, E., Sarmadi, H., Brannon, R. (2014). A continuum representation for soil disaggregation with subsequent recompression to model blast effects. Paper presented at the 17th U.S. National

Congress on Theoretical and Applied Mechanics, Michigan State University, East Lansing, MI. Good, S. P., et al. (2014). High frequency trends in the isotopic composition of Superstorm Sandy. In J.

B. Bennington, Farmer, E.C (Ed.), Learning from the Impacts of Superstorm Sandy (pp. 41 - 55): Academic Press.

Good, S. P., Mallia, D.V., Lin, J.C., Bowen, G.J. (2014). Stable Isotope Analysis of Precipitation Samples

Obtained via Crowdsourcing Reveals the Spatioitemporal Evolution of Superstorm Sandy. PLoS ONE, 9(3), e91117. doi: 10.1371/journal.pone.0091117

Goshayeshi, B., Sutherland, J.C. (2014). A comparison of various models in predicting ignition delay in single-particle coal combustion. Combustion and Flame, 161, 1900 - 1910. doi:

10.1016/j.combustflame.2014.01.010

Greene, T. (2014). Surrogate endpoints for CKD progression. Paper presented at the NKF Discussion of Design of Clinical Trials in Nephrology, San Francisco, CA.

Guo, H., Zheng, Z., et al. (2014). The clustering of galaxies in the SDSS-III Baryon Oscillation Spectroscopic Survey: modeling of the luminosity and colour dependence in the Data Release 10.

Monthly Notices of the Royal Astronomical Society, 441, 2398. Hall, S. J., Maurer, G., Hoch, s.W., Taylor, R., Bowling, D.R. (2014). mpacts of anthropogenic emissions

and cold air pools on urban to montane gradients of snowpack ion concentrations in the Wasatch

Mountains, Utah. Atmos. Environ., 98, 231 - 241. Hasan, M., Samimi, A., Sensale-Rodriguez, B., Simpson, J.J. (2014). Photonic nanojets: Subwavelength

detection, phototiodes, and nanoapertures. Paper presented at the International Conference on Metamaterials, Photonic Crystals, and Plasmonics (META), Singapore.

Hasan, M., Simpson, J.J. (2014, January ). Super-enhanced optical energy concentration through a subwavelength aperture using a photonic nanojet. Paper presented at the URSI National Radio Science Meeting.

Hasan, M., Simpson, J.J. (2014). Three-dimensional subwavelength confinement of a photonic nanojet using a plasmonic nanoantenna gap. Microwave and Optical Technology Letters, 56(11), 2700 -

2706. He, S., Narus, S.P., Facelli, J.C., Lau, L.M., Botkin, J.R., Hurdle, J.F. (2014). A domain analysis model for

eIRB systems: Addressing the weak link in clinical research informatics. Journal of Biomedical Informatics, 52, 121 - 129.

Hoch, S. W., Cherukuru, N.W., Calhoun, R., Whiteman, C.D., Lehner, M., Brown, W.J. (2014). LiDAR observations during METCRAX-II. Paper presented at the 6th Amer. Meteor. Soc. Conf. on Mtn Meteor, San Diego, CA.

Hoch, S. W., Jensen, D., Massey, J.d., Pardyjak, E.R., Fernando, H.J.S. (2014). Surface Energy Balance

Observations during MATERHORN (pp. poster): 16th Amer. Meteor. Soc. Conf. on Mtn Meteor., San Diego, CA.

Hocut, C. M., et al. (2014). Observations of slope and valley flow interactions during MATERHORN (pp. poster). 16th Amer. Meteor. Soc. Conf. on Mtn Meteor, San Diego, CA.

Homel, M. (2014). Constitutive Modeling of Fluid-Saturated Porous Rock in Material Point Method Simulations of Shaped-Charge Jet Penetration. Ph.D., University of Utah.

Homel M.A., G. J. E., Brannon, R.M. . (2014). Continuum Effective-Stress Approach for High-Rate Plastic

Deformation of Fluid-Saturated Geomaterials with Application to Shaped-Charge Jet Penetration. J. Applied Geophysics, submitted.

Homel M.A., G. J. E., Brannon, R.M. (2014). Mesoscale Validation of the Effective Stress Approach for Modeling the Plastic Deformation of Fluid-Saturated Porous Material. Mechanics of Materials, submitted.

Hu, H., Wang, Z., Liu, F. (2014). Half metal in two-dimensional hexagonal organometallic framework. Nanoscale Research Letters, 9, 690.

Hudait, A., Molinero, V. (2014). Ice Crystallization in Ultrafine Water-Salt Aerosols: Nucleation, Ice-Solution Equilibrium and Internal Structure. J. Am. Chem. Soc., 136, 8081 - 8093.

Jacobson, L. C., Ren, X., Molinero, V. (2014). Assessing the effects of crowding, pore size and

interactions on electro-osmotic drag coefficients. J. Phys. Chem. C, 118, 2093–2103 Jacobson, L. C., Kirby, R.M., Molinero, V. (2014). How short is too short for the interactions of a water

potential? Exploring the parameter space of a coarse-grained water model using Uncertainty Quantification. J. Phys. Chem. B, 118, 8190 - 8202.

Jadulco, R., Koch, M., Kakule, T., Schmidt, E., Orendt, A., He, H., Carter, G., Larson, E., Pond, C., Matainaho, T., Barrows, L. (2014). Isolation of Pyrrolocins A-C: cis- and trans-DecalinTetramic

Acid Antibiotics from an Endophytic Fungal-Derived Pathway. Journal of Natural Products, 77(11),

2537 - 2544. Jeglum, M. E., Hoch, S.W. (2014). Multi-Scale Interactions in the Planetary Boundary Layer over Complex

Terrain. Paper presented at the 16th Amer. Meteor. Soc. Conf. on Mtn Meteor, San Diego, CA. Jennings, S. G., Ahlstrom, J. B., Dubno, J. R. (2014). Modeling individual differences in overshoot: Effects

of age, hearing loss, and efferent feedback. The Journal of the Acoustical Society of America, 135(4), 2411.

Jensen, D., Pardyjak, E.R., Hoch, S.W. (2014). Monin-Obukhov Similarity Scaling Over Contrasting Surfaces During the Morning and Evening Transition. Paper presented at the 16th Conf. Mountain Meteor, San Diego, CA.

Jin, J., Miller, J.D., Dang, L.X. (2014). Molecular Dynamics Simulation and Analysis of Interfacial Water at Selected Sulfide Mineral Surfaces under Anaerobic Conditions. International Journal of Mineral Processing, 128, 55-67.

Jones, D. E., Igo, S., Hurdle, J., Facelli, J.C. (2014). Automatic Extraction of Nanoparticle Properties Using Natural Language Processing: NanoSifter an Application to Acquire PAMAM Dendrimer

Properties. PLoS ONE, 9(1), e83932. doi: 10.1371/journal.pone.0083932 Kambe, R., et al. (2014). Redox Control and High Conductivity of Nickel Bis(dithiolene) Complex

π-Nanosheet: A Potential Organic Two-Dimensional Topological Insulator. J. Am. Chem. Soc., 136, 14357 - 14360.

Kamojjala, K. (2014). Systematic code verification and validation of damage in high strength armor materials. Ph.D., University of Utah.

Kim, Y., Misra, M., Mohanty, S.K. (2014). Titanium Dioxide Nanotube Based Sensing Platform for

Detection of Mycobacterium tuberculosis Volatile Biomarkers. Nanotechnology, submitted. Lareau, M., Horel, J.D. (2014). Turbulent erosion of persistent cold-air pools: numerical simulations. J.

Atmos. Sci., online. doi: http://dx.doi.org/10.1175/JAS-D-14-0173.1

Lareau, N. P., Horel, J. D. (2014). Dynamically induced displacements of a persistent cold-air pool. Boundary-Layer Meteorology, 154(2), 291 - 316.

Lareau, N. P. (2014). The Dynamics of persistent cold-air pool breakup. Ph.D., University of Utah, Salt Lake City, UT.

Lawson, J., Horel, J. (2014). Analysis of the 1 December 2011 Wasatch downslope windstorm. Wea. Forecasting, 30, 115 - 135.

Lee, S. H., DeTar, C., Na, H., Mohler, D. (2014, 23 - 28 June 2014). Searching for the X(3872) and Z+C(3900) on HISQ lattices. Paper presented at the 323nd International Symposium on Lattice Field Theory, Columbia University, New York, NY.

Lehner, M., et al. (2014). A case study of downslope flows during MATERHORN. Paper presented at the

16th Amer. Meteor. Soc. Conf. on Mtn Meteor., San Diego, CA. Lehner, M., et al. (2014). Downslope-windstorm-type flows in Arizona's Meteor Crater - Initial findings

from METCRAX II. Paper presented at the EGU General Assembly 2014, Vienna, Austria. Lehner, M., Whiteman, C.D. (2014). Physical mechanisms of the thermally driven cross-basin circulation.

Quart. J. Roy. Meteor. Soc., 140, 895 - 907. Lehner, M., et al. (2014). Upstream flow and temperature conditions controlling

downslope-windstorm-type flows in Arizona's Meteor Crater. Paper presented at the 16th Amer.

Meteor. Soc. Conf. on Mtn Meteor., San Diego, CA Levkova, L., DeTar, C. (2014). Quark-gluon plasma in an external magnetic field. Phys. Rev. Lett., 112,

012002. Li, Z., Pu, Z., Sun, J., Lee, W-C. (2014). Impacts of 4D-VAR Assimilation of Airborne Doppler Radar

Observations on Numerical Simulations of the Genesis of Typhoon Nuri (2008). J. of Applied Meteorology and Climatology, 53, 2325 - 2343.

Li, Z., Pu, Z. (2014). Numerical simulations of the genesis of Typhoon Nuri (2008): Sensitivity to initial

conditions and implications for the roles of intense convection and moisture conditions. Wea. Forecasting, 29, 1402 - 1424.

Lin, F. C., Tsai, V.C., Schmandt, B. (2014). 3-D crustal structure of the western United States: application of Rayleigh-wave ellipticity extracted from noise cross-correlations. Geophys. J. Int, 198(2),

656-670.

Lin, F. C., Schmandt, B. (2014). Upper crustal azimuthal anisotropy across the contiguous US determined by Rayleigh wave ellipticity. Geophys. Res. Lett., 41. doi: 10.1002/2014GL062362

Lin, Z., Koch, M., Abdel Aziz, M., Tianero, D., Galindo, R., Cheatham III, T.E., Barrows, L., Reilly, C., Schmidt, E. (2014). Oxazinin A, A Pseudodimeric Natural Product of Mixed Bio-synthetic Origin

from a Filamentous Fungus. Organic Letters, 16, 4774 - 4777. doi: 10.1021/ol502227x

Liptak, J. (2014). Analysis of Arctic sea ice-atmoshere interaction. Ph.D., University of Utah. Liptak, J., Strong, C. (2014). A model-based decomposition of the sea ice-atmosphere feedback over the

Barents Sea during winter. Journal of Climate, 27, 2533 - 2544. Liptak, J., Strong, C. (2014). The winter atmospheric response to sea ice anomalies in the Barents Sea.

Journal of Climate, 27, 914 - 924. Liu, J., Wang, X., Depci, T., Miller, J.D. (2014). The Edge Surface of Kaolinite and Its Surface Chemistry.

Paper presented at the SME Annual Meeting, Salt Lake City, UT.

Liu, J., Miller, J.D., Yin, X., Gupta, V., Wang, X. (2014). Influence of Ionic Strength on the Surface charge and Interaction of Layered Silicate Particles. Journal of Colloid and Interface Science, 432,

270-277. Liu, J., Sandaklie-Nikolova, L., Wang, X., Miller, J.D. (2014). Surface Force Measurements at Kaolinite

Edge Surfaces Using Atomic Force Microscopy. Journal of Colloid and Interface Science, 35 - 40.

Liu, J. (2014). Surface Properties of Kaolinite Particles – Their Interactions and Flotation Considerations. MS, University of Utah.

Liu, M., Liu, F. (2014). Quantum Manifestation of Elastic Constants in Nanostructures. Nanotechnology(25), 135706. doi: arXiv:1209.0865

Lu, J., Qiu, Y., Baron, R., Molinero, V. (2014). Coarse-graining of TIP4P/2005, TIP4P/Ew, SPC/E and TIP3P water into monatomic anisotropic water models using relative entropy minimization. J. Chem. Theory and Comp, 10, 4104 - 4120.

Lund, M. D., Lambert, C., Jevremovic, T. (2014). High Performance Computing Simulations of Radiation shielding with GEANT4: Simulating Space Radiation Environment. Paper presented at the

Nuclear and Emerging Technologies for Space (NETS) 2014, Infinity Science Center, Mississippi. Lupi, L., Molinero, V. (2014). Does Hydrophilicity of Carbon Particles Improve their Ice Nucleation Ability?

J. Phys. Chem. A, 118, 7330-7337.

Lupi, L., Hudait, A., Molinero, V. (2014). Heterogeneous Nucleation of Ice on Carbon Surfaces. J. Am. Chem. Soc., 136, 3156–3164.

Lupi, L., Kastelowitz, N., Molinero, V. (2014). Vapor deposition of water on graphitic surfaces: formation of amorphous ice, bilayer ice, ice I and liquid water. J. Chem. Phys, 141, 18C508.

Mallia, D. V., Lin, J.C., Urbanski, S., Ehleringer, J., Nehrkorn, T. (2014). Impacts of upwind wildfire

emissions on CO, CO2, and PM2.5 concentrations in Salt Lake City, Utah. Journal of Geophysical Research: Atmospheres, 120. doi: 10.1002/2014JD022472

Massey, J. D., et al. (2014). Improving Boundary Layer and Near-Surface Temperatures Forecasts over Arid Mountainous Regions: Results from the MATERHORN Field Campaign. Paper presented at

the 16th Amer. Meteor. Soc. Conf. on Mtn Meteor., San Diego, CA Massey, J. D., Steenburgh, W.J., Hoch, S.W., Knievel, J.C. (2014). Sensitivity of Near-Surface

Temperature Forecasts to Soil Properties over a Sparsely Vegetated Dryland Region. J. Appl. Meteor. Clim., 53, 1976 - 1995.

Massey, J. S., WJ; Hoch, SW; Knievel, JC. (2014). Sensitivity of near-surface temperature forecasts to soil

properties over a sparsely vegetated dryland region. J Appl Meteor & Clim, 53, 1976 - 1995. doi: 10.1175/JAMC-D-13-0362.1

McNary, C. P., Armentrout, P.B. (2014). Cluster Chemistry: The Energy Dependence of FenCO+ (n = 4 −

17) Association Complexes in the Gas Phase (pp. poster). 2014 Lake Arrowhead Ion Chemistry Conference.

McNary, C. P., Armentrout, P.B. (2014). CO Bond Activation by Gas-Phase Iron Cluster Cations (pp. poster). 2014 Lake Arrowhead Ion Chemistry Conference.

McNary, C. P., Armentrout, P.B. (2014). Iron Cluster – CO Bond Energies from the Kinetic Energy Dependence of the Fen+ (n = 4 – 17) + CO Association Reactions. Phys. Chem. Chem. Phys, 16,

26567 - 26477. doi: doi:10.1039/c4cp02040e

Miao, L., Wang, Z.F., Gao, C.L., Liu, C., Liu, F., Qiang, D., Jia, J.F. (2014). Orbit- and Atom-Resolved Spin Textures of Intrinsic, Extrinsic and Hybridized Dirac Cone States. Phys. Rev. B, 89, 155116.

Miller, J. D., Zhang, Z., Wang, X. (2014). Surface Chemistry Aspects of Bastnaesite (Ce, LaFCO3) Flotation with Octyl Hydroxamate. Paper presented at the DOE 2014 Separation and Analysis PI

Meeting, Gaithersburg, Maryland.

Milo, A., Bess, E. N., Sigman, M.S. (2014). Interrogating selectivity in catalysis using molecular vibrations. Nature, 507, 210 - 215.

Ming, W., Liu, F. (2014). Tuning nucleation density of metal island with charge doping of graphene substrate. Appl. Phys. Lett., 105, 071609.

Mitchell, B. K., Steele, R.P. (2014). Nuclear Motion in the sigma-Bound Regime of Metal-H-2 Complexes: [Mg(H-2)(n=1-6)](2+) J Phys Chem A, 118, 10057-10066.

Mookherjee, A., Armentrout, P.B. (2014). Theoretical Investigation and Reinterpretation of the

Decomposition of Lithiated Proline and N-Methyl Proline. J. Mass Spectrom, 370, 16 - 28. doi: 10.1016/j.ijms.2014.06.012

Mookherjee, A., Armentrout, P.B. (2014). Thermodynamics and Mechanisms of Protonated TriGlycine Decomposition – Guided Ion Beam and Theoretical Approach (pp. poster): 20th International

Mass Spectrometry Conference, Geneva, Switzerland.

Neeman, E. M. (2014). Analysis and simulation of a cold-air pool and high wintertime ozone episode in Utah’s Uintah Basin. University of Utah.

Neemann, E. M., Crosman, E.T., Horel, J.D., Avey, L. (2014). Simulations of a cold-air pool associated with elevated wintertime ozone in the Uintah Basin, Utah. Atmos. Chem. Phys. Discuss., 14,

15953-16000. doi: 10.5194/acpd-14-15953-2014 Nguyen, A., Molinero, V. (2014). Cross-Nucleation between Clathrate Polymorphs: assessing the role of

stability, growth rate and structure matching. J. Chem. Phys, 140, 084506.

Nguyen, B. T., Simpson, J.J. (2014). A 3-D Stochastic FDTD model of electromagnetic wave propagation in magnetized ionosphere plasma. Paper presented at the Proc. URSI National Radio Science

Meeting, Boulder, CO. Nguyen, B. T., Furse, C., Simpson, J.J. (2014). Analysis of Electromagnetic Field Variability in Magnetized

Ionosphere Plasma using the Stochastic FDTD Method. Paper presented at the IEEE AP-S

International Symposium and USNC/URSI National Radio Science Meeting, Memphis, Tennessee. Nguyen, B. T., Simpson, J.J. (2014). An efficient stochastic approach to uncertainty quantification in 3-D

FDTD magnetized cold plasma. Paper presented at the International Conference on Electromagnetics in Advanced Applications (ICEAA), Palm Beach, Aruba.

Okal, A., Cornillie, S., Matissek, S.J., Matissek, K.J., Cheatham III, T.E., Lim, C.S. (2014). A

re-engineered p53 chimera with enhanced homo-oligomerization that maintains tumor suppressor activity. Mol. Pharm, 11(2442 - 2452).

Olson, J. K., Ivanov, A.S., Boldyrev, A. I. (2014). All-Nitrogen Analogue of Ozone: Li3N3 Species. Chem. Eur. J., 20, 6636 - 6640. doi: 10.1002/chem.201402572

Pasi, M., et al. (2014). μABC: A systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA. Nuc. Acids Res., 42, 12272-12283.

Pazmino, E., Trauscht, J., Dame, B., Johnson, W. P. (2014). Power Law Size-Distributed Heterogeneity

Explains Colloid Retention on Soda Lime Glass in the Presence of Energy Barriers. Langmuir 30(19), 5412 - 5421. doi: 10.1021/la501006p

Pazmino, E., Trauscht, J., Johnson, W.P. (2014). Release of Colloids from Primary Minimum Contact under Unfavorable Conditions by Perturbations in Ionic Strength and Flow Rate. Environmental Science & Technology, 48(16), 9227 - 9235.

Price, M., Ovcharenko, A., Thangaraj, R. (2014, June 23-24, 2014). Deformation of an ultra-thin diamond-like carbon coating on a magnetic recording head under combined loading. Paper

presented at the ASME 2014 Conference on Information Storage and Processing Systems, Santa Clara University, CA, USA.

Price, M., Ovcharenko, A., Thangaraj, R., Raeymaekers, B. (2014). Simulating nano-indentation of ultra-thin diamond-like carbon coatings. Paper presented at the 2014 STLE Tribology Frontiers

conference, Hyatt Regency Hotel, Chicago, IL.

Ray, R., Sarma, B., Mohanty, S.K., Misra, M. (2014). Theoretical and Experimental study of Sensing Triacetone Triperoxide (TATP) explosive through nanostructured TiO2 substrate. Talanta, 118,

304 - 311. Reichler, T. (2014). Poleward Expansion of the Atmospheric Circulation. In T. M. Letcher (Ed.), Climate

Change (2nd Edition ed.).

Roe, D. R., Bergonzo, C., Cheatham III, T.E. (2014). Evaluation of enhanced sampling provided by accelerated molecular dynamics with Hamiltonian replica exchange methods. J. Phys. Chem. B, 118, 3542 - 3552.

Rutz, J. J., Steenburgh, W.J., Ralph, F.M. (2014). Climatological characteristics of atmospheric rivers and

their inland penetration over the western United States. Mon. Wea. Rev., 142, 905 - 921. Sadeghirad, A., Liu, F. (2014). A three-layer-mesh bridging domain for coupled atomistic–continuum

simulations at finite temperature: Formulation and testing. Appl. Mech. Eng., 268, 299.

Samimi, A., Simpson, J.J. (2014). An efficient 3-D FDTD model of electromagnetic wave propagation in magnetized plasma. IEEE Trans. Antennas and Propagation, 63(1).

Sarswat, P., Sathyapalan, Y., Zhu, Y., Free, M.L. (2014). Advanced selective non-invasive ketone body detection sensors based on new ionophores. Mater. Res. Express 1, 1 - 16.

Schenkel, M. R. H., J.B.; Moran, M.J.; Robertson, L.A., Bedrov, D.; Gin, D.L. (2014). Effect of counter-ion

on the thermotropic liquid crystal behavior of bis(alkyl)-tris(imidazolium salt) compounds. Liquid Crystals, 41, 1668 - 1685.

Schmandt, B., Lin, F.C. (2014). P- and S-wave tomography of the mantle beneath the United States. Geophys. Res. Lett., 41. doi: 10.1002/2014GL061231

Scuba, W., et al. (2014). Knowledge Author: Creating Domain Content for NLP Information Extraction. Paper presented at the Proceedings of the 6th International Symposium on Semantic Mining in

Biomedicine (SMBM 2014), Aveiro, Portugal.

Singh, M., Dhabas, D., Nguyen, A.H., Molinero, V., Chakravarty, C. (2014). Competing Pair and Triplet Correlations in the transition from simple to tetrahedral liquids. Phys. Rev. Lett. , 112.

Skorczewski, T., Griffith, B., Fogelson, A. (2014). Multi-bond models of platelet adhesion and cohesion. Contemporary Mathematics, 628, 149 - 165.

Smith, K. (2014). Assessing the ability of CMIP5 models to capture connections between Great Basin precipitation and Pacific Ocean modes of variability and applying the assessment into the future. Master's degree, University of Utah.

Smith, K., Strong, C., Wang, S. (2014). Historical connections between Great Basin precipitation and Pacific Ocean variability (pp. poster). National Weather Association 39th Annual Meeting, Salt

Lake City, Utah, 18-23 October 2014.

Smith, K., Strong, C., Wang, S. (2014). Skill of Global Climate Models in Capturing Dependence of Great Basin Precipitation on Pacific Modes of Variability. (pp. poster). American Geophysical Union Fall

Meeting, San Francisco, California, 15-19, December 2014. Stadlbauer, P., Trantírek, L., Cheatham, T.E., Koca, J., Sponer, J. (2014). Triplex intermediates in folding

of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations. Biochimie 105, 22 - 35. doi: 10.1016/j.biochi.2014.07.009

Staten, P. W., Reichler, T., Lu, J. (2014). The transient circulation response to radiative forcings and

surface warming. J. Climate, 27(24), 9323 - 9336. Steele, R. P. (2014). Efficient anharmonic vibrational spectroscopy for large molecules using local-mode

coordinates J Chem Phys, 141, 104105. Strong, C., Kochanski, A.K., Crosman, E.T. (2014). A slab model of the Great Salt Lake for regional

climate simulation. J. Adv. Model. Earth Syst., 6, 602 - 615. doi: 10.1002/2014MS000305

Sutherland, J. C., Might, M., Earl, C., Saad, T.. (2014). Design Paradigms to Accommodate Architectural Uncertainty in Multiphysics Applications. Paper presented at the SIAM Parallel Processing

Conference, Portland, OR. Sutherland, J. C., Might, M., Earl, C., Saad, T., Bagusetty, A. (2014). Flexible, Efficient Abstractions for

High Performance Computation on Current and Emerging Architectures. Paper presented at the Algorithms and Abstractions for Assembly in PDE Codes Workshop, Albuquerque, NM.

Sweeney, A. F., Armentrout, P.B. (2014). Guided Ion Beam Studies of the Collision-induced Dissociation

of CuOH+(H2O)n (n = 1 – 4): Comprehensive Thermodynamic Data for Copper Ion Hydration. J. Phys. Chem. A, 118(10210 - 10222). doi: doi: 10.1021/jp508962d

Sweeney, A. F., Cooper, T.E., Armentrout, P.B. (2014). Transition Metal Hydration Studies: Experimental and theoretical investigation of binding energies for the Cu2+(H2O)n, n = 7 - 10 complexes (pp.

poster): 2014 Lake Arrowhead Ion Chemistry Conference.

Thatcher, L., Pu, Z. (2014). Characteristics of tropical cyclone genesis forecasts and underdispersion in high-resolution ensemble forecasting with a stochastic kinetic energy backscatter scheme. J. Meteor. Soc. Japan, submitted.

Thibault, J., Cheatham III, T.E., Facelli, J.C. (2014). iBIOMES Lite: Summarizing biomolecular simulation

data in limited settings. J. Chem. Info Model, 54, 1810- 1819. Thibault, J. C., Roe, D.R., Facelli, J.C., Cheatham, T.E. (2014). Data model, dictionaries, and desiderata

for biomolecular simulation data indexing and sharing. Journal of Cheminformatics, in press. Varble, A., et al. (2014). Evaluation of cloud-resolving and limited area model intercomparison simulations

using TWP-ICE observations: 1. Deep convective updraft properties. J. Geophys. Res., 119,

13891-13918. Varble, A., et al. (2014). Evaluation of cloud-resolving and limited area model intercomparison simulations

using TWP-ICE observations: 2. Precipitation microphysics. J. Geophys. Res., 119, 13919-13945.

Vellore, N. A., Baron, R. (2014). Epigenetic molecular recognition: a biomolecular modeling perspective. ChemMedChem, 9, 484 - 494.

Wang, Z. F., Chen, L., Liu, F. (2014). Tuning Topological Edge States of Bi(111) Bilayer Film by Edge Adsorption. Nano Lett, 14, 2879 - 2883.

Wen, J., Scoles, D.R., Facelli, J.C. (2014). Structure Prediction of Polyglutamine Disease Proteins: Comparison of Methods. BMC Bioinformatics, 15 (Suppl 7)(S11). doi:

10.1186/1471-2105-15-S7-S11

Whiteman, C. D. (2014). Meteorological aspects of our wintertime inversions and their air pollution consequences. Paper presented at the Joint Utah Conference on Safety and Industrial Hygiene,

Salt Lake City, UT. Whiteman, C. D., Hoch, S.W. (2014). Pseudo-vertical temperature profiles in a broad valley from lines of

temperature sensors on the sidewalls. J. Appl. Meteor. Clim., 53, 2430 - 2437.

Whiteman, C. D., Hoch, S.W. (2014). Relationship between particulate air pollution and meteorological variables in Utah's Salt Lake Valley. Atmos. Environ., 94, 742 - 753.

Whiteman, C. D., et al. (2014). The second Meteor Crater Experiment (METCRAX II) - An overview of the October 2013 field study. Paper presented at the 16th Amer. Meteor. Soc. Conf. on Mtn Meteor.,

San Diego, CA

Whittaker, S. (2014). Seismic Array Constraints on the D” discontinuity beneath Central America. M.S., University of Utah.

William, P. J., Markus, H. (2014). Upscaling colloid transport and retention under unfavorable conditions: Linking mass transfer to pore and grain topology. Water Resources Research 49(9), 5328-5341.

Yang, P., Liu, F. (2014). Understanding graphene production by ionic surfactant exfoliation: A molecular dynamics simulation study. J. Appl. Phys., 116, 014304.

Yu, H., Guo, B., Hanafy, S., Lin, F.C., Schuster, G.T. (2014). Direct detection of near-surface faults by

migration of back-scattered surface waves. SEG Technical Program Expanded Abstracts, 2135-2139. doi: 0.1190/segam2014-0737.1

Zabriskie, M. S., et al. (2014). BCR-ABL1 Compound Mutations Combining Key Kinase Domain Positions Confer Clinical Resistance to Ponatinib in Ph Chromosome-Positive Leukemia. Cancer Cell, 26,

428 - 442.

Zhang, H., Pu, Z. (2014). Influence of assimilating surface observations on the predicton of landfalls of Hurricane Katrina (2005) with ensemble Kalman filter. Mon. Wea. Rev., 142(8), 2915 - 2934.

Zhang, L. Z., Wnag, Z.F., Du, S.X., Gao, H.J., Liu, F. (2014). “Quantum size effect on dielectric function of ultrathin metal film: a first-principles study of Al(1 1 1). J. Phys.: Condens. Matter, 26, 505302.

Zhang, X., Du, H., Wang, X., Miller, J.D. (2014). Octyl Hydroxamate Adsorption by Bastnaesite - the Hydrophobic Surface State. Paper presented at the SME Annual Meeting, Salt Lake City, Utah.

Zhang, X. (2014). Surface Chemistry Aspects of Fluorite and Bastnaesite Flotation Systems. Ph.D.,

University of Utah, Salt Lake City, UT. Zhdanov., M. S., Endo, M., Toon, D., Cuma, M., Mattsson, J., Midgley, J. (2014). Anisotropic 3D inversion

of towed-streamer electromagnetic data: Case study from the Troll West Oil Province. Interpretaion, 2, SH97-SH113.

Zheng, Z., Wallace, J. (2014). Anisotropic Lyman-alpha Emission. Astrophysical Journal, submitted.

Zhou, M., Liu, Z., Ming, M., Wang, Z., Li, P., Liu, F. (2014). Epitaxial growth of large-gap quantum spin Hall insulator on semiconductor surface. Proc. Natl. Acad. Science, 111, 14378.

Zhou, M., Ming, Z., Liu, Z., Wang, Z., Yao, Y., Liu, F. (2014). Formation of quantum spin Hall state on Si surface and energy gap scaling with strength of spin orbit coupling. Sci. Rep., 4, 7102. doi: arXiv:

1401.3392 Zhou, M., Liu, Z., Ming, M., Wang Z., Liu, F. (2014). sd2 Graphene: Kagome Band in Hexagonal lattice.

Phys. Rev. Lett., 113, 236802.

Zhu, F., Liu, F., Scarpulla, M. (2014). Strain tuning of native defect populations: the case of Cu2ZnSn(S,Se)4. APL Materials, 2, 012110.

2013

Abu-Zayyad, T., et al. (2013). The energy spectrum of ultra-high-energy cosmic rays measured by the Telescope Array FADC fluorescence detectors in monocular mode. Astroparticle Physics, 48, 16 -

24. Alcott, T. I., Steenburgh, W. J. (2013). Orographic influences on a Great Salt Lake-effect snowstorm.

Mon. Wea. Rev., 141, 2432 - 2450. Armentrout, P. B. (2013). The Bond Energy of ReO+: Guided Ion-Beam and Theoretical Studies of the

Reaction of Re+ (7S) with O2. J. Chem. Phys., 139, 084305. doi: 10.1063/1.4818642

Armentrout, P. B., Tang, B., Rodgers, M.T. (2013). Metal Cation Dependence of Interactions with Amino Acids: Bond Energies of Rb+ and Cs+ to Met, Phe, Tyr, and Trp. J. Phys. Chem. B, 117, 3771 -

3781. Armentrout, P. B. (2013). The Power of Accurate Energetics (or Thermochemistry: What is it Good for?).

J. Am. Soc. Mass Spectrom., 24, 173 - 185.

Armentrout, P. B., Rodgers, M.T. (2013). Thermochemistry of Non-Covalent Ion-Molecule Interactions. Mass Spectrometry, 2, S0005.

Armentrout, P. B. L., F.-X. (2013). The Bond Energy of IrO+: Guided Ion-Beam and Theoretical Studies of the Reaction of Ir+ (5F) with O2. J. Phys Chem A, 117(7754 - 7766). doi: 10.1021/jp4063143

Armentrout, P. B. P., L.; Hinton, C.; Citir, M. (2013). Activation of Methane by Os+: Guided Ion Beam and

Theoretical Studies. ChemPlusChem (Memorial Issue for Detlef Schröder), 78, 1157 - 1173. doi: 10.1002/cplu.201300147

Ashton, N. R., DR; Weiss, RB; Cheatham, TE; Steward, RJ. (2013). Self-tensioning aquatic caddisfly silk: Ca2+-dependent structure, strength, and load cycle hysteresis. Biomacromoleculres, 14, 3668 -

3681. Asparouhova, E., Bessembinger, H., Kalcheva, I. (2013). Noisy Prices and Inference Regarding Returns.

Journal of Finance, 68(2), 665 - 714.

Austin, D. (2013). Verification and Validation of a geomechanical model aimed at simulating wellbore completion via shape-charge jet perforation of metal and penetration into sandstone. Ph.D.

Dissertation, University of Utah. Bailey, B., Stoll, R. . (2013). Turbulence in Sparse, Organized Vegetative Canopies: A Large-Eddy

Simulation Study. Boundary-Layer Meteorology, 147, 369 - 400.

Baron, R. (2013). Fast Sampling of A-to-B Protein Global Conformational Transitions: From Galileo Galilei to Monte Carlo Anisotropic Network Modeling. Biophysical Journal, 105, 1545 - 1546.

Beckvermit, J., Peterson, J., Harman, T., Bardenhage, S., Wight, C., Meng, Q., Berzins, M. (2013). Multiscale Modeling of Accidental Explosions and Detonations, Computing in Science and

Engineering. Computing in Science and Engineering, July, 76 - 86. Bergonzo, C., Galindo-Murillo, R., Cheatham, T.E. (2013). Molecular modeling of nucleic acid structure:

Electrostatics and solvation. Current Protocols Nucleic Acid Chemistry, 55, 7.9.1 - 7.9.27.

Bergonzo, C., Galindo-Murillo, R., Cheatham, TE. (2013). Molecular modeling of nucleic acid structure: Energy and Sampling. Current Protocols Nucleic Acid Chemistry, 54, 7.8.1 - 7.8.21.

Bergonzo, C. H., N; Roe, D; Swails, J; Roitberg, AE; Cheatham, TE. (2013). Multi-dimensional replica exchange molecular dynamics yields a converged ensemble of an RNA tetranucleotide. J Chem Theor Comput, 10(1), 492 - 499.

Bogenschutz, P. A., Krueger, S.K. (2013). A simplified PDF parameterization of subgrid-scale clouds and turbulence for cloud-resolving models. J. Adv. Model. Earth Syst., 5(2), 195 - 211. doi:

http://dx.doi.org/10.1002/jame.20018 Brown, S., Thorne, M.S. (2013). Viterbi Sparse Spike Detection. Geophysics, 78(4), 1 - 13. doi: doi:

10.1190/GEO2012-0209.1 Bullock, G., Molinero, V. (2013). Low-density liquid water is the mother of ice: on the relation between

mesostructure, thermodynamics and ice crystallization in solutions. Faraday Discussions, 167, 371

- 388. Charlton-Perez. A., e. a. (2013). On the lack of stratospheric dynamical variability in low-top versions of

the CMIP5 models. J. Geophys. Res. doi: 10.1002/jgrd.50125 Cheatham, I., T.E., and Case, D.A. (2013). Twenty-five years of nucleic acid simulations. Biopolymers,

99, 969 - 977.

Chen, D. P., J.H.; Hooper, J.B.; Klittnick, A.; Shen, Y.; Korblva, E.; Bedrov, D., Walba, D.M.; Glaser, M.A.; Maclennan, J.E., Clark, N.A. (2013). A Twist-bend Chiral Helix of 8nm Pitch in a Nematic Liquid

Crystal of Achiral Molecular Dimers. Proc. Natl. Acad. Sci. Chen, L., Wang, Z.F., Liu, F. (2013). Robustness of two-dimensional topological insulator states in bilayer

bismuth against strain and electrical field. Phys. Rev. B, 87, 235420. Crosman, E. T., N.P. Lareau, Horel, J.D. (2013). 2013 Large-Eddy Simulations of Cold Air Pools in Utah’s

Salt Lake Valley. Paper presented at the Western Air Western Air Quality Modeling Workshop –

Technical Methods and Applications, Boulder, CO. Davis, K., Price, R.C., Facelli, J.C. (2013). Implementing public health analytical services: Grid enabling of

MetaMap. Paper presented at the 26th IEEE International Symposium on Computer-Based Medical Systems.

Duan, H. X., Li, Y. H., Pu, Z. (2013). An application of assimilated dust concentration data and AMSU

Satellite radiance data in GRAPES_SDM model. J. of Desert Research, 4, 1150 - 1159. Faber, S., Bartholomew, K., Li, X., Paez, A., Nurul Habib, K.M. (2013). Social Equity in Distance Based

Transit Fares. Paper presented at the GIS in Transit Conference, Washington, D.C. Farber, S., Bratholomew, K., Li, X., Paez, A., Nural Habib, K.M. (2013). Social Equity in Distance Based

Transit Fares. Transportation Research Board.

Farber, S., Li, X. (2013). Urban Sprawl and Social Interaction Potential: an Empirical Analysis of Large Metropolitan Regions throughout the United States. Journal of Transport Geography, 31, 267 -

277. Fleming, A. M., Orendt, A.M., He, Y., Zhu, J., Dukor, R., Burrows, C.J. (2013). Reconciliation of Chemical,

Enzymatic, spectrosopic and Computational Data to Assign the Absolute Configuration of the DNA Base Lesion Spiroiminodihydantoin. J of American Chemical Society, 135, 18191 - 18204.

Galindo-Murillo, R. B., C; Cheatham, TE. (2013). Molecular modeling of nucleic acid structure. Current Protocols Nucleic Acid Chemistry, 54, 7.5.1 - 7.5.13.

Gonzales Solveryra, E., de la Llave, E., Molinero, V., Soler-Illia, G., Scherlis, D.A. (2013). Structure,

dynamics and phase behavior of water in TiO2 nanopores. J. Phys. Chem. C, 117, 3330–3342. González, S. I., Oña, O.B., Ferraro, M.B., Facelli, J.C. . (2013). Structure and electronic properties of

lithium-silicon clusters. Computational and Theoretical Chemistry, 1024, 61 - 68.

Greene, T. (2013). Validity and Statistical Power of Alternative eGFR-Based Endpoints: A Report from an NKF FDA Workshop. Paper presented at the American Society of Nephrology.

Hall, M., Beckvermit, J., Wight, C., Harman, T., Berzins, M. (2013). The Influence of an Applied Heat Flux on the Violence of Reaction of an Explosive Device. Paper presented at the XSEDE 2013.

Hasan, M. S., JJ. (2013, January 2013). Lightsabers (‘laser swords’) for improving photodetector speed and responsivity. Paper presented at the URSI National Radio Science Meeting, Boulder, CO.

Hasan, M. S., JJ. (2013). Photonic nanojet-enhanced nanometer-scale germanium photodiode. Applied Optics, 52(22), 5420 - 5425.

Henriksen, N. R., DR; Cheatham, TE. (2013). Reliable oligonucleotide conformational ensemble

generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulation. J Phys Chem B, 117, 4014 - 4027.

Hinton, C. S. C., M.; Armentrout, P. B. (2013). Guided Ion-Beam and Theoretical Studies of the Reaction

of Os+ (6D) with O2: Adiabatic and Nonadiabatic Behavior. Int. J. Mass Spectrom. (Memorial Issue for Detlef Schröder), 354 - 355, 87 - 98. doi: 10.1016/j.ijms.2013.05.015

Holten, V., Limmer, D.T., Molinero, V., Anisimov, A. (2013). Nature of the anomalies in the supercooled liquid state of the mW model of water. J. Chem. Phys, 138, 174501.

Jayamohan, H., Smith, Y. R., Gale, B.K., Misra, M., Mohanty, S. K. (2013). Platinum functionalized Titania Nanotube Array Sensor for Detection of Trichloroethylene in Water. IEEE Transactions.

Jensen, K. (2013). SPdKS analysis of ultra-low velocity zones beneath the western Pacific. M.S.,

University of Utah. Jensen, K. J. T., M.S.; Rost, S. (2013). SPdKS analysis of ultralow-velocity zones beneath the western

Pacific. Geophys. Res. Lett, 40, 1 - 5. doi: 10.1002/grl.50877 Kamojjala, K., Brannon, R. (2013). Data relocalization to mitigate slow convergence caused by

under-resolved stress fields in computational damage mechanics. J Eur Ceram Soc, 34(11), 2723

- 2730. doi: http://dx.doi.org/10.1016/j.jeurceramsoc.2013.12.016 Kamojjala, K., Lacy, J. M., Brannon, R.M. (2013). Effects of Statistical Variability of Strength and Scale

Effects on the Convergence of Unnotched Charpy and Taylor Anvil Impact Simulations. Paper presented at the ASME Verification and Validation Symposium, Las Vegas, NV.

Kochanski, A., Jenkins, M.A., Krueger, S., Mandel, J., Beezley, J. (2013). Real time simulation of 2007 Santa Ana fires. Forest Ecology and Management, 294, 136 - 149.

Krizmanic, J., Bergman, D., Sokolsky, P. (2013). The Non-Imaging CHErenkov Array (NICHE): A TA/TALE Extension to Measure the Flux and Composition of Very-High Energy Cosmic Rays. Paper presented at the The 33rd International Cosmic Ray Conference, Rio de Janeiro, Brazil.

Kulkarni, R. A., et al. (2013). Substrate selection influences molecular recognition in a screen for lymphoid tyrosine phosphatase inhibitors. Chembiochem, 14, 1640 - 1647.

Kulkarni RA, S. S., Vellore NA, Bliss MR, Krishnamurthy D, Baron R, Bottini N, Barrios AM. (2013).

Thiuram Disulfides as Pseudo-irreversible Inhibitors of the Lymphoid Tyrosine Phosphatase. Chem Med Chem, 8, 1561 - 1568.

Lapoutre, V. J. F. R., B.; van der Meer, A. F. G.; Oomens, J.; Bakker, J. M. Sweeney, A.; Mookherjee, A.; Armentrout, P. B. J. (2013). Structures of the Dehydrogenation Products of Methane Activation

by 5d Transition Metal Cations. Chem A, 117, 4115 - 4126. doi: 10.1021/jp400305k

Lehner, M., Rotunno, R., Whiteman, C. D. (2013). Initial simulations of flow over a small crater basin in preparation for an upcoming field experiment. Paper presented at the 32nd International

Conference on Alpine Meteorology, Kranjska Gora, Slovenia. Li B, Z. S., Rogers KE, de Oliveira CAF, Baron R, Cheng LT, McCammon JA. (2013). Variational

Implicit-Solvent Modeling of Host-Guest Binding: A Case Study on Curcubit[7]uril. J Chem Theor Comput, 9, 4195 - 4204.

Li, W.-L. I., AS; Federic, J; Romanexcu, C; Cernusak, I; Boldyrev, AI; Wang, L-S. (2013). On the way to

the highest coordination number in the planar metal-centred aromatic Ta©B10- cluster: Evolution of the Structures of TaBn- (n=3-8). J Chem Physics, 139, 104312.

Liu, J., Wang, X., Miller, J.D. (2013). Surface Chemistry Analysis of Collector Adsorption in Kaolinite Flotation Systems. Paper presented at the SME Annual Meeting, Denver, Colorado.

Lund, A. M., Orendt, A.M., Pagola, G.I., Ferraro, M.B., Facelli, J.C. . (2013). Optimization of crystal

structures of archetypical pharmaceutical compounds: A plane-wave DFT-D study using Quantum Espresso. Crystal Growth and Design, 13(5), 2181 - 2189.

Mejia, J. A. (2013). Characterization, Analysis and Simulation of Fine Coal Filtration. MS, University of Utah, Salt Lake City, UT.

Miller, N. E., Stoll, R. (2013). Surface Heterogeneity Effects on Regional-Scale Fluxes in the Stable Boundary Layer: Aerodynamic Roughness Length Transitions. Boundary-Layer Meteorology, 149,

277 - 301.

Mookherjee, A. A., P. B. . (2013). Role of Methylation on the Thermochemistry of Alkali Metal Cation Complexes of Amino Acids: N-Methyl Proline. Int. J. Mass Spectrom., 345-347, 109 - 119. doi:

10.1016/j.ijms.2012.08.021 Neuten, T. S., Farber, M., Delafontaine, M., Boussauw, K. (2013). Spatial Variation in the Potential for

Social Interaction: A Case Study in Flanders (Belgium). Computers, Environment and Urban Systems, 41, 318 - 331.

Nguyen, A. H., Molinero, V. (2013). Stability and metastability of bromine clathrate polymorphs. J. Phys. Chem. B, 117, 6330-6338.

Nguyen, B. T., Simpson, J.J. (2013). A stochastic FDTD model of electromagnetic wave propagation in magnetized ionospheric plasma. Paper presented at the IEEE AP-S International Symposium and USNC/URSI National Radio Science Meeting, Orlando, FL.

Oier, L., Matxain, J.M., Ruiperez, F., Uglade, J.M., Armentrout, P.B. (2013). Quantum chemical study of

the reactions between Pd+/Pt+ and H2O/H2S. Chem. Eur. J., 19, 8832 - 8838. doi: 10.1002/chem.201300222

Olson, J. K., Boldyrev, A.I. (2013). Planar to 3D Transition in the B6Hy Anions. J Phys Chem A, 117(7), 1614 - 1620. doi: 10.1021/jp310162v

Orendt, A. M., Pimienta, I.S.O., Badu, S. R., Solum, M.S., Pugmire, R.J., Facelli, J.C. (2013).

Three-dimensional Structure of the Siskin Green River Oil Shale Kerogen Model: A comparison between Calculated and Observed Properties. Energy & Fuels, 27(2), 702 - 710.

Price, M. O., A; Thangaraj, R; Raeymaekers, B. (2013, June 24 - 25, 2013). Delamination of ultra-thin diamond-like carbon coatings on magnetic recording heads under normal loading. Paper

presented at the 23rd ASME Annual Conference on Information Storage and Process Systems, Santa Clara University, CA, USA.

Prisbrey, K. (2013, March, 19 - 23, 2013). Experimental Measurement & Modeling Predictions of Performance of Surfactant Corrosion Inhibitors. Paper presented at the NACE International - 2013, Orlando, FL USA.

Pu, Z., Zhang, H., Anderson, J.A. (2013). Ensemble Kalman filter assimilation of near-surface observations over complex terrain: Comparison with 3DVAR for short-range forecasts. Tellus A, 65, 19620.

Qiu, S. (2013). Semileptonic B D decay at nonzero recoil with 2+1 flavor of improved staggered quarks. Ph.D., University of Utah.

Rajan, N. S., Gouripeddi, R., Facelli, J.C. (2013). Implementing public health analytical services: Grid enabling of MetaMap. Paper presented at the 26th IEEE International Symposium on

Computer-Based Medical Systems.

Rajan, N. S., Gouripeddi, R., Facelli, J.C. (2013). A service oriented framework to assess the quality of electronic health data for clinical research. Paper presented at the 2013 IEEE International

Conference on Healthcare Informatics. Robertson JC, H. N., Tortorici MB, Ciossani G, Borrello MT, Vellore NA, A Ganesan, Mattevi A, Baron R.

(2013). Expanding the Druggable Space of the LSD1/CoREST Epigenetic Target: New Potential Binding Regions for Drug-Like Molecules, Peptides, Protein Partners, and Chromatin. PLoS Comput Biol, 9(e1003158).

Roe, D. C., TE. (2013). PTRAJ and CPPTRAJ: Software for processing and analysis of molecular dynamics trajectory data. J Chem Theor Comput, 9, 3084 - 3095.

Rogers, K. O.-S., JM; Baron, R; Fajer, M.; deOliveira, CAF; McCammon, JA. (2013). On the Role of Dewetting Transitions in Host-Guest Binding Free Energy Calculations. J. Chem. Theory Comp., 9,

46 - 53.

Romanescu, C. G., TR; Li, W-L; Boldyrev, AI; Wang, L-S. (2013). Transition-Metal-Centered Monocyclic Boron Wheel Clusters (M©Bn): A New Class of Aromatic Borometallic Compounds. Acc Chem Res, 46, 350 - 358.

Romanescue, C. G., TR; Li, W-L; Boldyrev, AI; Wang, LS. (2013). Geometric and electronic factors in the

rational design of transition-metal-centered boron molecular wheels. J Chem Physics, 138, 134315.

Sarma, B., Jurovitzki, A.L., Smith, Y.R., Mohanty, S.K., Misra, M. (2013). Redox-Induced Enhancement in

Interfacial Capacitance of Titania Nanotube/Bismuth Oxide Composite Electrode. ACS Appl. Mater. Interfaces, 5(5), 1688 - 1699.

Sarma, B., Smith, Y.R., Jurovitzki, A.L., Ray, R. S., Mohanty, S. K., Misra, M. (2013). Supercapacitance Behavior of Porous Oxide Layer Grown on 302-type Stainless Steel Substrate. J of Power Sources, 236(August), 103 - 111.

Sarswat, P. K., Sathyapalan, A., Zhu, Y., Free, M.L. (2013). Design, synthesis and characterization of TPA-Thiophene based amide or imine functionalized molecule for potential optoelectronic devices.

J.of Theoretical and Applied Physics, 7(4). doi: 10.1186/2251-7235-7-4 Schmerr, N. C., Kelly, B. M., Thorne, M.S. (2013). Broadband array observations of the 300 km seismic

discontinuity. Geophys. Res. Lett, 40, 1 - 6. doi: 10.1002/grl.50257 Setny, P. B., R; Kekenes-Huskey, PM; MCCammon, JA, Dzubiella, J. (2013). Solvent Fluctuations in

Hydrophobic Cavity-Ligand Binding Kinetics. Proc. Natl. Acad. Sci USA, 110, 1197 - 1202.

Si, C., Duan, W., Liu, F. (2013). First-Principles Calculations on the Effect of Doping and Biaxial Tensile Strain on Electron-Phonon Coupling in Graphene. Phys Rev Lett, 111, 196802.

Skorczewski, T., Erickson, L. C., Fogelson, A. (2013). Platelet motion near a vessel wall or thrombus surface in 2D whole blood simulations. Biophysical Journal, 104(8), 174-172. doi:

10.1016/j.bpj.2013.01.061

Smith, Y. R., Sarma, B., Mohanty, S.K., Misra, M. (2013). Single-Step Anodization for Synthesis of Hierarchical TiO2 Nanotube Arrays on Foil and Wire Substrate for Enhanced Photoelectrochemical

Water Splitting. Int. J. Hydrogen Energ, 38, 2062 - 2069. Song, B., Molinero, V. (2013). Thermodynamic and structural signatures of water-driven

methane-methane attraction in coarse-grained mW water. J. Chem. Phys., 139, 054511. Sponer, J. M., A; Spackova, N; Cang, X; Cheatham, TE; Grimme, S. (2013). Relative stability of different

DNA guanine quadruplex stem topologies derived using large-scale quantum-chemical

computations. J American Chem Society, 135, 9785 - 9796. Stadbauer, P. K., M; Cheatham, TE; Koca, J; Sponer, J. (2013). Structural dynamics of possible late-stage

intermediates in folding quadruplex DNA studied by molecular simulations. Nuc. Acids Res., 41, 7128 - 7143.

Staten, P. W., Reichler, T. . (2013). On the ratio between shifts in the eddy-driven jet and the Hadley cell

edge. Clim. Dyn. doi: 10.1007/s00382-013-1905-7 Steele, R. P. (2013). Communication: Multiple-Timestep ab initio molecular dynamics with electron

correlation J Chem Phys, 139, 011102. Stevens, B., et al. (2013). The Atmospheric Component of the MPI-M Earth System Model: ECHAM6. J.

Adv. Model. Earth Syst., 5(2), 146-172. doi: 10.1002/jame.20015

Thatcher, L., Pu, Z. (2013). Evaluation of tropical cyclone genesis precursors with relative operating characteristics (ROC) in high-resolution ensemble forecasts: Hurrican Ernesto. Tropical Cyclone Research and Review, 2(3), 131 - 148.

Thibault, J. F., JC; Cheatham, TE. (2013). iBIOMES: Managing and sharing biomolecular simulation data

in a distributed environment. J Chem Inf Model, 53, 725 - 736. Thorne, M. S., Crotwell, H.P., Jahnke, G. (2013). An educational resource for visualizing the global

seismic wavefiled. Seismological Research Letters, 84(4), 1-7. doi: 10.1785/0220120134

Thorne, M. S., Zhang, Y., Ritsema, J. (2013). Evaluation of 1-D and 3-D seismic models of the Pacific lower mantel with S, SKS, and SKKS travetimes and amplitudes. Journal of Geophysical Research: Solid Earth, 118, 1 - 11. doi: 10.1002/jgrb.50054

Thorne, M. S., Garnero, E.J., Jahnke, G., Igel, H., McNamara, A.K. (2013). Mega ultra low velocity zone

and mantel flow. Earth and Planetary Science Letters, 364, 59 - 67.

Tortorici M, B. T., Tardugno M, Chiarelli L, Pilotto S, Ciossani G, Vellore NA, Bailey S, Cowan J, O’Connell M, Crabb SJ, Packham G, Mai A, Baron R, Ganesan A, Mattevi A. . (2013). Protein Recognition by

Small Peptide Reversible Inhibitors of the Chromatin-Modifying LSD1/CoREST Lysine Demethylase. ACS Chem Bio, 8, 1677 - 1682.

Vellore NA, B. R. (2013). Molecular Dynamics Simulations Indicate an Induced-Fit Mechanism for LSD1/CoREST-H3-Histone Molecular Recognition. BMC Biophys, 6, 15.

Wang, Z. F., Su, N., Liu, F. (2013). Prediction of a Two-Dimensional Organic Topological Insulator. Nano Lett., 13, 2842.

Wang, Z. F., Jin, S., Liu, F. (2013). Spatially separated spin carriers in spin-semiconducting graphene

nanoribbons. Phys Rev Lett, 111, 096803. Wei, L., Pu, Z., Wang, S. (2013). Numerical simulation of the life cycle of a persistent wintertime

inversion over Salt Lake City Boundary Layer Meteorology. Boundary Layer Meteorology. doi:

10.1007/s10546-013-9821-2 Wen, J., Scoles, D.R., Facelli, J.C. (2013). Structure Prediction of Polyglutamine Disease Proteins:

Comparison of Methods. Paper presented at the Biotechnology and Bioinformatics Symposium, BIOT 2013.

Yao, Y. (2013). Evaluation of one-dimensional seismic models of the Lunar interior. M.S., University of Utah.

Yeager, K. N., Steenburgh, W.J., Alcott, T.I. (2013). Contributions of lake-effect periods to the

cool-season hydroclimate of the Great Salt Lake Basin. J. Appl. Meteor. Climate, 52(2), 341 - 362. Yin, X., Yan, L., Liu, J., Xu, Z., Miller, J.D. (2013). Anisotropic Surface Charging of Chlorite Surfaces.

Clays and Clay Minerals, 61(2), 152 - 164. Zgarbova, M., Luque, F.J., Sponer, J., Cheatham, T.E., Otyepka, M., Jurecka, P. (2013). Toward improved

description of DNA backbone: Revisiting epsilon and zeta torsion force field parameters. J Chem Theor Comput, 9, 2339 - 2354.

Zhang, H., Pu, Z., Zhang, X. (2013). Examination of errors in near-surface temperature and wind from

WRF numerical simulations in regions of complex terrain. Weather Forecasting, 28(3), 893 - 914. Zhang, X., Wang, X., Yin, X., Du, H., Miller, J.D. (2013). Interfacial Chemistry Features of Selected

Fluorite Surfaces. Paper presented at the SME Annual Meeting, Denver, Colorado. Zhang, X., Du, H., Wang, X., Miller, J.D. (2013). Surface Chemistry Considerations in the Flotation of

Rare-earth and Other Semisoluble Salt Minerals. Minerals & Metallurgical Processing, 30(1),

24-37. Zhou, M., , Liu, Z., Wang, Z., Bai, Z., Feng, Y., Lagally, M.G., Liu, F. (2013). Strain-Engineered Surface

Transport in Si(001): Complete Isolation of the Surface State via Tensile Strain. Phys Rev Lett, 111, 246801.

Zhu, Y. (2013). Characterization of beta phase growth and Experimental Validation of Long Term Thermal Exposure Sensitization of AA5xxx Alloys. MS, University of Utah.

2012

Abu-Zayyad, e. a. (2012). The surface detector array of the Telescope Array experiment.

Nucl.Instrum.Meth, A689, 87-97. Alcott, T. I., Steenburgh, W.J., Laird, N.F. (2012). Great Salt Lake-effect precipitation: Observed

frequency, characteristics, and environmental factors. Wea. Forecasting, 27, 954 - 971. Andrews, N. (2012). Simulating the Diurnal Cycle of the Atmospheric Boundary Layer Using Large-Eddy

Simulation with Vertical Adaptive Mesh Refinement. MS, University of Utah. Badu, S., Pimienta, I.S.O., Orendt, A.M., Pugmire, R. J.. Facelli, J.C. (2012). Modeling of asphaltenes:

Assessment of sensitivity of 13C solid state NMR to molecular structure. Energy & Fuels, 26(4),

2161 - 2167. Baron, R., Vellore NA. (2012). LSD1/CoREST is an allosteric nanoscale clamp regulated by H3-histone-tail

molecular recognition. PANS. Baron, R., McCammon, J.A. (2012). Molecular Recognition and Ligand Association. . Ann. Rev. Phys.

Chem., 64.

Baron, R., Vellore NA. (2012). Reversible Opening/Closing Dynamics of LSD1/CoREST: Discovery of a Nanoscale Clamp for Chromatin and Protein Binding. Biochemistry, 51, 3151-3153.

Baron, R., Setney, P., Paesani, F. (2012). Water Structure, Dynamics, and Spectral Signatures: Changes Upon Model Cavity-Ligand Recognition. J. Phys Chem B, online.

Baron, R., Molinero, J. (2012). Water-Driven Cavity-Ligand Binding: Comparison of Thermodynamic Signatures from Coarse-Grained and Atomic-Level Simulations. Chem. Theory and Comp., 8,

3696–3704.

Baron, R. M., V. (2012). Water-driven Cavity-Ligand Binding with Coarse-Grained Solvent. J. Chem. Theory Comp., 7(under review).

Bedrov, D. (2012). Molecular dynamics simulation studies of the thermodynamics, structure, and transport properties of alkyl- and alkyne-imidazolium azide ionic liquids. J. Phys Chem, 116, 1114

- 1121.

Beveridge, D. L., Cheatham, T.E., Mezei, M. (2012). The ABCs of molecular dynamics simulations on B-DNA, circa 2012. J. Bioscience, 37, 379-397.

Chappanda, K. N., Smith, Y., Mohanty, S.K., Rieth, L.W., Tathireddy, P., Misra, M. (2012). Growth and characterization of TiO2 nanotubes from sputtered Ti film on Si substrate. Nanoscale Res Lett, July 12(7), 388.

Chappanda, K. N., Smith, Y., Misra, M., Mohanty, S.K. (2012). Site-specific and patterned growth of TiO2

nanotube arrays from e-beam evaporated thin titanium film on Si wafer. Nanotechnology, 23,

385601. Crockett, D. K., Ridge, P.G., Wilson, A.R., Lyon, E., Williams, M.S., Narus, S.P., Facelli, J.C., Mitchell, J.A.

(2012). Consensus: A framework for evaluation of uncertain gene variants in laboratory test reporting. Genome Medicine, 4, 48. doi: 10.1186/gm347

Crockett, D. K., Lyon, E., Williams, M.S., Narus, S.P., Facelli, J.C., Mitchell, J.A. . (2012). Utility of

gene-specific algorithms for predicting pathogenicity of uncertain gene variants. Journal of the American Medical Informatics Association, 19(2), 207 - 211.

Crosman, E., Horel, JD. (2012). The impact of the Great Salt Lake on Salt Lake Valley persistent cold air pools. Paper presented at the 15th Conference on Mountain Meteorology, Steamboat Springs,

CO. Crosman, E. T., Horel, J.D. (2012). Idealized Large-Eddy Simulations of Sea and Lake Breezes: Sensitivity

to Lake Diameter, Heat Flux, and Stability. Boundary-Layer Meteorology, 144(3), 309 - 328.

Cuma, M., Wilson, G.A., Zhdanov, M.S. (2012). Large-scale 3D inversion of potential field data. Geophysical Prospecting, 60, 1186 - 1199.

Davis, K., Staes, C., Duncan, J., Igo, S., Facelli, J.C. (2012). Identification of pneumonia and influenza deaths using the death certificate pipeline. BMC Medical Informatics and Decision Making, 12(37).

de la Llave, E., Molinero, V., Scherlis, D.A. (2012). Role of Confinement and Surface Affinity on Filling

Mechanisms and Sorption Hysteresis in Nanopores. J. Phys. Chem. C, 116, 1833 - 1840. DeTar, C., Kronfeld, A.S., Lee, S.H., Levkova, L., Mohler, D., Simone, J.N. (2012). Charmonium mass

splittings at the physical point. PoS LATTICE 257. Dixon, A. M., GD; Bruno, BJ; Constance, JE; Woessner, DW; Fidler, TP; Robertson, JC; Cheatham, TE;

Lim, CS (2012). Improved coiled-coil design enhances interaction with Bcr-Abl and induces

apoptosis. Mol. Pharm, 9, 187 - 195. Farber, S., Neutens, T., Miller, H.J., Li, X. (2012). The Social Interaction Potential of Metropolitan

Regions: A Time-Geographic Measurement Approach Using Joint Accessibility. Annals of the Association of American Geographers, 103(3), 483 - 504. doi:

DOI:10.1080/00045608.2012.689238 Farber, S., Neutens, T., Carrasco, J.A., Rojas, C. (2012). The Spatial Distribution of Face-to-face Social

Interactions. International Association of Travel Behaviour Research.

Fridlind, A. M., et al. (2012). A comparison of TWP-ICE observational data with cloud-resolving model results. J. Geophys. Res., 117, D05204.

Galeev, T. R., Romanescu, C., Li, W-L., Wang, L-S., Boldyrev, A.I. (2012). Observation of the Highest Coordination Number in Planar Species: Decacoordinated Ta©B10- and Nb©B10- Anions Angew. Chem. Int. Ed., 51, 2101-2105.

Greene, T. (2012). GFR Decline as an Endpoint for Clinical Trials in CKD. Paper presented at the Workshop sponsored by the National Kidney Foundation (NKF) and Food and Drug Administration

(FDA), Bethesda, MD. Hambrecht, K. (2012). Thesis. MS Thesis, University of Utah, Salt Lake City, Utah.

Harper, K. C., Bess, E.N., Sigman, M.S. (2012). Multidimensional steric parameters in the analysis of asymmetric catalytic reactions. Nat. Chem., 4, 366 - 374.

Henriksen, N. M., Davis, D.R., Cheatham, T.E. (2012). Molecular dynamics re-refinement of two different

small RNA loop structures using the original NMR data suggest a common structure. J. Biomol. NMR, 53, 321-339.

Hooper, J. B. S., O.N.; Borodin, O.; Bedrov, D.; Smith, G.D. (2012). Molecular dynamics simulation studies of the influence of imidazolium structure on the properties of imidazolium/azide ionic

liquids. J. Chem. Phys., 136, 194506.

Horel, J. D., Ander, C. (2012). Analysis of multiple stable layers in cold air pools. Paper presented at the 15th Conference on Mountain Meteorology, Steamboat Springs, CO

Horne, W. (2012). Flow Around a Solitary Tree in a Large Field Under Neutral Atmospheric Stratification. MS, University of Utah.

Ivanov, A. S., Boldyrev, A I. (2012). Reliable Predictions of Unusual Molecules Phys.Chem.Chem.Phys, 14, 15943 - 15952.

Jabes, B. S., Nayar, D., Dhabal, D., Molinero, V., Chakravarty, C. (2012). Water and Other Tetrahedral

Liquids: Order, Anomalies and Solvation. J. Phys. Cond. Matt., 24, 284116. Johnston, J. C., Molinero, V. (2012). Crystallization, Melting and Structure of Water Nanodroplets at

Atmospherically Relevant Temperatures. J. Am. Chem. Soc., 134, 6650-6659. Kamojjala, K., Swan, M.S., Brannon, R.M. (2012). Validation of Strain-Based Failure Models Using

Unnotched Charpy Tests. Paper presented at the ASME Verification and Validation Symposium,

Las Vegas, NV. Kim, J. (2012). Investigating Stratospheric Influences on Tropospheric Predictability. Ph. D., University of

Utah. Kim, Y. (2012). High-resolution regional climate simulations over mountainous terrain. MS, University of

Utah. Knott, C., Molinero, V., Doherty, M.F., Peters, B. (2012). Homogeneous nucleation of methane hydrates:

unrealistic at realistic conditions. J. Am. Chem. Soc., 134, 19544–19547.

Kochanski, A. K., Jenkins, M.A., Krueger, S.K. (2012). Lessons learned from multiscale atmosphere-fire simulations and their importance for WFDS development and a successful transition of FDS into a wildland fire model. Paper presented at the Building and Fire Research Laboratory Seminar Series, Gaithersburg, Maryland.

Krepl, M., Zgarbova, M., Stadlbauer, P., Otyepka, M., Banas, P., Koca, J., Cheatham, T.E., Jurecka, P.,

Sponer, J. (2012). Reference simulations of noncanonical nucleic acids with different chi variants of the AMBER force field: Quadruplex DNA, quadruplex RNA, and Z-DNA. J. Chem. Theory Comp., 8, 2506-2520.

Kwan, J. C., Donia, M.S., Han, W.H., Hirose, E., Haygood, M.G., Schmidt, E.W. (2012). Genome

streamlining and chemical defense in a coral reef symbiosis. PNAS.

Lareau, M., Horel, JD. (2012). Partial Removal of a Stable Boundary Layers in an Urbanized Mountain Basin. Paper presented at the 20th Symposium on Boundary Layers and Turbulence, Boston, MA.

Li, W.-L. R., C.; Galeev, T.R.; Wang, L-S.; Boldyrev, A.I. (2012). Transition-Metal-Centered Nine-Membered Boron Rings: M©B9 and M©B9. (M = Rh, Ir) J. Am. Chem. Soc., 134, 165 - 168.

Li, Z., Bedrov, D., Smith, G.D. (2012). Li+ Solvation and Transport Properties in Ionic Liquid/Lithium Salt Mixtures: A Molecular Dynamics Simulation Study. J. Phys. Chem. B., submitted.

Lin, Z., Flores, M., Fortez, I., Henriksen, N.M., Concepcion, G.P., Rosenber, G., Haygood, M.G., Olivera,

B.M., Light, A.R., Cheatham, T.E., Schmidt, E.W. (2012). Totopotensamides, polyketide-cyclic peptide hybrids from a Mollusk-associated bacterium Strepomyces sp. J. Natural Prod, 75,

644-649. Liu, C. C., D.; Zipser, E.J. (2012). Relationships between lightning flash rates and radar reflectivity

vertical structures in thunderstorms over the tropics and subtropics. J. Geophys. Res. Maojo, V., et al. (2012). Nanoinformatics: developing new computing applications for nanomedicine.

Computing, 94, 521 - 539.

Moore, E. B., Allen, J.T., Molinero, V. (2012). Liquid-ice coexistence below the melting temperature for water confined in hydrophilic and hydrophobic nanopores. J. Chem. Phys. C, 116, 7507-7514.

Mrowiec, A. A., Rio, C., Fridlind, A.S., Ackerman, A.S., DelGenio, A.D., Pauluis, O.M., Varble, A.C., Fan, J. (2012). Analysis of cloud-resolving simulations of a tropical mesoscale convective system

observed during TWP-ICE: Vertical fluxes and draft properties in convective and stratiform

regions. J. Geophys. Res., 117, D19201. doi: 10.1029/2012JD017759 Nguyen, A. H., Jacobson, L.C., Molinero, V. (2012). Structure of the clathrate/solution interface and

mechanisms of cross-nucleation of clathrate hydrates. J. Phys. Chem. C, 116, 19828–19838. Oates, R. (2012). Detection algorithms of stratospheric sudden warmings. MA, University of Utah.

Olson, J. K., Boldyrev, A.I. (2012). Electronic transmutation: Boron acquiring and extra electron

becomes 'carbon'. Chem Phys Lett, 523, 83 - 86. Osorio, E., Olson, J.K., Tiznado, W., Boldyrev, A.I. (2012). Analysis of Why Boron Avoids sp2

Hybridization and Classical Structures in the BnHn+2 Series Chem. Eur. J., 18, 9677-9681. Pare, P., Gribenko, A.V., Cox, L.H., Cuma, M., Wilson, A., Zhdanov, M.S., Legault, J., Smith, J., Polone, L.

(2012). 3D inversion of SPECTREM and ZTEM airborne electromagnetic data from the Pebble Cu-Au-Mo porphyry deposit. Alaska: Exploration Geophysics (Melbourne), 43, 104 - 115. doi:

10.1071/EG11044

Peterson, J., Beckvermit, J., Harman, T., Wight, C., Berzins, M. (2012). Multiscale Modeling of High Explosives for Transportation Accidents. Paper presented at the XSEDE ’12, New York, NY.

Pham., B. Q., Truong, T.N. (2012). Electronic spin transitions in finite-size graphene. Chemical Physics Letters, 535, 75 - 79.

Price, R. C., Huth, D., Smith, J., Harper, S., Pace, W., Pulver, G., Kahn, M.G., Schilling, L.M., Facelli, J.C.

(2012). Federated queries for comparative effectiveness research: Performance analysis Studies in Health Technology and Informatics, 175(9 - 18).

Prisbrey, K. (2012). Modeling experiences in materials processing“. Paper presented at the 2nd International Workshop on Materials Modeling and Simulations 2012, University of Malakand,

Chakdara, Pakistan. Pu, Z., Zhang, H. (2012). Assimilation of near surface observations over complex terrain: EnKF versus

3DVAR. Paper presented at the CMOS Congress 2012 & AMS 25th WAF/21st NWP, Montreal,

Quebec, Canada. Reicher, T., Kim, J., Manzini, E., Kroeger, J. (2012). A Stratospheric Connection to Atlantic Climate

Variability. Nature Geos, 783 - 787. doi: 10.1038/ngeo1586 Romanescue, C., Galeev, T.R., Sergeeva, A. P., Li, W-L., Wang, L-S, Boldyrev, A I. (2012). Experimental

and Computational Evidence of Octa- and Nona-Coordinated Planar Iron-Doped Boron Clusters:

Fe©B8- and Fe©B9- J. Organomet. Chem, 721-722, 148-154. Rutz, J. J., Steenburgh, J.W. (2012). Quantifying the role of atmospheric rivers in the interior western

United States. Atmos. Sci. Lett., 13(4), 257 - 261. Sarma, B., Smith, Y., Mohanty, S.K., Misra, M. (2012). Electrochemical Deposition of CdO on Anodized

TiO2 Nanotube Arrays for Enhanced Photoelectrochemical Properties. Materials Letters, 85(October), 33 - 36.

Setny, P. B., R; McCammon, JA. (2012). Comment on “Molecular-Driving Forces of the Pocket-Ligand

Hydrophobic Association” by G. Graziano, Chem. Phys. Lett. 533 (2012) 95. Chem Phys Lett(533), 95.

Shahrokh, K., Cheatham, T.E., Yost, G.S. (2012). Conformational dynamics of CYP3A4 demonstrate the important role of Arg212 coupled with the opening of ingress, egress and solvent channels to

dehydrogenation of 4-hydroxy-tamoxifen. Biochem. Biophys. Acta., 1820, 1605 - 1617.

Shahrokh, K. O., O.; Yost, G. S.; Cheatham, T.E. (2012). Quantum Mechanically Derived AMBER-Compatible Heme Parameters for Various States of the Cytochrome P450 Catalytic Cycle.

Journal of Computational Chemistry, 33, 119 - 133. Shepherd, T. D., Koc, M.A., Molinero, V. (2012). The quasi-liquid layer of ice under conditions of methane

clathrate formation. J. Phys. Chem. C, 116, 12172–12180.

Smith, Y. R., Sarma, B., Mohanty, S.K., Misra, M. (2012). Formation of TiO2-WO3 Nanotubular Composite via Single-Step Anodization and its Application in Photoelectrochemical Hydrogen Generation.

Electrochemistry Communications, 19(June), 131 - 134. Smith, Y. R., Sarma, B., Mohanty, S.K., Misra, M. (2012). Light Assisted Anodized TiO2 Nanotube Arrays.

ACS Appl. Mater. Interfaces, 4, 5883 - 5890. Sponer, J., Cang, X., Cheatham, T.E. (2012). Molecular dynamics simulations of G-DNA and perspectives

on the simulation of nucleic acid structures. Methods, 57, 25 - 39.

Staten, P. W. (2012). Understanding the causes and mechanisms of atmospheric circulation change. Ph.D., University of Utah.

Steenburgh, W. J., Massey, J.D., Painter, T.H. (2012). Episodic dust events of Utah's Wasatch Front and adjoining region. J. Appl. Meteor. Climate, 51, 1654 - 1669.

Steinmuller, B. M., M.; Hambrecht, K.; Smith, G.D.; Bedrov, D. (2012). Properties of random block

copolymer morphologies: Molecular dynamics and Single-Chain-in-Mean-Field simulations. Macromolecules, 45, 1107-1117.

Steinmuller, B. M., M.; Hambrecht, K.; Bedrov, D. (2012). Random Block Copolymers: Structure, Dynamics, and Mechanical Properties in the BUlk and at Selective Substrates. Macromolecules, 45, 9841 - 9853.

Stratton, S. (2012). Measurement of the Flux of Ultra-High Energy Cosmic Rays by the Telescope Array FADC Flourescence Detectors. Ph.S., State University of New Jersey, Rutgers.

Strong, C., Burian, S., Pomeroy, C. (2012, April 3 - 4, 2012). Climate Modeling to Support Urban Water Management in the Wasatch Range. Paper presented at the 2012 Spring Runoff Conference,

Logan, UT. Strong, C., Rassmussen, R., Ikeda, K. (2012). Dynamical downscaling of historical and projected winter

precipitation along the Wasatch Range for the CI-WATER project. Paper presented at the NCAR

Orographic Precipitation Workshop, Boulder, CO. Tokuno, e. a. (2012). New air fluorescence detectors employed in the Telescope Array experiment. A676,

54-65. Vatamanu, J., Borodin, O., Smith, G.D. (2012). Molecular Dynamics Simulation Studies of the Structure of

a Mixed Carbonate/LiPF6 Electrolyte near graphite Surface as a Function of Electrode Potential. J. Phys Chem, 116, 1114-1121.

Venkatasubramanian, S. (2012). Fast Multiple Kernel Learning using Multiplicative Weights Update.

submitted. Wall, C. L. Z., E.J.; Liu, C. (2012). A regional climatology of monsoonal precipitation in the southwestern

US using TRMM. J. Hydrometeor, 13, 310 - 323. Werner, E. W. M., T.-S.; Burckle, A. J. ; Sigman, M. S. (2012). Enantioselective Heck Arylations of Acyclic

Alkenyl Alcohols Using a Redox-Relay Strategy. Science, 338, 1455.

Whiteman, C. (2012). Meteorological Effects on Wintertime Cold-Air Pools in Utah's Salt Lake Valley. Paper presented at the 92nd Annual Meeting of the American Meteorological Society, New

Orleans, LA. Wilson, G. A., Cox, L.H., Cuma, M., Zhdanov, M.S. (2012). Inverting airborne geophysical data for

mega-cell and giga-cell 3D Earth models. The Leading Edge, 31, 316 - 321.

Xiong, J., White, H.S. (2012). The i–V response of an electrochemical cell comprising two polarizable microelectrodes and the influence of impurities on the cell response. J. of Electroanalytical Chem, 688, 354 - 359. doi: 10.1016/j.jelechem.2012.10.006

Young, J., Whiteman, C. (2012). Observing Characteristics of Wintertime Cold-Air Pools using Laser Ceilometers. Paper presented at the 15th Conference on Mountain Meteorology, Steamboat Springs, CO.

Zhang, L., Pu, Z., Lee, C., Zhao, Q. (2012). The influence of airborne Doppler radar data quality control

on numerical simulations of a tropical cyclone. Weather and Forecasting, 27, 231 - 239. Zhu, P., et al. (2012). A limited area model (LAM) intercomparison study of a TWP-ICE active monsoon

mesoscale convective event. J. Geophys. Res., 117, D11208. doi: 10.1029/2011JD016447 Zhu, Y., Kar, S., Free, M.L., Prisbrey, K. (2012). Long-term Corrosion Damage Prediction Modeling of

AA5083 Alloys Based on Experiment, Theory, and Molecular Dynamics Simulations. Paper

presented at the DoD Corrosion Conference.

2011

Armentrout, P. B. H., A. L.; Ye, S. J. (2011). Thermodynamics and Mechanisms for Decomposition of Protonated Glycine and Its Protonated Dimer. J Physical Chem A, 115, 11144 - 11155. doi:

10.1021/jp2025939

Bailey, B. (2011). THE IMPACT OF CANOPY GEOMETRY ON PARTICLE DISPERISON GRADIENTS IN SPARSE AGRICULTURAL CANOPIES. MA Thesis, University of Utah, Salt Lake City.

Bardwell, D. A., et al. (2011). Towards crystal structure prediction of complex organic compounds - a report on the fifth blind test. Acta Cryst., B67, 535 - 551.

Bikiel, D. E., Ramallo-Lopez, J.S., Requejo, F. G., Ona, O.B., Ferraro, M.B., Facelli, J.C., Doctorovich, F.

(2011). Formation of one dimensional linear chains by Ir-Ir bonds in cis-dicarbonyldicholoroiridate (I). Polyhedron, 30, 221 - 227.

Bogenschutz, P. A. (2011). Improving the representation of turbulence and clouds in cloud resolving models and general circulation models. Ph.D., University of Utah.

Burghardt, J. (2011). Nonlocal plasticity, instablility, and wellposedness of the elastic-plastic initial-boundary value problem. Ph.D., University of Utah, Salt Lake City, Utah.

Burghardt, J. A. (2011). Nonlocal plasticity, instablility, and well-posedness of the elastic-plastic initial-boundary value problem. Ph.D., University of Utah, Salt Lake City, UT.

Cang, X., Sponer, J., Cheatham, T.E. (2011). Explaining the varied glycosidic conformational, G-tract

length and sequence preferences for anti-parallel G-quadruplexes. Nuc. Acids Res., 39, 4499-4512.

Cang, X., spner, J., Cheatham, T.E. (2011). Insight into G-DNA structural polymorphism and folding from

sequence and loop connectivity through free energy analysis. J. Amer. Chem. Soc. Coon, J. (2011). HIFU treatment time reduction in superficial tumours through focal zone path selection.

International Journal of Hyperthermia, 27(5), 465 - 481. Coon, J. (2011). Treatment Time Reduction through Parameter Optimization in Magnetic Resonance

Guided High Intensity Focused Ultrasound Treatments. Ph.D., University of Utah, Salt Lake City, UT.

Cooper, T. E. A., P. B. (2011). Sequential Bond Energies and Barrier Heights for the Water Loss and

Charge Separation Dissociation Pathways of Cd2+(H2O)n, n = 3 – 11. J. Chem. Phys., 134. doi: 10.1063/1.3553813

Cooper, T. E. C., D. R.; Oomens, J.; Steill, J. D.; Armentrout, P. B. . (2011). Infrared Spectroscopy of Divalent Zinc and Cadmium Crown Ether Systems. J Physical Chem A, 115, 5408 - 5422. doi:

10.1021/jp202646y

Crosman, E. T. (2011). Idealized large-eddy simulation sensitivity studies of sea and lake breezes. Ph.D, University of Utah, Salt Lake City, UT. Retrieved from

http://content.lib.utah.edu/u?/us-etd3,20977 Crowl, L. M. F., A.L. (2011). Analysis of mechanisms for platelet near-wall excess under arterial blood

flow conditions. International Journal for Numerical Methods in Biomedical Engineering, 676,

348-375. DeMille, T., Cheatham, T, Molinero, V. (2011). A Coarse-Grained Model of DNA with Explicit Solvation by

Water and Ions. J. Phys. Chem. B., 115(1), 132 - 142. Dixon, A. S., Pendley, S.S., Bruno, B.J., Woessner, D.W., Shimpi, A.A., Cheatham, T.E., Lim, C.S. (2011).

Disruption of Bcr-Abl coiled coil oligomerization by design. J. Biol Chem, 286, 27751-27760. Ebbert, M. B., RL; Boucher, KM; Martin, M; Carrasco, E; Caballero, R; Stijleman, IJ; Bernard PS; Facelli,

JC. (2011). Characterization of uncertainty in the classification of multivariate assays:

application to PAM50 centroid-based genomic predictors for breast cancer treatment plans. Journal of Clinical Bioinformatics, 1(37), 1 - 9.

Facelli, J. C. (2011). Chemical shift tensors: Theory and application to molecular structural problems. Progress in Nuclear Magnetic Resonance Spectroscopy, 58, 176 - 201.

Ford, S. G., EJ; Thorne, MS. (2011). Differential t* measurements via instantaneous frequency matching:

observations of lower mantle shear attenuation heterogeneity beneath western Central America. Geophysical Journal International, 189, 513 - 523. doi: 10.1111/j.1365-246X.2011.05348.x.

Galeev, T. R., Chen, Q.; Guo, J.; Bai, H.; Miao, C.; Lu, H.; Sergeeva, A.P.; Li, S.; Boldyrev, A.I. (2011). Deciphering the mystery of hexagon holes in an all-boron graphene α-sheet. Phys. Chem, Chem Phys., 13, 11575 - 11578.

Galeev, T. R., Boldyrev, A.I. (2011). Planarity takes over in the CxHxP6−x (x = 0-6) series at x = 4. Phys.

Chem, Chem Phys.((DOI: 10.1039/C1CP21959F)).

Galeev, T. R., Romanescu, C., Li, W., Wang, L., Boldyrev, A.I. (2011). Valence isoelectronic substitution in the B8

- and B9- molecular wheels by an AI dopant atom: Umbrella-like structures of AIB7

- and

AIB8-. Journal of Chemical Physics, 135, 104301-104301 -104301-104307.

Galeev, T. R. I., A.S.; Romanescu, C.; Li. W.; Bozhenko, K.V.; Wang, l.; Boldyrev, A.I. (2011). Molecular

wheel to monocyclic ring transition in boron-carbon mixed clusters C2B6−

and C3B5−. Phys. Chem. Chem. Phys., 13(19), 8805-8810. Gerber, E., Reichler, T. . (2011). The Impact of Climate Change on the Spatial and Temporal Structure of

the Annular Modes. Paper presented at the WCRP open science conference, Session: Large-scale Climate Variability and Change, Denver, CO.

Gerber, E., Reichler, T. (2011). Stratosphere-Troposphere Coupling: Characterizing intraseasonal variability with the annular modes. Paper presented at the WCRP open science conference,

Denver, CO.

Gonzales Solveryra, E., de la Llave, Scherlis, D.A., Molinero, V. (2011). Melting and crystallization of ice in partially filled nanopores. J. Phys. Chem. B, 115, 14196–14204.

Harper, K. C., Sigman, M.S. (2011). Predicting and optimizing asymmetric catalyst performance using the principles of experimental design and steric parameters. Proc Natl Acad Sci U S A., 108(6), 2179.

Harper, K. C., Sigman, M.S. (2011). Three-Dimensional Correlation of Steric and Electronic Free Energy

Relationships Guides Asymmetric Propargylation. Science, 333, 1875 - 1878. Hofstetter, T. E. H., C.; Berden, G.; Oomens, J.; Armentrout, P. B. . (2011). Structural Elucidation of

Biological and Toxicological Complexes: Investigation of Monomeric and Dimeric Complexes of Histidine with Multiply Charged Transition Metal (Zn and Cd) Cations using IR Action

Spectroscopy. J. Phys Chem B, 115, 12648 - 12661. doi: 10.1021/jp207294 Huang, M., F. Cavallo, Feng Liu and M. G. Lagally. (2011). Nanomechanical Architecture of

Semiconductor Nanomembranes. Nanoscale, 3(96).

Huang, S. (2011). Characterization of shallow shear wave velocity structures in southwestern Utah. M.S., University of Utah.

Hujo, W., Jabes, B.S., Rana, V.K., Chakravarty, C., Molinero, V. (2011). The Rise and Fall of Anomalies in Tetrahedral Liquids. J. Stat. Phys, 145, 293.

J. Lu, C., G., Reichler, T., Kang, S. . (2011). Seasonality in the zonal mean circulation and response to climate change. Paper presented at the Workshop on Hierarchical Modeling of Climate, ICTP, Trieste, Italy.

Jacobson, J. C., Molinero, V. (2011). Can Amorphous Nuclei Grow Crystalline Clathrates? The Size and Crystallinity of Critical Clathrate Nuclei. J. Am. Chem. Soc., 133, 6458-6463.

Jacobson, L. C., Matsumoto, M., Molinero, V. (2011). Order parameters for the multistep crystallization of

clathrate hydrates. J. Chem. Phys., 135, 074501. Jenkins, M. A., Kochanski, A., Krueger, S. (2011). The fluid dynamics of steady-state fireline propagation.

Paper presented at the 9th Symposium on Fire and Forest Meteorology, Palm Springs, CA. Johansen, D., Jeffries, C. M. J., Hammouda, B., Trewhella, J. & Goldenberg, D. P. (2011). Effects of

macromolecular crowding on an intrinsically disordered protein characterized by small-angle neutron scattering with contrast matching. Biophysical Journal, 100, 1120 - 1128.

Johnston, J. C., Phippen, S., Molinero, V. (2011). A Single-Component Silicon Quasicrystal. J. Phys. Chem. Lett., 2, 384 - 388.

Kim, J., Austin, J., Gerber, E., Reichler, T. (2011). Stratosphere-Troposphere Coupling: Stability of the annular mode time scale and role of the stratosphere. Paper presented at the WCRP open science conference, Denver, CO.

Kochanski, A., . M.A. Jenkins, Krueger, S., Mandel, J., Beezley, J., Clements, C. (2011). Coupled atmosphere-fire simulations of the FireFlux experiment: Impacts of model resolution on its performance. Paper presented at the 9th Symposium on Fire and Forest Meteorology, Palm

Springs, CA. Kochanski, A., Jenkins, M.A., Sun, R., Krueger, S., Abedi, S., Charney, J.J. (2011). The importance of

low-level environmental vertical wind shear to wildfire propagation. International J. Wildland Fire. Le, L., Molinero, V. (2011). Nanophase Segregation in Supercooled Aqueous Solutions and their Glasses

Driven by the Polyamorphism of Water. J. Phys. Chem. B, 115, 132 - 142.

Leiderman K.; Fogelson, A. L. (2011). Grow with the flow: a spatial-temporal model of platelet deposition and blood coagulation under flow. Mathematical Medicine and Biology, 28, 47 - 84.

Levkova, L., DeTar, C. (2011). Charm annihilation effects on the hyperfine splitting in charmonium. Phys. Rev. D., 83, 074504.

Li, W.-L. R., C.; Galeev, T.R.; Wang, L-S.; Boldyrev, A.I. (2011). Aluminum Avoids the Central Position in

AlB9- and AlB10-: Photoelectron Spectroscopy and ab Initio Study J. Phys Chem A, 115, 10391 - 10397.

Liu, C. (2011). Rainfall contribution from precipitation systems with different sizes, intensities and durations. J. Hydrometeor, 12, 394 - 412.

Liu, C., Cecil, D., Zipser, E.J. (2011). Relationships between lightning flash rates and passive microwave brightness temperatures at 85 and 37 GHz over the tropics and subtropics. J. Geophys. Res, 116,

D12206. doi: 10.1029/2010JD015180

Liu, Z. L., C.X.; Wu, Y.S.; Duan, W. H.; Liu, F.; Wu, J. (2011). Stable Nontrivial Z2 Topology in Ultrathin Bi (111) Films: A First-Principles Study. Phys Rev Lett, 107, 136805.

Ma, H., Pazmino, E.F., Johnson, W.P. (2011). Gravitational settling effects on unit cell predictions of colloidal retention in porous media in the absence of energy barriers. Environmental Science & Technology, 45(19), 8306-8312. doi: DOI 10.1021/es200696x

Ma, H., Pazmino, E., Johnson, W.P. (2011). Surface heterogeneity on hemispheres-in-cell model yields all experimentally-observed non-straining colloid retention mechanisms in porous media in the

presence of energy barriers. Langmuir, 27(24), 14982-14994. doi: DOI 10.1021/la203587j Ma, M., Pu, Z., Wang, S., Zhang, Q. (2011). Characteristics and numerical simulations of extremely large

atmospheric boundary-layer heights over an arid region in north-west China. Boundary Layer Meteorology, 140, 163 - 176. doi: DOI:10.1007/s10546-011-9608-2

Meyers, M., and W. J. Steenburgh. (2011). Mountain weather prediction: Phenomenological challenges

and forecast methodology. In S. d. W. T. Chow, and B. Snyder (Ed.), Mountain Weather Research and Forecasting.

Moore, E. B., Moliero, V. (2011). Is it cubic? Ice crystallization from deeply supercooled water. Phys. Chem. Chem. Phys., 13, 20008-20016.

Moore, E. B., Moliero, V. (2011). Structural Transformation in Supercooled Water Controls the

Crystallization Rate of Ice. Nature, 479, 506-508. Niu, X. B. S., G. B.; Liu, F. (2011). Nonequilibrium Composition Profiles of Alloy Quantum Dots and their

Correlation with the Growth Mode. Phys Rev Lett, 107, 076101. Niu, X. B. S., G. B.; Liu, F. (2011). Phase separation in strained epitaxial InGaN islands. Appl. Phys. Lett,

99, 213102.

Olson, J. K., Boldyrev, A.I. (2011). Ab initio characterization of the flexural B3H8- anion found in the

reversible dehydrogenation. Computational and Theoretical Chemistry, 967, 1-4.

Olson, J. K., Boldyrev, A.I. (2011). Ab Initio Search for Global Minimum Structures of Neutral and Anionic B4H5 Clusters.

Optical Isomerism in B4H5 and B4H5. Chem. Phys. Lett., ASAP((DOI: 10.1016/j.cplett.2011.10.009)). Oña, O. B., Ferraro, M.B., Facelli, J.C. (2011). Transition from exo to endo Cu absorption in CuSin

clusters: A genetic algorithms density functional theory (DFT) study. Molecular Simulation(Feb),

1 - 11. Pennell, C., Reichler, T. (2011). On the effective number of climate models. J. Climate, 24(9),

22358-22367. Peterson, M. L., C. (2011). Global statistics of lightning in anvil and stratiform regions over tropics and

subtropics observed by TRMM. J. Geophys. Res., 1167, D23201. doi: 10.1029/2011JD15908

Reichler, T., Austin, J., Kim. J. (2011). Stratosphere-Troposphere Coupling: Evidence for Stratospheric Impacts on Ocean Circulation. Paper presented at the WCRP open science conference, Session:

Large-scale Climate Variability and Change, Denver, CO. Romanescu, C. G., T.R.; Li, W-L.; Boldyrev, A.I.; Wang, L-S. (2011). Aromatic Metal-Centered Monocyclic

Boron Rings: Co©B8− and Ru©B9−. Chem. Int. Ed., 50, 9334-9337. Rowley, J. W. O., A.J.; Tolley, N. D.; Hunter, B. N.; Low, E. N.; Nix, D.A.; Yost, C.C.; Zimmerman, G.A.;

Weyrich, A.S. (2011). e-Blood Genome-wide RNA-seq analysis of human and mouse platelet

transcriptomes. Blood, 118(doi:10.1182/blood-2011-03-339705). Shahrokh, K., Orendt, A., Yost, G.S., Cheatham, T.E. (2011). Quantum mechanically derived

AMBER-compatible heme parameters for various states of the cytochrome P450 catalytic cycle. J Comp Chem, 33(2), 119 - 133.

Smith, C. D., Zimin A, Holt C, Abouheif E, Benton R, Cash E, Croset V, Currie CR, Elhaik E, Elsik CG, Fave

MJ, Fernandes V, Gadau J, Gibson JD, Graur D, Grubbs KJ, Hagen DE, Helmkampf M, Holley JA, Hu H, Viniegra AS, Johnson BR, Johnson RM, Khila A, Kim JW, Laird J, Mathis KA, Moeller JA,

Muñoz-Torres MC, Murphy MC, Nakamura R, Nigam S, Overson RP, Placek JE, Rajakumar R, Reese JT, Robertson HM, Smith CR, Suarez AV, Suen G, Suhr EL, Tao S, Torres CW, van

Wilgenburg E, Viljakainen L, Walden KK, Wild AL, Yandell M, Yorke JA, Tsutsui ND. (2011). Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile). Proc Natl Acad Sci U S A., 108(14), 5673-5678.

Smith CR, S. C., Robertson HM, Helmkampf M, Zimin A, Yandell M, Holt C, Hu H, Abouheif E, Benton R, Cash E, Croset V, Currie CR, Elhaik E, Elsik CG, Favé MJ, Fernandes V, Gibson JD, Graur D,

Gronenberg W, Grubbs KJ, Hagen DE, Viniegra AS, Johnson BR, Johnson RM, Khila A, Kim JW, Mathis KA, Munoz-Torres MC, Murphy MC, Mustard JA, Nakamura R, Niehuis O, Nigam S,

Overson RP, Placek JE, Rajakumar R, Reese JT, Suen G, Tao S, Torres CW, Tsutsui ND,

Viljakainen L, Wolschin F, Gadau J. (2011). Draft genome of the red harvester ant Pogonomyrmex barbatus. Proc Natl Acad Sci U S A., 108(14), 5667-5672.

Staten, P., Lu, J., Reichler, T. . (2011). Structure and mechanisms of tropospheric circulation change in a warming climate. Paper presented at the WCRP open science conference, Session: Large-scale

Climate Variability and Change. Steenburgh, W. J., D. M. Schultz, B. Snyder, and M. Meyers,. (2011). Bridging the gap between

operations and research to improve weather prediction in mountainous regions. In S. d. W. T.

Chow, and B. Snyder (Ed.), Mountain Weather Research and Forecasting. Thomas, K. C., Ethirajan, M., Shahrokh, K., Sun, H., Lee, J., Cheatham, T.E., Yost, G.S., Reilly, C.A.

(2011). Structure activity relationship of capsaicin analogues and TRPV1-mediated human lung epithelial cell toxicity. J. Pharm. Exp. Ther, 337, 400-410.

Varble, A. F., A.M.; Zipser, E.J; Ackerman, A.S.; Chaboureau, J.P.; Fan, J; Hill, A.; McFarlane, A.S.;

Pinty, J.P.; Shipway, B. (2011). Evaluation of cloud-resolving model intercomparison simulations using TWP-ICE observations: Precipitation and cloud structure. J. Geophys. Res, 116, D12206.

doi: 10.1029/2010JD015180 Wang, Z., Y. Zhang, and Feng Liu. (2011). Formation of hydrogenated graphene nanoripples by strain

engineering and directed surface self-assembly. Phys Rev. B, 83, 041403 (R).

Wang, Z. F. L., F. (2011). Giant Magnetoresistance in Zigzag Graphene Nanoribbon. Appl. Phys. Lett, 99, 213102.

Wei, X., Henriksen, N.M., Skalicky, J.J., Harper, M.K., Cheatham, T.E., Ireland, C.M., VanWagoner, R.M. (2011). Araiosamines A-D: Tris-bromoindole cyclic quanidine alkaloids from the marine sponge

clathria (Thalysias) araiosa. J. Org. Chem,. 76, 5515- 5523. West, G. L., and W. J. Steenburgh. (2011). Influences of the Sierra Nevada on Intermountain cold-front

evolution. Mon. Wea. Rev., 139, 3184 - 3207.

Winkel, K., et al. (2011). Structural Study of Low Concentration LiCl Aqueous Solutions in the Liquid, Supercooled and Hyperquenched Glassy State. J. Chem. Phys., 134, 024515.

Wu, D. L., M.G.; Liu, F. (2011). Stabilizing Graphitic Thin Films of Wurtzite Materials by Epitaxial Strain. Phys Rev Lett, 107, 236101.

Wu, S., Haiying Zhang, and Cairns, B.R. . (2011). Genes for embryo development are packaged in blocks

of multivalent chromatin in zebrafish sperm Genome Research, 21(4), 578 - 589. Xing, L. B., O.; Smith, G.D., Li. W. (2011). A density functional theory study of the role of anions on the

oxidative decomposition reaction of propylene carbonate. J. Phys. Chem. A., 115, 13896 - 13905. Xu, L., Molinero, V. (2011). Is there a liquid-liquid transition in confined water? J. Phys. Chem. B, 115,

14210–14216. Yandell, M., Huff C, Hu H, Singleton M, Moore B, Xing J, Jorde LB, Reese MG. (2011). A probabilistic

disease-gene finder for personal genomes. Genome Research, 21(9), 1529-1542.

Zgarbova, M., Otyepka, M., Sponer, J., Mladek, A., Banas, P., Cheatham, T.E., Jurecka, P. (2011). Refinement of the Cornell et all nucleic acid force field based on reference quantum chemical

calculations of torsion profiels of the glycosidic torsion. J. Chem. Theory Comp. Zhang, L., Pu, Z. (2011). Four-dimensional Assimilation of Multi-time Wind Profiles Over a Single Station

and Numerical Simulation of a Mesoscale Convective System Observed During IHOP_2002. Mon. Wea. Rev., 139, 3369-3388.

Zhdanov, M. S., Cuma, M., Wilson, G., Velikhov, E. P., Black, N., Gribenko, A. (2011). Iterative

electromagnetic migration for 3D inversion of marine controlled-source electromagnetic data. Geophysical Prospecting, 59, 1101 - 1113.

Zhdanov, M. S., Wan, L., Gribenko, A., Cuma, M., Key, K., Constable, S. (2011). Large-scale 3D inversion of marine magnetotelluric data: Case study from the Gemini prospect, Gulf of Mexico.

Geophysics, 76, 77 - 87.

Zhdanov, M. S., Smith, R. B., Gribenko, A., Cuma, M., Green, M. (2011). Three-dimensional inversion of large-scale EarthScope magnetotelluric data based on the integral equation method: Geoelectrical

imaging of the Yellowstone conductive mantle plume. Geophys. Res. Lett, 38, L08307.

2010

Abbasi, R. U., et al. (2010). Analysis of large-scale Anisotropy of Ultra-High Energy Cosmic Rays in HiRes

Data. The Astrophysical Journal Letters, 713(1), L64 - L68. Alcott, T. I., Steenburgh, W. J. (2010). Snow-to-liquid ratio variability and prediction at a high elevation

site in Utah's Wasatch Mountains. Wea. Forecasting, 25(1), 323 - 337. Baldwin, M., Gillett, N., Forster, P., Gerber, E., Hegglin, M., Karpechko, A., Kim, J., Kushner, P.,

Morgenstern, O., Reichler, T., Son, s., Tourpali, K., . (2010). Effects of the stratosphere on the

troposphere. In T. G. S. V. Eyring, D. W. Waugh (Ed.), SPARC CCMVal (2010): SPARC CCMVal Report on the Evaluation of Chemistry-Climate Models.

Bhutia, S., Jenkins, M.A., Sun, R. (2010). Comparison of firebrand propagation prediction by a plume model and a coupled fire/admosphere large eddy simulator. J of Advances in Modeling Earth Systems, 2.

Bogenschutz, P. A., Krueger, S. K., Khairoutdinov, M. (2010). Assumed probability density functions for shallow and deep convection. J. Adv. Model. Earth Syst., 2(Art. #10). doi:

doi:10.3894/JAMES.2010.2.10 Burghardt, J. A. L., B.; Guilkey, J.E.; Xue, X.; Brannon, R. . (2010). Application of Uintah-MPM to shaped

charge jet penetration of aluminum. Paper presented at the 9th World Congress on

Computational Mechanics,. Ci, L., Son, L., Jin, C., Jariwala, D., Wu, D., Li, Y., Srivastava, A., Wang, Z.F., Storr, K., Balicas, L., Liu, F.,

Ajayan, P. M. (2010). Atomic layers of hybridized boron nitride and graphene domains. Nature Materials, 9, 430.

Ci, L., L. Song, C. Jin, D. Jariwala, D. Wu, Y. Li, A. Srivastava, Z.F. Wang, K. Storr, L. Balicas, Feng, & Liu, P. M. A. (2010). Atomic Layers of Hybridized Boron Nitride and Graphene Domains. Nature Materials, 9, 430.

Coon, J. (2010). Dose Delivery Time Reduction Through Optimization of Focal Zone Path, Power, and Size International Symposium on Therapeutic Ultrasound (Vol. Poster).

Crosman, E. T., Horel, J.D. (2010). Numerical and observational study of the Great Salt Lake Breeze. Paper presented at the 2010 Great Salt Lake Issues Forum, Salt Lake City, UT.

Crosman, E. T., Horel, J.D. (2010). The sensitivity of sea and lake breezes to variations in surface and atmospheric state in large-eddy simulations. Paper presented at the 14th conference on Mountain Meteorology, Olympic Village, CA.

Crowl, L., Fogelson, A. (2010). Computational model of whole blood exhibiting lateral platelet motion induced by red blood cells. Int j numer method biomed eng, 26(3-4), 471 - 487.

Cuma, M., Wilson, G.A., Zhdanov, M.S., Velikhov, E.P., Black, N., and Gribenko, A.V. (2010, October 17 - 22, 2010). Multiple inversion scenarios for enhanced interpretation of CSEM data using iterative

migration: A case study for the Shtokman gas field, Barents Sea. Paper presented at the SEG

Exhibition and 80th Annual Meeting, Denver, CO. De la Llave, E., Molinero, V., Scherlis, A. (2010). Water filling of a hydrophilic nanopore. J Chem Physics,

133, 034513. Du, J., Fogelson, A. (2010). A Cartesian Grid Method for Two-Phase Gel Dynamics on Irregular Domains.

International Journal for Numerical Methods in Fluids, 67(12). doi: 10.1002/fld.2445

Espejo, V. R., Le, X., Rainier, J.D. (2010). Cyclopropylazetoindolines as Precursors to C(3)-Quaternary-Substituted Indolinens. J American Chem Society, 132(24), 8282 - 8284.

Espinal, J. F., Mondragon, F., Truong, T. N. (2010). Thermodynamic evaluation of steam gasification mechanisms of carbonaceous materials. Carbon, 47(13), 3010 - 3018.

Freedman, H., Huynh, L. P., Le, L., Cheatam III, T.E., Tuszynski, J., Truong, T. N. (2010). Explicitly-Solvated Ligand contribution to Continuum solvation models for Binding Free Energies:

Selectivity of Theophylline Binding to an RNA Aptamer. Journal of Physical Chemistry B, 114(6),

2227 - 2237. Garcia-Hernandez, A., Facelli, J.C., Colom, L.C. (2010). Understanding synchronization and

hyper-synchronization in the septo-hippocampal system. Neuroscience, 11 (Suppl 1), 124. Gregg, K. L., Fogelson, A. (2010). Grow with the flow: A spatial-temporal model of platelet deposition

and blood coagulation under flow. Math Med Biology.

Gribenko, A. V., Green, A.M., Cuma, M., and Zhdanov, M.S. (2010). Efficient 3D inversion of MT data using integral equations and the receiver footprint approach application to the large-scale inversion of EarthScope data. Paper presented at the SEG Exhibition and 80th Annual Meeting, Denver, CO.

Halling, M. D., Orendt, A. M., Strohmeier, M., Solum, M.S., Tsefrikas, V. M., Hirao, T., Scott, L.T., Pugmire, R. J., Grant, D. M. (2010). Solid-state 13C NMR investigations of

4,7-dihydro-1H-tricyclopenta-[def,jkl, pqr]triphenylene (sumanene) and indeno

[1,2,3-cd]fluoranthene: Buckminsterfullerene moieties. Phys. Chem. Chem. Phys., 12, 7934 - 7941.

J. Lu, C., G., Frierson, D., Reichler, T. (2010). Differentiate the causes for the widening of the Hadley circulation through the regime change and seasonal cycle of mean circulation. Paper presented at

the American Geophysical Union Fall Meeting, San Francisco, CA.

Jacobson, L., Molinero, V. (2010). A Methane-water Model for Coarse-Grained Simulations of Solutions and Clathrate Hydrates. J. Phys. Chem. B, 114, 7302-7311.

Jacobson, L. C., Hujo, W., Molinero, V. (2010). Amorphous Precursor in the Nucleation of Clathrate Hydrates. JACS, 132, 11806 - 11811.

Jacobson, L. C., Huyo, W., Molinero, V. (2010). Nucleation Pathways of Clathrate Hydrates: Effect of

Guest Size and Hydrophilicity. J. Phys. Chem. B., 114, 13796 - 13807. Jeglum, M. E., W. J. Steenburgh, T. P. Lee, and L. F. Bosart. (2010). Multi-reanalysis climatology of

Intermountain cyclones. Mon. Wea. Rev., 138, 4035 - 4053. Jenkins, M. a., Kochanski, A., Krueger, S., McDermott, R., and Mell, W. (2010). The fluid dynamical forces

involved in grass fire propagation. Paper presented at the American Geophysical Union Fall Meeting, San Francisco, CA.

Jenkins, M. A., Kochanski, A., Krueger, S. (2010). The importance of wind in the fire environment. Paper

presented at the Wildland Fire Workshop, 24th Annual Advance Combustion Engineering Research Center, Provo, UT.

Johnston, J. C., Kastelowitz, N., Molinero, V. (2010). Liquid to quasicrystal transition in bilayer water. J. Chem. Phys., 133, 154516.

Kastelowitz, N., Johnston, J.C., Molinero, V. (2010). The Anomalously High Melting Temperature of

Bilayer Ice. J. Chem. Phys,, 132, 124511. Kochanski, A., Jenkins, M.A., Krueger, S., McGermott, R., Mell, W. (2010). Evaluation of the fire plume

dynamics simulated by WRF-fire. Paper presented at the American Geophysical Union Fall Meeting, San Francisco, CA.

Kochanski, A., . M.A. Jenkins, S. Krueger, R. McDermott, and W. Mell. (2010). Forecasting for Fire modeling. Atmospheric Sciences Department, University of Utah. Salt Lake City, UT.

Kochanski, A., Jenkins, M.A., Krueger, S., McGermott, R., Mell, W. (2010). Wind Forecasting for Fire Modeling. Building and Fire Research Laboratory, Nat'l Institute of Standards and Technology. Gaithersburg, MD.

Kochanski, A., Jenkins, M.A., Krueger, S. (2010). Wind Forecasting in the Fire Environment. Paper presented at the Wildland fire Workshop, 24th Annual Advance Combustion Engineering Research

Center, Provo, UT.

Lavery, R., Zakrezewska, K., Beveridge, D. L., Bishop, T.C., Case, D.A., Cheatham, T.E., Dixit, S., Jayaram, B., Lankas, F., Laughton, C., Maddocks, J. H., Michon, A., Osman, R., Orozco, M.,

Perez, A., Singh, T., Spackova, N., Sponer, J. (2010). A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in

B-DNA. Nuc. Acids Res., 38, 299 - 313. Le, L., Molinero, V. (2010). Nanophase segregation in supercooled aqueous solutions and their glasses

driven by the polyamorphism of water. J. Phys. Chem. A. Levesque, C. A., et al. (2010). Genome sequence of the necrotrophic plant pathogen Pythium ultimum

reveals original pathogenicity mechanisms and effector repertoire. Genome biology, 11, R73.

Liu, C. W., E.; Zipser, E.J.; Burns, G. (2010). Diurnal variations of global thunderstorms and electrified shower clouds and their contribution to the global electrical circuit. J. Atmos. Sci., 67, 309 - 323.

Liu, Z., J. Wu, W. Duan, M.G. Lagally and Feng Liu. (2010). Electron Phase Diagram of Single-Element

Silicon "Strain" Superlattice. Phys Rev Lett, 105, 016802. Lupton, E. M., Chen, L., Liu, F. (2010). Uniaxial Strain in Molecular Nanowires: A Case Study of B-phase

Polyfluorenes. Chem. Phys. Lett., 1, 1326. Ma, J., Johnson, W. P. (2010). Colloid Retention in Porous Media of Various Porosites: Predictions by the

Hemispheres-in-Cell Model. Langmuir, 26(3), 1680 - 1687. Manzini, E., Matthes, K., Blume, c., Bodeker, G., Cagnazzo, C., Calvo, N., Charlton-Perrex, A., Douglass,

A., Fogli, P., Gray, L., Kim J., Kodera, K., Kunze, M., Ortiz, C., Randel, B., Reichler, T.,

Stenchikov, G., Timmreck, C., Toohey, M., Yoden, S. (2010). Natural Variability of Stratospheric Ozone, Chapter 8. In T. G. S. V. Eyring, D.W. Waugh (Ed.), SPARC CCMVal (2010): SPARC CCMVal Report on the Evaluation of Chemistry-Climate Models

Martin, G. M., Senior, S F, Ineson, S., James, P., Milton, S.F., Brooks, M.E., Reichler, T., Kim, J. (2010).

Analysis and reduction of systematic errors through a seamless approach to modelling weather

and climate. J. Climate, 23, 5933 - 5957. Masiker, M. C., Mayne, M.C., Boone, B. J., Orendt A., Eyring, E.M. (2010). 7Li NMR chemical shift titration

and theoretical DFT calculation studies: solvent and anion effects on second-order complexation of 12-crown-4 and 1-aza-12-crown-4 with Lithium cation in several aprotic solvents. Magnetic Resonance in Chemistry, 48, 94 - 100.

Moore, E. B., de la Llave, E., Welke, K., Scherlis, D.A., Molinero, V. (2010). Freezing, Melting and Structure of Ice in a Hydrophobic Nanopore. Phys. Chem. Chem. Phys., 12, 4124 - 4134.

Moore, E. B., Molinero, V. (2010). Ice crystallizatioin in water's "no-man's land. J. Chem. Phys., 132, 244504.

Oler, A., Alla RK, Roberts DN, Wong A, Hollenhorst PC, Chandler KJ, Cassiday PA,, & Nelson CA, H. C., Graves BJ, Cairns B.R. (2010). Human RNA polymerase III transcriptomes and relationships to

Pol II promoter chromatin and enhancer-binding

factors. Nat Struct Mol Biol, 17(5), 620 - 628. Olson, J. (2010). AB INITIO SEARCH FOR NOVEL BXHY BUILDING BLOCKS WITH POTENTIAL FOR

HYDROGEN STORAGE. Ph.D. Dissertation, Utah State University, Logan, UT. Oppermann, C., Crosman, E., Horel, J.D. (2010). Observational study of the Great Salt Lake Breeze.

Paper presented at the Annual Meeting of the American Meteorological Society, Atlanta, GA.

Patterson, O., Igo, S., Hurdle, J.F. (2010). Automatic Acquisition of Sublanguage Semantic Schema: Towards the Word Sense Disambiguation of Clinical Narratives. Paper presented at the AMIA

2010. Paulsen, R. B., Seth, P.P., Swayze, E.E., Griffey, R.H., Skalicky, J.J., Cheatham, T.E., Davis, D.R., .

(2010). Inhibitor induced structure change in the HCV IRES domain IIa RNA. Proc. Natl. Acad. Sci., 107(16), 7263 - 7268. doi: 10.1073/pnas.0911896107

Pennell, C., Reichler, T. (2010). On the effective number of climate models. J. Climate, e-View. doi:

10.1175/2010JCLI3814.1 Price, R. C., Pettey, W., Freeman, T., Keahey, K., Leecaster, Samore, M., Tobias, J., Facelli, J.C. (2010).

SaTScan on a Cloud: On-Demand Large Scale Spatial Analysis of Epidemics. Online Journal of Public Health Informatics, 2(1), 1-11.

Pu, S., Zhang, L., Emmitt, G.D. (2010). Impact of airborne Doppler wind lidar data on numerical

simulation of a tropical cyclone. Geophys. Res. Lett., 37, L05801. Rai, K., Sharmistha Sarkar, Talmage J. Broadbent, Matthew Voas, Kenneth F., Grossmann, L. D. N.,

Somaye Dehghanizadeh, Fanuel T. Hagos, Yumei Li,, Rachel K. Toth, S. C., Timothy M. Bahr, W. Evan Johnson, Brad Sklow,, & Randall Burt, C. B. R., David A. Jones. (2010). DNA Demethylase

Activity Maintains Intestinal Cells in an Undifferentiated State Following Loss of APC. Cell. Cell, 142(6), 930-942.

Ratkiewicz, A., Bieniewska, J., Truong, T. N. (2010). Kinetics of the Hydrogen Abstraction R-OH + H -->

R-O* + H2 Reaction class. International Journal of Chemical Kinetics, 43(2), 78 - 98. Rost, S., Garnero, E.J, Thorne, M.S., Hutko, A.R. (2010). On the absence of an ultralow-velocity zone in

the North Pacific. Journal of Geophysical Research, 115, B04312. doi: 10.1029/2009JB006420 Rutz, J., Reichler, T., Lu, J. (2010). Atmospheric circulation trends in millenium-length climate

simulations. Paper presented at the AMS 22nd Conf. on Climate Variability and Change, Atlanta,

GA. Rutz, J. (2010). Past shifts in the general circulation: Causation, structure, and effects on hydroclimate.

MS, University of Utah. Sharma, N., Pan J.-j., and Poulter C.D. (2010). Type II Isopentenyl diphosphate isomerase: probing the

mechanism with alkyne/allene diphosphate substrate analogues. Biochemistry, 49, 6228 - 6233. Shingleton, N. (2010). Coupling a Land-Surface Model to Large-Eddy Simulation to Study the Nocturnal

Boundary Layer. MA Thesis, University of Utah, Salt Lake City.

Smith, C. R., et al. (2010). Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile). PNAS. Retrieved from

Smith, C. R., et al. (2010). Draft genome of the red harvester ant (Pogonomyrmex barbatus). PNAS. Retrieved from

Staten, P., Reichler, T., Rutz, J.J., Kim, J. (2010). How Ozone Depletion Causes Southern Hemispheric

Climate Change. Eos Trans. AGU, 91(26), Jt. Assem. Suppl., Abstract A42A-03. Staten, P. W., Reichler, T., Lu, J. (2010). Understanding the direct and indirect circulation response to

radiative forcings. Paper presented at the American Geophysical Union Fall Meeting, San Francisco, CA.

Truong, T., Freedman, H., Le, L., Cheatham, T.E., Tuszynski, J., Huynh, L. (2010). Explicitly-solvated

ligand contribution to continuum solvation models for binding free energies: selectivity of theophylline binding to an RNA aptamer. J. Phys Chem B, 114, 2227 - 2237.

Wang, Z., Feng Liu. (2010). Manipulation of Electron Beam Propagation by Hetero-Dimensional Graphene Junctions. ACS Nano, 4, 2459.

Welker, M. C., Pavelec, D.M., Nix, D.A., Duchaine, T. F., Kennedy, S., Bass, B.L. (2010). Dicer's Helicase Domain is Required for Accumulation of Some, but not all, C. Elegans Endogenous siRNAs. RNA, 16(5), 893 - 903.

Werner, E. W., Sigman, M.S. (2010). A Highly Selective and General Palladium Catalyst for the Oxidative Heck Reaction of Electronically Nonbiased Olefins. J. Am. Chem. Soc., 132(40), 13981 - 13983.

West, G. L., Steenburgh., W.J. (2010). Life cycle and mesoscale frontal structure of an Intermountain cyclone. Monthly Weather Review, 138(7), 2528 - 2545.

Wilson, G. A., Cuma, M., Zhdanov, M.S., Gribenko, A., and Black, N. (2010, December 13 - 17, 2010). A quantitative comparison of the effects of stabilizing functionals in 3D regularized inversion of marine CSEM data. Paper presented at the AGU Fall Meeting, San Francisco, CA.

Xu, L., Molinero, V. (2010). Liquid-vapor Oscillations of Water Nanoconfined Between Hydrophobic Disks: Thermodynamics and Kinetics. J. Phys. Chem. B, 114, 7320 - 7328.

Xu, W. Z., E.J.; Liu, L.; Jiang, J. (2010). On the relationships between lightning frequency and thundercloud parameters of regional precipitation systems. J. Geophys. Res, 115, D12203. doi:

10.1029/2009JD013385

Zhdanov, M. S., Cuma, M., Ueda, T. (2010). 3D Electromagnetic Holographic Imaging in Active Monitoring of Sea-Bottom Geoelectric Structures. In J. Kasahara, Korneev, V., Zhdanov, M.S.

(Ed.), Active Geophysical Monitoring (pp. 317-342): Elsevier. Zhdanov, M. S., Cuma, M., Gribenko, A., Wilson, G. and Black, N. (2010). 3D inversion of marine CSEM

data: A feasibility study for the Shtokman gas field in the Barents Sea. Paper presented at the

International Workshop on Electrical, Gravity and Magnetic Methods, Capri, Italy. Zhdanov, M. S., Cuma, M., and Wilson, G. (2010). 3D iterative migration of marine controlled-source

electromagnetic data with focusing regularization. Paper presented at the 72nd EAGE Conference and Exhibition, Barcelona, Spain.

Zhdanov, M. S., Velikhov, E. P., Cuma, M., Wilson, G., Black, N., and Gribenko, A. (2010). Exploring multiple 3D inversion scenarios for enhanced interpretation of marine CSEM data in an iterative

migration analysis of the Shtokman gas field in the Barents Sea. First Break, 28(3), 95 - 101.

Zhdanov, M. S., Cuma, M., Wilson, G. A., Black, N., and Gribenko, A. (2010). Exploring multiple 3D inversion scenarios for enhanced interpretation of marine electromagnetic data. Paper presented

at the Brazilian Geophysical Society Non-Seismic Geophysics Forum, Rio de Janeiro, Brazil. Zhdanov, M. S., Cuma, M., and Wilson, G. (2010). Large-scale 3D iterative migration of marine

controlled-source electromagnetic data with focusing regularization Paper presented at the Progress in Electromagnetic Research Symposium, Boston, MA. Zhdanov, M. S., Green, A. M., Gribenko, A. V., Cuma, M. and Wilson, G. A. (2010). Large-scale

three-dimensional inversion of EarthScope MT data from the northwestern United States. Paper presented at the International Workshop on Electromagnetic Sounding in memory of Mark

Berdichevsky and Peter Weidelt, Moscow, Russia. Zhu, J., Feng Liu, and G. B. Stringfellow. (2010). Enhanced cation-substituted p-type doping in GaP from

dual surfactant effects. Crys. Growth, 312, 174.

Zhu, J., Feng Liu, G. B. Stringfellow, and S.-H. Wei. (2010). Strain-Enhanced Doping in Semiconductors: Effects of Dopant Size and Charge State. Phys Rev Lett, 105, 195503.

2009

Abbasi, R. U., et al. (2009). Measurement of the flux of ultra high energy cosmic rays by the stereo technique. Astroparticle Physics, 32, 53 - 60.

Abbasi, R. U., et al. (2009). A Search for Three and Four Point Correlation in HiRes Stereo Data. online(arXiv:0901.3740v2).

Bankiewicz, B. H., L. K.; Ratkiewicz, A.; Truong, T. N. (2009). Kinetics of 1,4 Hydrogen Migration in Alkyl

Radical Reaction Class. J Physical Chem A, 113, 1564-1573. Belz, J. (2009). Overview of Recent HiRes Results. Nuclear Physics B, 190, 5 - 11.

Coon, J., Christensen, D., Vyas, U., Roemer, R., Payne, A. (2009). Dose Delivery Time Reduction through Focal Zone (FZ) Size and Path Optimization in HIFU. Paper presented at the Society of Thermal

Medicine, Tucson, AZ. Coon, J. (2009). HIFU Dose Delivery Time Reduction: Focal Zone Size and Path Optimization. Paper

presented at the Society for Thermal Medicine Annual Meeting, Tucson, AZ.

Crosman, E. T., Horel, J.D. (2009). Idealized large-eddy simulations of sea and lake breezes. Paper presented at the 13th Congerence on Mesoscale Processes, Salt Lake City, UT.

Crosman, E. T., Horel, J.D. (2009). Observational and numerical study of the Great Salt Lake. Paper presented at the 10th Annual WRF User's Workshop, Boulder, CO.

Day, G., Cooper, T.G., Cruz Cabeza AJ, Hejczyk KE, Ammon HL, Boerrigter SXM, Tan J, Della Valle RG,

Venuti E, Jose J, Gadre SR, Desiraju GR, Thakur TS, van Eijck BP, Facelli JC, Bazterra VE, Ferraro MB, Hofmann DWM, Neumann M, Leusen FJJ, Kendrick J, Price SL, Misquitta AJ, Karamertzanis

PG, Welch GWA, Scheraga HA, Arnautova YA, Schmidt MU, van de Streek J, Wolf A, Schweizer B. (2009). Significant progress in predicting the crystal structures of small organic molecules

– a report on the fourth blind test. Acta Crystallogr. B, B65, 107 - 125. Demille, R., Molinero, V. (2009). Coarse-grained Ions Without Charges: Reproducing the Solvation

Structure of NaCl in water using Short-Ranged Potentials. J. Chem. Phys., 131(3), 034107.

Du, J., Wright, G., Fogelson, A. (2009). A Parallel Computational Method for Simulating Two-Phase Gel Dynamics. International Journal for Numerical Methods in Fluids, 60, 633-649. doi:

10.1002/fld.1907 Endo, M., Cuma, M., and Zhdanov, M. S. (2009). Large-Scale Electromagnetic Modeling for Multiple

Inhomogeneous Domains. Commun. Comput. Phys, 6, 269 - 289.

Endo, M., Cuma, M., and Zhdanov, M. S. (2009). Three-dimensional electromagnetic modeling in complex geoelectric structures with multiple inhomogeneous domains. Paper presented at the EOS.

Endo, M. C., M.; Zhdanov, M.S. (2009). Multiple domain integral equation method for 3D electromagnetic modeling in complex geoelectric structures. Paper presented at the SEG International Exposition

and 79th Annual Meeting, Houston, TX. Facelli, J. C., Orendt, A.M. (2009). Chapter 8: Chemical Shifts: Basics & Solid-state Molecular-level

Structure. In R. K. Harris (Ed.), NMR Crystallography: Wiley.

Facelli JC, O. A. (2009). Chapter 5: Magnetic Shielding & Chemical Shifts: Basics. In R. K. Harris (Ed.), NMR Crystallography: Wiley.

Fadrna, E., Spackova, N., Sarzynska, J., Koca, J., Orozco, M., Cheatham, T.E., Kulinski, T., Sponer, J. (2009). Single stranded loops of quadruplex DNA as key benchmark for testing nucleic acids force

field. J. Chem. Theory Comp., 5, 2514 - 2530.

Hammoud, S., Nix, D., Haiving Z., Purwar J., Carrell D., Cairns B.R. . (2009). Distinctive Human Sperm Chromatin Packages Genes Guiding Embryo Development. Nature, Epub(Jun 14), PMID:

19525931. Hammoud, S. S., Nix, D.A., Zhang, H., Purwar, J., Carrell, D.T., Cairns, B.R. (2009). Distinctive Chromatin

in Human Sperm Packages Genes for Embryo Development. Nature, 460, 473 - 478. Han, T. S., Zhang, M. M., Walewska, A., Gruszczynski, P., Robertson, C.R., Cheatham, T.E., Yoshikami,

D., Olivera, B. M., Bulaj, G. (2009). Structurally-minimized ?conotoxin analogs as sodium channel

blockers: Implications for designing conopeptide-based therapeutics. Chem. Med. Chem., 4, 406 - 414.

Hollenhorst, P. C., Chandler, K. J., Poulsen, R.L., Johnson, W.E., Speck, N.A., Graves, B.J. (2009). DNA Specificity Determinants Associate With Distinct Transcription Factor Functions. PLoS Genet, 5(12), e1000778.

Hooper, J. B., Bedrov, D., Smith, G. D., Borodin, O., Dattelbaum, D. M., Kober, E. (2009). A Molecular Dynamics Simulation Study of the Pressure-Volume-Temperature Behavior of Polymers Under

High Pressure. J. Chem. Phys., 130, 144904. Huang, e. a. (2009). Quantum Manifestations of Graphene Edge Stress and Edge Instability: A First

Principles Study. Physical Review Letters, 102, 166404.

Huynh, L. K., Tirtowidjojo, M., Truong, T. N. (2009). Theoretical study on kinetics of the H2CO + O2 --> HCO + HO2 reaction. Chemical Physics Letters, 469, 81 - 84.

Jacobson, L. C., Hujo, W., Molinero, V. (2009). Thermodynamic Stability and Growth of Guest-Free Clathrate Hydrates, A Low-Density Crystal Phase of Water. J Physical Chem B, 113, 10298 -

10307. Jenkins, M. A., Bhutia, S., Sun, R. (2009). Impacts of Fire/Atmosphere Coupling and Boundary-Layer

Turbulence on Firebrand Propagation. Paper presented at the 8th Symposium on Fire and Forest

Meteorology, Kalispell. Jenkins, M. A., S. Bhutia, and R. Sun. (2009). Impacts of Fire/Atmosphere Coupling and Boundary--Layer

Turbulence on Firebrand Propagation. Paper presented at the 8th Symposium on Fire and Forest Meteorology, American Meteorological Society, Kalispell, Montana.

Johnston, J. C., Iuliucci, R.J., Facelli, J.C., Fitzgerald, G., Mueller, K.T. (2009). Intermolecular shielding

contributions studies by modeling the 13C chemical-shift tnesors of organic single crystals with plane waves. Journal of Chemical Physics, 131, 144503.

Joung, I. S., Etinkol, P., Hud, N.V., Cheatham, T.E. (2009). Molecular dynamics simulations and coupled nucleotide substitution experiments indicate the nature of AoA base pairing and a putative

structure of the coralyne-induced homo-adenine duplex. Nuc. Acids Res., 37, 7715 - 7727. Joung, I. S., Cheatham, T. E. (2009). Molecular dynamics simulations of the dynamic and energetic

properties of alkali and halide ions using water-model specific ion parameters. J. Phys. Chem B, 113, 13279 - 13290.

Kang, J., Gemberlling, M., Nakamura, M., Whitby, F.G., Handa, H., Fairbrother, W.G., Tantin, D. (2009).

A General Mechanism for Transcription Regulation by Oct1 anmd Oct4 in Response to Genotoxic and Oxidative Stress. Genes Dev., 23(2), 208 - 222.

Kim, S., Orendt, A.M., Ferraro, M. B., Facelli, J. C. (2009). Crystal Structure Prediction of Flexible

Molecules Using Parallel Genetic Algorithms with a Standard Force Field. Journal of Computational Chemistry, 30 1973 - 1985.

Kochanski, A., Jenkins, M.A., Krueger, S., McGermott, R., Mell, W. (2009). Capabilities of current wildfire models when simulating topographical flow. Paper presented at the American Geophysical Union

Fall Meeting, San Francisco, CA. Kochanski, A., . M.A. Jenkins, and S. Krueger. (2009). Fire Spread and Hill Flow. Paper presented at the

Wildland-Urban Interface (WUI) Fires Workshop, Building and Fire Research Laboratory Annual

Fire Conference, NIST, Gaithersburg, MD. Kochanski, A., Jenkins, M.S., Krueger, S. (2009). Fire spread and Hill Flow. Wildland-Urban Interface

(WUI) Fires Workshop. NIST. Gathersburg, MD. Kochanski, A., Jenkins, M.a., and Krueger, S.K. (2009). Flow over a simple hill and its impact on wind

speed, variability and turbulence. Paper presented at the 8th Symposium on fire and Forest

Meteorology, Kalispell, MT. Kochanski, A., M.A. Jenkins, and S.K. Krueger. (2009). Flow over a simple hill and its impact on wind

speed, variability, and turbulence. Paper presented at the 8th Symposium on Fire and Forest Meteorology, American Meteorological Society, Kalispell, Montana.

Krueger, S. L., Kochanski, A.K. (2009, 24 - 27 May 2009). What can Cloud-Resolving Models Tell us About Critical Phenomena in Atmospheric Precipitation? Paper presented at the 2009 Joint Assembly,

Toronto, Canada.

Le, L., Lee, E., Schulten, K., Truong, T. N., . (2009). Molecular modeling of seine influenza A/H1N1, Spanish H1N1, and avian H5N1 flu N1 meuraminidases bound to Tamiflu and Relenza. Public Library of Science (PLoS) Currents Influenza, August 27, 2009.

Li, X., Pu, Z. (2009). Sensitivity of numerical simulations of the early rapid intensification of Hurricane

Emily (2005) to cumulus parameterization schemes in different model grid resolutions. J. Meteorol. Soc. Japan, 87, 403 - 421.

Li, Y. Y., Liu, M., Ma, D.Y., Yu, D.C., Chen, X., Ma, X.C., Xue, Q.K., Xu, K.W., Jia, J.F., Liu, F. (2009).

Bistability of Nanoscale Ag Islands on Si(111)-4 x 0) - In surface Induced by Anisotropic Stress. Phys. Rev. Lett., 103, 076102.

Liu, C. Z., E.J. (2009). Implication of the day vs. night differences of water vapor, carbon monoxide and

thin cloud observations near tropical tropopause. J. Geophys. Res, 114, S09303. doi: 10.1029/2008JD011524

Liu, C. Z., E.J. (2009). "Warm rain" in the tropics: Seasonal and regional distribution based on 9 years of TRMM data. J. Climate, 22, 767 - 779. doi: 10.1175/2008JCLI2641.1

Lu, J., C. Deser, and T. Reichler. (2009). Cause of the widening of the tropical belt since 1958. Geophys. Res. Lett, 36, L03803, doi:03810.01029/02008GL036076.

Ma, J., Pedel, J., Fife, P., Johnson, W. (2009). Hemispheres-in-Cell Geometry to Predict Colloid Deposition

in Porous Media. Environ. Sci, Technol, 43, 8573-8579. Maran, U., Britt, D., Fox, C. B., Harris, J. M., Orendt, A., Conley, H., Davis, R., Hlady, V., Stang, P. J.

(2009). Self-Assembly of a Triangle-Shaped, Hexaplatinum-Incorporated, Supramolecular Amphiphile in Solution and at Interfaces. Chem. Eur. J., 15, 8566 - 8577.

McDermott, R. (2009). A Workshop to Build Three Simple Tensegrity Models for K-12 Mathematics Classrooms. Paper presented at the Bridges 2009: Mathemmatics, Music, Art, Architecture Culture, Banff, Alberta, Canada.

Molinero, V., Moore, E. B. (2009). Water Modeled as an Intermediate Element between Carbon and Silicon. J Physical Chem B, 113, 4008.

Moore, E. B., Molinero, V. (2009). Growing correlation length in supercooled water. J Chem Physics, 130(24), 10298-10307.

Muszynska, M., Ratkiewicz, A., Huynh, L. K., Truong, T. N. (2009). Kinetics of the Hydrogen Abstraction

C2H3 + alkane --> C2H4 + alkyl radical Reaction Class. Journal of Physical Chemistry, 113(29), 8327 - 8336.

Nguyen, H. G., Konya, G., Eyring, e., Hunter, D., Truong, T. N. (2009). Theoretical Study on the Interaction between Zenon and Positively Charged Silver Clusters in Gas Phase and on the (001)

Chabazite Surface. Journal of Physical Chemistry 113(29), 12818 - 12825.

Novoa, J. J., Stephens, P. W., Weerasekare, M., Shum, W. W., Miller, J.S. (2009). The Tetracyanopyrazinide Dimer Dianion [TCNP]2

2- 2 Electron 8 Center (2e-/8c) Bonding. J. Am. Chem. Soc., 131, 9070.

Orendt, A. M., Facelli, J. C. (2009). Chemical Shifts & Solid-state Molecular-level Structure NMR Cystallography (pp. 99 - 111): John Wiley & Sons, Ltd.

Orrego, J., Zapata, F., Truong, T. N., Mondragon, F. (2009). Heterogeneous CO2 Evolution from Oxidation

of Aromatic Carbon-based Materials. Journal of Physical Chemistry A, 113(29), 8415 - 8420.

Pendley, S. S., Yu, Y.B., Cheatham, III, T. E. (2009). Molecular Dynamics Guided Study of Salt Bridge Length Dependence in Both Fluorinated and Non-Fluorinated Parallel Dimeric Coiled-Coil Proteins.

Proteins, 74, 612 - 629. Pennell, C., Reichler, T. (2009). On the effective number of climate models Paper presented at the

American Geophysical Union Fall Meeting, San Francisco, CA.

Pu, Z., Li, X., Zipser, E. (2009). Diagnosis of the initial and forecast errors in the numerical simulation of the rapid insstensification of Hurrican Emily (2005). Wea. Forecasting, 24, 1236 - 1251.

Pu, Z., Li, X., Sun, J. (2009). Impact of airborne Doppler radar data assimilation on the numerical simulation oof intensity changes of Hurricane Dennis near a landfall. J. Atmos. Sci. , 66, 3351 -

3365. Reichler, T., J. Kim, and C. Pennell. (2009). How well do coupled models simulate present-day climate?

Paper presented at the Climate research division seminar, Environmental Canada, Toronto,

Canada. Reichler, T., J. Kim. (2009). Validation of tropospheric and stratospheric climate. In V. Eyring, T.

Shepherd, D. Waugh, editors. (Ed.), SPARC Report on Evaluation of Chemistry Climate Models: CCMVal.

Reichler, T., and J. Kim. (2009, June 1-5). Validation of tropospheric and stratospheric climate. Paper

presented at the CCMVal 2009 Workshop, Univ. of Toronto,Toronto, Canada. Shum, W. W., Epstein, A. J., Miller, J.S. (2009). Spin polarized electronic structure for the layered

two-dimensional [FeII (TCNE)(NCMe)2[FeIIICl4] Organic-based Magnet. Phys. Rev B, 80, 064403. Sokolsky, P. (2009). Observation of the GZK cutoff by the HiRes Experiment. Nuclear Physics B, 196, 67 -

73.

Staes, C. Z., W.; LeFevre, S.; Price, R.; Narus, S.P.; Gundlapalli, A.; Rolfs, R.; Nangle, B.; Samore, M.; Facelli, J. C. (2009). A case for using grid architecture for state public health informatics: the

Utah perspective. BMC Medical Informatics and Decision Making 2009, 9(32). Steenburgh, W. J., Neuman, C.R., West, G.L., Bosart, L.F. (2009). Discrete frontal propagation over the

Sierra-Cascade Mountain and Intermountain West. Monthly Weather Review, 137, 2000 - 2020. Sun, R., and S.K. Krueger, M.A. Jenkins, M.A. Zulauf, J.J. Charney. (2009). The importance of

fire/atmosphere coupling and boundary--layer turbulence to wildfire spread. International Journal for Wildland Fire., 18, 50 - 60.

Sun, R. K., S. K.; Jenkins, M.A.; Charney, J.J. (2009). The Importance of Fire/Atmosphere Coupling and

Boundary-Layer Turbulence to Wildfire Spread. International Journal for Wildland Fire., 18(1), 50 - 60.

Trujillo, E. M. (2009). Modeling Acid Rock Drainage in a Mine Rock Pile Using a Modified Version of TOUGHREACT. Paper presented at the TOUGH 2009 Symposium, Berkeley, California.

Trujillo, E. M. (2009). A User Friendly Graphic Interface for TOUGHREACT. Paper presented at the

TOUGH 2009 Symposium, Berekely, California. Wang, H., Cheatham, III, T. E., Lewis, J. (2009). Differential Electronic States Observed During the A-B

DNA Duplex Conformational Transitions. Soft Matter, 5, 685 - 690. Xu, W. Z., E.J.; Liu, C. (2009). Rainfall characteristics and Convective properties of Mei-Yu precipitation

systems over south China and Taiwan, Part I: TRMM observations. Wea. Rev., 137, 4261 - 4275.

Zhang, Y., Ritsema, J., Thorne, M. (2009). Modeling the ratios of SKKS and SKS amplitudes with ultra-low velocity zones at the core-mantle boundary. Geophysical Research Letters, 36, L19303. doi:

10.1029/2009GL040030 Zhdanov, M. S., Cuma, M. (2009). Electromagnetic migration of marine CSEM data in areas with rough

bathymetry. Paper presented at the SEG International Exposition and 79th Annual Meeting,

Houston, TX. Zhdanov, M. S., Cuma, M., Gribenko, A., and Wilson, G. (2009). Large-scale 3D inversion of marine

controlled-source electromagnetic data using the integral equation method. Paper presented at the AGU Fall Meeting.

2008

Abassi, R. U., et al. (2008). Air fluorescence measurements in the spectral range 300-420 nm using 28.5 GeV electron beam. Astroparticle Physics, 29, 77 - 86.

Austin, J., Reichler, T. (2008). Long-term evolution of the cold point tropical tropopause: Simulation results and attribution analysis. J. Geophys. Res, 113, D00B10.

Cantarel, B. K., I.; Robb; S. M. C.; Parra, G.; Ross, E.; Moore, B.; Holt, C.; Sanchez-Alvarado, A.; Yandell,

M. (2008). An Easy-to-use Annotation Pipeline Designed for Emergin Model Organism Genones. Genome Reserach, 18(188-196).

Chen, et al. (2008). Magnetism in Nanopatterned Graphite Film. Applied Physical Letters, 93, 223106. Corrigan, J. (2008). Martha Tomhave Blauvelt. The Work of the Heart: Young Women and Emotion,

1780-1830. The American Historical Review, 113(3), 827-828. doi: doi:10.1086/ahr.113.3.827 Dutrow, N., Nix, D.A., Holt, D., Milash, B., Dalley, B., Westbroek, E., Parnell, T.J., Cairns, B.R. (2008).

Dynamic Transcriptome of Schizosaccharomyces Pombe shown in RNA-DNA Hybrid Mapping. Nat Genet., 40(8), 977 - 986.

Espinal, J. F. T., T. N.; Mondragon, F. (2008). Mechanisms of carbon gasification reactions using

electronic structure methods. In L. Nemes, Irle, S. (Ed.), Spectroscopy, Dynamics, and Molecular Theory of Carbon Plasma and Vapors.

Facelli, J. C., Orendt, A. M., Ferraro, M., Pimienta, I., Bazterra, V. (2008). Crystal Structure Prediction (CSP) of Flexible Molecules with Genetic Algorithms and Standard Force Field [Abstract]. Paper presented at the Proceedings of the XII Congress of the International Union of Crystallography.

Facelli, J. C. (2008). The Impact of Grid Computing in Biomedical Informatics. Paper presented at the INFOLAC2008 - AAIM.

Fennick, J. R. K., J.B.; Leonard, R. H.; Truong, T. N.; Lewis, J. P. (2008). A cyberenvironment for

crystallography and materials science and an integrated user interface to the Crystallography Open Database and Predicted Crystollography Open Database. J of Applied Crystallography, 41,

471 - 475. Fennick, J. R. K., J.B.; Leonard, R. H.; Truong, T. N.; Lewis, J. P. (2008). A cyberenvironment for

cystallography and materials science and an integrated user interface to the Crystallography Open Database and Predicted Crystallography Open Database. Journal of Applied Crystallography, 41, 471-475.

Freedman, H. L., L.; Tuszynski, J. A.; Truong, T. N. (2008). Improving the Performacne fo the Coupled Reference Interation Site Model (RISM)/Simulation Method for Absolute Free Energy of Solvation.

J. Phys Chem B, 112, 2340 - 2348. Green, A., Bribenko, A., Cuma, M., Zhdanov, M.S. (2008). Preliminary results of 3D Inversion of the

EarthScope Oregon MT Data Using the Integral Equation Method. AGU 2008 Fall Meeting.

Han, Y. H., M.; Tringides, M.C.; Liu, F. (2008). Quantum Modulation of Island Nucleation on Top of a Metal Nanomesa. Surf. Sci, 602, 62.

Han, Y. L., F. (2008). Coulomb Sink Effect on Coarsening of Metal Nanostructures on Surfaces. Front. Phys. China, 3, 41.

Han, Y. L., F.; Li, S.; Jia, J.; Zue, Q.; Lee, B. (2008). Kinetics of Mesa Overlayer Growth: Climbing of Adatoms onto the Mesa Top. Appl. Phys. Lett, 92, 021909.

Hanlon, W. (2008). The Energy spectrum of Ultra High Energy Cosmic Rays Measured by the High Resolution Fly's Eye Observatory in Stereoscopic Mode. Ph.D. Ph.D. Dissertation, University of Utah, Salt Lake City, UT.

Huynh, L. K. Z., S.; Truong, T. N. (2008). Kinetics of hydrogen abstraction O (3P) + alkane --> OH+alkyl reaction class: An application of the reaction class transition state theory. Combustion and Flame, 152(1/2), 177 - 185.

Jenkins, M. A., and S.K. Krueger. (2008). The Importance of a LES approach to coupled wilfire/atmosphere modeling. Paper presented at the BFRL Annual Fire Conference 2008, NIST,

Gaithersubrg, MD. Joung, I. S., Cheatham, T. E. (2008). Determination of Alkali and Halide Monovalent Ion Parameters for

Use in Explicitly Solvated Biomolecular Simulations. J. Phys. Chem B, 112(30), 9020 - 9041. Kim, J., Chen, G., Reichler, T. (2008, August 31 - September 5). A possible mechanism for the

tropospheric response to stratospheric forcing. Paper presented at the SPARC 4th General

Assembly, Bologna, Italy. Kim, J., Kumar, A., Reicher, T. (2008, April 13 - 18, 2008). Predictability of the Arctic Oscillation

Associated With Stratospheric Influences in Operational Forecasts. Paper presented at the EGU General Assembly, Vienna, Austria.

Kim, J., Reichler, T. (2008, August 31 - September 5). Simulation of Stratospheric Intraseasonal Variability with the GFDL climate model: A low-top and high-top comparison. Paper presented at the SPARC 4th General Assembly, Bologna, Italy.

Kim, J., Reichler, T. (2008). Uncertainties in the Climate Mean State of Global Reanalyses, Observations, and the GFDL Climate Model. Paper presented at the EGU General Assembly, Vienna, Austria,

April 13-18. Krikov, S. P., R.; Allen-Brady, K.; Cannon-Albright, L. A.; Facelli, J. C. (2008). Enablign GeneHunter as a

Grid Service: A Case Study for Implementing Analytical Services for Biomedical Grids [a poster]. Paper presented at the American Medical Informatics Association's Annual Symposium, Washington, D.C.

Li, X., Pu, Z. (2008). Sensitivity of numerical simulations of early rapid intensification of Hurricane Emily (2005) to cloud microphysical and planetary boundary layer parameterizations. Monthly Weather Review, 136, 4819 - 4838.

Liu, C. Z., E.J.; Cecil, D. J.; Nesbitt, S.W.; Sherwood, S. (2008). A cloud and precipitation feature database from 9 years of TRMM observations. J. Appl. Meteor. Climate, 47, 2712- 2728. doi:

10.1175/2008JAMC1890.1 Liu, C. Z., E.J.; Mace, G.G.; Benson, S. (2008). Implications of the differences between daytime and

nighttime CloudSat observations over the tropics. J. Geophys. Res, 113, D00A04. doi:

10.1029/2008JD009783 Lu, J., C. Deser, T. Reichler. (2008). Cause of the widening of the tropical belt since 1958. Paper

presented at the American Geophysical Union Fall Meeting, San Francisco (CA). Maran, U. C., H.; Frank, M.; Arif, A.; Orendt, A.; Britt, D.; Hlady, V.; Davis, R.; Stang, P. (2008). Giant

Micelles of Organoplatinum(II) Gemini Amphiphiles. Langmuir, 24, 5400 - 5410. McDermott, R. H., W. (2008). A Computer Aided Geometric Model of a Ten-Plane Polyhedral

Transformation: Explosion-Implosion. Paper presented at the submitted for presentation at

Bridges 2008. Orendt, A. M., Guo, X, Facelli, JC. (2008). 13C chemical shielding calculations of actinide complexes

[Abstract]. American Chemical Society. Orrego, J. F. T., T. N.; Mondragon, F. (2008). A Linear Energy Relationship between Activation Energy

and Absolute Hardness: A Case Study with the O(3P) Atom-Addition Reactions to Polyaromatic

Hydrocarbons. J Physical Chem A, 112(36), 8205 - 8207. Price, R. C. B., W.; Bazterra, V. E.; Facelli, J. C. (2008). Digital Sherpa: A Set of High Level Tools to

Manage Scientific Applications in a Computational Grid. Paper presented at the 2008 MardiGras Conference on Developing Grid Based Applications, Baton Rouge, LA.

Pu, Z. (2008). Assimilation of satellite data in improving numerical simulations of tropical cyclones: progress, challenge and development Data Assimilation for Atmospheric Oceanic, and Hydrologic

Applications: The Springer-Verlag.

Pu, Z. (2008). High resolution numerical simulation of tropical cyclone intensity change with assimilation of satellite, radar, and in-situ data. Ph. D., University of Utah, Salt Lake City, Utah.

Pu, Z., X. Li, C., Velden, W. T. Liu. (2008). Impact of aircraft dropsonde and satellite wind data on the numerical simulation of two landfalling tropical storms during TCSP. Weather and Forecasting, 23, 62 - 79.

Pu, Z., Xu, L. (2008). MODIS/Terra observed snow cover over the Tibet Plateau: Distribution, variation and possible connection with the East Asian summer monsoon (EASM). Theor. Appl. Climatol., doi: 10.1007/s00704-00008-00749.

Pu, Z. H., J. (2008). Ensemble-based Kalman filers in strongly non-linear dynamics. Advances in Atmospheric Sciences, 26, 373 - 380.

Pu, Z. L., X.; Velden, C.; Aberson, S.; Liu, W. T. (2008). Impact of aircraft dropsonde and satellite wind

data on numerical simulation of two landfalling tropical storms during TCSP. Weather and Forecasting, 23, 62 - 79.

Rai, K., Huggins IJ, James SR, Karpf AR, Jones DA, Cairns B.R. (2008). DNA demethylation in zebrafish

involves the coupling of a deaminase, a glycosylase, and gadd45. Cell, 135(7), 1201 - 1212. Rausch, T. T., A.; Camp, N. J.; Cannon-Albright, L. A.; Facelli, J. C. (2008). A Parallel Genetic Algorithm

to Discover Patterns in Genetic Markers that Indicate Predisposition to Multifactorial Disease.

. Computuers in Biology and Medicine, 38, 826-836. Reichler, T., Chen, G., Lu, J. (2008). Decadal trends in the width of the tropical belt. Paper presented at

the EGU General Assembly, Vienna, Austria, April 13-18.

Reichler, T., Kim, A. (2008). How well do coupled models simulate present-day climate? Paper presented at the Atmospheric Physics Laboratory, Department of Physics, Universidad Mayor de San Andres,

La Paz, Bolivia.

Reichler, T., Kim, A. (2008). How well do coupled models simulate present-day climate? A comparison of three generations of coupled models. Bull. Amer. Meteor. Soc, 89(3).

Reichler, T., and J. Austin. (2008, April 13-18). Long-Term Trends in the Tropical Cold Point Tropopause: Simulation Results and Attribution Analysis. Paper presented at the EGU General Assembly,

Vienna, Austria.

Reichler, T. (2008). A performance metric for climate models. Paper presented at the SPARC DynVar workshop, Toronto, Canada, March 27-28.

Reichler, T., Chen, G., Lu, J. (2008). Poleward shift of the global circulation under climate change - a low-top / high-top sensitivity study with the GFDL climate model, Toronto, Canada, March 27-28.

Reichler, T., J. Lu, and G. Chen. (2008, August 31 - September 5.). Stratospheric role for the widening of the general circulation. Paper presented at the SPARC 4th General Assembly, Bologna, Italy.

Reichler, T., J. Kim, and C. Pennell. (2008, November 20). Towards an objective quantification of climate model performance. Paper presented at the International Development and Globalization Program (IGERT, Columbia University, NY, NY.

Reichler, T., Kim, J. (2008). Uncertainties in the climate mean state of global observations, reanalyses, and the GFDL climate model. J. Geophys. Res, 113, D05106.

Reichler, T., Kim, J. (2008). Uncertainties in the climate mean state of global reanalyses, observations, and a modern climate model. Paper presented at the Proceedings of the 2nd WCRP International Conference on Reanalysis, Tokyo, Japan, January.

Reichler, T., and J. Austin. (2008). What determines tropical tropopause parameters? A modelling study of past and future trends with the AMTRAC coupled chemistry climate model. Paper presented at

the SPARC 4th General Assembly, Bologna, Italy.

Reichler, T. C., G.; Lu, J. (2008). Decadal Trends in the Width of the Tropical Belt. Paper presented at the Geopysical Research Abstracats.

Reichler, T. C., G.; Lu, J. (2008). Poleward shift of the global circulation under climate change -- A low-top / high-top sensitivity study with the GFDL climate model. Toronto, Canada.

Rocha, R., Hurdle, J., Matney, S., Narus, S., Meystre S, LaSalle B, Deshmukh V, Hunter C, Mineau G, Facelli JC, Mitchell J. (2008). Utah's Statewide Informatics Platform for Translational and Clinical

Science [poster]. Poster retrieved from

Shafer, J. C., Steenburgh, W.J. (2008). Climatology of strong Intermountain cold fronts. Monthly Weather Review, 136, 784 - 807.

Shum, W. W. (2008). Magnetic Interactions in Novel Molecule-based Materials. Ph.D. Dissertation, University of Utah, Salt Lake City, UT.

Smith, G. D., Borodin, O., Li, L., Kim, H. (2008). A Comparison of Ether- and Alkyl-derivatized

Imidazolium-Based Room Temperature Ionic Liquids: A Molecular Dynamics Simulation Study. PhysChemChem Phys, 10, 6301 - 6312.

Sobczyk, M. N., D.; Simons, J. (2008). Theoretical study of through-space and through-bond electron transfer within positive charged peptides in the gas phase. Inter. J. Mass Spec., 269, 149 - 164.

Staes, C., LeFevre, S., Price, R., Xu, W., Duncan, J., Scott, W., Contreras, J., Lui, Z., Gundlapalli, A., Facelli, J.C. . (2008). Utah phGRID demonstration project: grid-enabling the Environmental Public Health Tracking Network [Abstract]. Paper presented at the PHIN Conference.

Staes CJ, X. W., LeFebre D, Narus SP, Gundlapalli A, Samore M, Facelli JC. (2008). A Case for Using Grid Architecture in State Public Health Informatics: The Utah Perspective [poster].

Steenburgh, W. J., Alcott, T.I. (2008). Secrets of the "Greatest Snow on Earth". Bull. Amer. Meteor. Soc, 89, 1285 - 1293.

Stoll, R. P.-A. (2008). Large-eddy simulation of the stable atmospheric boundary layer using dynamic

models with different averaging schemes. Boundary-Layer Meteorology, 126(1), 28. Svozil, D., Sponer, J.E., Marchan, I., Perez, A., Cheathan, III, T. E., Luque, J., Orozco, M., Sponer, J.

(2008). Geometrical and Electronic Structure Variability of the Sugar-Phosphate Backbone in Nuceic Acids. J Physical Chem B, 112(27), 8188 - 8197.

Videla, A. R. L., C. L.; Miller, J. D. (2008). Simulation of Saturated Fluid Flow in Packed Particle Beds - The Lattice-Boltzmann Method for the Calculation of Permeability from XMT Images. Journal of the Chinese Institute of Chemical Engineers, 39(2), 117 - 128.

Wang, Y., Truong, T. N. (2008). Cluster formation Model in Vapor Deposition of Pd Atoms on the Perfect Mg (100) Surface and on its Surface Oxygen Vacancy. J Physical Chem C, 112(13674 - 13680).

Zhu, J., et al. (2008). Dual-Surfactant Effect to Enhance p-Type Doping in III-V Semiconductor Thim Films. Physical Review Letters, 101, 196103.

Zhu, J. Y., Liu, F., Stringfellow, G. B. (2008). Dual-surfactant effect on enhancing p-type doping in III-V

semiconductor thin films. Physical Review Letters, 101, 196103.

2007

Abassi, R. U., et al. (2007). Studies of systematic uncertainties in the estimation of the monocular

aperture of the HiRes experiment. Abbasi, R. U., et al. (2007). Alternative Methods to Finding Patterns in HiRes Stereo Data.

Auffinger, P. C., T. E.; Vaiana, A.C. (2007). Spontaneous Formation of KCL Aggregates in Biomolecular Simulations: A Force Field Issue? J. Chem. Theory Comp., 3, 1851 - 1859.

Bazterra, V. E. T., M.; Ferraro, M.; Facelli, J.C. (2007). A Distributed Computing Method for Crystal Structure Prediction of Flexible Molecules: An Application to N-(2-dimethyl-4,5-dinitrophenyl)

Acetamide. J Chem Theor Comput, 3, 201 - 209.

Bhat, M. H. M., V.; Soignard, E.; Solomon, V. C.; Sastry, S.; Yarger, J. L.; Angell, C. A. (2007). Vitrification of a monatomic metallic liquid. Nature, 448, 787- 791.

Borodin, O. L., Q.; Smith, G. D. (2007, October 7 - 12, 2007). Quantum Chemistry and MD Simulation Studies of Fluorinated Ionomers. Paper presented at the 212th ECS, Washington, D.C.

Borodin, O. S., G. D.; Rees, R. (2007). Molecular Dynamics Simulations of Ionic Liquids and Lithium Transport in Them. Paper presented at the Annual AIChE Meeting, Salt Lake City, UT.

Borodin, O. S., G. D. (2007, October 7 - 12, 2007). Molecular Dynamics Simulations of Lithium Transport in Bulk Electrolytes and at Interfaces. Paper presented at the 212th ECS, Washington, D.C.

Borodin, O. S., G. D. (2007). Molecular Dynamics Simulations of Lithium Transport in Bulk Electrolytes and at the Electrolyte/electrode Interface. Paper presented at the Annual AIChE Meeting, Salt Lake City, UT.

Cantarel, B. K., I.; Robb; S. M. C.; Parra, G.; Ross, E.; Moore, B.; Holt, C.; Sanchez-Alvarado, A.; Yandell,

M. (2007). MAKER: An Easy-to-Use Annotation Pipeline Designed for Emerging Model Organism Genomes. Genome Reserach, 18, 188 - 196.

Chen, H., Ilan, B., Wu, Y., Zhu, F., Tajkhorshid, E., Schulten, K., and Voth, G.A. (2007). Electrostatics and Charge Delocalization in Proton Channels, I: The Aquaporin Channels and Proton Blockage.

Biophysical Journal, 92(1), 46 - 60.

Endo, M. C., M.; Zhdanov, M.S. (2007). Multigrid IE method for large-scale models with inhomogeneous background. SEG Expanded Abstracts, 26, 554.

Espinal, J. F., Truong, T.N., Mondragon, F. (2007). Mechanisms of NH3 formation during the reaction of H2 with nitrogen containing carbonaceous materials. CARBON, 45(11), 2273-2279.

Facelli, J. (2007). Modeling NMR Chemical Shifts Modern Magnetic Resonance (pp. 49-58): Springer. Florez, E. M., F.; Truong, R. N.; Fuentealba, P. (2007). Density functional theory characterization of the

formation of copper clusters on Fs and Fs+ center on a MgO surface. Surface Science, 601(3),

656-664. Hawkins, W., McDermott, R. (2007). A Ten-Plane Polyhedral Transformation: Explosion-Implosion.

unpublished. Huynh, L. K., Rakiewicz, A., Truong, T.N. (2007). Kinetics of the Hydrogen Abstraction CHO+ Alkane -->

HCHO + Alkyl Reaction Class: an Application of the Reaction Class Transition State Theory.

Theoretical Chemistry Accounts, 120, 107 - 118. Huynh, L. P., S.; Ratkiewicz, A.; Truong, T. N. (2007). An Ab Initio Study of the Kinetics of Hydrogen

Abstraction for the H+ Alkene --> H2 + Alkenyl Reaction Class. J Physical Chem A, 111(11), 2156 - 2165.

Jenkins, M. A., Sun, R., Krueger, S., Charney, J., Zuluaf, M. (2007). Effect of Vertical Wind Shear on Grassfire Evolution. Paper presented at the 7th Symposium on Fire and Forest Meteorology, Bar

Harbor, Maine.

Johnson, W. P., Li, X.; Yal, G. (2007). Colloid Retentioin in Porous Media: Mechanistic Confirmation of Wedging and Retention in Zones of Flow Stagnation. Environ. Sci, Technol, 41, 1279 - 1287.

Kalcher, J., Skurski, P., Simons, J. (2007). Electron binding capabilities of some silylenes having small singlet-triplet splitting triplet ground states. J. Phys. Chem., A 111, 401 - 410.

Krishnamurthy, M., Simon, K., Orendt, A., Beal, P. A. (2007). Macrocyclic Helix-Threading Peptides for

Targeting RNA. Angew. Chem. Int. Ed., 46, 7044 - 7047. Lui, Q. B., O.; Smith, G. D. (2007). The Hydration and Proton Dissociation in the Interaction Between

Fluorocarbon-Based Phosphonic Acid and Water Clusters. Paper presented at the AIChE Meeting, Salt Lake City, UT.

Ma, Z., Halling, M. D., Solum, M. S., Harper, J. K., Orendt, A. M., Facelli, J.C., Pugmire, R., Grant, D. M.,

Amick, A. W., and Scott L. T. (2007). Ring Current Effects in Crystals, Evidence from 13C Chemical Shift Tensors for Intermolecular Shielding in 4,7-Di-t-butylacenaphthene versus

4,7-Di-t-butylacenaphythylene. Journal of Physical Chemistry A, 111, 2020 - 2027. Ma, Z., Facelli, J.C., Pugmire, R.J., Dunn, B.C., Turpin, G.C., Eyring, E.M., Ernst, R.D. (2007). Solid State

13C NMR and Quantum Chemical Investigation of Metal Diene Complexes. Magn Reson Chem, 45, 393-400.

McDermott, R. (2007). Building Models to Transition From Dimension to Dimension. Paper presented at

the Bridges Donostia -- Mathematical Connections in Art, Music and Science, San Sebastian (Donostia), Spain.

Mell, W., Jenkins, M.A., Gould, J., Cheney, P. (2007). A Physics Based Approach to Modeling Grassland Fires. International Journal for Wildland Fire, 16(1 - 22).

Novoa, J. N., Ribas-Arino, J., Shum, W. W., Miller, J. S. (2007). Control of Two-Electron Four-Center

(2e-/4c) C-C Bond Formation Observed for Tetracyanoethenide Dimerization, [TCNE22-. Inorganic

Chemistry, 46, 103-107.

Orendt, A. M., Facelli, J.C. (2007). Solid State Effects on NMR Chemical Shifts [review]. Annual Reports on NMR Spectroscopy, 62(115-178).

Perez, A., Marchan, I., Svozil, D., Sponer, J., Cheatham, T.E., Laughton, C.A., Orozco, M. (2007). Refinement of the AMBER force field for nuclleic acids. Improving the description of /

conformers. Biophys. J., 92(11), 3817 - 3829.

Reichler, T. (2007). Widening of the Tropics During the 20th Century: Observations vs. Simulations. Paper presented at the American Geophysical Union Fall Meeting, San Francisco, CA.

Robb, S. M. C., Ross, E., Sanchez-Alvarado, A. (2007). SmedGD: the Schmidtea mediterranea Genome Database. Nucleic Acids Research, 36, D599-D606.

Shao, J. T., S. W.; Thompson, N.; Cheatham, T. E., . (2007). Clustering Molecular Dynamics Trajectories:

I. Characterizing the Performance of Different Clustering Algorithms. J. Chem. Theory Comp. , 3, 2312.

Skurski, P., Sobczyk, M., Joakowski, J., and Simons, J. (2007). Possible mechanisms for protecting

N-Cbonds in helical peptides from electron-capture (or transfer) dissociation Inter. J. Mass. Spec., 265(2-3), 197 - 212.

Theodore, M., Sobczyk, M., Simons, J. (2007). Cleavage of Thymine N3-H bonds by low-energy electrons

attached to base π*orbitals. Chem. Phys., 329(1-3), 139 - 147. West, G. L., Steenburgh, W.J., Cheng, W. Y. (2007). Spurious grid-scale precipitation in the North

American Regional Reanalysis. Monthly Weather Review, 135, 2168 - 2184. Wierzbicki, A., Cheatham, T.E., Dalal, P., Knickelbein, J.E., Haymet, A.D.J., and Madura, J.D. (2007).

Antifreeze proteins at the ice/water interface: Three calculated discriminating properties for orientation of type I proteins. Biophys. J., 93(5), 1442 - 1451.

Wu, Y., Ilan, B., Voth. G.A. (2007). Electrostatics and Charge Delocalization in Proton Channels. II. The

Synthetic LS2 Channel and Proton Selectivity. Biophysical Journal, 92( 1), 61 - 69. Zhdanov, M. S. G., A.; and Cuma, M. (2007). Regularized focusing inversion of marine CSEM data using

minimum vertical-support stablizer. SEG Expanded Abstracts, 26, 579. Zhdanov, M. S. U., T. (2007). Joint iterative migration of electric and magnetic-field data. SEG Expanded

Abstracts 26, 599.

2006

Anusiewicz, I., Berdys-Kochanska, J., Skurski, P., Simons, J. (2006). Simulating Electron Transfer

Attachment to a Positively Charged Model Peptide. J. Phys. Chem. A, 110, 1261 - 1266. Bagnato, J. D., Shum, W., Strohmeier, M., Grant, D., Atta, M. A., Miller, J. S. (2006). The Structure of

Fractinoally Charged Tetracyanobenzenen- Present in [TCNB]32-. Angew. Chem. Int. Ed., 45,

5322 - 5326. Cardoen, W., Gdanitz, R. J., Simons, J. (2006). Barrier height, exothermicity, and van der Waals wells on

the F + H2 F Ground-State Surface Calculated at the r12=ACPF-2 level. J. Phys. Chem. A, 110,

564-571.

Cardoen, W., Simons, J., Gdanitz, R. J. (2006). F + H2 FH + H Potential Energy Surface:

Construction of the Reference Configuration State Function Space and MR-ACPF-2 Results. International Journal of Quantum Chemistry, 106, 1516 - 1527.

Cardoen, W., Gdanitz, R. J., Simons, J. (2006). Transition-State Energy and Geometry, Exothermicity, and

van der Waals Wells on the F + H2 FH + H Ground-State Surface Calculated at the r12-ACPF-2

Level. Journal of Phys. Chem. A, 110, 564 - 571.

Cheatham, I., T.E., and Case, D.A. (2006). Applying AMBER biomolecular simulation methods to DNA and

RNA: Insight into the dynamics, interactions and energetics of varied nucleic acid structures. In J. a. L. Sponer, F. (Ed.), Computational Studies of DNA and RNA (pp. 45 - 72).

Cheatham, T. E., III., Case, D. A. (2006). Using AMBER to simulate DNA and RNA. In J. Sponer, Lankas, F. (Ed.), Computational Studies of DNA and RNA (pp. 45 - 72): Wiley.

Chevallier, C., Bugni, T. S., Feng, X., Harper, M. K., Orendt, A. M., Ireland, C. M. (2006). Tedanolide C: A

Potent New 18-Membered-Ring Cytotoxic Macrolide Isolated from the Papua New Guinea Marine Sponge Ircinia sp. Journal of Organic Chemistry, 71, 2510 - 2513.

Chu, J.-W., and G.A. Voth. (2006). Coarse-Grained Modeling of the Actin Filament Derived from Atomistic-Scale Simulations. Biophys. J., 90(5), 1572 - 1582.

Difley, S., Simons, J. (2006). The Role of Angular Electron Pair Correlation in Stablilizing C602-. Inter. J.

Quantum Chem, 507-513.

Ehlers, J. R., N.G.; Huynh, L.K.; Pham H.; Marks, M.; Truong, T. N. (2006). Theoretical study on

mechanism of epoxy-amine curing reactions. Macromolecules, 40(12), 4370 - 4377. Facelli, J. C. (2006). Intermolecular Shielding by Molecular Magnetic Susceptibility. A New View of

Intermolecular Ring Current Effects. Magnetic Resonance in Chemistry, 44, 401-408. Florez, E., Mondragon, F., Truong, T. N., Fuentealba, P. (2006). Transition-metal atom adsorption on an

Fs defect site of MgO (100) and the interaction with a hydrogen atom. Physical Review B: Condensed Matter and Materials Physics, 73(11), 115423/115421-115423/115427.

Harper, J. K., Grant, D. M., Zhang, Y., Lee, P. L., Von Dreele, R. (2006). Characterizing Challenging

Microcrystalline Solids with Solid-State NMR Shift Tensor and Synchrotron X-ray Powder Diffraction Data: Structural analysis of Ambuic Acid. J American Chem Society, 128, 1547 -

1552. Huynh, L. K., Ratkiewicz, S., Truong, T. N. (2006). Kinetics of the Hydrogen Abstraction OH + Alkane -->

H2O + Alkyl Reaction Class: An Application of the REaction Class Transition State Theory.

Journal of Phys. Chem. A, 110(2), 473-484. Kick, E., Davis, B., and Kentor, J. (2006). A Cross-National Analysis of Militarization and Inequality.

Journal of Political and Military Sociology, 34(2 (Winter)), 319-337. Kick, E. L., Fraser, J.C., and Davis, B. L. (2006). Performance Management, Managerial Citizenship, and

Worker Commitment: A Study of the United States Postal Service with Some Global Implications.

Economic and Industrial Democracy, 27, 137-172. Li, X., Zhaoxia P. (2006, 24 - 28 April, 2006). Sensitivity of numerical simulations of Hurrican Emily (2005)

to cumulus and microphysical parameterizations. Paper presented at the AMS 27th Conference on Hurricane and Tropical Meteorology.

Massoth, F. W., Politzer, P., Concha, M.C., Murray, J.S., Jakowski, J., Simons, J. (2006). Catalytic Hydrodeoxygenation of Methyl-Substituted Phenols: Correlations of Kinetic Parameters with

Molecular Properties. J. Phys. Chem. B, 110, 14283 - 14291.

Massoth, F. W., Politzer, P., Concha, M.C., Murray, J.S., Jakowski, J., Simons, J. (2006). Kinetics of catalytic hydrodeoxygenation of methyl-substituted phenols: Correlations with molecular

properties. J. Phys. Chem 110, 14280-14291. Maupin, C. M., K.F. Wong, A.V. Soudakov, S. Kim, and G.A. Voth. (2006). A Multi-State Empirical Valence

Bond Description of Protonatable Amino Acids. J. Phys. Chem. A., 110( 2), 631 - 639.

McDermott, R. (2006). Building Simple and Not So Simple Stick Models. Paper presented at the Bridges London -- Mathematical Connections in Art, Music, and Science, London, England.

McDermott, R. (2006). Transformations of Vertices, Edges and Faces to Derive Polyhedra. Paper presented at the Bridges London -- Mathematical Connections in Art, Music, and Science, London

England.

Moision, R. M., and P. B. Armentrout. (2006). The Special Five-Membered Ring of Proline: An Experimental and Theoretical Investigation of Alkali Metal Cation Interactions with Proline and Its

Four- and Six-Membered Ring Anaglogs. J. Phys. Chem. A., 110( 11), 3933 - 3946. Nichols, C., Deal, S., Rogers, TJ, Miklavcic, J., Miklavcic, B., Ayromlou, M., Wachtel, R., Mercer, P.,

Humbert, J., King, R. (2006, November 6 - 11, 2006). Musical Performance over Internet2 using the AccessGrid. Paper presented at the International Computer Music Conference, Tulane

University, New Orleans, LA.

Ona, O., Bazterra, V., Caputo, M., Facelli, J., and Ferraro, M. (2006). Global Optimization of Atomic cluster Structures Using Parallel Genetic Algorithms. Paper presented at the Material Res. Soc.

Symposium Proceedings. Ona, O., Bazterra, V., Caputo, M., Facelli, J., Fuentealba, P., and Ferraro, M. (2006). Modified genetic

algorithms to model cluster structures in medium-sized silicon clusters: Si18-Si60. Physical Review, A 73, 053203-053201 - 053203-053211.

Orendt, A., Roberts, SW, and Rainier, JD. (2006). The Role of Asynchronous Bond Formation in the

Diastereoselective Epoxidation of Cyclic Enol Ethers: A Density Functional Theory Study. Journal of Organic Chemistry, 71, 5565-5573.

Orendt, A. M., Roberts, Rainier, J. (2006). The Role of Asynchronous Bond Formation on the Diastereoselective Epoxidation of Cyclic Enol thers: A Density Functional Theory Study. J. Org.

Chem,. 71, 5565 - 5573.

Paesani, F., Zhang, W., Case, D.A., Cheatham, T.E., and Voth, G.A. (2006). An accurate and simple quantum model for liquid water. J. Chem. Phys., 125, 184507.

Paramore, S., G.S. Ayton, and G.A. Voth. (2006). Extending a Spectrin Repeat Unit I. Linear Force-Extension Response. Biophys J, 90(1), 92 - 100.

Pu, Z., Li, X. (2006, 24 - 28 April, 2006). Assimilation of satellite and in situ observations during TCSP for understanding tropical cyclone intensification. Paper presented at the AMS 27th Conference on Hurricane and Tropical Meteorology.

Pu, Z., Li, X. (2006, June 19 - 22, 2006). Numerical simulations of tropical cyclones during TCSP: The impact of data assimulation and sensitivity to cumulus and microphysical schemes in the WRF model. Paper presented at the 7th Annual WRF User's workshop, Boulder, CO.

Sefzik, T. H., Fidler, J. M., Iulicci, R., Facelli, J. C. (2006). Modeling the 13C Chemical-shift Tensor in

Organic Single-crystals by Quantum Mechanical Methods: Finite Basis Set Effects. Magnetic Resonance in Chemistry, 44, 390-400.

Shafer, J. c., Steenburgh, J.A., Cox, J.A. W., Monteverdi, J. P. (2006). Terrain influences on synoptic

storm structure and mesoscale precipitation distribution during IPEX IOP3. Monthly Weather Review, 134, 478 - 497.

Simons, J. (2006). How Do Low-Energy (0.1 - 2 eV) Electrons Cause DNA-Strand Breaks? Accounts of Chemical Research, 39(10), 772 - 779.

Simons, J. (2006). How very low-energy (0.1 - 2 eV) electrons cause DNA strand breaks. Advances in Quantum Chemistry, 52, 171 - 188.

Sobczyk, M., Simons, J. (2006). Distance dependence of through-bond electron transfer rates in

electron-capture and electron-transfer dissociation. International Journal of Mass Spectrometry, 253, 274 - 280.

Sobczyk, M., Simons, J. (2006). The Role of Excited Rydberg States in Electron Transfer Dissociation. J. Phys. Chem. B, 110, 7519 - 7527.

Spackova, N., Cheatham, T.E., and Sponer, J. (2006). Molecular dynamics simulations of nucleic acids. In

F. L. J. Sponer (Ed.), Computational Studies of DNA and RNA (pp. 301-326). Stoll, R. P.-A. (2006). Dynamic subgrid-scale models for momentum and scalar fluzes in large-eddy

simulations of neutrally stratified atmospheric boundary layers over heterogeneous terrain. Water Resources Res, 42, W01409.

Strohmeier, M., Barich, D. H., Grant, D. M., Miller, J. S., Pugmire, R. J., Simons, J. (2006). Solid-state

NMR Spectra and Long Intradimer Bonds in the [TCNE]22- Dianion

J. Phys. Chem. A, 110(25), 7962 - 7969. Sun, R., Jenkins, M.A., Krueger, S., and Charney, J. (2006). An evaluation of fire plume properties

simulated with the FDS and Clark coupled wildfire model. Canadian Journal of Forest Research, 36(11), 2894 - 2908.

Sun, R., Jenkins, M.A., Krueger, S., and Charney, J. (2006). Wildfire evolution in the convective boundary layer. Paper presented at the 17th Symposium on Boundary Layers and Turpulence, San Diego, CA

Sun, R. J., M.A.; Krueger, S.; Charney, J. (2006). An Evaluation of Fire Plume Properties Simulated with

the FDS and Clark Coupled Wildfire Model. Can. J. For. Res., 36, 2894 - 2908. Truong, T. N., Nayak, M., Huynh, H., Cook, T., Mahajan, P., Tran, L., Bharath, J., Jain, S., Pham, H.,

Boonyasiriwat, C., Nguyen, N., Andersen, E., Kim, Y., Choe, S., Choi, J., Cheatham, T.E., Facelli, J. (2006). Computational Science and Engineering Online (CSE-Online): A Cyber-Infrastructure

for Scientific Computing. Journal of Chem. Inf. Model., 46, 971- 984. Violi, A. a. V., A. (2006). Combustion-generated nanoparticles produced in a bensene flame: A

multiscale approach. Journal of Chemical Physics, 125(054302).

Wang, Y., Florez, E., Mondragon, F., Truong, T.N. (2006). Effects of metal-support interactions on the electronic structures of metal atoms adsorbed on the perfect and defective (100) surfaces.

Surface Science, 600(9), 1703-1713. Wijitkosoom, A., Tonmunphean, S., Truong, T.N., Hannongbua, S. (2006). Structural and dynamical

properties of a full-length HIV-1 integrase: molecular dynamics simulation. Journal of

Biomolecular Structure and Dynamics, 23(6), 613-624.

Wu, Y., H.L. Tepper, and G.A. Voth. (2006). A Flexible Simple Point-Charge Water Model with Improved Liquid-State Properties. J. Chem. Phys., 124(2 ), 024503.

Yu, J., G.T. Schuster, and R. Estill. (2006). Prestack Migration Deconvolution. Geophysics., 71(2), S53 - S62.

Zhang, H. R., Pham, M., Truong, T. N., Eddings, E.G., Sarofim, A.F. (2006). Polymerization reactions of

aromatics in a fuel-rich 20 torr naphthalene premixed flame enhanced by ring closure steps. Preprints of Symposia, American Chemical Society, Division of Fuel Chemistry, 51(2), 733-735.

Zhdanov, M. S. L., S. K.; Yoshioka, K. (2006). Integral equation method for 3D modeling of electromagnetic fields in complex structures with inhomogeneous background of conductivity.

Geophysics, 71, G333 - G345.

2005

Abbasi, R. U., et al. (2005). Observation of the Ankle and Evidence for a High-Energy Break in the Cosmic

Ray Spectrum. Phys. Lett. B., 619( ), 271-280. Abbasi, R. U., et al. (2005). A Search for Arrival Direction Clustering in the HiRes 1 Monocular Data Above

1019.5 eV. . Astrophys. J., 22, 139-149.

Abbasi, R. U., et al. (2005). Search for Global Dipole Enhancements in the HiRes-I Monocular Data above 1018.5 e V. . Astroparticle Phys., 21, 111-123.

Abbasi, R. U., et al. (2005). Search for Point Sources of Ultra-High Energy Cosmic Rays above 4.0 1019 eV Using a Maximum Likelihood Ratio Test. . Astrpohys. J., 623, 164-170.

Abbasi, R. U., et al. (2005). Study of Small-Scale Anisotropy of Ultra-High Energy Cosmics Rays Observed in Stero by HiRes. Astrophys. J., 610, 73-76.

Abbasi, R. U., et al. (2005). A Study of the Composition of Ultra-High Energy Cosmic Rays Using the High

Resolution Fly's Eye. Astrophys. J., 622, 910-926. Anusiewicz, I., Jasionowski, M., Skurski, P., Simons, J. (2005). Backbone and Side-Chain Cleavages in

Electron Detachment Dissociation (EDD). J. Phys. Chem. A, 109, 11332 - 11337. Anusiewicz, I., Berdys-Kochanska, Joanna, Czaplewiski, Cezary, Sobcyk, Monika, Daranowski, Emma,

Skurski, Piotr, Simons, Jack. . (2005). Charge Loss in Gas-Phase Multiply Negatively Charged

Oligonucleotides. J. Phys. Chem. A., 109, 240-249. Anusiewicz, I., Berdys., J.; Sobczyk, M.; Sawicka, A.; Skurski, P.; Simons, J. (2005). Coulomb-Assisted

Dissociative Electron Attachment: application to a Model Peptide. J. Phys. Chem, A109, 250 - 258.

Anusiewicz, I., Berdys-Kochanska, Joanna, Simons, Jack. (2005). Electron Attachment Step in Electron

Capture Dissociation (ECD) and Electron Transfer Dissociation (ETD). J. Phys. Chem. A., 109( ), 5801-5813.

Anusiewicz, M. S., Berdys-Kochanska, J., Skurski, P., and Simons, J. (2005). A theoretical model for indirect dissociative electron attachment. Journal of Physical Chemistry, A 109, 484-492.

Ayton, G., Tepper, H.L., Miriganian, D. T., and Voth, G.A. (2005). A New Perspective on Coarse-grained Dynamics of Fluids. Journal of Chemical Physics, 120, 4074-4088.

Ayton, G. S., McWhirter, J. L. McMurtry, P. and Voth, G.A. (2005). Coupling field theory with continuum

mechanics: a simulation of domain formation in giant unilammellar vesicles. Biophys J, 88, 3855-3869.

Bazterra, V. E., Cuma, M., Ferraro, M. B., Facelli, J. C. (2005). A General Framework to Understand Parallel Performance in Heterogeneous Clusters: Analysis of a New Adaptive Parallel Genetic

Algorithm. J. of Parallel and Distributed Computing, 65, 48-57.

Bazterra, V. E. (2005). Modified Genetic Algorithm to Model Crystal Structures: III. Determination of Crystal Structure Allowing Simultaneous Molecular Geometry Relaxation. International Journal of Quantum Chemistry, 96, 312-320.

Blood, P. R., G.S. Ayton, and G.A. Voth. (2005). Probing the Molecular-Scale Lipid Bilayer Response to

Shear Flow using Nonequilibrium Molecular Dynamics. J. Phys. Chem. B., 109, 18673-18679. Borges, C. R., Taccogno, J., Crouch, D. J., Le, L. Truong, T. N. (2005). Structure and mechanism of

formation of an important ion in doping control. International Journal of Mass Spectrometry, 247(1-3), 48-54.

Burns, T. J., Kick, E.L., Davis, B. L. (2005). Theorization and a Cross-National Analysis of Deforestation

Globalization and the Environment. Leiden, England: Brill Academic Publishers. Case, D. A., Cheatham, T. E., III, Darden, Gohlke, H., Luo, R., Merz, K. M., Jr., Onufrieve, A., Simmerling,

C., Wang, B., Woods, R. . (2005). The AMBER Biomolecular Simulation Programs. J. Comp. Chem., 26, 1668 - 1688.

Chang, R., G.S. Ayton, and G.A. Voth. (2005). Multi-Scale Coupling of Mesoscopic and Atomistic-Level

Lipid Bilayer Simulations. J. Chem. Phys., 122, 244716. Cheatham, T. E., III. (2005). Molecular Modeling and Atomistic Simulation of Nucleic Acids. Ann. Reports

Comp. Chem, 1, 75-89. Chu, J. W. a. V., G.A. (2005). Allostery of Actin Filaments: Molecular Dynamics Simulations and

Coarse-Grained Analyses. Proc. Natl Academy of Science, 102(13111-13116).

Day, G. M., Motherwell, W. D. S., Ammon, H. Boerrigter, S. X. M., Della Valle, R. G., Venuti, E., Dzyabchenko, A., Dunitz, J., van Eijck, B. P., Erk, P., Facelli, J. C., Bazterra, V. E., Ferraro, M. B.,

Hofmann, D. W. M., Leusen, F. J. J. Liang, C., Pantelides, C., Karamertzanis, P. G., Price, S. L., Lewis, T. C. Torrissi, A., Nowell, H., Scheraga, H., Arnautova, Y., Schmidt, M. U. Schweizer, B.,

Verwer, P. . (2005). A Third Blind Test of Crystal Structure Prediction. Acta Crystall, B61,

511-527. Difley, S., Simons, J. (2005). Role of Angular Electron Pair Correlation in Stabilizing C2-60. International

Journal of Quantum Chemistry, 106, 507 - 513. Dixit, S. B., Beveridge, D. L., Case, D. A., Cheatham, T. E., III., Giudice, S., Lankas, F., Lavery, R.,

Maddocks, J., Osman, R., Sklenar, H., Thayer, K. M., Varnai, P. . (2005). Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Obligonucleotides. II.

Sequence Context Effects on the Dynamical Structures of the 10 Unique Dinucleotide Steps. .

Biophys J., 89, 3721-3740. Espinal, J. F., Truong, T.N., Mondragon, F. (2005). Mechanisms for methane and ethane formation in the

reaction of hydrogen with carbonaceous materials. Carbon, 43(9), 1820-1827. Facelli, J. C., Sefzik, T.H., Turco, D., and Iuliucci, R.J. (2005). Modeling NMR Chemical Shift: A Survey of

Density Functional Theory Approaches for Calculating Tensor Properties. Journal of Physical Chemistry, 109, 1180-1187.

Freedman, H., Truong, T.H. (2005). An Application of Coupled Referenced Interaction Site Model

(RISM)/Molecular Dynamics (MD) Method to the Conformational Analysis of the Alanine Dipeptide. J. Phys. Chem. B. , 121(24), 12447-12457.

Freedman, H., Truong, T. N. (2005). A coupled reference interaction site model/molecular dynamics

study of the potential of mean force curve of the SN2 Cl-+CH3Cl reaction in water. Journal of Physical Chemistry B, 109(10), 4726-4730.

Geva, E., S. Jang, and G.A. Voth. (2005). Chapter 5: Quantum Rate Theory: A Path Integral Centroid Perspective. In S. Yip (Ed.), Handbook of Materials Modeling: SpringerLink.

Hone, T. D., Izvekob, S., and Voth, G.A. (2005). Fast Centroid Molecular Dynamics: A Force-Matching Approach for the Predetermination of the Effective Centroid Forces. J . Chem. Phys., 122,

054105(054101-054107).

Huynh, L. K., Truong, T. N. (2005). First-priciples kinetics for combustion systems using reaction class transition state theory. Preprints of Symposia - American Chemical Society, Division of Fuel Chemistry, 50(1), 82 - 85.

Iyengar, S. S., Day, T. J. F., and Voth, G.A. (2005). On the Amphiphilic Behavior of the Hydrated Proton:

An Ab Initio Molecular Dynamics Study. Int. J. Mass Spec., 241, 197-204.

Iyengar, S. S., M.K. Petersen, T.J.F. Day, C.J. Burnham, V.E. Tiege, and G.A. Voth. (2005). The Properties of Ion-Water Clusters. I. The Protonated 21-Water Cluster. J. Chem. Phys., 123,

084309. Izvekov, S., and Voth, G.A. (2005). Ab Initio Molecular Dynamics Simullation of Aqueous Proton Solvation

and Transport Revisited. J. Chem. Phys., 123, 044505 (044501-044509). Izvekov, S., and G.A. Voth (2005). Effective Force Field for Liquid Hydrogen Fluoride from Ab Initio

Molecular Dynamics Simulation Using the Force-Matching Method. J. Phys. Chem. B., 109,

6573-6586. Izvekov, S., and G.A. Voth. (2005). Multi-Scale Coarse-Graining of Liquid State Systems. J. Phys. Chem.,

123(134105). Izvekov, S., A. Violi, and G.A. Voth. (2005). Systematic Coarse-Graining of Nanoparticle Interactions in

Molecular Dynamics Simulation. J. Phys. Chem. B., 109, 17019-17024

Jenkins, M. A., Mell, W., Sun, R., Krueger, S., Zuluaf, M., and Charney, J. (2005). Numerical modeling of wildfires. Paper presented at the Workshop on Firest Fires and Point Processes., University of

Toronto. Jeon, J., and G.A. Voth. (2005). The Dynamic Stress Responses to Area Change in Planar Lipid Bilayer

Membranes. Biophys. J., 88, 1104-1119 Jiang, Z., J. Yu, B. Hornby, and G.T. Schuster. (2005). Migration of Multiples. The Leading Edge, 24,

315-318.

Jui, C. H., et. al. (2005). Observation of the Ankle and Evidence for a High-Energy Break in the Cosmic Ray Spectrum. Phys. Letters B, 619(3-4), 271 - 280.

Jui, C. H., et. al. (2005). Search for Point Sources of Ultra-High Energy Cosmic Rays above 4.0 1019 eV Using a Maximum Likelihood Ratio Test. Astrophys. J., 623, 164-170.

Jui, C. H., et. al. (2005). A Study of the Composition of Ultra-High Energy Cosmic Rays Using the High

Resolution Fly's Eye. Astrophys. J., 622, 910-926. Jungsuttiwong, S., Limtrakul, J., Truong, T.H. (2005). Theoretical study of modes of adsorption of water

dinner on H-ZSM-5 and H-Faujasite Zeolites. Journal of Physical Chemistry B, 109(27), 13342-13351.

Ka, B. J., and G.A. Voth. (2005). An Efficient and Accurate Implementation of Centroid Molecular Dynamics Using a Gaussian Approximation. J. Phys. Chem. A., 109(50 ), 11609 - 11617.

Kim, W. S., J. Kim, J.K. Park, S.Mukamel, S.K. Rhee, Y.K. Choi, and J.Y. Lee (2005). Stacking Effect of

Polyfluorene on the Chemical Shift and Electron Transport. J. Phys. Chem. B., 109, 2686-2626

Kungwan, N., Truong, T. N. (2005). Kinetics of the Hydrogen Abstraction .bul.CH3 + Alkane -->CH4 +

Alkyl Reaction Class: An Application of the Reaction Class Transition State Theory. Journal of Physical Chemistry A, 109(34), 7742-7750.

Lloyd, R. D., F.W. Bruenger, G.N. Taylor, and S.C. Miller (2005). Search for a Genetic Link for Mammary

Cancer in a Beagle Colony. In Vivo, 19, 723-728. Lu, G., Huang, Feng L. (2005). Towards Quantitative Understanding of Formation and Stability of Ge Hut

Island on Si(001). Phys. Rev. Lett., 94, 176103.

Lu, G.-H., Cuma, M., Feng Liu. (2005). First-prinicples Study of Strain Stabilization of Ge(105) Facet on Si(001). Phys. Rev. Lett. B., 72, 125415.

Lu, G.-H., M. Huang, M. Cuma, and F. Liu. (2005). Relative Stability of Si Surfaces: a First Principles Study. Surface Science, 588, 61-70.

McDermott, R. (2005). A Physical Proof for Five and Only Five Regular Solids. Paper presented at the Renaissance Banff -- Bridges: Mathematical Connections in Art, Music and Science.

McDermott, R. (2005). Polyhedral Transformation: Explosion-Implosion. Paper presented at the

Renaissance Banff -- Bridges: Mathematical Connections in Art, Music and Science, Banff, Alberta, Canada.

McDermott, R. (2005). A Ukrainian Easter Egg Monument Stands for Thirty Years. Paper presented at the Renaissance Banff -- Bridges: Mathematical Connections in Art, Music and Science, Banff,

Alberta, Canada.

Oku, K., M. Kurose, M. Kubota, S. Fukuda, M. Kurimoto, Y. Tujisaka, A. Okabe, and M. Sakurai (2005). Combined NMR and Quantum Chemical Studies on the Interaction between Trehalose and Dienes

Relevant to the Antioxidant Function of Trehalose. J. Phys. Chem. B., 109, 3032-3040. Ona, O., Bazterra, V. E., Caputo, M. C., Ferraro, M. B., Facelli, J. C. (2005). ab Initio Global Optimization

of the Structures of Si_n H, n = 4-10, Using Parallel Genetic Algorithms. Phys. Rev. A., 72. Orendt, A., Haymore, B., Richardson, D., Robb, S., Sanchez Alvarado, A., Facelli, J. C. (2005). Design,

Implementation and Deployment of a Commodity Cluster for Periodic Comparisons of Gene

Sequences. High Performance Computing Paradigm and Infrastruture, 733-744. Paramore, S., G.S. Ayton, and G.A. Voth. (2005). Extending a Spectrin Repeat Unit II. Rupture Behavior.

Biophys. J., 90( 1), 101 - 111. Petersen, M. K., Wang, F., Blake, N.P., Metiu, H., and Voth, G.A. (2005). Excess Proton Solvation and

Delocalization in a Hydrophilic Pocket of the Proton Conducting Polymer Membrane Nafion. J. Phys. Chem. B, 109, 3727-3730.

Pratt, L. M., Le, L. T., Truong, T. N. (2005). A Computaional Study of Mixed Aggregates of

Chloremethyllithium with Lithium Dialkylamides. Journal of Organic Chemistry, 70(21), 8298-8302.

Ratkiewicz, A., Truong, T.N. (2005). Automated mechanism generation: From symbolic calculation to complex chemistry. Internal Journal of Quantum Chemistry, 106(1), 244-255.

Reichler, T., Kushner, P.J., and Polvani, L.M. (2005). The Coupled Stratosphere -Troposphere Response

to Impulsive Forcing from the Troposphere. J. of the Atmospheric Sciences, 62, 3337 - 3352. Sawicka, A., Skurski, Piotr, Simons, Jack. (2005). Inverse Potassium Hydride: A Theoretical Study. J.

Phys. Chem. A., 109, 922-927. Sawicka, A., Berdys-Kochanska, J., Skurski, P., and Simons, J. (2005). Low-Energy (0.1 eV) Electron

Attachment S-S Bond Cleavage Assisted by Coulomb Stablization. International Journal of Quantum Chemistry, 102, 838-846.

Schuster, G. T. (2005). Fermat's interferometric principle for target-oriented traveltime tomography.

Geophysics, 70(4), U47 - U50. Sefzik, T., Turco, D., Iuliucci, R., Facelli, J. C. . (2005). Modeling NMR Chemical Shift: A Survey of Density

Functional Theory Approaches for Calculating Tensor Properties. J. Phys. Chem. A., 109, 1180-1187.

Shi, Q., and Voth, G. A. (2005). Multi-Scale Modeling of Phase Separation in Mixed Lipid Bilayers.

Biophys. J., 89(4), 2385 - 2394. Sirigaraensre, J., Truong, T. N., Limtrakul, J. (2005). Density Functional Study of the Mechanism of the

Beckmann Rearrangement Catalyzed by H-ZSM-5: A Cluster and Embedded Cluster Study. Journal of Physical Chemistry B, 109(24), 12099-12106.

Sobczyk, M., I. Anusiewicz, J. Berdys-Kochanska, A. Sawicka, P. Skurski, and J. Simons. (2005).

Coulomb-Assisted Dissociative Electron Attachment: Application to a Model Peptide. J. Phys. Chem. A., 109, 250-258.

Sobczyk, M., Skurski, Piotr, Simons, Jack. (2005). Dissociative Low-Energy Electron Attachment to the C-S Bond of H3CSCH3 Influenced by Coulomb Stailization. Advances in Quantum Chemistry, 48,

239-251.

Sun, R., S.K. Krueger, M.A. Jenkins, W. Mell, and J. Charney. (2005). An Evaluation of FDS and Clark Coupled Wildfire Model. Accepted by 6th Symposium on Fire and Meteorology and the 19th Interior West Fire Council Meeting, Conmore, AB, Canada(Accepted by 6th Symposium on fire and meteorology and the 19th Interior west fire council meeting, Conmore, AB, Canada).

Sun, R., Krueger, S., Jenkins, M.A., Mell, W., and Charney, J. (2005). An evaluation of the Fire Dynamics Simulator and the coupled Clark wildfire model using plume observations. Paper presented at the

6th Symposium on Fire and Forest Meteorology, Canmore, B.C., Canada.

Tepper, H. L., and G.A. Voth. (2005). A Coarse-Grained Model for Double-Helix Molecules in Solution: Spontaneous Helix Formation and Equilibrium Properties. J. Chem. Phys., 122, 124906.

Tepper, H. l., and Voth, G. A. (2005). Protons May Leak Through Pure Lipid Bilayers via a Concerted Mechanism. Biophys. J., 88, 3095-3108.

Tiznado, W., Ona, O., Bazterra, V. E., Caputo, M. C., Ferraro, M. B., Facelli, J. C., Fuentealba, P. (2005).

Theoretical Study of the Adsorption of H and Si_n Clusters (n = 3-10). J. Chem. Phys., 123, 214302.

Treesukol, P. S., K., Limtrakul, J., Truong, T. N. (2005). Nature of the Metal-Support Interaction in Bifunctional Catalytic Pt/H-ZSM-5 Zeolite. Journal of Physical Chemistry B, 109(24), 11940-11945.

Venkatnathan, A., and G.A. Voth. (2005). Superposition State Molecular Dynamics. J. Chem. Theory Comp., 1, 36-40.

Wang, F., and Voth, G. A. (2005). A Linear-Scaling Self-Consistent Generalization of the Multi-State

Empirical Valence Bond Model for Multiple Excess Protons in Aqueous Systems. J. Chem. Phys., 122, 144105(144101-144109).

Wang, Y., Truong, T. N. (2005). Correlation between electronic structures of metal-intercalated single wall carbon nanotubes with their field emission properties. Journal of Theoretical & Computational Chemistry, 4(Special Issue), 657-668.

Wang, Y., S. Izvekov, T. Yan, and G.A. Voth. (2005). Multi-Scale Coarse-Graining of Ionic Liquids. J. Phys. Chem. B., 110( 8), 3564 - 3575.

Wang, Y., and G.A. Voth. (2005). Unique Spatial Heterogeneity in Ionic Liquids. J. Am. Chem. Soc., 127, 12192-12193

Wu, Y., and G.A. Voth. (2005). A Computational Study of the Open and Closed States of the Influenza A M2 Proton Channel. Biophys. J., 89( ), 2402-2411.

Xu, J., and Voth, G. A. (2005). Computer Simulation of Explicit Proton Translocation in Cytochrome c

Oxidase: The D-Pathway. Proc. Nat. Academy of Science, 102, 6795-6800. Ye, S. J., R. M. Moision, and P. B. Armentrout (2005). Sequential Bond Energies of Water to Sodium

Clycine Cation. Int. J. Mass. Spec., 240, 233-248. Yu, J. a. S., G. T. (2005). Crosscorrelation migration of inverse vertical seismic profile data. Geophysics,

71(1), S1 - S11.

2004

Abbasi, R. U., et al. (2004). Measurement of the Flux of Ultrahigh Energy Cosmic Rays from Monocular

Observations by the High Resolution Fly's Eye Experiment. Phys. Rev. Lett., 92, 151101. Abbasi, R. U., et. al. (2004). Monocular Measurement of the Spectrum of UHE Cosmic Rays by the FADC

Detector of the HiRes Experiment.

Anusiewicz, I., J. Berdys, M. Sobczyk, P. Skurski, and J. Simons. (2004). Effects of Base Pi-Stacking on Damage to DNA by Low-Energy Electrons. J. Phys. Chem. A., 108, 11381-11387.

Ayton, G. S., and G.A. Voth. (2004). Mesoscopic Lateral Diffusion in Lipid Bilayers. Biophys. J., 87, 3299-3311

Ayton, G. S., and G.A. Voth. (2004). The Simulation of Biomolecular Systems at Multiple Length and Time

Scales. Int. J. for Multiscale Comp. Eng. (IJMCE) (Special Issue: Invited Article), 2, 291-311 Bazterra, V. E., Cuma, M., Ferraro, M. B., Facelli, J. C. (2004). A general framework to understand

parallel performance in heterogeneous clusters: analysis of a new adaptive parallel genetic algorithm. Journal of Parallel and Distributed Computing, 65, 48-57.

Bazterra, V. E., Ona, Ofelia, Caputo, Maria C., Ferraro, Marta B., Fuentealba, Patricio, Facelli, J. C. (2004).

Modified Genetic Algorithms to Model Cluster Structures in Medium-size Silicon Clusters. [Journal]. Phys. Rev. A., 69, 053202.

Berdys, J. A., Iwona, Skurski, Piotr, Simons, J. . (2004). Damage to Model DNA Fragments from Very Low-Energy (<1 eV) Electrons. J. Am. Chem. Soc., 126(20), 6441-6447.

Cheng, W. Y. Y., and W. J. Steenburgh. (2004 ). Evaluation of Surface Sensible Weather Forecasts by the WRF and Eta Models Over the Western United

States. Wea. Forecasting, 20, 812-821.

Clawson, J., Anderson, K., Pugmire, R., Grant D. (2004). 15N NMR Chemical Shift Tensors of Substituted Hexaazaioswurtzitanes: The Intermediates in the Synthesis of CL-20. J. Phys. Chem. A., 108,

2638-2644. Davis, B. L., E.L. Kick, and T.J. Burns. (2004). Change Scores, Composites and Reliability Issues in

Cross-National Development Research. International J. of Comparative Sociology, 45, 299-314.

Del Popolo, M. G., and Voth, G. A. (2004). On the structure and dynamics of ionic liquids. Journal of Physical Chemistry, B 108, 1744-1752.

Di Fiori, N., Orendt, A.M., Caputo, M.C., Ferraro, M.B., and Facelli, J.C. (2004). Modeling Solid-state Effects on NMR Chemical Shifts Using Electrostatic Models. Magnetic Resonance in Chemistry, 42,

41-47. Espinal, J., Montaya, A., Mondragon, F., Truong, T.N. (2004). A DFT Study of Interaction of Carbon

Monoxide with Carbonaceous Materials. J. Phys. Chem. B., 108, 1003-1008.

Espinal, J. F., Mondragon, Fanor, Truong, T.N. (2004). Density Functional Theory Study of Carbon-H2O Reactions during Gasification with Steam. Am. Chem. Soc., 49, 822.

Facelli, J. C. (2004). Calculations of Chemical Shielding: Theory and Applications. Concepts in Mag. Res. Part A, 20A, 42-69.

Freedman, H., Truong, T.H. (2004). A Coupled Reference Interaction Site Model (RISM)/Molecular

Dynamics (MD) Study of Potential Mean Force of the SN2CI + CH3CI Reaction. J. Phys. Chem. A. , 109, 4726-4730.

Freedman, H., Truong, T.N. (2004). Coupled Reference Interaction Site Model/Simulation Approach for Thermochemistry of Solvation: Theory and Prospects. J. Chem. Phys., 121( ), 2187.

Freedman, H., Nguyen, H, Truong, T.H. (2004). A Study of the Tautomic Equilibria of 2-hydroxypyridine/2-oxopyridine and of Cystosine in Water Using the Coupled Reference

Interaction Site Model (RISM)/Molecular Dynamics (MD) Approach. J. Phys. Chem. B. , 108,

19043. Gregory, E., Cheatham, III T.E., Facelli, J.C. (2004). Data Mining Atomic Motions from Computer

Siimulations of Nucleic Acids: A Wavelet Study of the Differential Bending of d[GA_4 T_4 C]_n and d[GT_4 A_4 C]_m. . In A. Gramada (Ed.), Currents in Computational Mol. Bio (pp. 528).

Hart, K., Steenburgh, W. J., Onton, D., Siffert, A. (2004). An Evaluation of Mesoscale-Model-Based Model

Output Statistics (MOS) during the 2002 Olympic and Paralympic Winter Games. Wea. Forecasting, 19, 200-218.

Hart, K. A. (2004). An evaluation of high-resolution modeling and statistical forecast techniques over complex terrain. Ph.D. Doctoral dissertation University of Utah, Salt Lake City.

Hart, K. A., W. J. Steenburgh, and D. J. Onton. (2004 ). Model Forecast Improvements with Decreased Horizontal Grid Spacing Over Fine-scale Intermountain

Orography During the 2002 Olympic Winter Games. Wea. Forecasting, 20, 558-576.

Hone, T. D., and Voth, G.A. . (2004). A centroid moelcular dynamics study of liquid para-Hydrogen and ortho-Deuterium. J. Chem. Phys., 121, 6412-6422.

Huang, M. H., Cuma, M., Lagally, M.G., Feng Lui. (2004). Bending of Nanoscale Thin Si Film Induced by Growth of Ge Islands: Hut vs. Dome. MRS Procedding, 791(Q6.4), 1-6.

Ilan, B., E. Tajkhorshid, K. Schulten, and G. A. Voth. (2004). The Mechanism of Proton Exclusion in

Aquaporin Channels. Proteins: Structure, Function, and Bioinformatics, 55, 223-228 Izvekov, S., Parrinello, M., Burnham, C. J., Voth, G. A. (2004). Effective Force Fields for Condensed Phase

Systems From Ab Initio Molecular Dynamics Simulation: A New Method for Force-matching. [Journal]. J. Chem. Phys., 120(23), 10896-10913.

Jenkins, M. A. (2004). Investigating the Haines Index Using Parcel Model Theory. Int. J. of Wildland Fire, 13, 1 - 13.

Jui, C. H., et. al. (2004). Study of small-scale anisotrphy of ultra-high energy cosmic rays observed in

stereo by HiRes. Astrophysics Journal, 610, L73-76. Ka, B. J., Voth, G. A. (2004). Combining the Semiclassical Initial Value Representation with Centroid

Dynamics. [Journal]. J. Phys. Chem B., 108(21), 6883-6892. Lapid, H., Agmon, N., Petersen, M.K. and Voth, G.A. (2004). A bond-0rder analysis of the mechanism for

hydrated proton mobility in liquid water. Journal of Chemical Physics, 122, 1 - 11.

Limtrakul, J., Inntam, Chan, Truong, T.N. (2004). Density Functional Theory Study of the Ethylene Epoxidation over Ti-substituted Silicalite (TS-1): An Application of Cluster and Embedded Cluster

Methods. J. of Molecular Catalysis A: Chemical, 207(139). McWhirter, J. L., Ayton, G.S., and Voth, G.A. (2004). Coupling Field Theory with Mesoscopic Dynamical

Simulations of Multi-component Lipid Bilayers. Biophysical Journal, 87.

Nguyen, H. N., Zhang, S., Peeters, J., Truong, T.N., Nguyen, M.T. (2004). Direct ab initio Dynamics Studies of the Reactions of HNO with H and OH radicals. Chem. Phys. Lett., 388(94).

Ona, O., V. E. Bazterra, M. C. Caputo, M. B. Ferraro, P. Fuentealba, J. C. Facelli. (2004). Modified Genetic Algorithms to Model Atomic Cluster Structures: CuSi Clusters. J. Mol. Struct., 681, 149-155.

Pala, R., Feng Liu. (2004). Determining the Adsorptive and Catalytic Properties of Strained Metal Surfaces using Adsortion-induced Stress. J. Chem. Phys., 120(7720).

Petersen, M. K., S.S. Iyengar, T.J.F. Day, and G.A. Voth. (2004). The Hydrated Proton at the Water

Liquid/Vapor Interface. J. Phys. Chem. B., 108, 14804-14806 Rega, N., S. S. Iyengar, G. A. Voth, H. B. Schlegel, T. Vreven, and M. J. Frisch. (2004). Hybrid Ab Initio

Empirical Molecular Dynamics: Combining the ONIOM Scheme with the Atom-centered Density Matrix Propagation (ADMP) Approach. J. Phys. Chem. B., 108, 4210 - 4220

Schuster, G. T., J. Yu, J. Sheng, and J. Rickett. (2004). Interferometric/daylight Seismic Imaging. GJI, 157, 838-852.

Stokes, B. T., Jui, C.C. H., and Matthews, J.N. (2004). Using fractal dimensionality in the search for

source models of ultra-high energy cosmic rays. Astroparticle Phys., 21, 95. Strohmeier, M., Grant D. M. . (2004). Experiemental and Theoretical Investigation of the 13C and 15N

Chemical Shift Tensors in Melanostatin - Exploring the Chemical Shift Tensor as a Structural Probe. J. Am. Chem Soc., 126, 966-977.

Sun, R., Jenkins, M. A., Krueger, S. K. (2004). Effects of atmospheric stability, moisture, and wind speed

on wildfire behavior and indications of Haines Index. . Internal Journal of Wildland Fire. Truong, T. N. (2004). Computational Science and Engineering Online: An Integrated Web-based

Environment for Multi-scale Modeling of Complex Reaction Systems. (Proceedings of the 2nd International Conference on Foundations of Molecular Modeling and Simulations). Molecular Phys., 102, 353.

Violi, A., A.F. Sarofim, and G.A. Voth. (2004). Kinetic Monte Carlo-Molecular Dynamics Approach To Model Soot Inception. Combust. Sci. and Tech., 176, 991-1005

Violi, A., Truong, T.N., Sarofim, A.F. (2004). Kinetics of Hydrogen Abstraction Reactions From Polycyclic Aromatic Hydrocarbons by H atoms. J Phys. Chem. A., 108(4846).

Wang, Y., Truong, T.N. (2004). Theoretical Study of Adsorption of Water Dimer on the Perfect MgO (100) Surface: Molecular Adsorption versus Dissociative Chemisorption. J. Phys. Chem. B., 108,

3289-3294.

Yan, B., Liu, F., Lagally, M.G. (2004). Local Strain-mediated Chemical Potential Control of Quantum Dot Self-organization in Heteroepitaxy. Phys. Rev. Lett., 92( ), 025502.

Yan, t., Burnham, C. J., Del Popola, M.D., and Voth, G.A. (2004). Molecular dynamics simulation of ionic liquids: The effect of electronic polarizability. Journal of Physical Chemistry B 108, 11777-11881.

Zang, J., Treibergs, Andrejs, Han, Y., Feng Liu. (2004). Geometry Constant Defining Shape Transitions of

Carbon Nanotubes under Pressure. Phys. Rev. Lett., 92, 105501.

2003

Ahn, E., Hari, P., Whitaker, J., Williams, G.A., Taylor, P.C., and Facelli, J. (2003). Evidence of indirect spin

-- spin coupling in srystalline and glassy As-chalcogen compounds. Journal of Non-Crystalline Solids 326 & 327, 64 - 67.

Bazterra, V. E., Ferraro, M. B., Facelli, J. C. (2003). Modified Genetic Algorithm to Model Crystal Structures. III. Determination of Crystal Structures Allowing Simultaneous Molecular Geometry

Relaxation. International J. of Quantum Chemistry, 96, 312-320. Blair, S. (2003). Self-focusing of Narrow 1-D Beams in Photoni Microcavity Arrays. J. of the Optical

Society of America, B 20, 1520-1526.

Burns, T. J., Kick, E.L., and David, B.L. (2003). Theorizing and Rethinking Linkages between the Natural Environment and the Modern World-System: Deforestation in the Late 20th Century. Journal of World-Systems Research, 9, 357-392.

Cummings, M. P., Handley, S. A., Myers, D. S., Reed, D. L., Rokas, A., Winka, K. (2003). Comparing

Bootstrap and Posterior Probability Values in the Four-taxon Case. Systematic Biology, 52,

477-487. Erkoc, S., Leblebicioglu, Kemal, Halici, Ugur. (2003). Application of Genetic Algoritms to Geometry

Optimization of Microclusters: A Comparative Study of Empirical Potential Energy Functions for Silicon. Materials and Manufacturing Processing, 18, 329-339.

Fogelson, A., and R. Guy. (2003). Platelet-Wall Interactions in Continuum Models of Platelet Aggregation. Biophys. J., 80( ), 1050-1074.

Freedman, H., Truong, T.N. (2003). A Coupled RISM/MD or MC Simulation Methodology for Solvation

Free Energies. Chem. Phys. Lett., 381, 362. Jenkins, M. A., Krueger, S. K., Sun, R. (2003, November 2003). Using a Simple Parallel Model to

Investigate the Haines Index. Paper presented at the 5th Symposium on Fire and Forest Meteorology, Orlando, FL.

Lee, L., and LeVeque, R.J. (2003). An immersed interface method for incompressible Navier-Stokes

equations. SIAM J Sci. Comp, 25, 832-856. Lewis, J. P., Cheatham, T. E., III, Starikov, E.B., Wang, H., Sankey, O.F. (2003). Dynamically Amorphous

Character of Electronic States in Poly(dA)-Poly(dT) DNA. J. Phys. Chem. B., 107, 2581-2587. Montoya, A., Mondragon, F., Truong, T.N. (2003). CO2 Adsorption on Carbonaceous Surface: A Combined

Experimental and Theoretical Study. Carbon, 41, 29. Myers, D. S., Cummings, M. P. (2003). Necessity is the Mother of Invention: a Simple Grid Computing

System using Commodity Tools. J. of Parallel and Distributed Computing, 63, 578-589.

Oklejas, V., and Harris, J. M. (2003). In-Situ Investigation of Binary Component Self-Assembled Monolayrs: A SERS-Based Spectroelectrochemical Study of the Effects of Monolayer Composition

on Interfacial Structure. Langmuir, 19, 5794-5801. Oklejas, V., Sjostrom, C., and Harris, J. M. (2003). Surface Enhanced Raman Scattering Based Vibrational

Stark Effect as a Spatial Probe of Interfacial Electric Fields in the Diffuse Double Layer. J. Phys. Chem. B., 107, 7788-7794.

Ratkiewicz, A., Truong, T.N. (2003). Application of Chemical Graph Theory for Automated Mechanism

Generation. J. of Chemical Information and Computer Sciences, 43, 36. Schuster, G. T., Katz, L., Followill, F., and Yu, J. (2003). Autocorrelogram migration theory. Geophysics

68, 1685-1694. Shapolav, V., Yan Wang, Truong, T.N. (2003). Theoretical Analysis of the Electronic Spectra of Water

Adsorbed on the Rutile TiO2 (110) and MgO (100) Surfaces. Chem. Phys. Lett., 381, 362.

Sheley, D., Crosby, T., Zhou, M., Giacoma, J., Yu, J., He, R., and Schuster, G. (2003). 2-D seismic trenching of colluvial wedges and faults in contributions to Neotectonics and seismic hazard from

shallow geophysical imaging. Tectonophysics, 368, 51-69. Sheley, D., and G. Schuster. (2003). Reduced-time Migration of Transmission P-S Waves. Geophysics, 68,

1695-1707.

Sheng, J., and Schuster, G.T. (2003). Finite-frequency resolution limits of wave path traveltime tomography for smoothly varying models. Geophysical J. Int, 152, 669-676.

Solum, M. S., Veranth, J. M., Jiang, Y. J., Orendt, A. M., Sarofim, A. F., Pugmire, R J. (2003). The Study of Anthracene Aerosols by Solid-State NMR and ESR. Energy & Fuels, 17(3), 738 - 743.

Sun, H., and G.T. Schuster. (2003). 3D wavepath migration. Geophysical Prospecting, 51, 421-430.

Sun, R. (2003). Effect of low-level atmospheric stablity and moisture on wildfire behavior. Master of Science, University of Utah, Salt Lake City, UT.

Sun, R., and M.A. Jenkins. (2003). Effects of Near-Surface Atmospheric Stability and Moisture on Wildfire Behavior and Consequences for Haines Index. Paper presented at the 5th Symposium on Fire and

Meteorology and the 2nd International Wildland Fire Ecology and Fire Management Congress, Orlando, FL.

Whitaker, J., Ahn, E., Hari, P., Williams, G. A., Taylor, P. C., Facelli, J. C. (2003). Indirect (J) coupling of

inequivalent 75As nuclei in crystalline and glassy As2Se3 and As2S3. J. Chem. Phys., 119, 8519-8525.

Zhang, S., Truong, T.N. (2003). Kinetics of Hydrogen Abstraction Reaction Class H + H-C(sp3): First-Principle Predictions Using the Reaction Class Transition State Theory. J. Phys. Chem. A., 107.

Zhang, S., Nguyen, H.N., Truong, T.N. (2003). Theoretical study of Mechanism, Thermodynamics and Kinetics of the Decomposition of Gas phase HMX

(Octahydro-1,3,5,7-Tetranitro-1,3,5,7-Tetrazocine. J. Phys. Chem. B., 107, 2981.

2002

Anderson, K. L., Merwin, L.H., Wilson, Facelli, J.C. (2002). 15N Chemical Shifts in Energetic Materials:

CP/MAS and ab Initio Studies of Aminonitropyridines, Aminonitropyrimidines, and Their N-Oxides. Int. J. Mol. Sci., 3, 858-872.

Anusiewicz, I. a. P. S. (2002). An Ab Initio Study on BeX3 Superhalogen Anions (X=F, C1, Br). Chem.l Phys. Lett., 358, 426-434.

Ayton, G., Voth, G. A. (2002). Bridging Microscopic and Mesoscopic Simulations of Lipid Bilayers. Biophys J., 83, 3357-3370.

Bazterra, V. E., Ferraro, M. B., Facelli, J. C. . (2002). Modified Genetic Algorithm to Model Crystal

Structures. I. Benzene, Naphthalene and Anthracene. J. Chem. Phys., 116, 5984-5991. Bazterra, V. E., Ferraro, M. B., Facelli, J. C. (2002). Modified genetic algortithm to model crystal

structures. II. Determination of a polymorphic structure of benzene using enthalpy minimization. Journal of Chemical Physics, 116, 5992-5995.

Clawson, J. S., Strohmeier, M., Stueber, D., Orendt, A. M., Barich, D. H., Asay, B., Hiskey, M. A.,

Pugmire, R. J., Grant, D. M. (2002). 15N Chemical shift Tensors of -HMX. J Physical Chem A, 106(26), 6352 - 6357.

Day, T. J. F., Soudackov, M., Cuma, M., Schmitt, U. W., Voth, G. A. (2002). A Second Generation

Multi-State Empirical Valence Bond Model for Proton Transport in Aqueous Systems. J. Chem. Phys., 117, 5839-5849.

Fogelson, A., H. Yu, A. Kuharsky. (2002). Computational Modeling of Blood Clotting: Coagulation and

Three-dimensional Platelet Aggregation. Polymer and Cell Dynamics: Multiscarel Modeling and Numerical Simulations.

Harper, J. K., J.C. Facelli, D.H. Barich, G. McGeorge, A.E. Mulgrew, D.M. Grant. (2002). 13C NMR Investigation of Solid-State Polymorphism in 10-Deacetyl Baccatin III. J. Am. Chem. Soc., 124,

10595.

Horel, J., Potter, T., Dunn, L., Steenburgh, W. J., Eubank, M., Splitt, M., Onton, D. J. (2002). Weather support for the 2002 Winter Olympic and Paralympic Games. Bulletin of American Meteorolgic Society, 83, 227-240.

Izvekov, S., Voth, G. A. (2002). Carr-Parrinello Molecular Dynamics Simulation of Liquid Water: New

Results. J. Chem. Phys., 116, 10372-10376. Jenkins, M. A. (2002). A Examination of the Sensitivity of Numerically Simulated Wildfires to Low-level

Atmospheric Stability and Moisture, and the Consequences for the Haines Index. International Journal of Wildland Fire, 11, 213-223.

Jenkins, M. A., Sun, R. (2002, August 2003). What Coupled Wildfire-atmosphere Numerical Models Can Do. Paper presented at the 4th International Workshop on Disturbance Dynamics in Boreal Forest, Prince George, British Columbia.

Lankas, F., T. E. Cheatham, III, P. Hobza, J. Langowski, N. Spackova, and J. Sponer. (2002). Critical

Effect of the N2 Amino Group on Structure, Dynamics and Elasticity of DNA Polypurine Tracts. Biophys. J., 82, 2592-2609.

Reil, K. (2002). The Energy Spectrum of Ultra High Energy Cosmic Rays Measured by the High Resolution Fly's Eye Detectors.

Rienstra, C. M., Kellogg, L. T., Jaroniec, C. P., Hohwy, M., Reif, B., McMahon, M. T., Tidor, B. Perez,

T. L., Griffin, R. G. . (2002). De Novo Determination of Peptide Structure with Solid-state Magic-angle Spinning NMR Spectroscopy. PNAS, 19, 10260-10265.

Schlegel, H. B., Iyengar, S. S., Li, X., Milliam, J. M., Voth, G. A., Scuseria, G. E., Frisch, M. J. (2002). Ab Initio Molecular Dynamics: Propagating the Density Matrix with Gaussian Orbitals. III.

Comparison with Born Oppenheimer Dynamics. J. Chem. Phys., 117, 8694-8704. Schultz, D. M., Steenburgh, W. J., Trapp, R.J., Horel, J., Kingsmill, D.E., Dunn, L.B., Rust, W.D., Cheng,

L., Bansemer, A., Cox, J., Daugherty, J., Jorgensen, D.P., Meitin, J., Showell, L., Smull, B.F.,

Karp, K., Trainor, M. (2002). The Intermountain Precipitation Experiment. Bulletin of American Meteorolgic Society, 83, 189-210.

Schuster, G. T. (2002). Geophysics is Kid's Play. The Leading Edge, 24( ), 315-318. Skurski, P., I. Dabkowska, A. Sawicka, J. Rak. (2002). Dipole-bound and Dispersion-bound Anions

Supported by the Asymmetric Tautomers of Aminophosphine: H3NPH and HNPH3. Chemical

Physics, 279, 101-111.

Smondyrev, A. M. a. G. A. V. (2002). Molecular Dynamics Simulation of Proton Transport Near the Surface of a Phospholipid Membrane. Biophysical Journal, 82, 1460.

Spackova, N., T. E. Cheatham, III, F. Ryjcek, F. Lankas, L. van Meervelt, P. Hobza and J. Sponer. (2002). Molecular Dynamics Simulations and Thermodynamics Analysis of DNA - Drug Complexes. I.

Minor groove binding between 4',6-diamidino-2-phenylindole (DAPI) and DNA duplexes in

solution. Journal of American Chemical Society. Steenburgh, W. J. (2002). Using Real-time Mesoscale Modeling in Undergraduate Education. Bulletin of

American Meteorolgic Society, 10, 1147-1451. Stefl, R., T.E. Cheatham III, N. Spackova, E. Fadrna, I. Berger, J. Koca and J. Sponer. (2002). Formation

Pathways of a Guanine-quadruplex DNA revealed by Molecular Dynamics and Thermodynamical Analysis of the Substates. Journal of American Chemical Society.

Stewart, J., Whiteman, D., Steenburgh, W. J., Bian, X. . (2002). A Climatological Study of Thermally

Driven Wind Systems of the U.S. Intermountain West. Bulletin of American Meteorological Society, 83, 699-708.

Stueber, D., Orendt, A. M., Facelli, J. C., Parry, R. W., Grant, D. M. (2002). Carbonates, Thiocarbonates, and the Corresponding Monoalkyl Derivatives: III. The 13C Chemical Shift Tensors in Potassium

Carbonate, Bicarbonate and Related Monomethyl Derivatives. Solid State Nuclear Magnetic Resonance, 22, 29 - 49.

Violi, A., Kubota, A., Truong, T., Pitz, W., Westbrook, C., Sarfofim, A. . (2002). A Fully-Integrated Kinetci Monte Carlo / Molecular Dynamics Approach for the Simluation of Soot Precursor Growth. Paper presented at the Proceedings of the 29th International Symposium on Combustion Sapporo,

Japan. Violi, A., A. Sarofim, T. Truong. (2002). Mechanistic Pathways to Explain H/C Ratio of Soot Precursos.

Paper presented at the Second Mediterranean Combustion Symposium, Sharm el Sheik, Egypt.

2001

Archbold., G. (2001). A Fiber-optic Based Calibration Systems for the HiRes Experiment. Proceedings of

ICRC, 1.

Bellido, J., Belz, J., Dawson, B., Schindel, M., Stokes, B. (2001). Anisotropy Studies of Ultra-High Energy Cosmic Rays as Observed by the High Resolution Fly's Eye (HiRes). Proceedings of ICRC, 1.

Bergman, D. R. (2001). Determining the Alignment of HiRes Optics Using a CCD Camera. Proceedings of ICRC, 1.

Bergman, D. R. (2001). A Monocular Spectrum Analysis Using FADC Timing at HiRes. Proceedings of ICRC 2001, 1.

Cao, Z. (2001). A Measurement of the Average Longitudinal Development Profile of Cosmic Ray Air

Showers Between from 1017 eV and 1018.3 eV. Proceedings of ICRC 2001, 1. Cao, Z. (2001). Measurement of the Cosmic Ray Energy Spectrum from 1017 to 1018.3 eV Using a Hybrid

Technique. Proceedings of ICRC 2001, 1. Cao, Z. (2001). Monte Carlo Simluation of the HiRes Experiment. Proceedings of ICRC, 1.

Cheatham, I., T. E., Young, M. A. (2001). Molecular Dynamics Simulations of Nucleic Acids: Successes,

limitations and promise. Biopolymers, 56, 232-256. Clay, R. W., B.R. Dawson, R.T. Pace, D.S. Riordan, A.G.K. Smith, N.R. Wild. (2001). Cloud Detection at

the High Resolution Fly's Eye. Proceedings of ICRC, 1. Facelli, J. C., Nakagawa, B. K., Orendt, A. M., Pugmire, R. J. (2001). Cluster analysis of 13C Chemical

Shift Tensor Principal Values in Polycyclic Aromatic Hydrocarbons. J Physical Chem A, 105(31),

7468 - 7472. Izvekov, S., and G. A. Voth. (2001). Ab Initio Molecular Dynamics Simulation of the Ag(111)-Water

Interface. J. Chem. Phys., 115, 15. Jones, B. F., Matthews, J. N., Moore, S.A., Thomas, S. (2001). Calibration and Stability of the High

Resolution Fly's Eye Detector. Proceedings of ICRC 2001, 1. Jui, C. H. (2001). Measurement of the Ultrahigh Energy Cosmic Ray Spectrum Using Monocular Data

From the High-Resolution Fly's Eye Experiment. Proceedings of ICRC, 1.

Kerber, R., Boucher, K. (2001). Pseudolikelihood Estimation of Genetic Parameters for Arbitrarily Complex Pedigrees. Poster presented at the Tenth Conference of the International Genetic Epidemiology Society, Garmisch, Germany.

Kick, E. L., Davis, B.L., and Parker, C.R. (2001). Macrosocial Causes of Suicide and Homicide: A

Research-In-Progress Report. International Journal of Comparative Criminology 1, 120-126.

Kick, E. L., and Davis, B.L. (2001). World-System Structure and Change: An Analysis of Global Networks and Economic Growth Across Two Time Periods. American Behavioral Scientist, 44, 1561-1578.

Kuharsky, A., and A. Fogelson. (2001). Surface-mediated Control of Blood Coagulation: The Role of Binding Site Densities and Platelet Deposition. Biophys. J., 80, 1050-1074.

Lefohn, A. E., Ovchinnikov, M., Voth, G. A. . (2001). A Multistate Empirical Valence Bond Approach to Polarizable and Flexible Water Model. J. Phys. Chem B., 105, 6628.

Mathews, J. N. (2001). Description of the High Resolution Fly's Eye Detector. Proceedings of ICRC, 1.

Menashe, D., Bihma, O., Laikhtman, B. D. . (2001). Thermodynamic Fluctuations of Site Energies and Occupation Numbers in the Two-dimensional Coulomb Glass. Physical Review B., 64, 115209.

Morrison, P. a. L. W. (2001). Measuring Air Shower Speeds with the HiRes Fluorescence Detectors. Proceedings of ICRC, 1.

Reil, K. A., R. W. Springer. (2001). Preliminary Stereo Results from the High Resolution Fly's Eye Cosmic

Ray Observatory. Proceedings of ICRC, 1. Roberts, M. D. (2001). Atmospheric Analysis Techniques at HiRes. Proceedings of ICRC, 1.

Roberts, M. D. (2001). Atmospheric Monitoring at HiRes - Hardware Systems 1. Proceedings of ICRC, 1. Schmitt, U. W., and G. A. Voth. (2001). The Isotope Substitution Effect on the Hydrated Proton. Chem.

Phys. Lett., 329, 36. Smith, J. D., S.B. Thomas, L.R. Wiencke. (2001). Absolute GPS Time Event Generation and Capture for

Remote Locations. Proceedings of ICRC, 1.

Song, C. (2001). Study of the Longitudinal Development of Air Showers with CORSIKA. Proceedings of ICRC, 1.

Strohmeier, M., Orendt, A. M., Alderman, D. W., Grant, D. M. (2001). Investigatioin of the Polymorphs of dimethyl-3, 6-Dichloro-2, 5-Dihydroxyterephthalate by 13C Solid-State NMR Spectroscopy. J American Chem Society, 123(8), 1713 - 1722.

Violi, A., Truong, T., D'Anna, A. D'Alessio, A., Sarofim, A. . (2001). Quantum Mechanic Study of High Molecular Mass Compounds in Combustion Conditions. Proceedings of the 2nd Joint Meeting of the US Sections of the Combustion Institute. Oakland, CA.

Wiencke, L. R. (2001). Atmospheric Monitoring at HiRes - Hardware Systems 2. Proceedings of ICRC, 1.

Wiencke, L. R. (2001). Atmospheric Monitoring at HiRes - The Atmosphere at Dugway. Proceedings of ICRC, 1.

Zech, A. (2001). Comparisons of CORSIKA-generated Showers with HiRes Data. Proceedings of ICRC, 1.

2000

Amicangelo, J., Armentrout, P. . (2000). Absolute Binding Energies of Alkali-Metal Cation Complexes with

Benzene Determined by Threshold Collision-Induced Dissociation Experiements and ab Initio

Theory. J. Phys. Chem. B., 104, 11420-11432. Barich, D. H., Orendt, A. M., Pugmire, R. J., Grant, D. M. (2000). Carbon-13 Chemical-Shift Tensors in

Polycyclic Aromatic Compounds. 9. Biphenylene. J Physical Chem A, 104(35), 8290 - 8295. Cuma, M., U. W. Schmitt and G. A. Voth. (2000). The Multi-Scale Empirical Valence Bond Model for

Acid-Base Chemistry in Aqueous Solution. Chem. Phys. Lett., 258, 187.

Davis, B. L., and E.L. Kick. (2000). Human Capital Issues and Information Technology in Education in the New Millennium. In G. D. Garson (Ed.), Social Dimensions of Information Technology: Issues for the New Millennium. Hershey, PA: Idea Group Publishing.

Facelli, J. C. (2000). Nitrogen-15 chemical shift in the pyridine-methanol complex. Chem. Phys. Lett., 322,

91-96. Fogelson, A., and J. Keener. (2000). Immersed Interface Methods for Neumann and Related Problems.

SIAM J. Sci Comput., 22, 1630-1654.

Green, R. J., Qian, Jun, Kim, Ho-Tae, Anderson, Scott L. (2000). Hydride Abstraction by NO+ from Ethanol: Effects of Collision Energy and Ion Rotation State. J. Chem. Phys., 113, 3002.

Gutowski, M., Skurski, P., Li, X., Wang, L.S. (2000). (MgO) n (n = 1-5) Clusters: Multipole-Bound Anions and Photodetachment Spectroscopy. Phys. Rev. Lett., 85, 3145.

Kick, E., Davis, B.L., Lehtinen, M., Wang, L. (2000). Family and Ecnomic Growth: A World-System

Approach and a Cross-National Analysis. International Journal of Comparative Sociology, 41, 225-244.

Kick, E. L., Davis, B.L., Lehtinen, M., and Burns, T.J. (2000). A Cross-National Analysis of Democracy, Political Instability, and National Development Outcomes. Journal for Political and Military Sociology 28, 131-155.

Koizumi, H., . Zhang, Armentrout, P. . (2000). Collision-Induced Dissociation and Theoretcial Studies of

Cu+-Dimethyl Ether Complexes. J. Phys. Chem. A., 105, 2444-2452.

Mass, C. F., Steenburgh, W. J. (2000). An Observational and Numerical Study of an Orographically Trapped Wind Reversal Along the West Coast of the U. S. Mon. Wea. Rev., 129, 1318-1338.

Montoya, A., Truong, T, Sarofim, A. (2000). Spin Contamination in Hartree-Fock and Density Functional Theory Wavefuntions in Modeling of Adsorption on Graphite. J. Phys. Chem. A., 104, 6108-6110.

Orendt, A. M., Facelli, J. C., Bai, S., Rai, A., Gossett, M., Scott, L. T., Boerio-Goates, J., Pugmire, R. J.,

Grant, D. M. (2000). Carbon-13 Shift Tensors in Polycyclic Aromatic Compounds. 8. A Low-Temperature NMR Study of Coronene and Corannulene. J Physical Chem A, 104(1), 149 -

155. Pernice, M. (2000). A Hybrid Multigrid Method for the Steady-State Incompressible Navier-Stokes

Equations. Electronic Transactions on Numerical Analysis, 10, 74. Skurski, P., and M. Gutowski. (2000). Excited Electronic States of Anion of

7,7,8,8-tetracyanoquinodimethane (TCNQ). J. of Molecular Structure, 531, 339.

Truong, T., Maity, D. K. . (2000). A Combined Reaction Class Approach with Integrated Molecular Orbital+Molecular Orbital (IMOMO) Methodology: A practical tool for Kinetic modeling. J. Chem. Phys., 112, 24-30.

Wang, Y. (2000). Modeling and Imaging by a New Adaptive Grid Finite-Difference Method. Ph.D.,

University of Utah, Salt Lake City, Utah.

Weiss, J. A., R.D. Rabbitt and B.N. Maker. (2000). Use of Image Data to Regularize Ill-Posed Problems in Solid Mechanics. International Journal for Numerical Methods in Engineering.

1999

Bell, R., Simons, J. (1999). Unusual Thresholds and Isotope Effects in AI+ + H2/D2/HD Reactions. J. Phys. Chem. A., 103, 539.

Bowden, A. E., Rabbit, R., Weiss, J. . (1999). Stress and Strain in the Human Distal Phalanx Under Indentation. Proc. 21st Annual EMBS Conference (1st joint with BMES), 512.

Calhoun, A., Voth, G.A. (1999). Electrochemical Bond-Breaking Reactions: A Comparison of Large Scale Simulation Results with Analytical Theory. J. Phys. Chem. B., 103, 3442.

Calhoun, A., Koper, T. M., Voth, G. A. . (1999). Large-Scale Computer Simulation of an Electrochemical

Bond-Breaking Reaction. Chem. Phys. Lett., 305, 94. Eskicioglu, M. R., Marsland, T., Hu, W., Shi, W. (1999). Evaluation of the JIAJIA Software DSM System on

High Performance Computer Architectures. IEEE Transactions on Antennas and Propagation, 76. Gutowski, M., Skurski, P. . (1999). Electron Binding Energies in Linear Bipole-Bound (HCN)n - (n=2-5).

Chem. Phys. Lett., 300, 331.

Gutowski, M., Skurski, P. (1999). Electronic Structure of Dipole-bound Anions. Res. Devel. Physical Chem., 3, 245-260.

Gutowski, M. (1999). Favorable Performance of the DFT Methods in Predicting the Minimum-Energy Structure of the Lowest Triplet State of WF4. International Journal of Quantum Chemistry, 73,

369. Gutowski, M., and P. Skurski. (1999). Theoretical Study of the Dipole-Bound Anion (HF). Res. Devel.

Physical Chem., 3, 245.

Gutowski, M., Skurski, P. (1999). Theoretical Study of the Quadrupole-Bound Anion (BeO)-. Chem. Phys. Lett., 303, 65.

Jang, S., Y. Pak and G. A. Voth. (1999). Quantum Dynamical Simulation of the Energy Relaxation Rate of the CN- Ion in Water. J. Phys. Chem. A., 103, 10289.

Jang, S., S. Jang, and G. A. Voth. (1999). Quantum Molecular Dynamics Simulations of Low Temperature

High Energy Density Matter: Solid p-H2/Li and p-H2/B. J. Phys. Chem. A., 103, 9512. Johnson, M. A., T. N. Truong. (1999). High-Level ab Initio and Density Functional Theory Evaluation of

Combustion Reaction Energetics: NO2 and HONO Elimination from Dimethylnitramine. J. Phys. Chem. A., 103, 8840-8846.

Johnson, M. A., Truong, T. N. . (1999). Importance of Polarization in Simluations of Condensed Phase Energetic Materials. J. Phys. Chem B., 102, 9392-9393.

Maity, D., Bell, R., Truong, T. . (1999). Mechanism and Quantum Mechanical Tunneling Effects on Inner

Hydrogen Atom Transfer in Free Base Porphyrin: A Direct ab Initio Dynamics Study. J. Am. Chem. Soc., 63, 861.

Maity, D. K., W. T. Duncan, T. N. Truong. (1999). Direct Ab Initio Dynamics Studies of the Hydrogen Abstraction Reactions of Hydrogen Atom with Fluoromethanes. J. Phys. Chem. A., 103,

2152-2159.

Morey, D., Schuster, G. . (1999). Paleoseismicity of the Oquirrh Fault, Utah from Shallow Seismic Tomography. GJI, 138, 25.

Orendt, A. M., Facelli, J. C., Grant, D. M. (1999). A theoretical study of the acetate 13C chemical shift tensor in cadmium acetate dihydrate. Chemical Physics Letters, 302, 499 - 504.

Pak, Y., Voth, G. A. (1999). Reactive Flux Calculations of Methyl Vinyl Ketone Reacting with Cyclopentadiene in Water. J. Phys. Chem. A., 103, 925.

Pavese, M., Berard, D. R., Voth, G. A. . (1999). Ab initio Centroid Molecular Dynamics: A Fully Quantum

Method for Condensed Phase Dynamics Simulations. Chem. Phys. Lett., 300, 93. Pernice, M., Bockelie, J., Swensen, D., Smith, P. (1999). Progress, Results, and Experiences in Developing

an Adaptive Solver for Steady State Turbulent Reacting Flows in Industrial Boilers and Furnaces, Structured Adaptive Mesh Refinement (SAMR) Grid Methods. IMA Volumes in Mathematics and its Applications, 117.

Rabbitt, R. D. (1999). Directional Coding of Three Dimensional Movements by Vestibular Semicircular Canals. Biological Cybernetics, 80, 417.

Skurski, P., Gutowski, M. . (1999). Ab Initio Study of the Dipole-Bound Anion (H2O…HC1). J. Chem. Phys., 111, 3004.

Skurski, P., M. Gutowski and J. Simons. (1999). Dipole-Bound Anion of the HNNH3 Isomer of Hydrazine.

An Ab Initio Study. J. Phys. Chem. A., 103, 625. Skurski, P., Gutowski, M., Simons, J. . (1999). Theoretical Study of the Dipole-Bound Anion (HPPH3). J.

Chem. Phys. A., 100, 274. Tinniswood, A., Lazzi, G., Gandhi, O.P. (1999). The Use of the Expanding Grid FDTD Method for

Simulation of CAD-derived Personal Wireless Telephones. Technical Report, University of Utah. Truong, T. N., Truong, T. T. . (1999). A Reaction Class Approach with the Integrated Molecular Orbital +

Molecular Orbital Methodology. Chem. Phys. Lett., 314, 529.

Truong, T. N. (1999). Thermal Rates of Hydrogen Exchange of Methane with Zeolite: A Direct ab Initio Dynamics Study on the Importance of Quantum Tunneling Effects. J Phys. Chem. B., 101, 2750.

Vollmer, J. M., Srefanovich, E., Truong, T. . (1999). Molecular Modeling of Interactions in Zeolites: An Ab Initio Embedded Cluster Study of Nh3 Adsorption in Chabazite. J. Phys. Chem. B., 103, 9415.

Wang, L. L., Boldyrev, A. I., Simons, J. . (1999). Tetracoordinated Planar Carbon in the Al4C- Anion. A

Combined Photoelectron Spectroscopy and ab Initio Study X. J. Phys. Chem. A., 103, 503. Yu, H. (1999). Three Dimensional Computational Modeling of Platelet Aggregation on Parallel Computers.

Ph.D., University of Utah, Salt Lake City, Utah.

1998

Bowden, A. E., Rabbitt, R. D., Weiss, J. A. . (1998). Anatomical Registration and Segmentation by

Warping Template Finite Element Models. SPIE, 3254, 469. Calhoun, A., Voth, G.A. (1998). The Computer Simulation of Correlated Electron Transfer Across the

Electrode/Electrolyte Interface Involving Multiple Redox Species. J. Phys. Chem. B., 109, 4569. Calhoun, A., and G. A. Voth. (1998). Computer Simulation of Electron Transfer Processes across the

Electrode/Electrolyte Interface: A Treatment of Solvent and Electrode Polarizability. J. Electroanalytical Chemistry, 405, 253.

Calhoun, A., Voth, G.A. (1998). Isotope Effects in Electron Transfer Across the Electrode-Electrolyte

Interface: A Measure of Solvent Mode Quantization. J. Phys. Chem. B., 102, 8563. Eskicioglu, M. R., and T. Marsland. (1998). Evaluation of JIAJIA Software DSM System on High

Performance Architecture. Proceedings of the 32nd Hawaii International Conference on System Sciences and the Proceedings of the 1998 IBM Center for Advanced Studies Conference.

Eskicioglu, M. R., Marsland, T. . (1998). Shared Memory Computing on SP2: JIAJIA Approach. IBM Center for Advanced Studies Conference (CASCON'98).

Fogelson, A., and A. Kuharsky. (1998). Membrane Binding-site Density Can Modulate Activation

Thresholds in Enzyme Systems. J. Theor. Biol., 193, 1-18. Gardiner, J., Weiss, J. (1998). Experimental Testing and Computational Modeling to Determine the

Stress-Strain Distribution in the Human Medical Collateral Ligament. 44th Annual Meeting, Orthopedic Research Society.

Grunbaum, D., D. Eyre, and A. Fogelson. (1998). Functional geometry of ciliated tentacular arrays in

active suspension feeders. J. Exp. Biol., 201, 2575-2589. Keener, J. P., Bogar, K. (1998). A Numerical Method for the Solution of the Bidomain Equations in Cardiac

Tissue. CHAOS, 8, 234. Kick, E. L., Davis, B.L., Kiefer, D., and Burns, T.J. (1998). A Cross-National Analysis of Militarization and

Well-Being Relationships in Developing Countries. Social Science Research, 27, 351-370.

Maity, D., W. Duncan and T. Truong. (1998). Direct ab Initio Dynamics Studies of the Hydrogen Abstraction Reactions of Hydrogen Atom with Fluormethanes. Journal of Physical Chemistry, A 103, 3152.

Michael, J., Barton, R., Saffle, J., Mone, M., Markewitz, B., Hillier, K., Elstad, M., Campbell, E., Troyer, B.,

Whatley, R., Liou, T., Samuelson, W., Carveth, H., Hinson, D., Morris, S., Davis, B. L., and Day,

R. (1998). Inhaled Nitric Oxide Versus Conventional Therapy: Effects on Oxygenation in ARDS. American Journal of Respiratory Critical Care Medicine 157, 1372-1380.

Newren, E. (1998). Multilevel Distributed-Memory Solutions of Poisson's Equation. Masters of Science, University of Utah, Salt Lake City, Utah.

Nowaryta, J. P. (1998). Theoretical Study of Inhomogeneous Fluids. Doctoral dissertation, University of

Utah. Orendt, A. M., Facelli, J. C., Jiang, Y. J., Grant, D. M. (1998). NMR at Cryogenic Temperatures: A 13C

NMR Study of Ferrocene. J Physical Chem A, 102(39), 7692 - 7697. Pernice, M., C. Johnson, P. Smith, and A. Fogelson. (1998). Final Report: Symposium on Adaptive

Methods for Partial Differential Equations. Pernice M., W., H. . (1998). NITSOL A Newtown Iterative Solver for Nonlinear Systems. Society of

Industrial and Applied Mathematics, 19, 302.

Skurski, P., and M. Gutowki. (1998). Theoretical Study of the Dipole-Bound Anion (H2O...NH3). Journal of Chemical Physics, 108, 6303.

Taccardi, B. a. S. V. (1998). Multiple Components in the Unipolar Electrogram: A Simulation Study in a Three-Dimensional Model of Ventricular Myocardium. Journal of Cardiovascular Electrophysiology, 9, 1062.

Tinniswood, A., Gandhi, O. P. . (1998). Head and Neck Resonance in a Rhesus Monkey - A Comparison with Results from a Human Model. Technical Report, University of Utah.

Tinniswood, A. D., Furse, C. M., Gandhi, O. P. (1998). Computations of SAR Distributions for Two Anatomically Based Models of the Human Head Using CAD Files of Commercial Telephones and

the Paralleled FDTD Code. IEEE Transactions on Antennas and Propagation, 46, 829. Tinniswood, A. D., Furse, C.M., Gandhi, O.P. (1998). Power Deposition in the Head and Neck of an

Anatomically Based Human Body Model for Plane Wave Exposures. Phys. Med. Biol., 43, 2361.

Truong, T., Duncan, W., Tirtowidjojo, M. . (1998). A Reaction Class Approach for Modeling Gas Phase Reaction Rates. Faraday Transactions, 1, 1061.

Weiss, J., P. Moulis, H. Ayliffe, T. Rosenberg and V. Cooley. (1998). Finite Element Simulation of Stresses in Healing Cartilage Defects. ASME Winter Annual Meeting.

Weiss, J., Rabbitt, R., Bowden, A., Maker, B. . (1998). Incorporation of Medical Image in Data in Finite

Element Models to Track Strain in Soft Tissues. SPIE, 3254, 277. Weiss, J. A. (1998). Stresses in the Human Medial Collateral Ligament During Valgus Loading. 5th

Japan-USA-Singapore-China Conference on Biomechanics.

1997

Abu-Zayyad, T., et al. (1997). Atmospheric Monitoring at the High Resolution Fly's Eye: Data from the

HiRes2 Flasher Array. Presented at the 25th ICRC, Durban, South Africa. Abu-Zayyad, T., et al. (1997). Calibration and Stability Measurements of a FADC Based Data Acquisition

System for the HiRes Fly's Eye Experiement. Presented at the 25th ICRC, Durban, South Africa. Abu-Zayyad, T., et al. (1997). The Capabilities of the High Resolution Fly's Eye Detector. Presented at the

25th ICRC, Durban, South Africa.

Abu-Zayyad, T., et al (1997). Cosmic Ray Composition Measured by HiRes in Coincidence with FE2. Presented at the 25th ICRC, Durban, South Africa.

Abu-Zayyad, T., et al. (1997). The HiRes Detector: Absolute Calibration and Alignment. Presented at the 25th ICRC, Durban, South Africa.

Abu-Zayyad, T., et al. (1997). A Monte Carlo Study of Reconstruction of Monocular Events Having Limited Track Lengths for the High Resolution Fly's Eye. Presented at the 25th ICRC, Durban, South Africa.

Abu-Zayyad, T., et al. (1997). Multi-Component Observations of 1017 eV East with a Hybrid Fluorescence and Surface Detector. Presented at the 25th ICRC, Durban, South Africa.

Abu-Zayyad, T., et al. (1997). Physics with HiRes Stage 0.5 and Stage 2. Presented at the 25th ICRC, Durban, South Africa.

Abu-Zayyad, T., et al. (1997). Radio Controlled Light sources ofr Atmospheric Monitoring at HiRED.

Nuclear Instruments and Methods. Presented at the 25th ICRC, Durban, South Africa. Abu-Zayyad, T., et al. (1997). Radio Controlled Zenon Flashers for Atmospheric Monitoring at the HiRes

Cosmic Ray Observatory. Presented at the 25th ICRC, Durban, South Africa. Abu-Zayyad, T., et al. (1997). Status of the High Resolution Fly's Eye Detector: Operation and

Installation. Paper presented at the 25th ICRC, Durban, South Africa.

Abu-Zayyad, T., et al. (1997). Stereo Reconstruction of Eas With the HiRes Detector. Presented at the 25th ICRC, Durban, South Africa.

Abu-Zayyad, T., et al. (1997). Testing the High Resolution Fly's Eye Using Laserscope. Presented at the 25th ICRC, Durban, South Africa.

Abu-Zayyad, T., et al. (1997). Trigger Sensitivity of the FADC Instrumented HiRes Fly's Eye. Presented at the 25th ICRC, Durban, South Africa.

Abu-Zayyad, T. e. a. (1997). Atmospheric Monitoring at the High Resolution Fly's Eye: Atmospheric

Scattering. Presented at the 25th ICRC, Durban, South Africa. Bowden, A. E., R. D. Rabbitt, J. A. Weiss and B. N. Maker. (1997). Use of Medical Image Data to

Compute Strain Fields in Biological Tissue. ASME BED, 34, 191. Burns, T. J., Davis, B. L., and Kick, E. L. (1997). Position in the World-System and National Emissions of

Greenhouse Gases. Journal of World-Systems Research, 3, 432-466.

Dai, H. Y., Loh, E. C., Sokolsky, P. (1997). The OWL Detector: Simulation and Reconstruction. Internal Report, University of Utah-UUHEP, 97, 4.

Dai, Y., Loh, E. C., Sokolsky, P. (1997). The OWL Detector: Neutrino Aperture, Detector Spacing and Track Reconstruction. Internal Report, University of Utah, UUHEP, 97, 5.

Fain, H., Kick, E.L., Davis, B.L. and Burns, T.J. (1997). World-System Position, Tropical Climate, National Development and Infant Mortality: A Cross-National Analysis of 86 Countries. Human Ecological

Review, 3(2), 197-202.

Gardiner, J. C., and J. A. Weiss. (1997). Representation of Anisotropy in constitutive Models of Biological Soft Tissues. J. of Biomech. Eng., 120, 233.

Liu, F., Orendt, A. M., Alderman, D. W., Grant, D. M. (1997). Carbon-13 Chemical Shift Tensors in Pentaerythritol. J American Chem Society, 119(38), 8981 - 8984.

Orendt, A., Hu, J., Jiang, Y., Facelli, J.C., Wang, W, Pugmire, R. Ye, C., Grant, D. M. (1997). Solid State 15N and 13C NMR Study of Several Metal 5,10,15,20-Tetraphyenylporphyrin Complexes, Journal of the American Chemical Society. J. Phys. Chem. A., 119, 7114.

Puso, M., Weiss, J. (1997). Finite Element Implementation of Anisotropic Quasilinear Viscoelasticity Using a Discrete Spectrum Approximation. ASME J. of Biomechanical Engineering, 33, 347.

Sellers, B. J., Davis, B. L., Larkin, P. W., Morris, S. E., and Saffle, J. R. (1997). Early Prediction of Prolonged Ventilator Dependence in Thermally Injured Patients. Journal of Trauma, 43(6),

899-903.

Strohmeier, M., Orendt, A. M., Facelli, J. C., solum, M. S., Pugmire, R. J., Parry, R. W., Grant, D. M. (1997). Solid State 15N and 13C NMR Study of Several Metal 5, 10, 15, 20-Tetraphenylporphyrin

Complexes. J American Chem Society, 119(30), 7114 - 7120. Truong, T. (1997). Thermal Rates of Hydrogen Exchange of Methane with Ziolite: A Direct ab Initio

Dynamics Study on the Importance of Quantum Tunneling Effects. J. Phys. Chem. B., 101.

Weiss, J. A., Gardiner, J.C., Quapp, M. (1997). Material Models for the Study of Soft Tissue Mechanics. ASME BED, 249.

1996

Davis, B. L., and E.L. Kick. (1996). Human Capital Issues in the Use of Information Technology in

Education. Social Science Computer Review, 14, 169-180.

Dillon, R., L. Fauci, A. Fogelson, and D. Gaver. (1996). Modeling Biofilm Processes Using the Immersed Boundary Method. J. Sci. Comput., 129, 57-73.

Facelli, J. C., Orendt, A. M., Jiang, Y. J., Pugmire, R. J., Grant, D. M. (1996). Carbon-13 Chemical Shift Tensors and Molecular conformation of Anisole. J. Phys Chem, 100(20), 8268 - 8272.

Kick, E. L., Burns, T. J., Davis, B. L., Murray, D. A., and Murray, D. (1996). Impacts of Domestic

Population Dynamics and Foreign Wood Trade on Deforestation: A World-System Perspective. Journal of Developing Societies, 12(1), 68-87.

Kick, E. L., Davis, B. L., Burns, T. J., and Li, L. (1996). World System and National Institutional Effects on Infant Mortality in Third World Countries. International Third World Studies Journal and Review 7, 61-67.

Orendt, A., Facelli, J. C., Radziszewski, J. G., Horton, W. J., Grant, D. M., Michl, J. (1996). C dipolar NMR Spectrum of Matrix-Isolated 0-Benzyne-1, 2-13 C2. Am Chem Society, 118, 846 - 852.

Weiss, J. A., B. N. Maker and S. Govindjee. (1996). Finite Element Implementation of Incompressible, Transversely Isotropic Hyperelasticity. Computer Methods In Applied Mechanics and Engineering, 135, 107.

Weiss, J. A., D. A. Schauer and J. C. Gardiner. (1996). Modeling Contact in Biological Joints Using Penalty

and Augmented Lagrangian Methods. Advances in Bioengineering ASME, 34, 347.

1995

Kick, E. L., Davis, B. L., and Burns, T. J. (1995). International Multiple Networks in World-System

Approaches. International Conference on Social Networks, 3, 237-248.

Saffle, J. R., Davis, B. L., and Williams, P. (1995). Recent Outcomes in the Treatment of Burn Injury in the United States: A Report from the American Burn Association Patient Registry. Journal of Burn Care & Rehabilitation, 16, 219-232.

Saffle, J. R., and Davis, B. L. (1995). A Simple Guide to the Burn Registry. Burns: Journal of the International Society for Burn Injuries 21, 230-236.

1994

Burgess, Y., Davis, B. L., and Kick, E. L. (1994). Militarization and Well-Being: An Analysis of Third World

Women and Men. International Third World Studies Journal and Review, 5, 9-23. Davis, B. L. (1994). Economic and Human Development Assessment by Cross National Comparison:

Methodological Obstacles to Empirical Verification of Prevailing Theories. Ph.D., University of

Utah, Salt Lake City, UT.

1993

Fauci, L., and Fogelson, A. (1993). Truncated Newton Methods and the Modelling of Complex Immersed Elastic Structures. Pure Applied Math, 46, 787-818.

Saffle, J. R., Davis, B. L., Kagan, R., et. al. (1993). Development of a Computerized Registry for the

Patient With Burns: Part I. Journal of Burn Care & Rehabilitation, 14, 199-206. Saffle, J. R., Davis, B. L., Kagan, R., et. al. (1993). Development of a Computerized Registry for the

Patient With Burns: Part II. Journal of Burn Care & Rehabilitation, 14, 368-375.

1992

Fogelson, A. (1992). Continuum Models of Platelet Aggregation: Formulation and Mechanical Properties.

SIAM JAM, 52, 1089-1110.