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RESEARCH TEAM GRANTS IN SCIENCE AND TECHNOLOGY 2006

FINAL REPORT

I. PROJECT PRESENTATION

PROJECT TITLE CODE

Computer Simulation Laboratory of Nanomaterials and Biological Systems of Experimental Interest ADI-24

PROJECT DIRECTOR SIGNATURE

Gonzalo Gutiérrez Gallardo

CONTACT INFORMATION Las Palmeras 3425, Ñuñoa; Región Metropolitana - MAIN INSTITUTION

Universidad de Chile PERIOD INFORMED

April-07 - April 2011

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a) Main researchers’ information

MAIN RESEARCHER (Complete Name) SIGNATURE

Eduardo Menendez-Proupin WORKING ADDRESS PHONES EMAIL Dept. Física, Fac. Ciencias, U. de Chile eariel99@gmail.com

MAIN RESEARCHER (Complete Name) SIGNATURE

Fernando Danilo Gonzalez-Nilo

WORKING ADDRESS PHONES EMAIL

Center for Bioinformatics and Molecular Simulations (CBSM) Universidad de Talca 2 Norte 685, Casilla 721, Talca - Chile

danilo.gonzaleznilo@gmail.com

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b) Associated researchers’ information

ASSOCIATED RESEARCHER (Complete Name) SIGNATURE

Walter Orellana

WORKING ADDRESS PHONES EMAIL

Dept. Fisica, UNAB worellana@unab.cl

ASSOCIATED RESEARCHER (Complete Name) SIGNATURE

David Laroze

WORKING ADDRESS PHONES EMAIL Instituto de Alta Inv., U. Tarapaca david.laroze@gmail.com

ASSOCIATED RESEARCHER (Complete Name) SIGNATURE

Jaime Henriquez

WORKING ADDRESS PHONES EMAIL Center for Bioinformatics and Molecular Simulations (CBSM) Universidad de Talca 2 Norte 685, Casilla 721, Talca - Chile

II. EXECUTIVE SUMMARY

The Project Anillo ACT-24 is entitled Computer simulation laboratory of Nanomateriales andbiological systems of experimental interest, and its main research goal was a) the study of struc-tural, dynamic, mechanic, electronic, magnetic and optical properties of nanomaterialsand b) the study of biological systems such as transmembrane proteins (TRP channels)and the catalytic reaction mechanism in enzymes (PEPCK). During the course of the pro-ject, new topics arose, such as the interface between an organic material and a metal, shock wavesand hypervelocity impacts. These studies were performed by means of computer simulation at themolecular level, which has shown to be a very useful technique in the theoretical study of systemswith time and length scale going from the atomic to nanoscopic and, eventually, to microscopicsize, such as the systems studied in this proposal. In addition, we explored methodological andtechnical topics, such as the development of a molecular dynamics code, the installation of a highperformance computing system (304 cores) and a database web platform for nanoparticles. Theresults of these investigations present an interest not only from a basic point of view, but also theyare capable of being applied to strategic researchs interest for the development of our country, inareas such as nanotechnology and biotechnology.

The Anillo ACT-24 rested on two fundamental pillars: the Group of NanoMaterials, www.gnm.cl,of the Departamento de Fısica, Facultad de Ciencias of the Universidad de Chile (GNM), and theCenter of Bioinformatic and Molecular Simulation,http://cbsm.utalca.cl/, of the Universidad deTalca (CBSM). The synergy generated by this union allowed us to expand the research issues ini-tially pointed out, as well as venture in more applied areas and interactions with the public sectorthat, in other way, would have been impossible to do. The Anillo begun with a nucleus of threetitular researchers, three reasearch associates and a group of collaborators both from Chile andabroad, as well as 10 graduate and undergraduate students. These researchers and students camefrom Antofagasta, La Serena, Santiago, Talca, Valdivia and Puerto Montt, with collaborators inBrazil, France and Spain, USA, India, Italy, Japan and Sweden. Through the three years of resear-ch, our collaborators net grew up, and 4 postdoctoral researchers, 25 graduate and undergraduatestudents, as well as foreign researchers joined the team. During the course of the project, we workeddriving three main areas: scientific research, human resources training and outreach of the researchresults, to both specialized audience and public at large.

The main results obtained by our research are embodied in the 56 (ISI) published papers, as wellas more than 100 congress and conference presentations, in addition to other articles published injournals of continental and national circulation. In the issue nano structured materials and bulkproperties, we studied the properties of the aluminium oxide in amorphous state and its crystallinephase γ-Al2O3, developing a structural model that presents a good agreement with experiments,which let us quantify the ionic character of the bond, as well as elucidate the change in its vibrationalproperties as the sample is put under pressure. In the same line, we studied the compound CdTeOx,a material of current importance in the search for greater efficiency in photovoltaic cells: using ab-initio molecular dynamics calculations on this compound in amorphous state, we could correlatethe structure to the emission spectra of photoelectrons (XPS) obtained experimentally. Anotheramorphous material investigated was the CuZr, alloy that forms a metallic glass, which has manyapplications as structural material due to its excellent mechanical properties. Here we studied,by means of computer simulation, its structure and vibrational states in liquid and amorphousstate, determining that the fundamental building block is a distorted icosahedron. The study of themechanic and elastic properties of materials is an issue that can be addressed with high precision

by means of calculations based on quantum mechanics. In this way, we performed a theoretical-experimental work focused on platinum, that allowed us to determine its elastic constants in a widerange of pressures, getting an excellent agreement with the experiments in those ranges where thedata is available. Using the same calculation technique, we studied the mechanical properties of thehydroxiapatite and fluorapatite, key components of the enamel and body of the teeth. In particular,the fluorapatite is found in sick teeth, degrading its mechanical strength.

Properties of surfaces and interfaces was another research topic, for both semiconductorand metallic systems. Here we performed basic studies, as well as applications to specific materialphysics problems and biological systems, working the researchers from GNM (U. de Chile) and theCBSM (U. Talca) in close contact. Thus, joining efforts and experiences, we could address pro-blems from a theoretical-experimental point of view, in organic and inorganic systems. Below wehighlight the main achievements. In collaboration with researchers from Universidad de Sevilla, westudied the adsorption of gold atoms in anatase nitrogen surfaces, a titanium oxide variant withphotocatalytic properties of great current interest in the search for stable and cheap catalyzers thatcan be activated by light. Another study of surface properties was carried out together with anexperimental group from U. de Chile: we studied the influence of edges in the electric conductivityof thin gold films. Also, we determined the potential energy barrier between grain boundaries usingquantum mechanics calculations and images of the TEM microscope. In the area of interfaces be-tween organic and metallic systems, we highlight the study about adsorption of the oligopeptideRGD in titanium dioxide. This topic has direct relationship with the response of tissues to tita-nium implants, vastly used nowadays in medicine, since the titanium oxide is the natural interfacebetween tissues and titanium (see figure). In the field of biology is possible also to identify certainimmunological responses through the interactions between atomic gold structures and proteins suchas opsonin, fibronectin and others. We modeled such a system with gold clusters interacting withthiols, obtaining that the interaction of the organic compound was energetically more stable in thedeprotonated state than in the protoned state. Finally, another study performed is realted to thecorrosion of metallic oxides by organic acids, a problem of practical importance both in industryas in laboratory. In particular, we studied copper and zinc oxides attacked by formic acid, findingthrough quantum mechanics calculations that copper has a much higher resistence, due to theinteraction that, unlike zinc, covers an hydroxylated layer and a molecule of water.

(a) Aspartate molecule on TiO2 surface. (b) AGS-FA-PAMAM-QDot in tu-moral cell

Figura 1: Example of metal-organic interfaces and QD-dendrimers.

The sutdy of quantum dots was an issue raised from the beginning, but was soon extendedto its interaction with organic systems. This issue was addressed in different levels of complexityand approximations. One of the studies undertaken is related to the behavior of a quantum dotunder a non-constant magnetic field, using the approximation of effective mass. In the same way, westudied the magneto-optic properties of the semiconductor CdxZn1−xSe, showing that the thermalannealing produces evaporation of Cd, modifies the form of quantum confinement and allows totune in its magnetic properties. The theoretical-experimental study undertaken jointly with theInstitute of Chemistry of the U. de Talca, in relation with the synthesis and characterization ofthe complex dendrimer-quantum dot, is particularly interesting and of great importance due to itsapplication to obtaining images of tumor cells. In fact, such is the progress in this investigationthat a first test has become possible in the cell imaging system, distinguishing tumor cells fromhealthy ones.

Carbon Nanotubes (CNT) is another issue initially proposed, in particular its interactionwith molecules, and its possible use as sensors. We studied the absorption of NH3, NO2, H2O andO2 over CNT that had a double vacancy, assuming it would act as active site. However, due toa weak van der Waals interaction, our results suggest that such a defective CNT is not a goodcandidate for a sensor. We also studied CNTs as hydrogen storage materials, a hot topic because ofthe search for new energy sources; the energy involved in the H2 absortion and desorption process,obtained by means of molecular dynamics, indicate that nanopores produced by irradiation couldbe successfully used as a hydrogen storage system. Another project explores the covalent and non-covalent mechanism for the attachment iron porphyrins (FeP) on the surface of single-walled CNT.

Nanomagnetism, that is, the magnetic properties of nano-materials was an important topicstudied in the Anillo. Our contribution in this area ranges from analysis of thermal and dynamicsproperties of magnetic chain (nanowires), caracterization of ferrofluids, to quantum level studies ofthe adsorption of magnetic nanoparticles (Fe) on semiconductors surfaces, as well as the influenceof the co-linear magnetism to the total energy in iron at high pressure.

In the study of biological systems by large-scale computer simulation our Anillo didimportant contributions. For example, we performed molecular level simulation of K+ chan-nels: potassium channels are undoubtedly one of the most enigmatic and more studied proteins inbiophysics. These transmembrane proteins are the clue for electrical signals of our nervous system,as well as being involved in several neurodegenerative diseases. Several studies have found that insome kind of cancer, like gastric cancer, these proteins are over-expressed and probably have animportant role in this disease. In the field of therapies pain relief the K+ channels are used asan important target for design of new anesthetics. Results from molecular simulations allowed usto reinterpret the functional importance of two key aminoacids participating in the sensed tempe-rature TRPV1 K+ channel activation. In the same way, computational predictions based in theanalysis of long molecular dynamics simulations allowed us to identify the aminoacids involvedin the modulation of electrostatic potential, which regulates the pass of ions across the hSlo K+channels.

The study of enzymatic catalysis represent another successful application of computer simu-lation to proteins. Using a hybrid scheme which include quantum mechanics/molecular mechanics(QM/MM), we performed, together with U. Santiago researchers, a structural study of the transi-tion states of the decarboxylation reaction that takes place in the active site of the PEPCK protein.The results obtained so far have allowed us to analyze in detail the role of two metals that takepart of the catalytic reaction of this enzyme, as well as transitory deprotonation processes, that are

not feasible to analyze by other means.Computational assisted drug design in also an area where the our experience in the use of

different techniques allowed to tackle several problems, mainly associated to protein-ligand inter-actions. Thus, by means of a hybrid QM/MM method, we studied non-covalent bonds (hydrogenbonds) between ligands and active sites in kinasas proteins which appear in cancer, Alzheimer andother pathologies. For example, one of our results shows the energy of the hydrogen bond is theprincipal component of the interaction.

Following the research-driving idea that some biological problems can be better understoodthrough a molecular level model, we explore the study of systems far from equilibrium. Wehave collaborated with physicians of Arauco Clinic to study of the effect of shock waves onbiological systems. The motivation is the increasing use of shock wave therapy in the treatmentof fractures and wounds, and the lack of knowledge about the interaction of shock waves withhuman tissue. To assist in this regard, preliminary we have simulated at atomic level the effects ofshock waves in inorganic systems like an argon block, describing in detail the fracture process thatoccurs there. At the same time to these efforts, we want to describe at the atomic level the damageproduced by the impact of small projectiles on organic and inorganic matter. Promisingresults in the case of a copper nano projectile against a target allows us to look with optimism theresults of this line of research.

Interestingly, our activities not only consisted of “papers” research, but also applied scientificwork at international level. In this sense, we are proud of two achievements: the creation of theCollaboratory for Structural Nanobiology (http://nanobiology.utalca.cl/), in collaboration to theNational Institute of Cancer, USA, which is a web tool to facilitate the interaction of researcherswho are working in nanobiology, health and medicine. Also, we created “from scratch.a computersimulation package called Las Palmeras Molecular Dynamics, www.lpmd.cl, which can be used tosimulate systems at the atomic level, and to visualize the atoms or molecules; it is freely distributedunder the GPL license.

Regarding scientific infrastructure, it included the creation of three laboratories: the la-boratory of the Group of Nanomaterials (www.gnm.cl) at the U. Chile, the Protein Engineeringlaboratory and the Electron Microscopy lab, at U. of Talca. Besides these laboratories, we installedthe Center of High Performance Computing, funded jointly by our Anillo and U. Talca, which hasa total of 308 cores interconnected with an InfiniBand network, ideal to run parallel software, andwhere we have performed most of the large-scale simulations. We have also installed a smaller clus-ter at the University of Chile. The design, setup and running of these facilities has been a majoreffort from the standpoint of technical and administrative work, which has given us vast experienceof scientific management.

The Project Anillo has played a fundamental role in the education of students and youngresearchers. During its development 23 undergraduate students have worked in their title projectand research, as well as 4 masters and 11 doctoral students have done their thesis. In addition, 4doctors are performing their postdoctoral training in our Anillo. The tasks of training researchershas been strongly favored by the scientific exchange we made, both our trips to research groupabroad (over 14), and the visits of professors and students from outside, where we received over24 researchers, which allowed us to to establish new collaborations with groups of Universidad deSevilla (Spain), Universidade Federal de Sao Carlos and Universidade Federal de Uberlandia (Bra-zil), Harvard University and University of Pittsburgh (USA), University of Antioquia (Colombia),ICIMAF (Cuba), University of Chihuahua (Mexico), University of Udine (Italy), KTH (Sweden),

Fraunhoffer Institute (Germany), which adds to our former links to U. Califormia Southern, Flori-da International University, Iowa State University and the National Cancer Institute in the USA,Uppsala University in Sweden, U. Sao Paulo, Brazil, CNRS-University of Nancy in France.

Outreach activities have been on two levels: technical meetings for specific audiences, aswell as activities for public at large. In the first area, we highlight the organization of 14 schoolsand workshops, including 4 of an international character: Latin American School of ComputationalMaterials Science (www.gnm.cl / school), together ICTP Italy, in Santiago (2008), Advanced Courseon Free Energy Calculations: Theory and Practice, together Action Grid FP7 of the EC, in Talca(2009). Also, we co-organized two international conferences: Computing modeling and data driven:Y Symposium at the 11th International Conference on Advanced Materials, ICAM09 in Rio deJaneiro, 2009, and the First International Conference on Bioinformatics (SoIBio) in Chillan, 2010.Besides these, we have been invited as speakers in 16 international and 6 national events, and havepresented papers and posters in 31 international and 42 national events, as well as more than 12conferences and seminars in different universities of the country and abroad. Regarding the outreachto the public at large, our researchers and students have made over 10 activities, from lectures incolleges and schools, exhibitions to open house activities, reaching more than 1500 people acrossthe country. We have also appeared on radio, television and interviews on printed media, describingour scientific work.

Finally, it is interesting to note that our research activities have allowed us naturally to establishinteraction with the productive sector, in a couple of initiatives that we are sure are just thebeginning of a more regular basis. In fact, we worked with a company of the mining sector in theproject Thermophysical Properties of mining tires, to optimize their use in trucks, us performing thesimulations and the advice at field tests. On the other hand, together with the Faculty of Agronomyand the Institute of Chemistry of the U. Talca we are working on the project Nanobiology applied tothe food industry, which has the support of the Fraunhoffer Institute and local businesses. Also, weare participanting in the education area, through the project Collaborative learning besed in growinginfrastructure of GRID, in collaboration with the Bioinformatics group at PUC, Foundation for LifeSciences and the support from Microsoft-Chile, HP and Coffe Business.

All in all, we can say that the support of the Bicentennial Program through the Project Anilloover these years has been the mainstay of our research groups, vital in joining together, consolidateand project them forward.

III. RESUMEN EJECUTIVO

El Proyecto Anillo ACT-24 se titula Laboratorio de simulacion computacional de nanobio sis-temas y su objetivo principal en investigacion era a) el estudio de propiedades estructura-les, dinamicas, mecanicas, electronicas, magneticas y opticas de nanomaterials y b)el estudio de sistemas biologicos como proteınas transmembranales (canales TRP) ymecanismo de reaccion catalıtica en enzimas (PEPCK). Durante el desarrollo del proyectosurgieron nuevos temas de investigacion, tales como el estudio de la interfase entre un materialorganico y un metal y ondas de choque e impactos a hipervelocidades. Estos estudios se realizaronpor medio de simulacion computacional a nivel molecular, la cual ha probado ser una tecnica muyutil en el estudio teorico de sistemas donde su escala de longitud y tiempo va desde lo atomico a lonanoscopico y eventualmente a lo microscopico. Unido a esto, exploramos temas de caracter meto-dologico y tecnico, como fue el desarrollo exitoso de un codigo de dinamica molecular, la instalacionde un sistema de computo de alto rendimiento (304 cores), y una plataforma web de nanopartıcu-las. Los resultados de estas investigaciones no solo tienen interes desde un punto de vista basico,sino tambien estan en condiciones de ser aplicados en investigaciones de interes estrategico para eldesarrollo del paıs, en areas tales como nanotecnologıa y biotecnologıa.

El Anillo ACT-24 descanso sobre dos pilares fundamentales: el Grupo de NanoMateriales,www.gnm.cl, del Departamento de Fısica de la Facultad de Ciencias de la Universidad de Chi-le (GNM), y el Centro de Bioinformatica y Simulacion Molecular, http://cbsm.utalca.cl/, de laUniversidad de Talca (CBSM). La sinergia producida de esta union nos permitio ampliar los temasde investigacion inicialmente planteados, ası como incursionar en areas mas aplicadas e interaccionescon el sector productivo, que de otra manera habrıa sido imposible realizar. El Anillo comenzo conun nucleo de tres investigadores titulares, tres asociados y un conjunto de colaboradores tanto deChile como del exterior, ası como cerca de 10 estudiantes, desde pregrado hasta doctorado. Estosinvestigadores y estudiantes eran de Antofagasta, La Serena, Santiago, Talca, Valdivia y PuertoMontt, con colaboradores en Brasil, Francia, Espana, EE. UU, India, Italia, Japon y Suecia. A lolargo de los tres anos de actividades nuestra red de colaboradores crecio, incorporandose 4 inves-tigadores postdoctorales, 25 estudiantes de postgrado y de pregrado, asi como colaboradores delexterior. Durante todo el desarrollo del proyecto trabajamos impulsando tres areas principales: in-vestigacion cientıfica, la formacion de recursos humanos y la difusion de los trabajos de investigaciontanto publico a especializado como general.

Los principales resultados de investigacion alcanzados, que se describen a continuacion,estan plasmados en los 56 papers (ISI) publicados, ası como en las mas de 100 presentaciones encongresos y conferencias, ademas de los artıculos publicados en revistas de circulacion continental ynacional. En el tema de materiales nanoestructurados y propiedades del bulto, estudiamoslas propiedades del oxido de aluminio en estado amorfo y su fase cristalina γ-Al2O3, desarrollan-do un modelo estructural que presenta un muy buen acuerdo con los experimentos, lo que nospermitio cuantificar el caracter ionico del enlace, ası como dilucidar el cambio de sus propieda-des vibracionales a medida que la muestra es sometida a presion. En la misma lınea, estudiamosel compuesto CdTeOx, un material de importancia actual en la busqueda de mayor eficiencia enceldas fotovoltaicas: utilizando calculos de dinamica molecular ab-initio sobre este compuesto enestado amorfo, pudimos correlacionar los espectros de emision de fotolectrones (XPS por sus siglasen ingles) obtenidos experimentalmente con la estructura. Otro material amorfo investigado fue elCuZr, aleacion que forma un vidrio metalico, con variadas aplicaciones, por ejemplo como materialestructural debido a sus excelentes propiedas mecanicas. El estudio de las propiedades mecanicas

y elasticas de materiales es un tema que se puede abordar con gran precision mediante calculosbasado en mecanica cuantica. Ası, realizamos un trabajo teorico-experimental sobre platino quepermitio determinar constantes elasticas en un amplio rango de presiones del Pt sometido a altapresion, obteniendo un excelente acuerdo con los experimentos en aquellos puntos donde estos datosestan disponibles. Usando la misma tecnica de calculo, abordamos el estudio de las propiedadesmecanicas de la hidroxiapatita y la fluorapatita, componentes claves del esmalte y cuerpo de losdientes.

Otro tema de investigacion fueron las propiedades de superficies e interfaces, tanto se-miconductoras como metalicas. Aquı realizamos estudios de caracter basico, ası como aplicacionesa problemas concretos de fısica de materiales y sistemas biologicos, en estrecho contacto entre losinvestigadores del GNM (U. de Chile) y el CBSM (U. Talca). De este modo, sumando esfuer-zos y experiencias, pudimos abordar problemas desde un punto teorico-experimental, en sistemasinorganicos y organicos. En colaboracion con investigadores de la Universidad de Sevilla estudia-mos la adsorcion de atomos de oro en superficies nitrogenadas de anatasa, una variedad de oxidode titanio con propiedades fotocatalıticas, de gran interes actual en la busqueda de catalizadoresestables y baratos que pueden ser activados por luz. Otro estudio de propiedades de superficie fuellevado a cabo junto a un grupo experimental de la U. de Chile: se estudio, en pelıculas delgadas deoro, la influencia de bordes en la conductividad electrica de la pelıcula. En el area de interfaces entresistemas metalicos y organicos, destacamos el estudio sobre la adsorcion del oligopeptido RGD endioxido de titanio. Este topico tiene directa relacion con la respuesta de los tejidos a los implantesde titanio, de gran uso actualmente en medicina, pues el oxido de titanio es la interface natural entrelos tejidos y el titanio. En el campo de la biologıa es tambien posible indentificar ciertas respuestasinmunologicas a traves de interaciones entre estructuras atomicas de oro y proteınas tales como laopsonina, fribronectina y otras. Para representar esto, modelamos un sistema donde interactuanclusters de oro con tioles, resultando que la interaccion del compuesto organico era energeticamentemas estable en el estado desprotonado que en el protonado. Finalmente, otro estudio realizado tie-ne relacion con la corrosion de oxidos metalicos por acidos organicos, un problema de importanciapractica tanto a nivel insdustrial como de laboratorio. En particular, estudiamos oxidos de cobrey de zinc atacados por acido formico, encontrando a traves calculos de mecanica cuantica que elcobre resiste mucho mejor, debido la interacciondirecta entre el oxıgeno y el metal, a diferencia delzinc, que envuelve una capa hidroxilada y una molecula de agua.

(a) Molecula de aspartato sobre superficie deTiO2

(b) AGS-FA-PAMAM-QDot encelula tumoral

Figura 2: Ejemplos de interface metal-organica y puntos cuanticos-dendrımeros.

Puntos cuanticos (quantum dots) fue un tema planteado desde los inicios, pero que prontofue extendido a su interaccion con sistemas organicos. Esto fue abordado en diferentes niveles decomplejidad y aproximaciones. Uno de los estudios emprendidos esta relacionado con el compor-tamiento de un punto cuantico sometido a un campo magnetico variable, usando la aproximacionde masa efectiva. Del mismo modo, estudiamos las propiedades magneto-optica del semiconductorCdxZn1−xSe, demostrando que el recocido termico produce evaporacion del Cd, modifica la formadel confinamiento cuantico y permite sintonizar sus propiedades magneticas. Particularmente in-teresante es el estudio teorico-experimental emprendido en conjunto con el Instituto de Quımica dela U. de Talca, respecto de la sıntesis y caracterizacion del complejo punto cuantico-dendrımero, degran importancia por su aplicacion para obtener imagenes de celulas tumorales. En efecto, tales sonlos progresos en esta investigacion, que se ha podido realizar ya una primera prueba en el sistemade imageneolgıa celular, distinguiendo celulas tumorales de las sanas.

Nanotubos de carbono (CNT) es otro tema planteado inicialmente, en particular su interac-cion con moleculas y el posible uso como sensores. Primeramente estudiamos la absorcion de NH3,NO2, H2O y O2 sobre CNT que tenıan una vacancia doble y que podrıa actuar como sitio activo.Sin embargo, debido a una debil interaccion de van der Waals, nuestro resultados sugieren que unCNT con estos defectos no es buen candidato para ser usado como sensor. Luego estudiamos lasposiblidades del uso de CNT como materiales para almacenar hidrogeno, un tema candente debidoa la busqueda de nuevas fuentes y formas de energıa. Las energıas involucradas en el proceso deabsorcion y desorpcion del H2, calculadas en base a dinamica molecular cuantica, sugieren queCNT con nanoporos producidos por irradiacion podrıan ser usados con exito como depositos dehidrogeno. Otro de los proyectos abordados estudia las condiciones en que las porfirinas de hie-rro (FeP) se pegan a un CNT, y por tanto las posiblidades de usar un CNT como soporte parapegar macrociclos metalicos en su superficie, cuya actividad electrocatalıtica ha sido reportadaexperimentalmente.

Nanomagnetismo, es decir, propiedades magneticas de los nano-materiales es un topico degran importancia hoy dıa. En esta area nuestra contribucion radica en varios aspectos: desde estu-dios de propiedades dinamicas y termicas de cadenas magneticas (“nanohilos”) basados en simula-cion computacional de dinamica de espines, pasando por ferrofluidos, hasta estudios a nivel cuanticode adsorcion de nanoparticulas magneticas (Fe13) en superficies de semiconductores, ası como lacontribucion del magnetismo no-colineal en la energıa total del hierro a alta presion.

En el estudio de sistemas biologicos mediante simulacion computacional de granescala nuestro Anillo ha realizado aportes significativos, ya sea en el aspecto metodologico, en lainterpretacion de experimentos y ası como en la prediccion de fenomenos, tales como diseno dedrogas asistida por computador. En efecto, estudiamos canales ionicos de la membrana celu-lar, tales como el canal de postasio K+. Esta importante proteına transmembranal juega un papelclave en la senal electrica de nuestro sistema nervioso, esta involucrada en enfermedades neuro-degenerativas y se sobre-expresa cuando se presentan ciertos canceres, como el gastrico. Nuestrasimulacion computacional a gran escala nos permitio calcular la energıa libre, determinar las pro-piedades estrcuturales y dinamicas de esta proteına, siendo capaces de interpretar la importanciafuncional de dos aminoacidos claves que participan en el canal K+ activado. Del mismo modo, y enconjunto investigadores de la U. Valparaiso, logramos establecer el mecanismo electrostatico usadoen el transporte ionico a traves de esas membranas.

El estudio de la catalisis enzimatica representa otra aplicacion exitosa de metodos compu-tacionales a proteınas. Mediante el empleo de un esquema hıbrido que une mecanica molecular y

mecanica cuantica (QM/MM) estudiamos, junto a investigadores de la U. Santiago, los estados detransicion en la reaccion de decarboxilacion que ocurre en el sitio activo de la proteına PEPCK.Hemos analizado en detalle el rol que juegan dos metales que toma parte en la reaccion catalıticade la enzima PEPCK, ası como el proceso de deprotonizacion, cuestion imposible de resolver porotros medios.

El diseno de drogas asistido por computador tambien fue un area de investigacion explo-rada por nuestro Anillo, donde nuevamente nuestra experiencia en el uso de distintas metodologıascomputacionales permitio afrontar con exito varios problemas, principalmente asociado a las inter-acciones proteına–ligando. En efecto, mediante un metodo hıbrido QM/MM ası como otros tecnicas,estudiamos interacciones no-covalentes (puente de hidrogeno) entre ligandos y sitios activos en cier-tas proteınas kinasas, que participan en cancer, Alzheimer y otras patologıas. Por ejemplo, nuestrosresultados muestran que la energıa asociada al enlace puente de hidrogeno es la principal compo-nente de la interaccion e indentificamos los principales residuos involucrados en el potencial delcompuesto.

Siguiendo en la lınea de investigacion en problemas biologicos que pueden entenderse mejor atraves de un modelo a nivel molecular, abordamos el estudio de sistemas lejos del equilibrio.Hemos colaborado con medicos de la Clınica Arauco en el estudio del efecto de ondas de choqueen sistemas biologicos. La motivacion central es el uso creciente de la terapia de ondas de choqueen el tratamiento de fracturas y diversas heridas y el escaso conocimiento sobre la interaccionde ellas con el tejido humano. Para contribuir en este aspecto, hemos simulado a nivel atomico,primeramente, los efectos de ondas de choque en sistemas inorganicos como un bloque de argon,describiendo en detalle el proceso de fractura que allı ocurre. Unidos a estos esfuerzos, tambiennos interesa describir a nivel atomico el dano producido por el impacto de pequenos proyectilesen materia organica e inorganica. Resultados promisorios en el caso de un nanoproyectil de cobresobre un blanco nos permiten mirar con optimismo los resultados de esta lınea de investigacion.

Nuestras actividades no solo se traducen en resultados cientifıcos propiamente tal, sino tambienplataformas de trabajo e infraestrucura cientıfica de alcance internacional. En este sentido, esta-mos orgullosos de dos logros: hemos creado una base de datos para nanobiologıa, Collaboratory forStructural Nanobiology (http://nanobiology.utalca.cl/) y una suite para simulacion computacionalllamada Las Palmeras Molecular Dynamics (www.lpmd.cl), ambos, hasta donde sabemos, las pri-meras de su genero en latinoamerica y de categorıa mundial. La base de datos Collaboratory forStructural Nanobiology ha sido desarrollada en conjunto con el Instituto Nacional del Cancer, EE.UU, y esta concebida como un espacio para facilitar la interaccion entre los investigadores que tra-bajan en nano-biotecnologıa, salud y medicina. El paquete computacional Las Palmeras MolecularDynamics, que ha sido desarrollado complementa en nuestro Anillo, es un programa que permitela simulacion y visualizacion de materiales a nivel atomico y molecular, liberado con licencia GPL.

En cuanto a infraestructura cientıfica, destaca la creacion de tres laboratorios: el laborariodel Grupo de NanoMateriales, en la U. de Chile, y los laboratorios de ingenierıa de proteınas yde microscopıa electronica en la U. de Talca. Junto a estos laboratorios, instalamos un Centro decomputacion de alto rendimiento, financiado en forma conjunta por nuestro Anillo y la U. Talca, quetiene un total de 308 cores interconectados con una red infiniband, ideal para calculos en paralelo,en el cual hemos realizado la mayorıa de las simulaciones de gran escala. Asimismo, hemos istaladoun cluster mas pequeno en la Universidad de Chile. El diseno, instalacion y puesta a punto de estosequipos a sido un esfuerzo mayor desde el punto de vista tecnico y administrativo que nos ha dadouna enorme experiencia de gestion cientıfica.

El proyecto Anillo ha jugado un rol fundamental en la formacion de estudiantes e investiga-dores jovenes. Durante su desarrollo han trabajado en su memoria y unidades de investigacion23 estudiantes de pregrado y han desarrollado sus tesis 4 estudiantes de magister y 11 estudian-tes de doctorado. Ademas, 4 doctores realizan su entrenamiento postdoctoral en nuestro Anillo.Las tareas de formacion de investigadores se ha visto fuertemente favorecidas por el intercambiocientıfico que hemos podido realizar, tanto de nuestras salidas a centros del exterior (mas de 14),como visitas de profesores y estudiantes del exterior a nuestros laboratorios, donde hemos recibidoa 24 investigadores, lo cual nos ha permitido establecer nuevas colaboraciones con grupos de laUniversidad de Sevilla, Universidade Federal de Sao Carlos, Universidade Federal de Uberlandia,Harvard University, University of Pittsburgh, University of Antioquia, ICIMAF (Cuba), Universityof Chihuahua, University of Udine, KTH (Sweden), Fraunhoffer Institute, que se agregan a nuestrosantiguos colaboradores de U. Southern Califormia y Florida International University en EE. UU,Uppsala University en Suecia, U. Sao Paulo, Brasil, CNRS-University of Nancy, Francia y NationalCancer Institute de EE.UU.

En cuanto difusion de la actividad cientıfica, esta se ha dado en dos planos: encuentros tecnicospara publico especializados, ası como actividades para el publico general. En el primer ambito,destaca la organizacion de 14 escuelas y workshops, 4 de ellos de caracter internacional: Latin Ame-rican School of Computational Materials Science (www.gnm.cl/school), en conjunto con el ICTPde Italy, en Santiago, 2008; Advanced Course on Free Energy Calculations: Theory and Practice, enconjunto con FP7 Action Grid de la CE, en Talca; tambien co-organizamos otras dos conferenciasinternacionales: Computing modeling and data driven, Simposio Y de la 11th International Confe-rence on Advanced Materials, ICAM09, en Rio de Janeiro, 2009; y First International Conferenceon Bioinformatics (SoIBio), en Chillan, 2010. Junto a esto, hemos dado charlas invitados en 16eventos internacionales y en 6 nacionales, y hemos presentado trabajos y posters en 31 eventosinternacionales y en 42 nacionales, ası como mas de 12 coloquios y seminarios en diferentes univer-sidades del paıs y exterior. Respecto de la difusion cientıfica a todo publico, nuestros investigadoresy estudiantes han realizado sobre 10 actividades, desde charlas en liceos y colegios, exposiones yactividaes de puertas abiertas, con llegada directa a mas de 1500 personas a lo largo del paıs.Tambien hemos tenido comparencencias en la radio, television y en entrevistas en medios escritos,dando a conocer nuestro trabajo cientıfico.

Finalmente, es interesante destacar que nuestras actividades de investigacion nos han permitidointeractuar de manera natural con el sector productivo, en un par de inciativas que, estamos seguros,son solo el comienzo de una relacion mas regular. En efecto, hemos trabajado junto a una empresadel sector minero en el projecto Propiedades termofısicas de neumaticos mineros, para optimizar eluso de ellos en los camiones, haciendo nosotros las simulaciones y asesoramiento de las pruebas enterreno. Por otro lado, junto a la Facultad de Agronomıa y el Instituto de Quımica de la U. de Talcatrabajamos en el proyecto Nanobiologıa aplicada para la industria de alimentos, que cuenta con laayuda del Instituto Fraunhoffer de Alemania y empresas locales. En el area de educacion tambienestamos participando, a traves del proyecto Aprendizaje colaborativo basado en infrestructura deGRID, junto al grupo de Bioinformatica de la PUC, Fundacion Ciencias para la Vida y el apoyoMicrosoft-Chile, HP y Cofe Bussines.

En definitiva, podemos decir que el apoyo del Programa Bicentenario a traves de estos anos,por medio del Proyecto Anillo, ha sido un pilar fundamental y decisivo para unir, consolidar, yproyectar hacia adelante a nuestros grupos de investigacion.

IV. RESULTS IN RESEARCH

The main results in research of our project consists in the ones about the proposed topics, awell as new topics that emerged during the development of the project. They are reflected in themore than 100 contributions to national and international conferences (see Section V) and in morethan 60 published papers that are listed in Section VII. Here we will review only some of thoseresults, stressing the novelty and interelation of the different topics.

The areas considered in our original proposal, which has been consolidated as research topicsin our groups thanks to this project, are:A ) physical properties of nanostructured materials (mechanics of nanomaterials, nanotubes, nano-magnetism, semiconductor nanoparticles), leaded by the U. Chile team andB) Molecular simulation (MD and QM/MM) of biological systems (transmembrane proteins, enzy-matic catalysis and protein-ligand interactions) and structural characterization of dendrimers, lea-ded by the U. Talca team.

Also, along this project we have developed other related areas that emerged during these years:C) nanobiology, computational drug design, metal-organic interfaces, shock waves in biologicalsystems, hypervelocity impact, code development, among others. Most important, we have strengt-hened the research and academic links between the two teams thanks to these new topics. Thus,the synergy has specific results expressed as collaborations, mentoring of undergraduate and post-graduate thesis, postdoctoral fellows, as well as mobility of researchers and students.

The scientific achievements can be also measured in the number of invitations at Plenary lec-tures, given in national and international conferences by almost all members of Project Anillo (seeSec.IV), the collaboration and scientific exchange with several group and colleagues around theworld, as well as the organization of several international schools and simposia (see Sec.VIII).

It is interesting to note that during these years, we have incorporated as collaborators severalPhd. researchers and graduate student, from different universities, like Univ. Austral Valdivia, U.Tarapaca, U. Tec. Fedrico Santa Marıa, Univ. Andres Bello, as well as as Postdoctoral Fellows(supported by a Fondecyt grant). In addition, colaboration arise with other Anillos team, like theone of Non-linear physics at Fac. Cs. Fis. y Mat-U. de Chile, leaded by Dr. E. Tirapegui and Dr.M. Clerc (Proyecto Anillo ACT-15), and Experimental Plasma Physics, P4, from CCHEN, leadedby Dr. L. Soto, (Proyecto Anillo ACT-26).

In the next pages, we describe the main research activities developed, pointing out both, thesuccess and the difficulties we experienced in the different projects. We will begin describing theresearch results on the topics proposed in our original proposal, and then the new ones.

A ) Physical properties of nanostructured materials

IV.1. Nanostructured and bulk materials

In this area, the main efforts have been directed to simulated structural and mechani-cal properties of nanocrystalline materials. In this respect, and in order to have a completedomain over the simulation techniques and how to perform it according our needs, we ha-ve been developing a molecular dynamic program, as well as several tools to analyze theresults. The outcome of this efforts is the Las Palmeras Molecular Dynamics (LPMD) pa-ckage (http://www.lpmd.cl), developed mainly by PhD sutdents at GNM: S. Davis (KTH,Sweden, and member of GNM, now Fondecyt postdoctoral fellow at GNM.), J. Peralta and

C. Loyola (both graduated in 2010 and now a postdoctoral fellow at Iowa State University),F. Gonzalez (current PhD student). LPMD is a molecular dynamics (MD) code writtenfrom scratch in C++, as user-friendly, modular and multiplatform as possible. Some of itsfeatures are: it is an Open Source code, it works using plugins, it reads simple and intuitiveconfiguration files, and includes utility software to perform analysis, conversion, and visuali-zation of MD simulations. Today, the stable branch 0.6 in its latest version is 0.6.1. This lastversion includes new features such as more friendly control files, more efficient simulationtimes, a new API version (2.0). On the latest tests, LPMD has shown good agreement withother software, but longer simulation times; an issue which we hope to improve in futurereleases. One of the aims for the next version is to optimize the linkedcell method, for bet-ter performance in more massive simulations. The Fig. 3 show the number of lines of C++code, from the version 0.5.0 to the lastest stable version 0.6. We expect the future code linesincreasing to be only in the plugins, consolidating the API code. The last stable versionhave in their distribution python-code lines. LPMD includes additional software to computeproperties from previous simulations, such as Analyzer : for output files (from other softwa-re or LPMD itself), to obtain pair distribution function, angular distribution, coordinationnumber, Common Neighbor Analysis, correlation, Density/Temperature Profiles. Converter:converts between different MD file formats: XYZ, POSCAR (VASP), CONFIG (DLPOLY),mol2, lpmd (LPMD). Visualizer: to animate MD simulations. See more detail in the web pagewww.lpmd.cl, and the recently published paper entitled Las Palmeras Molecular Dynamics:A Flexible and Modular Molecular Dynamics Code in Computer Physics Communications,Sec. VII [43].

(a) Number of lines of C++ code progress, fromthe version 0.5.0 to the latest stable version

(b) Nanocrystal built with a utilityof LPMD

Figura 3: LPMD package. Most of the incremental improvement has been in the plugins principally,consolidating the API code.

Other achievements in materials calculation have been:

molecular dynamics and X-ray photoelectron spectroscopy study of CdTeOx, was pu-blished (Sec.VII [29, 38, 39]). We obtained structural models for the amorphous mate-rials a-CdTeOx, (0,2 < x < 3), using ab initio molecular dynamics, and we have madea detailed description of the variety of atomic environments found in these materials.

These structural models, in the form of xyz coordinates of the atoms in a supercell,were used subsequently to calculate the XPS spectra and validate them by comparisonwith experimental data.

the experimental and theoretical study of the strength of polycrystalline coarse-grainedplatinum to 330 GPa and of nanocrystalline platinum up to 70 GPa was done andpublished, Sec. VII [16].

amorphous alumina under pressure has been studied and a manuscript submitted toPRL. Referees recommend no to publish in PRL, but have a favorable opinion foranother journal. We worked in that comment and submit it to PRB, Sec. VII [59].

amorphous alumina by ab-initio calculation has been studied and published in Sec.VII [45], and a detailed report has been submitted, Sec. VII [60].

amorphous germania under pressure has been studied and the results presented inseveral conferences (See Sec.IV [41, 43]). Two articles were published Sec. VII [22, 45]

vibrational properties and infrared spectra and of γ−alumina were studied, and theresults were presented in several conferences (See Sec. IV [40, 42, 47]) and published inone article Sec. VII [46]. In this work, the vibrational properties of the four availablestructural models of γ−alumina were computed, looking relatively similar. However,the simulated infrared spectra (depend on the dynamical dipole moments of the vbra-tional modes) show remarkable differences that could be observed in low temperaturemeasurements.

in the 2 months visit of PhD student C. Valencia from U. Antioquia we studied struc-tural and dynamical properties of Cu46Zr54 bulk metallic glasses (BMG), a hot topictoday because the unique mechanical properties of BMG. A paper has been publishedSec. VII [50].

mechanical properties of Hydroxyapatite (HAP) and fluorapatite(FAP). Hydroxyapa-tite (HAP) is an essential components of dental enamel and bone, and the elastic pro-perties of single crystal HAP are not know. Fluorapatite(FAP) is found in sick teeth(fluorosis) and degrades its mechanical resistance. We made a computational study ofthe elastic properties of HAP and FAP using ab initio and forcefield techniques. Ourab initio HAP stiffness constants differ from previous calculations, but follow similartrends. The pseudo single-crystal HAP experimental stiffness constants in current useare critically reviewed. Combining the data from the ab initio simulations with the ex-perimental FAP stiffness constants, several new HAP stiffness constants are proposed.We found that the properties mismatch between HAP and FAP is evidently too smallto assume it directly responsible for the dental enamel mechanical degradation withfluorosis desease. One article has been accepted (Sec. VII [56]).

IV.2. Semiconductors: surfaces, interfaces, quantum dots

Several research projects have been conducted in this area, mainly leaded by E. Menendez.Among them:

in collaboration with a team of the University of Sevilla (Prof. Fernandez-Sanz), we havestudied the adsorption of gold atoms on nitrogenated surfaces of anatase, a polymorphof titanium dioxide with photocatalytic properties. Nitrogenation and deposition oftransition metal atoms is an active line of research, oriented to find stable and cheapphotocatalysts that are activated with visible light. The manuscript recently accepted(Sec. VII [55]).

we contributed to a study of magneto-optical properties of CdxZn1−xSe semiconductorquantum dots, demonstrating that thermal annealing produce the evaporation of Cdmaterial, modifies the shape of the quantum confinement and allows to tune magneticproperties. This a collaboration between six institutions in Brazil, Chile, France, andGermany. Our role was the ab initio calculation of the strain effects in the quantum dotsand analysis and support the zincblende lattice model of the quantum dots. Besides,the work includes high quality experiments and multiband effective mass calculationsof excitons states. An article was recently published, Sec. VII [41].

the study of Schottky barriers in the CdSe/Au interface, was cancelled. After submit-ting one article during the first year of the project, one referee asked to do tests ofconvergence with the size of the model system. The subsequent calculations revealedan artificial electric field across the interface which makes impossible to fit a barrierheight. Several alternatives have been tried to eliminate this artifact, but none provedto be effective.

we did calculation of the potential energy barrier in a model of grain boundary ingold nanofilms. This work, in collaboration with an experimental group at U. of Chile,consisted on an ab initio calculation of the potential barrier associated with a twingrain boundary identified with the help TEM images by the experimental group. Thiswould be an input for a phenomenological theory of conductivity limited by grainborders. A talk was given in a group meeting and a report was written (Sec.IV[19]),and although, regretfully, the ab initio calculation revealed that for a twin boundarythere is no potential barrier, this project is the beginning of a collaboration betweena theoretical and experimental groups of our University, an important issue for bothgroups.

we studied quantum dots at several levels of complexity and approximation. In onestudy, Sec.VII[4], using the effective mass approximation, we have studied the dyna-mical behavior of a quantum dot under variable magnetic fields. The subproject ofelectron-phonon coupled states in quantum dots nanocrystals, stated in the originalprojects for the first two years, was cancelled. This subproject had been delayed inbenefit of arising collaborations with experimental groups. The experimental work onquantum dots was made by the group of Talca and is described below. In support of theexperiments, we tried to establish good methods to calculate the structural and electro-nic properties with quantum mechanical atomistic methods. In particular, we wantedto study quantum dot phenomena related to their surface functionalization. Regretfullywe obtained poor performance of the semiempirical methods (PM3,PM6,CNDOL) andextremely long computation times (for our cluster) with the DFT methods.

IV.3. Nanotubes

The interaction of carbon nanotubes (CNTs) with molecules and their possible use assensors was one of our proposed works. We studied the adsorption of NH3, NO2, H2O andO2 onto a semiconducting CNT containing a divacancy, assumed as a possible active site.In general, we observe weak Van der Waals interactions, which do not introduce significantelectronic perturbations in the CNT band structure to alter conduction properties in theCNT. Thus, our results suggest that defective CNTs would not be able for sensor applications.In the original project, we also proposed to study the functionalization of CNT with polymers.However, the description of this system by first-principles calculations proved to be complexand very computational demanding which could not be initated because our computationalfacilities (the Anillo cluster) took a couple of year to be fully operational. The unsuccessfulresults and the delay in the cluster start off led us to redirect the project on CNTs lookingfor both interesting and less computational-demanding systems. After a search we decidedto focus in two problems: catalysis and energy needs. Thus, we studied CNTs as hydrogenstorage materials and as support to attach metallomacrocycles for solid-gas heterogeneouscatalysis: (i) H2 storage inside single-walled carbon nanotubes: The interaction of hydrogenmolecules with multivacancy defects in CNTs and their subsequent incorporation insideat room temperature were investigated by ab initio molecular dynamic simulations. Wefind endohedral binding energies for H2 close to those estimated optimal for a reversibleadsorption-desorption process, suggesting that nanoporous CNTs as produced by electronirradiation could be an effective hydrogen storage medium, allowing the access to the CNTinner space. Storage capacity of about 4 wt% are estimated for a 11 A. CNT, with thepossibility to be increased for CNTs with larger diameters. One article has been publishedin this issue, Sec.VII[30]. (ii) Iron Porphyrin attached on carbon nanotube sidewalls: Weexplore covalent and non-covalent mechanisms to attach iron porphyrins (FeP) on the surfaceof single-walled carbon nanotubes (CNTs). We studied the stability and electronic propertiesof several FeP-CNT assemblies to shed light in the experimentally reported electrocatalyticactivity of carbon-supported Fe macrocycles and the role of the linking structure. One articlehas been published in this issue, Sec. VII [40]. The catalytic activity of this supramolecularcomplex for the oxygen reduction reaction is currently under investigation. This work is partof the Ph.D. thesis of Igor Ruiz-Tagle at U. Andres Bello (UNAB) in Santiago under thesupervision of W. Orellana.

In other activities concerning the study of CNTs, we have collaborated with an inter-national team in a research on excited states and optical properties of single walled carbonnanotubes. We have studied these properties using an approximate method to the Hartree-Fock self-consistent method and a subsequent configurations interaction calculation. Onearticle has been published, Sec. VII [42]. The optical properties of several types of carbonnanotubes were studied and compared with high level ab initio calculations with satisfactoryaccuracy. The promise of this method is that, being computationally light, can be appliedto a number of interesting phenomena related to finite and defective nanotubes, as well asin interaction with other nanostructures (Menendez and Orellana).

IV.4. Nanomagnetism

Several topics has been treated here, among them:

Strongly interacting systems: we have studied the dynamical behavior of strongly inter-acting systems for few and large number of magnetic particles. In particular, for two,three, four and five particles we focus in different geometric configurations. In all thiscases, the conservative dynamics present a rich types of behaviors such that transitionsbetween chaos and regular motion depending on the parameters. In the case of largenumber of particles (N � 100) we studied a chain geometric configuration. We exploredboth dissipative and conservative systems. We found that due to the dipolar interactionthe absolute value of the total magnetization is not conserved, see Sec. VII [1, 9, 10].Finally, the statistical mechanics properties for a large number of particles for differenttypes of magnetic interactions were analyzed.

Ferrofluids: we studied magnetic fluids formed by a stable colloidal suspension of mag-netic nano-particles dispersed in a carrier liquid. Different types of carrier liquids wereconsidered, such as Newtonian, Maxwellian and General Visco-elastic fluids. The mainproblem was the convection phenomenon. We also analyzed the influence of magne-tophoretic effect and the coupling between the concentration and magnetic effect inthe rotating convective thresholds of the binary magnetic mixtures We showed thatrotation stabilizes the convection produced by heat injection. Amplitudes equationswere derivate close to the bifurcations. Some of these results can be found in Refs. Sec.VII [2, 31, 57].

Magnetic nanowires: another topic explored deals with the dynamical behaviors onquasi-reversal systems, where 1-D magnetic systems are typical examples. In particu-lar, we derived a new amplitude equation for dissipative system under a parametricalforcing, Sec.VII [14, 32, 33]. In addition, we characterized a new type of localized struc-tures and some spontaneous breaking of symmetry that can appear in these systems.This work was done in collaboration with Anillo Project ACT-15.

Adsorption of magnetic nanoparticles on surfaces: We studied the electronic and mag-netic properties of iron nanoparticles with 13 atoms (Fe13) adsorbed on self-organized1D structures onto semiconducting surfaces. These 1D structures are bismuth dimersperfectly aligned on the Si(001) surfaces. The Bi lines are very long (> 1 nm) but only0.63 nm wide, they form after Bi evaporation from Si(001) at above 450 C. Our goalwith this project is to shed light on the possibility to contruct 1D magnetic nanowireon semiconducting surfaces using the Bi lines as template. Our results show that theFe13 nanoparticles are strongly adsorbed between the Bi lines, with binding energiesof about 5 eV, nucleating as nanowires along the Bi lines after the adsorption. Thisnanowire shows interesting properties like metallic half-metal behavior along the wi-re, having magnetic moment of 2.6 µB/Fe-atom. Additionally, it exhibits a magneticbistability in the plane normal to the wire direction. The calculated Fe-nanowire mag-netic anisotropy energy is found to be of 1.6 meV/Fe-atom. The article describing theabove results is currently under preparation. Motivated by the interesting properties

of surface-supported nanoparticles, we started another project in this issue, not consi-der in the original proposal. It deals with nanoparticles of noble metals (Au, Pd, Pt)adsorbed on metal-oxide surfaces [TiO2(110) and CeO2(111)] and their application incatalysis. The above systems have shown superior catalytic properties for important re-actions like the oxygen reduction and the carbon monoxide oxidation. We are exploringthe origin of such as catalytic properties (Orellana).

Heat diffusion in spin chains: the thermodynamic properties magnetic chains in themicro-canonical ensemble Sec.VII [28] and in classical dipolar systems has also beendone, including the heat transport in magnetic chains. In fact, in two Master thesis (F.Cuturrufo and E. Valdebenito) directed by G. Gutierrez have explored the validity ofthe Fourier law in the case of 1-D system with anisotropy and external magnetic field.

Non-collinear magnetism: by non-collinear magnetism ab-initio methods, our associatedR. Lizarraga and E. Holstrom from U. Austral have studied the high pressure phase ofiron (Sec.VII [20]).

B) Molecular simulation (MD and QM/MM) of biological systems

IV.5. Large-scale Molecular simulation of K+ channels

Potassium channels are undoubtedly one of the most enigmatic and more studied pro-teins in biophysics. These transmembrane proteins are the clue for electrical signals of ournervous system, as well as they are involved in several neurodegenerative diseases. Severalstudies have found that in some cancers, like gastric cancer, these proteins are over-expressedand probably have an important role in this disease. In the field of therapies pain relief theK+ channels are used as an important target for design of new anesthetics. U. Talca team(D. Gonzalez and students) has implemented and developed modern methods of molecularsimulation that are applied successful to these kind proteins. The knowledge at an atomiclevel of the structural and dynamic properties of these systems has a high impact in scientificresearch, contributing with novel hypothesis and contributing with the implementation ofmore efficient experimental strategies in the search of the mechanisms related to the activa-tion of these proteins (Sec.VII [23, 24].

Inportant progress was made in the implementation of advanced methods for evaluationof free energy and large scale molecular simulations of transmembrane proteins. K+ channelshave very complex activation mechanisms which are constituted by structural motifs wellconserved along each family, however they can not be necessarily identified from a simplesequence analysis. In this context we highlight works, published as articles of great impact, inwhich results from molecular simulations allowed us to reinterpret the functional importanceof two key aminoacids participating in the sensed temperature TRPV1 K+ channel activa-tion. One of them is described in detail in the paper entitled Dissection of the componentsfor PIP2 Activation and thermosensation in TRP channels, published in Proceeding of theNational Academy of Sciences (see Sec. VII [6]).

In the same way, computational predictions based in the analysis of long molecular dy-namics simulations allowed us to identify the aminoacids involved in the modulation of

electrostatic potential, which regulates the pass of ions across the hSlo K+ channels. Inthis study, we performed a huge, both experimental and theoretical, effort to establish theelectrostatic mechanism used in the ion transport across these transmembrane proteins. Theaforementioned work was published in the prestigious Journal of General Physiology (Sec.VII [12]) and it was awarded, by the editorial committee, appearing in the cover of the jour-nal. Both articles, are the product of a well coordinated and fruitful colaboration betweenthe experimental group leaded by Dr. Ramon Latorre from Universidad de Valparaso, andthe modeling group leaded by Dr. Danilo Gonzalez from Universidad de Talca.

IV.6. Enzymatic Catalysis

Another developed area of the Anillo has been the structural study of the transition statesof the decarboxylation reaction that take place in the active site of the PEPCK protein. Toconduct these studies, leaded by U. Talca team, we have implemented hybrid calculationmethods like the quantum mechanics/molecular mechanics (QM/MM) scheme. The resultsobtained so far have allowed us to analyze in detail the role of two metals that take partof the catalytic reaction of this enzyme (Sec.VII [25, 17]). It also has allowed us to analyzetransitory deprotonation processes that are not feasible to analyze by other means. Theset of theoretical results have been discussed in detail with Dr. Emilio Cardemil from theUniversity of Santiago, who is a well-known expert in this protein. This studies allowed toperform the undergraduate dissertations of Hector Urbina (2008), Xaviera Lopez (2009) andRomina Sepulveda (2010), bioinformatics engineering students at the U. Talca. Thus, thetheoretical results have been also included in undergraduate and graduate thesis from Dr.Cardemils students.

IV.7. Quantum Dot-Dendrimer complex

This area of research, with application in cancer cell imaging, bring together the exper-tise of U. Talca team (D. Gonzalez) and U. Chile team (E. Menendez) in the synthesis andstructural characterization of Q Dots-dendrimer complexes, and we have the support fromDr. Leonardo Santos at Chemistry Institute of U. Talca, who kindly allow us to use hislaboratory and facilities. In fact, Dr. Daniela Geraldo, a postdoc associated to UTalca groupthat has implemented the synthesis and characterization of quantum dots and dendrimers.It is important to highlight the significant progress made in this area, where this multidisci-plinary collaboration between Dr. Santos and CBSM has led to the first test for cell imagingsystem to distinguish tumor cells from normal cells, Sec.VII[54] (see Figure).

IV.8. Protein-ligand interactions and computational assisted Drug Design

2008-2010: During this period, we developed and applied diverse methods for predictionof physical-chemistry properties useful in the study of quantitative structure activity rela-tionships. Methods such as CoMFA, CoMSIA and QSAR 3D were used in our research. Thatfield had an accelerated development in our group during 2008 due to the incorporation ofJulio Caballero to the PhD program of Applied Sciences at U. Talca. Moreover, the im-plementation of hydrid calculation methods, like quantum mechanics/molecular mechanics

(a) AGS-FA-PAMAM-QDot on tu-mor cells

(b) Dendrimer model of PAMAMG4 interacting with ibuprofen.Drug delivery

Figura 4: Examples of QD-dendrimers and drug deliver research

(QM/MM) and ONIOM, has allowed us to study not only enzymatic reactions, but noncovalent interactions (hydrogen bonds) between ligands and active site of some protein kina-ses participating in cancer, Alzheimer disease and other pathologies. It is worthy to say thatthese hybrid methods have became useful in the study of interaction energies between inhibi-tors and protein, which in turn has allowed to establish good structural-activity correlation,mainly in protein kinase systems. This research area is leaded by Dr. Jans Alzate-Morales,who was hired recently by UTalca after his postdoctoral stay research at CBSM. In a firststudy, the ONIOM method was applied to study the hydrogen bond interactions betweensome CDK2 inhibitors and various models of the active site in CDK2/CyclinA system. Itwas found that according with the models size, a good description of the molecular inter-actions inside the active site can be obtained. From best model, it was possible to obtain areliable correlation between the total ONIOM energy and the biological activity reported forcompounds studied. The results show that H-bond interaction energy is the principal com-ponent in this proteinligand interaction and residues Lys89 and Asp86 are essential for greatpotency of compound NU6102. The main results of this work were published in ChemicalPhysics Letters Journal, Sec.VII[26].

In a second work, we performed Comparative molecular field analysis (CoMFA) andQM/MM hybrid calculations on 9H- purine derivatives as CDK2 inhibitors. CoMFA wascarried out to describe the activities of 78 analogues. The models were applied to a trainingset including 64 compounds. The best CoMFA model included steric and electrostatic fields,had a good Q2 value of 0.845, and adequately predicted the compounds contained in thetest set. Furthermore, plots of the steric CoMFA field allowed conclusions to be drawn forthe choice of suitable inhibitors. In addition, the dynamical behavior of compounds with 4-(aminosulfonyl)phenyl, 4-[(methylamino)sulfonyl]phenyl, 4-[(dimethylamino)sulfonyl]phenyl,and [3-methoxy-4-(aminosulfonyl)]phenyl groups at position 2 of the 9H-purine scaffold in-side the CDK2 active site were analyzed by QM/MM calculations. The interactions of thesecompounds with residues Lys89, Asp86, and Ile10 were characterized, see Sec.VII[49]. Thisresearch area will be reinforced by recent FONDECYT project granted to Dr. Jans Alzate-

Morales.

C) New topics: a synergy between U. Chile and U. Talca teams

IV.9. Metal-organic interfaces

(a) Aspartate molecule (asparte acid desprotona-de) on a TiO2 (rutilo) surface

(b) Cistein aminoacid interactingwith a defect on the bottom of Au8 cluster

Figura 5: Metal-organics interfaces

IV.9.1. Biological oligopeptide (RGD) on titanium oxide surface

We have studied the adsorption of aminoacids on surfaces of rutile, which is the moststable polymorph of titanium dioxide and the natural interface between titanium implantsand biological tissues. This investigation was a joint effort of U. de Chile (E. Menendez) andU. Talca (J. Henriquez ) teams and produced two Bioinformatics Engineering thesis works(R. Urzua and J. Mansilla). The aim of this investigation was to elucidate the main inter-actions involved on the phenomenon of adsorption of the oligopeptide RGD, on titanium ata fundamental level, using the molecular simulation tools, such as quantum mechanics andminimization techniques. From the molecular mechanics minimization it was found that theRGD peptide was localized on a fibronectin protein loop (1TTF), orientated toward outside(water face), accordingly with those results, that sequence enabled interaction with the TiO2

surface. We have employed several quantum mechanical codes to study this interaction: MO-PAC, VASP, and SIESTA. We have found that MOPAC does not produce good geometries,at difference with a test of truly ab initio calculations with VASP and SIESTA. The ener-gies of adsorption of Arginine, Aspartic Acid and Lysine were obtained using two ab initioelectronic structure packages (VASP and SIESTA). The first part of this work consisted indetermining the model system with the minimal number of atoms needed to obtain consis-tent results of adsortion energies. It was established in this work, that to model the TiO2

(110) surface in interaction with water molecules, it is required minimum a supercell with40 oxygen atoms and 20 titanium atoms, arranged in 15 atomic layers, keeping the bottomsix layers with the atomic positions fixed at the ideal crystal positions. The atomic positionsof the top layers are allowed to relax, and the fixed bottom layers simulate the effect of the

underlying thick material. To model amino acid adsorption, the TiO2 surface unit cell mustbe replicate at least twice in the two surface directions. Our model is severely limited due tonot considering the rest of the water molecules surrounding the amino acid in aqueous envi-ronment. The amino acids arginine and aspartic present charged states (by proton transfer)in conditions of neutral pH. These protonation states were included in the simulations, andproduces a strong dependence of the adsorption energy with the size of the unit cell, whichmake the results untrustable. The electrostatic interaction must be screened by the presenceof water, with is not included in the simulation. The inclusion of water can be done usinga solvent model (using a different program) or include explicit water molecules, multiplyingthe computer resources need. The main result of this research line is the results on wateradsorption energies and the advances toward a realistic model system for simulation of theRDG interaction with the TiO2 surface. The results are still contradictory and more researchis needed before submitting a publication.

IV.9.2. Amino acid contained sulphur atoms on interaction with gold cluster

In the biological field is possible to characterize some immunological responses throughinteractions involving on gold atoms structures and proteins such as opsosines (serum proteinthat binds to microbes to facilitate their phagocytosis in macrophages), tumor necrosis fac-tor therapy of Aaurimune, fibronectin, and so on. The aim of this investigation is to suggesta theoretical model about the main interaction of biological compound contained sulphuron gold cluster defects. Theoretical calculations were made on surface of Au cluster interac-ting to thiols compound. Computational chemistry was performed using the hybrid methodB3LYP. The gold defects structures were modeling as cluster concepts. The studies showedthe interaction of organic compounds with its unprotonated state on Au cluster energeticallymore stable than its protonated state. In the case of methionine, its structural feature, asmean: absence of sulphydryl group, the interaction with the metal surface was mediatedby the electronic density of sulphur. This investigation also was done by J. Henriquez formU. Talca and E. Menendez U. Chile and it resulted in Bioinformatics Engineering thesis ofWaldo Acevedo (graduated on March of 2009).

IV.9.3. Organics Acid on metallic oxides surfaces: Cu2O and ZnO

The experimental evidence shows that zinc oxide and copper oxide can suffer corrosion byorganic acid derivatives. This research is an effort to explain the interaction involves on thatkind system at molecular level and, in this way, give a characterization of the atmosphericcorrosion process. The quantum mechanics calculations indicate that the interaction energybetween the organic compound and metallic surface is stronger for Zinc that the copper. Thiscould be due at the direct metal-oxygen interaction in the zinc case, while, on the coppercase this interaction involves the hydroxylated layer and one molecular water. The energeticand hardness analysis show that contained Zinc system was more stable than the containercopper one. In the other hand the Cu2O-formate system was harder than the ZnO-formatesystem, therefore, the Zn systems are more easily corroded by the organic acid than thecopper (see Sec.VII [15]).

IV.10. Shock wave simulation and hypervelocity impact

a)

b)

c)

(a) Solid argon, simulated withLPMD package by C. Loyola

(b) Water, simulated with NAMDpackage by D. Aguayo

Figura 6: Shock waves simulations

In recent years the use of extra-corporeal shock waves therapy (ESWT) in the treatmentof different ailments in human beings have been steadily increasing since its first applicationin 1981. The success of these procedure has mostly depended on clinical evidence, becausethe scarcity of our knowledge of the interaction between shock waves and biological tissuesat the molecular or functional level. In order to gain a fundamental understanding of theeffects of shock waves on biological materials, a research project has been established in theFacultad de Ciencias, U. de Chile, with the participation of physicians at Arauco Salud Clinicand Facultad de Medicina, U. de Chile, researchers from U. Windsor (Dr. Aroca), Canada,and the Lab. of Raman spectroscopy, Dr. Campos and Clavijo) and GNM of Facultad deCiencias, U. de Chile In this transdisciplinary project, our contribution shall be to simulatethe behavior of this phenomenon at various levels of complexity. In addition, we have aFondecyt postdoctoral fellow (Dr. Encina, Advisor: G. Gutierrez) working in this proposal.Also, we gave a course in the topic (see Sec.VIII, Course [9]). After a year of joint efforts ofU. de Chile and U. Talca team, we have now some results. In the figure 6 we display picturesof the shock wave simulation on solid argon and in water. In both cases the methodologyis similar: we assign to the piston certain velocity, generating a shockwave front. When thepiston stop, a rarefaction wave developed, producing at the end the fail of the sample. Infact, in figure 6 we display three stage of this process: a) the shockwave advance just afterthe piston stopped. Note the clear difference between the high density shockwave front atone side (right) and the undisturbed material in the other side (left); b) the shockwave frontis reaching the other extreme of the sample, developing a rarefaction wave behind it, andleaving a structure different to the initial fcc one; c) finally void growth can be seen. Thisstudy has been published in Computational Materials Science, Sec. VII [44], and form partof the PhD thesis of Claudia Loyola, at GNM. The research is conducted by PhD students atSantiago (solid argon) and at Talca (water), under direction of G. Gutierrez and D. Gonzalezrespectivaly. Now we will continue in this line, introducing biological material, like proteinsor membranes. Also, we have study the physics of hypervelocity impact, that is, collisions atvelocity above sound velocity, between two nano-object (clusters). Preliminary results hasbeen presented in seminars and Conferences Sec. IV [90, 91]. We stressed the fact that theseprojects, as well as the one on Quantum Dot-Dendrymer complex (see below, Sec.III.9), have

enabled us to the develop new lines of research, where is needed the expertise both of theGNM team at U. de Chile and the CBSM team of U. Talca.

IV.11. Convection of polymeric solutions

In this field we have developed a model for convection polymer solutions in a liquid, suchas DNA. We have shown that the effect of rotation stabilizes the threshold of convection,see Sec.VII[2, 5].

IV.12. Structural database of Nanobiology

From 2008 to date, U. Talca team signed a contract of a sole source (the first one in LatinAmerica) on behalf of SAIC-NCI, USA, which allowed us to jointly develop databases ofnanoparticle structures CNS. The beta version is available in http://nanobiology.utalca.cl/.At present we are working on molecular simulation protocols that enable us an efficientfilling of that database. This work was key in the current colaboration between FraunhoferInstitute and UTalca team to develop the line research of NanoBiotechnology in Food.

IV.13. High performance computing facility

One of our goal was the develpment of a top level scientific computer lab, and the final setup of a high performance computing system. After almost one and a half year of negotiationwith Hewlett Packard, the high performance computing (HPC) system was finally installedon December 2008 at Universidad de Talca. The system consists of 38 blades, each one with2 Quadcore Xeon processors, suming in total 304 cores. The nodes are interconnected withInfiniband (20 Gbps) and Gigabit Ethernet networks. The total investment on the computersystem was $ 160 million pesos. The Anillo Project provided 65 million pesos (40%) and theUniversity of Talca made a contribution of 95 million pesos (60%). Currently, the cluster isrunning with high production quotas, with a system of queues (PBS) that has respondedproperly to the demands of researchers and students associated to the scientific Anillo.

Other notable achievement is the settlement of a physical space for the Group of Nano-materials at the University of Chile, which is on operation since April 2008. During 2008we adquired a Dell computer with 4 Quadcore Xeon Processors that is being used for cal-culation. It had has an intermediate cost between the personal computers and the HPC ofTalca. All this infrastructure now will be complemented with the CONICYT project formajor equipment in HPC, titled “National Laboratory for High-Performance Computing(NLHPC)”.

V. NATIONAL AND INTERNATIONAL COLLABORATION

Here we list the main activities related to increases the link and collaboration with othergroups and researchers both at national and international level. Several of them have beensupported by the Grant for International collaboration ACI-52, awarded by our Anillo atthe beginning of 2008.

In the activities, a highlight are the Invited talks at international Conferences.

Invited Talks, International Conferences

[1] G. Gutierrez, Thermophysical properties of novel ceramic, Invited Talk, USA- AirForcewindows on science, AFOSR meeting, Arlington, USA, 11-17 May 2008.

[2] G. Gutierrez, Computer simulations in amorphous compounds, Invited Talk, Interna-tional Conference Material Informatics and DFT, Oran, Algeria from 11 to 13 October2008.

[3] G. Gutierrez, Ab-initio molecular dynamics for amorphous alumina and spin dynamicsfor magnetic systems, Invited Talk, Latin American School in Computational MaterialsScience, ICTP-UChile-UNAB, Santiago, Enero2009.

[4] E. Menendez, Ab initio molecular dynamics of CdTe oxides, Invited Talk, Latin Ame-rican School in Computational Materials Science, ICTP-UChile-UNAB, Santiago, Ja-nuary 2009.

[5] D. Gonzalez, Invited Talk as Plenary Lecturer, Bioinforsalud, First EuropeanCommission-Funded Initiative to Analyze Biomedical Informatics, Grid Technologiesand Nanoinformatics, PAIS, March 2009.

[6] D. Gonzalez, Invited Talk as Plenary Lecturer, First Workshop for Proteomics in theNew World. LNCC, Petropolis, Rio de Janeiro, Brazil May 12-16, 2008.

[7] D. Gonzalez, Collaboratory for Structural Nanobiology: Nanoparticles database, InvitedTalk as Plenary Lecturer, 6th Workshop of Computational Chemistry and MolecularSpectroscopy, October 21-24, 2008. Punta de Tralca, Chile May 12-16, 2008.

[8] D. Gonzalez, Nanobiology -The Next Frontier for Molecular Simulations, Invited Talk,Latin American School in Computational Materials Science, ICTP-UChile-UNAB, San-tiago, Enero2009.

[9] W. Orellana, Magnetic nanoestructures on semiconducting surfaces: First principlescalculations, Invited Talk, 17 International Material Research Congress, Cancun, Mexi-co, (August 2008).

[10] W. Orellana, Self-organized Fe nanowires on semiconducting surfaces, Invited Talk,Latin American School on Computational Material Science, ICTP-UChile-UNAB, San-tiago (January 2009).

[11] D. Laroze, Dinamica de sistemas Quasi-reversibles, Invited Talk as Plenary Lecturer,Sociedad Boliviana de Fisica, SOBOFI, La Paz, Bolivia (Nov. 2008).

[12] Gonzalo Gutierrez was invited for an Invited lecture at the symposium on Science andEngineering of Nanoscale Systems: Scientific Discovery through Advanced Computationand Experimental Validation at the 2009 International Conference on Computational &Experimental Engineering and Sciences, ICCES’09 , 8-13 April 2009, Phuket, Thailand.Did not go because force majeure.

[13] Dr. J. Alzate participated in the first International Congress in Pharmaceutical, Bio-chemical and Biotechnological Sciences that will take place between 1 and 5 of June2009 in the Santa Maria Catholic University, Arequipa, Peru. Plenary Lecture

[14] G. Gutierrez:

– Co-chair Simposio Y - Computational Modeling and Data Driven Materials Discovery,ICAM09 (11th International Conference on Advanced Materials), Rio de Janeiro, 20-25de Septiembre 2009.

– Invited speaker at III Workshop on Novel Methods for ElectronicStructure Calculations, La Plata, Argentina, 14-16 de octubre 2009. Seehttp://congresos.unlp.edu.ar/index.php/NMESC/

[15] W .Orellana, invited speaker at Simposio Y - Computational Modeling and Data DrivenMaterials Discovery, ICAM09 (11th International Conference on Advanced Materials),Rio de Janeiro, 20-25 de Septiembre.

[16] We note that E. Menendez also was invited as a Speaker at ICAM2009 and at IIIWorkshop on Novel Methods for Electronic Structure Calculations, but he can not gofor personal reasons.

Invited Talks, National Conferences

[17] G. Gutierrez, Heat transport in magnetic sytems, Invited Talk, Topicos en Fısica NoLineal, Santiago, Chile (Oct. 2008)

[18] D. Laroze, Localized waves in magnetic wires, Invited Talk, Topicos en Fısica No Lineal,Santiago, Chile (Oct. 2008)

[19] E. Menendez, Potential energy barrier in models of grain boundary in gold, Meeting ofthe Group of Nanotechnology of the Faculty of Physical and Mathematical Sciences ofthe Univ of Chile. 16 October 2008.

[20] D. Laroze, Modelos extendidos en dinamica de Poblaciones: Efectos del Ruido, InvitedTalk, Taller de Arqueologıa Matematica, Arica, Chile, Oct. 2008.

[21] D. Laroze, Magnetoconveccion no lineal, Invited Talk, Mini-Workshop Nucleo Milenio?Magnetismo basico y aplicado, Renaca, Chile.

[22] E. Menendez, Calculo de barrera de potencial en intercaras metal semi–conductor pormetodos de primeros principios, Invited Talk, II Escuela de Nanoestructuras, Valpa-raıso, Chile, Jan. 2009.

Contributed talks and posters, International Conferences

[23] O. Suarez, P. Vargas, D. Laroze, Scaling of Magnetic phases as function of length in1D linear Chain, CLACSA XIII, Santa Marta, Colombia (Dic. 2007)

[24] W. Orellana, Fe adatoms along Bi nanolines on H/Si(001): Patterning atomic magneticchain, 13th Brazilian Workshop of Semiconductor Physics Sao Paulo, Brazil (Abril2007)

[25] D. Holmes, F. Gonzalez-Nilo, S. Brauchi, R. Latorre, M.I. Niemeyer, F. Sepulveda, anScience Paradigm for Latin America. 3rd IEEE Internacional Conference on e-Scienceand Gris Computing, Virtual Institute for Integrative Biology (VIIB):Belgrado, India,(Dic. 2007)

[26] F. Gonzalez-Nilo, Charla plenaria titulada: Biomolecular simulations and structurebioinformatics of transmembrane protein: K+ channels. international workshop oncollaborative bioinformatics EMBnet- RIBCentro de Bioinformatica y Simulacion Mo-lecular, Malaga, Espana, (Junio 2007)

[27] H. Digenova, A. Ruiz-Lara S. F.D.Gonzalez-Nilo, Structural analysis: Guanine Nucleo-tide Dissociation (GDI), in Solanum chilense (tomato). Mendoza, Argentina (2007)

[28] C. Avila, F.D. Gonzalez-Nilo, R. Chehin, Blind docking studies of phosphatydil-serineto Glyceraldehyde-3-phosphate dehydrogenase, Dpto Bioquımica de la Nutricion, Uni-versidad Nacional de Tucuman, san Miguel de Tucuman, Argentina (2007)

[29] R. E. Cachau, M. J. Fritts, I. Topol, S. K. Burt, F. D. Gonzalez-Nilo, M. Matties,New modeling strategies for the computational characterization of nanobioparticles.Biophysical society-51th annual meeting, Baltimore, EEUU. (Marzo 2007)

[30] F. D. Gonzalez-Nilo, M. I. Niemeyer, L. Zuniga, W. Gonzalez, P. L. Cid, F. V. Sepul-veda. Neutralization of a single arginine residue gates open a two-pore domain, alkali-activated K+ channel. Biophysical society-51th annual meeting, Baltimore, EEUU.(Marzo 2007)

[31] G. Orta, M. Salazar, W. Gonzalez, C. Mascayano, N. Raddatz, E. Rosenmann,F. Gonzalez-Nilo, S. Brauchi, R. Latorre. Dissecting phosphatidylinositol 4,5-bisphosphate activation and thermosensation in Trp channels.Biophysical society-51thannual meeting, Baltimore, EEUU. (Marzo, 2007)

[32] I. Carvacho, W. Gonzalez, P. Orio, S. Brauchi, O. Alvarez, F. D. Gonzalez-Nilo, R.Latorre. External surface charge neutralization induces outward rectification on theCalcium- and Voltage- activated potassium channel BK.

[33] J. Henrıquez-Roman, C. Leygraf , H. Gil. A model of the interaction betweenorganicacid ion with oxidized metallic surfaces in presence of water molecules, ElectronicStated and Excitation on nanostructures. PASI-2007 Pan American Advanced StudyInstitute 2007. Zacatecas, Mexico, (Junio 2007)

[34] W. Orellana, Stability of finite single-walled carbon nanotubes adsorbed on Si(001),American Physical Society Meeting, New Orleans, (Marzo 2008)

[35] G. Gutierrez, High pressure behavior of amorphous Al2O3: a molecular dynamics study,NanoTech 2007, Santa Clara, EE. UU, Mayo 2007.

[36] G. Gutierrez, S. Davis, Structural, dynamic and electronic properties of amorphousAl2O3: abinitio molecular dynamics calculations, American Physical Society Meeting,New Orleans, (Marzo 2008)

[37] G. Gutierrez, E. Valdebenito, S. Davis, Heat diffusion in a classical Heisenberg chain,American Physical Society Meeting, New Orleans, (Marzo 2008)

[38] W. Orellana, Fe-porphyrins attached to single-walled carbon nanotubes: Electronicand dynamical properties from ab initio calculations. IFSC Universidade de Sao Paulo,Brazil, August 2010.

[39] W. Orellana, Fe-porphyrins adsorbed on single-walled carbon nanotubes for hetero-geneous catalysis. American Physical Society 2010 March Meeting. Portland, USA,March 2010.

[40] Vibrational properties of gamma alumina, con C. Loyola y E. Menendez,poster en CCP5 “Methods in Molecular Simulation Summer School2008”(http://www.ccp5.ac.uk/SSCCP5/main.html) del 6-15 de julio de 2008 enSheffield, Inglaterra.

[41] Germania under pressure, con J. Peralta, poster en CCP5 ”Methods in MolecularSimulation Summer School 2008”(http://www.ccp5.ac.ukgxz/SSCCP5/main.html) del6-15 de julio de 2008 en Sheffield, Inglaterra.

[42] Vibrational properties of gamma alumina, con C. Loyola y E. Menendez, poster en 29thInternational Conference on the Physics of Semiconductor, del 21 julio al 1 de Agosto2008 en Rio de Janeiro, Brasil (http://www.icps2008.org).

[43] Germania under pressure, con J. Peralta, poster en 29th International Conference onthe Physics of Semiconductor, del 21 julio al 1 de Agosto 2008 en Rio de Janeiro, Brasil(http://www.icps2008.org)

[44] Ab-initio molecular dynamics study of amorphous CdTeOx alloys, poster presentadapor E. Menendez en 29th International Conference on the Physics of Semiconductor,del 21 julio al 1 de Agosto 2008 en Rio de Janeiro, Brasil (http://www.icps2008.org)

[45] Ab initio study of Au/CdSe Schottky barriers, poster, Menendez en 29th InternationalConference on the Physics of Semiconductor, del 21 julio al 1 de Agosto 2008 en Riode Janeiro, Brasil (http://www.icps2008.org)

[46] Germania under pressure, con J. Peralta, Poster en Latin American School in Compu-tational Materials Science, ICTP-UChile-UNAB, Santiago, Enero2009.

[47] Vibrational properties of gamma alumina, con C. Loyola y E. Menendez, Poster en LatinAmerican School in Computational Materials Science, ICTP-UChile-UNAB, Santiago,Enero2009.

[48] W. Orellana, Stability and bonding properties of finite single-walled carbon nanotu-bes adsorbed on Si(001). 6th Workshop of Computational Chemistry and MolecularSpectroscopy, Punta de Tralca, Chile, (October 2008).

[49] W. Orellana, Fe13 clusters adsorbed along Bi nanolines on H/Si(001), 19 InternationalConference on the Physics of Semiconductors, Rio de Janeiro, Brazil, (August 2008).

[50] Igor Ruiz-Tagle and W. Orellana, Theoretical investigation of Fe-phthalocyanine andFe-porphyrin adsorbed on single-wall carbon nanotubes. 6th Workshop of Computatio-nal Chemistry and Molecular Spectroscopy, Punta de Tralca, Chile, (October 2008).

[51] D. Laroze, J. Martinez-Mardones, Amplitude equation for stationary convection in aviscoelastic magnetic fluid. MEDYFINOL08, Punta del Este, Uruguay. (Talk)

[52] M. G. Clerc, S. Coulibaly, D. Laroze, Dynamical Behavior of a magnetic wire. MEDY-FINOL08, Punta del Este, Uruguay. (Poster)

[53] P. Diaz, D. Laroze, L.M. Perez, Configurational Temperature for a Dipolar MagneticChain. MEDYFINOL08, Punta del Este, Uruguay. (Poster)

Contributed talks and posters, National Conferences

[54] D. Laroze, L.M.Perez, P. Diaz, Classical Spin Dynamics of four in interacting magneticparticles on a square LAWNP07, Arica, Chile (Oct. 2007)

[55] D. Laroze, A. Toloza, C. Mendoza, J. Martınez-Mardones. Amplitude equation forstationary convection in a rotating binary ferrofluid LAWNP07, Arica, Chile (Oct.2007)

[56] M. G. Clerc, S. Coulibaly and D. Laroze, Amplitude equation for a parametricallyforced magnetic wire LAWNP07, Arica, Chile (Oct. 2007)

[57] M. G. Clerc, S. Coulibaly and D. Laroze, Localized states beyond asymptotic parame-trically driven amplitude equation LAWNP07, Arica, Chile (Oct. 2007)

[58] G. Aguero, G. Gutierrez, D. Laroze, G. Sanchez, Transferencia de Calor entre dossolidos con geometrıa cilındrica, Emfimin07, Santiago, Chile (Nov. 2007).

[59] M. G. Clerc, S. Coulibaly, P. Diaz, D. Laroze and L.M. Perez, Dynamical Behavior ofmagnetic system Instabilities and Nonequilibrium Structures XI, Vina del Mar, Chile(Dic. 2007)

[60] M. G. Clerc, S. Coulibaly and D. Laroze, Localized states beyond asymptotic para-metrically driven amplitude equation Instabilities and Nonequilibrium Structures XI,Vina del Mar, Chile (Dic. 2007)

[61] P. Diaz, D. Laroze, L.M.Perez, Classical Spin Dynamics of four in interacting magneticparticles on a square Instabilities and Nonequilibrium Structures XI, Vina del Mar,Chile (Dic. 2007)

[62] D. Laroze, Localization and domain wall in magnetic wires, Mini workshop on Magne-tism, Renaca, Chile (Abr. 2008)

[63] W. Orellana, Structural and electronic properties of nanostructures from ab initio,Workshop on Free Energy Calculations Applied to Biomolecules, Talca, Chile (Nov.2007)

[64] W. Orellana, Estabilidad y propiedades de enlace de nanotubos de carbono de unapared depositados sobre la superficie de silicio (001), VI Encuentro de Modelos Fısicosy Matematicos en Ingenierıa, Santiago, Chile (Nov. 2007).

[65] M. Vidal, H. Urbina, W. Gonzalez, I. Carvacho, y R. Latorre, F. Gonzalez-Nilo, Cavi-dad intracelular del canal de potasio Hslo: rol de residuos hidrofobicos en la conduc-tancia de iones potasio. XXX Reunion Anual de la Sociedad de Bioquımica y BiologıaMolecular de Chile. Chillan, Chile. (Sep. 2007).

[66] D. Genova, F. Gonzalez-Nilo Fernando, F. Sepulveda, M.Niemeyer, Analisis Termo-dinamico del Sensor de pH Presente en el Canal de Potasio task-2. XXX ReunionAnual de la Sociedad de Bioquımica y Biologıa Molecular de Chile. Chillan, CHILE(Sep. 2007).

[67] H. Urbina, I.Tobar, Cardemil, F. Gonzalez, Rol Estructural del Residuo R457 en laafinidad de ADPDP en Carboxiquinasa Fosfoenolpiruvica de Saccharomyces Cerevi-siae. XXX Reunion anual de la Sociedad de Bioquımica y Biologıa Molecular de Chile.Chillan, Chile (Sep. 2007).

[68] A. Vergara, H. Urbina, C. Gonzalez, M. Holmgren, F. Gonzalez-Nilo, Inactivacion delCanal de Potasio Shaker. XXX Reunion Anual de la Sociedad de Bioquımica y BiologıaMolecular de Chile. Chillan, Chile (Sep. 2007).

[69] C. Navarro, H. Urbina, T. Bar-Magen, C. Mascayano, J. Patton, F. Gonzalez-Nilo Re-conocimiento de RNA en RNA Polimerasa de Rotavirus RNA-Dependiente. DinamicaMolecular Dirigida y Simulacion de Acoplamiento. XXX Reunion Anual de la Sociedadde Bioquımica y Biologıa Molecular de Chile. Chillan, Chile (Sep. 2007).

[70] F. Gonzalez Nilo Base de datos para estructura de Nanobiologıa. IV SimposioArgentino-Chileno de Polımeros. Vina del Mar, Chile (Dic. 2007).

[71] M. Saavedra, J. Caballero, F. Gonzalez Nilo. Estudio de interaccion poli-e- caprolac-tona/ciclodextrina mediante Simulacion Molecular. IV Simposio Argentino-Chileno dePolimeros. Vina del Mar. Chile. (Dic.2007)

[72] J. Caballero, F. Gonzalez Nilo. Estudio de la formacion del complejo progesterona-b-ciclodextrina usando dinamica molecular dirigida. IV Simposio Argentino-Chileno dePolimeros. Vina del Mar. Chile. (Dic.2007)

[73] J. Henrıquez-Roman, C. Leygraf, Interaction of carboxilate ion on Metallic oxidedsurface representation in presence of water molecules. XXVII Jornadas Chilenas deQuimica. Chillan, Chile. (Oct. 2007)

[74] J. Henrıquez-Roman, E. Gonzalez, L. Padilla-Campos, M. A. Paez, Aminoacidos comoinhibidores de la corrosion de cobre en medio acido clorhıdrico. Una mirada experi-mental y teorica. XXVII Jornadas Chilenas de Quımica. Chillan, Chile. (Oct. 2007)

[75] E. Menendez, Simulacion de la estructura de vidrios de CdTeOx. VI Encuentro deModelos Fısicos y Matematicos en Ingenierıa, Santiago, Chile (Nov. 2007)

[76] C. Loyola, G. Gutierrez y E. Menendez, Estudio a nivel atomico de las propiedades vi-bracionales de γ-Al2O3. VI Encuentro de Modelos Fısicos y Matematicos en Ingenierıa,Santiago, Chile (Nov. 2007)

[77] J. Peralta, Las Palmeras Molecular Dynamics: Dinamica Molecular Flexible y Modula,VI Encuentro de Modelos Fısicos y Matematicos en Ingenierıa, Santiago, Chile (Nov.2007)

[78] E. Valdebenito, Transporte en sistemas magneticos, VI Encuentro de Modelos Fısicosy Matematicos en Ingenierıa, Santiago, Chile (Nov. 2007)

[79] G. Gutierrez, C. Esparza, Calculo de momentos de inercia mediante sumas finitas, XXICongreso de Educacion en Ingenierıa, SOCHEDI, Santiago, octubre 2007

[80] G. Gutierrez, Estudio teorico de (nano)materiales, Encuentro de Fısica teorico-experimental, FCFM, U. de Chile, Julio 2007

[81] G. Gutierrez, Heat transfer in magnetic systems, Escuela de nanoestructuras, UTFSM,Valparaıso, Enero 2008

[82] Fractura de argon por medio de ondas de choque, con C. Loyola, charla Simposio So-ciedad Chilena de Fısica, Valparaıso, Nov. 2008.

[83] Germania a altas presiones, con J. Peralta, poster en II Escuela de nanoestructuras,UTFSM, Valparaıso, Enero 2009.

[84] Structural and vibrational properties of amorphous GeO2 under pressure: a moleculardynamics study, con J. Peralta. Charla Simposio Sociedad Chilena de Fısica, Valpa-raıso, Nov. 2008.

[85] D. Laroze, J. Martinez-Mardones, L. M Perez and Y. Rameshwar, Amplitude equationfor stationary convection in a rotating binary ferrofluid, SOCHIFI08, Valparaiso, Chile.(Talk)

[86] Calculo y representacion grafica de sumas finitas mediante gnuplot, con C. Esparza,XXII Congreso Chileno de Educacion en Ingenierıa, La Serena, Octubre 2008.

[87] Igor Ruiz-Tagle and W. Orellana, Theoretical investigation of Fe-phthalocyanine andFe-porphyrin adsorbed on single-wall carbon nanotubes, XVI Simposio Chileno de Fi-sica, Valparaiso, (November 2008).

[88] W. Orellana, Self-organized Fe nanowires on a semiconducting surface: Structural,electronic and magnetic properties from ab initio, XVI Simposio Chileno de Fısica,Valparaiso, (Noviembre 2008).

[89] W. Orellana, G. Gutierrez, Stability and dynamical properties of Ti2SiC3(0001) at hightemperatures: First-principles calculations. XVII Simposio Chileno de Fısica, Pucon,Chile, Noviembre 2010.

[90] C. Loyola, G. Gutierrez, Impactos a hipervelocidad: simulacion por medio de dinamicamolecular,

[91] N. Amigo, C. Loyola, S. Davis, G. Gutierrez, Impactos supersonicos de nano-proyectilesde cobre: un estudio mediante dinamica molecular, XVII Simposio Chileno de Fısi-ca, Pucon, Chile, Noviembre 2010. XVII Simposio Chileno de Fısica, Pucon, Chile,Noviembre 2010.

[92] F. Gonzalez-Cataldo, F. Gonzalez-Wasaff, Y. Navarrete, G. Gutierrez, Rebote de unaesfera sobre una superficie: estudio a nivel atomico, XVII Simposio Chileno de Fısica,Pucon, Chile, Noviembre 2010.

[93] F. Gonzalez-Cataldo, J. Peralta, C. Loyola, S. Davis, Visualizacion 3D en tiempo realpara dinamica molecular clasica: LPMD y LPVISUAL, XVII Simposio Chileno deFısica, Pucon, Chile, Noviembre 2010.

[94] C. Rioseco, J. Rojas, N. Amigo, G. Gutierrez, S. Davis, Estudio a nivel atomico de lacolision inelastica entre dos nano-objetos metalicos, XVII Simposio Chileno de Fısica,Pucon, Chile, Noviembre 2010.

[95] J. Peralta, G. Gutierrez, W. Orellana, Propiedades elasticas y electronicas del compues-to laminar Ti2GaN sometido a presion: estudio de primeros principios, XVII SimposioChileno de Fısica, Pucon, Chile, Noviembre 2010.

Visits from abroad and from other parts of Chile

[1] Prof. S. Saxena, de Florida International Univ, Marzo 2007 (1 semana), visita FC, Uch.

[2] Dr. Norge Cruz, Universidad de Sevilla, Espana, Noviembre (4 semanas), visita FC,Uch.

[3] Dr. Chris Chipot, CNRS, Nancy, Francia, Noviembre 2007 (1 semana).

[4] Prof. R. Lagos, U. Estdual Paulista, Rio Claro, Brasil, Enero 2008 (1 semana), visitaFC, Uch.

[5] Visit of Sergio Davis, PhD student of the KTH, Sweden, and member of Group of Na-noMaterials. Sergio, who visited us in two opportunities, is one of the leader developersof the Las Palmeras MD package, and also help with cluster installation and gave a mi-nicourse of Python (NanoTaller de Python). June 2007, July 2008, and December2008-January 2009. Now, he is incorparated at GNM as a FONDECYT postdoc.

[6] Visit of Prof. Carlos Camacho (University of Pittsburgh). Delivered a set of Lectureson Physics of Proteins from 11-14 August 2008, 4.5 hrs. 18 persons (PhD student, un-dergraduate and researchers) attended. Conversation on the topic of protein submittedunder shock waves with Prof. G. Gutierrez and Dr. M. Branes.

[7] Visit of Prof. Roberto Miwa, Universidade Federal de Uberlandia, Brasil, from 29 Sept.- 3 Oct. 2008. Collaboration with Prof. W. Orellana on ab-initio calculation of metal-oxides surfaces.

[8] Visit of Dr. Raul Cachau, National Cancer Institute-USA: 2 working visits at CBSB,U. Talca, November 14-20, 2008 and April 5 to 11, 2009. Both visits were related tothe nanobiology project led by Prof. D. Gonzalez. From these visits, we expect thewriting of at least 2 articles during the 2009 year and the co-tutor of 2 PhD theses and2 or 3 under-graduate thesis. It has also initiated the development of a laboratory ofcrystallography of proteins and of electronic microscopy, both initiatives are providedwith the support of the SAIC-NCI.

[9] Visit of Prof. Giorgios Tsironis, Dept. Physics, University of Crete, Greece, from 11-19 nov. 2008. Seminars at Dept. of Physics, Simposio Chilean Physical Society andconversations on topics of statistical physics. Possible collaboration on calculation ofbreathers in solid: Si, Ge by ab-initio calculations (see Appendix Sec.IV).

[10] Visit of Camilo Valencia Balvin, PhD Student of the University of Antioquia, to acquirepractice on Molecular dynamics calculation, under Prof. G. Gutierrez. See the reportand the manuscript to be submitted on the topic of structural and dynamical propertiesof CuZr amorphous alloy . This visit is related to the one of Dr. Jorge Osorio-Guillen,and is the first step in our collaboration project. From Nov. 2008 to Jan 2009.

[11] Visit of Prof. Jorge Osorio-Guillen, from Dept. Physics, Universidad de Antioquia,Medellin, Colombia, from 18-ene to 31 ene 2009. Participation in the LatinamericanSchool on Computational Materials Science as Invited Speaker and collaboration onbulk metallic glasses with G. Gutierrez.

[12] Visit of Dr. Marcos Sotomayor, postdoctoral fellow at Harvard University, betweenDecember 12 and January 3, 2009. He taught courses Methods of Molecular Simulation,Advanced Course on Free Energy Calculations. Theory and Practice at CBSM-Talca.Additionally, he discussed cooperation issues. The course took 45 hours, 5 days. Dr.Sotomayor also gave a lecture on Protein Mechanics at the Group of NanoMaterials,Universidad de Chile., 28 Dec. 2008.

[13] Dr. Chris Chipot came from Universite de Nancy, France, between December 12 and 19of 2008. He taught courses Methods of Molecular Simulation, Advance Course on FreeEnergy Calculation: Theory and Practice at CBSM-Talca. The course had 45 hours,5 days. During the visit of Dr. Chipot coordinated two under-graduate thesis and tworesearch units for students of the Ph.D. program in Applied Science.

[14] Visit of Javier Fernandez Sanz, University of Seville. This is a long term collaboration,initiated in 2005, with Prof. E. Menendez, and presently focused on the computationof surface and interface properties. He also gave a lecture at the Latinamerican Schoolon Computational Materials Science as Invited Speaker.

[15] Visit of Profs. Dr. E. Holstrom and Dr. R. Lizarraga of Universidad Austral at Valdivia,to U. of Chile. 18-24 de enero 2009. They are now permanent collaborators of ourProject Anillo, and together Prof. Menendez, are working with Prof. A. Amezaga onalculation of XPS spectra (see below). .

[16] Visits of Prof A. Amezaga, from Universidad Austral at Puerto Montt. Work on thecalculation of core level shifts with Prof. Menendez. He is a permanent collaborator ofthe Anillo, and plan to begin his PhD studies at Universidad de Chile. He is comingto Santiago twice a month.

[17] Visit of M. C. Alexander Odriazola Diaz, researcher at the Instituto de Cibernetica,Matematica y Fisica de Cuba from 2 April- 30 May, to work on Raman calculation ofsemiconductor quantum dots with Professor Eduardo Menendez.

[18] Dr. Norge Cruz, de la Universidad de Sevilla, Espana, 6-15 de november de 2009.Gave a short course on Methods for Materials Simulations, and woerked on topics ofimpurities in titanium dioxide surfaces and aminoacid desposited on the same surfaces.

[19] Dr. Jorge Kohanoff, (http://titus.phy.qub.ac.uk/group/Jorge ) University of Belfast.17-21 August 2009. He taught a short course “Simplified methods in electronic structurecalculations”. The content of this course is the Chapter 10 of his book “Electronicstructure calculations for Solids”.

[20] Dr. Volker Eyert, del Center for Electronic Correlations and Magnetism, Institute forPhysics, University of Augsburg, week 28 de September 2009. Talk: All-Electron Full-Potential Calculations at O(ASA) Speed.

[21] Dr. Luis Montero, Faculty of Chemitry, University of Havana, 28/mar/2010-3/abr/2010. This visit is related with the work on electronic structure calculationsin large molecules and nanostructures using approximate semi empirical wavefunctionmethods (CNDOL). He gave talk to the group of nanomaterials and discussed topicson the calculations of uantum dots.

[22] Dr. Jose Manuel Garcia de La Vega, Faculty of Science, Autonomous University ofMadrid 30/mar/2010 al 2/abr/2010. This visit is related to the visit of Dr. Montero.Both visits were supported by an external project of international cooperatiion. Hegave a talk to the Department of Physics.

[23] Dra. Maria E. Fuentes, Fac. Chemistry, Autonomous University of Chihuahua, Mexi-co. 28/mar/2010-5/abr/2010. Related to the visits of Drs. Montero and Garcia de laVega. Also worked on the properties of hydroxiapatite, and simulations of ferroelectricmaterials.

[24] Dr. Alain Delgado Gran. Centro de Estudios Aplicados al Desarrollo Nuclear, Cuba.28/ene/2010-8/mar/2010. We came to make applications of the CNDOL method to theelectronic structure of quantum dots. His visit was supported partially by the Anilloand by a grant from the Thirld World Academy of Sciences (http://www.twas.org).

Research visits to other institutions

[1] G. Gutierrez, visited the Collaboratory for Advanced Computing and Simulations(CACS), University of Southern California, May 2007.

[2] E. Menendez, Universidad de Sevilla, Octubre 2007. He was invited under a projectmanaged in Sevilla from the Agencia Espanola de Cooperacion Internacional. In thisoccasion he engaged in a research on impurities in a titanium dioxide crystal.

[3] G. Gutierrez y W. Orellana, Cesmec, FIU, Marzo 2008

[4] Prof. D. Gonzalez was invited by Ministry of Education and Science of Germany toattend to HannoverMesse 2008, showcase for industrial technology, Hannover, Germanyand also is member of the commission for collaboration Chile-NCI of ministry of Healthof Chile.

[5] Dr. J. Alzate was invited by Ministry of Education and Science of Germany to attendto HannoverMesse 2009, showcase for industrial technology, Hannover, Germany thattook place during the recent month of April.

[6] Prof. E. Menendez visited the group of Prof. Javier Fernandez Sanz, Department ofPhysical Chemistry, University of Sevilla. This is a long term collaboration initiatedin 2005, and presently focused on the computation of surface and interface properties,particularly, working on the calculation of Schottky barrier heights. 23/nov to 22/decof 2008.

[7] Prof. E. Menendez visited Prof. M. E. Fuentes Montero, at the University of Chihuahua,from 12 to 25 Feb 2009. The program consisted in teaching a tutorial course on thesimulation package Quantum-ESPRESSO and to explore cooperation in topics of ma-terials science. From this visit the following lines appeared as cooperation projects tobe delivered in the next year: Computation of elastic properties of hydroxyapatite. Thisis a mineral that composes most the bones and dental enamel. Computation of excitedstates and optical properties of carbon nanotubes and quantum dots using quantumchemistry semi-empirical methods.

[8] Prof. E. Menendez visited the Autonomous University of Madrid, from 27/january to 3February 2010. He visited the group of Prof. Jose Garcıa de la Vega in the framework of

the project of computation of excited states and optical properties of carbon nanotubesand quantum dots using quantum chemistry semi-empirical methods.

International and national grants: awarded and applicated

[1] Grant Cooperacion internacional para simulacion de nanobio ACI-52, Ch$20 000,-,awarded in Janaury 2008. This grant has played a key rol in our international activitiesand collaboration.

[2] PROYECTOS DE COOPERACION INTERUNIVERSITARIA UAM-SANTANDERcon America Latina, application submitted, April 2009, led by E. Menendez y W.Orellana. Title: Estados electronicos de grafenos, nanotubos de carbono, fulerenos ynanocristales con posibles dopantes Director: Jose Manuel Garcia de la Vega, Deptode Quimica Fisica Aplicada, Universidad Autonoma de Madrid. Participation: UAM,UChile, UNAB-Chile, U. Autonoma de Chihuahua-Mexico, UHabana-Cuba, 2009-2010

[3] Walter Orellana, Principal Investigator of the project: FONDECYT regular (2009-2013) Theoretical investigation of nanoscale catalyst based on metallic nanoparticlesand metallo-macrocyclic complexes

[4] Daniel Laroze, Principal Investigator Proyecto Fondecyt Iniciacion, (2008-2010) NON-VARIATIONAL EFFECTS IN THE PARAMETRICALLY DRIVEN QUASIREVER-SIBLE SYSTEMS

[5] MAT2005-1872: Simulacion de catalizadores: reactividad de superficies de TiO2 y SnO2

dopadas con C, N y Sb, interfase metal/soporte, y propiedades electronicas de sistemasde tipo colorante/soporte. Director: Javier Fernandez Sanz; participation: U. de Sevilla-Espana, U. de Chile, 2008-2011

[6] Agencia Espnola de Cooperacion Internacional (PCI/2006) Director: Norge Cruz peri-dodo: 2006

Participations in schools

[1] E. Menendez, Spring College on Water in Physics, Chemistry and Biology, Trieste,Italia (Apr. 2007)

[2] C. Loyola, E. Valdebenito, J. Peralta, Minicurso de Nanomecanical, Santiago, Chile(Jun 2007)

[3] C. Loyola, E. Valdebenito, J. Peralta, Minisimposio de Fısica Teorico-Experimental,Fısica Nuclear, Fısica de Sistemas Nanoscopicos y Nanomateriales, Santiago, Chile (Jul2007)

[4] C. Loyola, J. Peralta, Segundo Congreso Nacional de e-ciencia, Santiago, Chile (Sep.2007

[5] C. Loyola, E. Valdebenito, J. Peralta, Escuela de Nanoestructuras, Valparaıso, Chile(Ene. 2008)

[6] C. Loyola, E. Valdebenito, J. Peralta, Minicurso sobre Respuesta Mecanica de Mate-riales Desordenados, Santiago, Chile (Abr 2008)

[7] G. Gutierrez, Diplomado en biologıa celular y molecular, Facultad de Ciencias, Univ.De Chile, Abril-Diciembre 2007

[8] W. Orellana, Diplomado en biologıa celular y molecular, Facultad de Ciencias, Univ.De Chile, Abril- Diciembre 2007

[9] C. Loyola and J. Peralta, CCP5 “Methods in Molecular Simulation Summer School2008” (http://www.ccp5.ac.uk/SSCCP5/main.html) 6-15 de july 2008 in Sheffield,United Kingdom.

9

VI. TRAINING OF STUDENTS, POST-GRADUATES AND YOUNG RESEARCHERS This section consists mainly in the following table. Nevertheless, if there are special highlights that you consider should be mentioned in addition to the information required, please refer to Section III (RESEARCH RESULTS) making specific reference to the student or young researcher work.

No. Name of student Gender

(M/F) Thesis Title

Type of degree

1

Degree denomination

Status2 Tutor's name

Category in the Project

University that gives the degree

1 Nicolas Viaux M Computer simulation of materials

1 Resaerch Unit, 4th year student Physics

F-2008 Eduardo Menendez Titular University of Chile

2 Varinia Bernales F Introduction to materials simulation

1 Summer practice, Chemistry student

F-2008 Eduardo Menendez Titular University of Chile

3 Erick Nicolas Perez M Introduction to materials simulation

1 Summer practice, Chemistry student

F-2008 Gonzalo Gutierrez Director University of Chile

4 SAMUEL MORALES NAVARRO

M

Análisis mediante simulación molecular de los determinantes estructurales de la activación dependiente de volta je en canales de potasio de Arabi- dopsis thaliana

1 Biochemist F-2008 Danilo González Nilo Titular Catholic University of Chile

5 RODRIGO URZUA LEIVA

M

Estudio de la interacción de las cadenas laterales de los aminoáci- dos que conforman el oligopeptido RGD sobre superficies de TIO2

1 Bioinformatics Engineer

F-2009

Jaime Henríquez Roman Eduardo Menendez Proupin

Associate Titular

University of Talca

6 VALERIA MARQUEZ MIRANDA

F

Caracterizaci´on del rol del residuo F380 en la conductancia a traves del canal de potasio hSlo

1 Bioinformatics Engineer

F-2008 Danilo González Nilo Titular University of Talca

1 Undergraduate degree or professional title (1); Master or equivalent (2); Ph.D. or equivalent (3). 2 Finished (F-year) or In Progress (IP)

10

7 CRISTELL NAVARRO NAVARRO

F

Estudio del perfil de Energıa Libre de iones de K+ en el canal de potasio TASK-2

1 Bioinformatics Engineer

F-2008 Danilo González Nilo Titular University of Talca

8 WALDO ACEVEDO CASTILLO

M

Caracterización de la interacción entre cluster de Aun y amino acidos azufrados

1 Bioinformatics Engineer

F-2009

Danilo Gonzáalez Nilo Jaime Henríquez Roman

Titular Associate

University of Talca

9 XAVIERA LOPEZ CORTES

F

Estudio in- silico de la descarboxilación del oxaloacetato en fosfoenolpiruvato carboxiquinasa de Saccharomyces cerevisiae

1 Bioinformatics Engineer

F-2008

Danilo Gonzáalez Nilo Jaime Henríquez Roman

Titular Associate

University of Talca

10 ARIELA VERGARA JAQUE

F

Structural and Electrostatic properties in the permeation pat- hway of Shaker potassium channel and the mutants P475D and P475Q

1 Bioinformatics Engineer

F-2008 Danilo González Nilo Titular University of Talca

11 Diego Cohen M Molecular dynamics of cluster collisions

1 Research Unit, 4th year Physics student

F-2009 Claudia Loyola G. Gutierrez

PhD student Director

University of Chile

12 Yasmin Navarrete F Visualization for the LPMD code

1 Research Unit, 4th year Physics student

F-2009 Joaquin Peralta G. Gutierrez

PhD student Director

University of Chile

13 Pablo Ravelo M Visualization for the LPMD code

1 Research Unit, 3rd year Physics student

F-2009 Joaquin Peralta G. Gutierrez

PhD student Director

University of Chile

14 Rodrigo deNegri M Molecular dynamics of hypervelocity impact

1 Research Unit, 3rd year Physics student

F-2009 Claudia Loyola G. Gutierrez

PhD student Director

University of Chile

15 Daniela Riuz F Ab initio clculations 1 4th year chemistry un dergraduate

IP E. Menendez Titular University of Chile

16 Ricardo Osorio Pulgar M Elastic constants of hydroxiapatite,

1 training, 2nd year student of physics

F-2010 E. Menendez Titular University of Chile

17 Jorge Mansilla Sierra M

Interaction of the amino acids of the RGD sequence with titanium dioxide surfaces

1 Engineer in Bioinformatics

F-2010 E. Menendez Titular University of Talca

18 Mauricio Franco Cisterna M Introduction to atomistic materials simulation

1 Research unit, 3rd year student of Physics

F-2010 E. Menendez Titular University of Chile

11

19 Nicolas Amigo M Hypervelocity impact 1 Research unit, 4rd year student of Physics

F-2009 Gonzalo Gutiérrez Director University of Chile

20 Diego Contreras M

Mechanical properties of proteins by computer simulation techniques

1 Research unit, 3rd year student of Physics

F-2010 Gonzalo Gutiérrez Director University of Chile

21 Felipe Gonzalez Wassaf M

Bouncing of a cube under gravity: molecular dynamics simula- tion

1 Research unit, 3rd year student of Physics

F-2010 Gonzalo Gutiérrez Director University of Chile

22 Camila Rioseco F Impact of nanosphere: molecular dynamics simulation

1 Research unit, 3rd year student of Physics

F-2010 Gonzalo Gutiérrez Director University of Chile

23 José Rojas M Impact of nanosphere: molecular dynamics simulation

1 Research unit, 3rd year student of Physics

F-2010 Gonzalo Gutiérrez Director University of Chile

24 Eduardo Valdebenito M 2 Master in Science IP Gonzalo Gutiérrez Director University of Chile

25 Fernando Cuturrufo M 2 Master in Physics F-2009 Gonzalo Gutiérrez Director University of La Serena

23 Omar Suarez M

PROPIEDADES ESTÁTICAS Y DINÁMICAS DE NANOESTRUCTURAS MAGNÉTICAS INTERACTUANTES CON GEOMETRÍA CILÍNDRICA

2 Master in Physics

Patricio Vargas David Larozze

Associate

Universidad Federico Santa Maria

24 Marcelo Tuesta M 2 Magister en Educación Física

Jorge Cancino D. Laroze

Associate

Universidad Mayor

25 Joaquin Peralta M

Physical properties of new materials by means of computer simulation methods

3 Phd in Physics F-2010 Gonzalo Gutiérrez Director University of Chile

26 Claudia Loyola F

Study at atomic level of nanostructured materials by means of computer simulation methods

3 Phd in Physics F-2010 Gonzalo Gutiérrez Director University of Chile

27 Felipe González M

Materiales en condiciones extremas: aplicaciones al estudio del interior de planetas

3 Phd in Physics IP Gonzalo Gutiérrez Director University of Chile

12

solares y extrasolares

28 Igor Ruiz-Tagle M

Catalytic properties of metallomacrocycles attached to carbon nanos- tructures: A theoretical study

3 PhD in Chemistry IP Walter Orellana Associate Universidad Andres Bello

29 Paula Escobar F 3 Phd in Physics IP Eduardo Menendez Titular University of Chile

30 DANIEL AGUAYO VILLEGAS

M

Insights into role of the induced conformational changes in the VP1/VP2/RNA complexes on the rotavirus SA11 RNA replication.

3 PhD Program of Applied Science

IP Danilo González Nilo Titular University of Talca

31 WENDY GONZALEZ DIAZ

F

Structural, molecular and phenotype characterization of vol- tage, pH and abiotic stress regulation in KAT1 and SKOR channels of Arabidopsis thaliana

3 PhD Program of Biotechnology

F-2009

Danilo González Nilo Simon Ruiz

Titular

University of Talca

32 HEGALY MENDOZA VILCHES

F

Implementation of chemical conditions for protein crystalliza- tion using chips based on semiconductors

3 PhD Program of Applied Science

IP Raul Cachau Associated University of Talca

33 JULIO CABALLERO M

Models and molecular dynamic simulations of dendrimer-related systems

3 PhD Program of Applied Science

IP Danilo González Nilo Titular University of Talca

34 Laura Milena Perez F

Theoretical studies on the dynamical behaviours of magnetic system

3 Dr. in Materials Science

IP Stella Ordóñez D. Laroze

Associate

University of Santiago

35 Pablo Diaz M Spatiotemporal dynamics of Bose-Fermi mixtures

3 Dr. in Physics IP Iván Schmidt David Larozze

Associate

Universidad Federico Santa Maria

36 DANIELA GERALDO F PAMAM-QDs based nanocomposite for

4 Postodoctoral F-2009 Danilo González Nilo Titular University of Talca

13

fluorescent labelling of early stage cancer

37 PABLO ENCINA M

STUDY OF BIOLOGICAL SYSTEMS UNDER THE EFECT OF SHOCK WAVES

4 Postodoctoral IP Gonzalo Gutiérrez Director University of Chile

38 SERGIO DAVIS M

STUDY OF MELTING OF SOLIDS USING ATOMISTIC COMPUTER SIMULATION TECHNIQUES

4 Postodoctoral IP Gonzalo Gutiérrez Director University of Chile

39 GERMAN MIÑO M

MECHANICAL AND COOPERATIVE PROPERTIES OF DIMERIC PROTEINS. A COMPUTATIONAL SIMULATION STUDY

4 Postdoctoral IP Gonzalo Gutiérrez Director University of Chile

40 Fernanda Lopez F training in ab initio calculations

3 PhD in chemistry IP Antonio Galdamez Eduardo Menendez

Titular University of Chile

N

Note: Please consider all the students registered in previous progress reports.

VII. PUBLICATIONS

Papers Abril 2007-2010

[1] Magnetostatic interactions between two magnetic wires, R. Picin, D. Laroze, M. Knobel,P. Vargas, M. Vazquez, Europhysics Letters 78, 67004 (2007).

[2] Thermal Convection in a Rotating Binary Maxwell liquid Mixture, D. Laroze, J. Mar-tinez Mardones, J. Bragard, European Physical Journal S.T. 146, 291 (2007).

[3] A detailed analysis of dipolar interactions in arrays of bi-stable magnetic nanowires,D. Laroze, J. Escrig, P. Landeros, D. Altbir, M. Vazquez, P. Vargas, Nanotechnology18, 415708 (2007)

[4] On the probably transition of a quantum dot in a time dependent magnetic field, D.Laroze, R. Rivera, Revista Mexicana de Fısica S 53, 112 (2007).

[5] Realistic rotating convection in a DNA suspension, D. Laroze, J. MartinezMardones,J. Bragard, C. PerezGarcia Physica A 385, 433 (2007).

[6] Dissection of the components for PIP2 activation and thermosensation in TRP chan-nels, S. Brauchi, G. Orta, C. Mascayano, Salazar M, N. Raddatz, H. Urbina, E. Ro-senmann, F. Gonzalez-Nilo, R. Latorre, Proc Natl Acad Sci U S A 104, 10246 (2007).

[7] In-silico nanobio-design. A new frontier in computational biology, R.E. Cachau, FDGonzalez-Nilo, O.N. Ventura, M.J. Fritts, Curr Top Med Chem. 7, 1537 (2007).

[8] Molecular in situ studies of atmospheric corrosion, C. Leygraf, J. Hedberg, P. Qiu, H.Gil, J. Henriquez, and C. M. Johnson, Corrosion 63, 715 (2007).

[9] Classical spin dynamics of four interacting magnetic particles on a ring, D. Laroze, L.M. Perez, Physica B 403, 473 (2008).

[10] Dynamics of two interacting dipoles, D. Laroze, P. Vargas, C. Cortes, G. Gutierrez,Journal of Magnetism and Magnetic Materials 320, 1440 (2008).

[11] Intrinsic electrostatic potential in the BK channel pore: role in determining single chan-nel conductance and block, I. Carvacho, W. Gonzalez, Y.P. Torres, S. Brauchi, O. Al-varez, F.D. Gonzalez-Nilo, R. Latorre, J. Gen. Physiol. 131, 147 (2008)

[12] 2D Autocorrelation, CoMFA, and CoMSIA modeling of protein tyrosine kinasesınhibi-tion by substituted pyrido[2,3-d]pyrimidine derivatives, J. Caballero, M. Fernandez, M.Saavedra, F.D. Gonzalez-Nilo, Bioorg. Med. Chem. 16, 810 (2008).

[13] A CoMSIA study on the adenosine kinase inhibition of pyrrolo[2,3-d]pyrimidine nucleo-side analogues, J. Caballero, M. Fernandez, F.D. Gonzalez-Nilo, Bioorg. Med. Chem.16, 5103 (2008).

[14] Localized states beyond asymptotic parametrically driven amplitude equation, M. G.Clerc, S. Coulibaly and D. Laroze, Physical Review E 77, 056209 (2008).

[15] Initial Atmospheric Corrosion of Zinc exposed to Formic acid, Investigated by in-situVibrational Sum Frequency Spectroscopy and Density Functional Theory calculations,J. Hedberg, J. Henriquez, S. Baldelli, M. Johnson, C. Leygraf, Journal of PhysicalChemistry C, 113, 2088-2095 (2008).

[16] Strength of polycrystalline coarse-grained platinum to 330 Gpa and of nanocrystallineplatinum up tu 70 Gpa from high-pressure x-ray diffraction data, A. K. Singh, H-P.Liermann,Y. Akayama, S. K.Saxena, and E. Menendez-Proupin, Journal of AppliedPhysics 103, 063524 (2008).

[17] Study of the interaction between progesterone and beta-cyclodextrin by electrochemicaltechniques and steered molecular dynamics. Caballero J, Zamora C, Aguayo D, YanezC, Gonzalez-Nilo FD. , J Phys Chem B. 112(33):10194-201. Aug 21 (2008). Epub 2008Jul 30.(ISI:4,086)

[18] Stability and bonding properties of finite single-walled carbon nanotubes adsorbed onSi(001), W. Orellana, Applied Physics Letters 92, 093109 (2008).

[19] Iron silicide wires patterned by Bi nanolines on the H/Si(001) surface: Spin-densityfunctional calculations, R.H. Miwa, W. Orellana and G.P. Srivastava, Physical ReviewB 78, 115310 (2008)

[20] Noncollinear magnetism in the high-pressure hcp phase of iron, Raquel Lizarraga, LarsNordstrom, Olle Eriksson, and John Wills, Phys. Rev. B 78, 064410 (2008)

[21] Dynamics of a rotating particle under a time-dependent potential: exact quantum solu-tion from the classical action, D. Laroze, G. Gutierrez, R. Rivera and J. Yanez, PhysicaScripta 78, 015009 (2008).

[22] Structural and vibrational properties of amorphous GeO2: a molecular dynamics study,J. Peralta, G. Gutierrez and J. Rogan, J. Phys.: Conden. Matter 20, 145215 (2008).

[23] Distinct roles of the last transmembrane domain in controlling Arabidopsis K+ channelactivity. Gajdanowicz P, Garcia-Mata C, Gonzalez W, Morales-Navarro SE, SharmaT, Gonzalez-Nilo FD, Gutowicz J, Mueller-Roeber B, Blatt MR, Dreyer I. New Phytol.182(2):380-91 (2009). Epub 2009 Jan 14(ISI:5,249)

[24] Shared and Group-Specific Features of the Rotavirus RNA Polymerase Reveal PotentialDeterminants of Gene Reassortment Restriction. S. M. McDonald, D. Aguayo, F. D.Gonzalez-Nilo, and J. T. Patton, Journal of Virology, , p. 000 Vol. 83, No. 12. 0022,June 2009 (ISI:5,332)

[25] Docking and quantitative structure-activity relationship studies for sulfonyl hydrazidesas inhibitors of cytosolic human branched-chain amino acid aminotransferase. Caba-llero J, Vergara-Jaque A, Fernandez M, Coll D. Mol Divers. Apr 7(2009)(ISI: 2,708)

[26] A computational ONIOM model for the description of the H-bond interactions betweenNU2058 analogues and CDK2 active site Alzate-Morales, JH; Caballero, J; Gonzalez-Nilo, FD; Contreras, R., Chemical Physics Letters, 479, 149-155, (2009)

[27] Saldias C, Gargallo L, Sandoval C, Leiva A, Radic D, Caballero, Saavedra M, Gonzalez-Nilo FD, POLYMER 50 (13), 2926-2932 (2009)

[28] Configurational temperature for interacting anisotropic magnetic particles, P. Diaz andD. Laroze, International Journal of Bifurcation and Chaos 19, 3485-3498 (2009).

[29] Ab initio molecular dynamics study of amorphous CdTeOx alloys: Structural properties,E. Menendez-Proupin, P. Giannozzi, J. Peralta, and G. Gutierrez, Phys. Rev. B 79,014205 (2009).

[30] Reaction and incorporation of H2 molecules inside single-walled carbon nanotubes th-rough multivacancy defect, W. Orellana, Physical Review B 80, 075421 (2009).

[31] Amplitude equation for stationary convection in a rotating binary ferrofluid, D. La-roze, J. Martinez-Mardones, L. M. Perez, Y. Rameshwar , International Journal ofBifurcation and Chaos, Vol. 19, No. 8 (2009) 2755-2764.

[32] Localized states and non-variational IsingBloch transition of a parametrically driveneasy-plane ferromagnetic wire, Marcel G. Clerc , Saliya Coulibaly, and David Laroze,Physica D 239, 72-86 (2009).

[33] Nonvariational IsingBloch transition in parametrically driven systems, M. G. Clerc, S.Coubaly, and D. Laroze, International Journal of Bifurcation and Chaos, Vol. 19, No.8 (2009) 2717-2726.

[34] Investigation of interface properties of Ni/Cu multilayers by high kinetic energy pho-toelectron spectroscopy, Sari Granroth, Ronny Knut, Moreno Marcellini, Gabriella An-dersson, Svante Svensson, Olof Karis, Mihaela Gorgoi, Franz Schafers, Walter Braun,Wolfgang Eberhardt, Weine Olovsson, Erik Holmstrom, Nils Martensson, PHYSICALREVIEW B 80, 094104 (2009)

[35] Modularity density of network community divisions, Erik Holmstrom, Nicolas Bock,Johan Brannlund Physica D 238 (2009) 1161-1167

[36] Ab initio method for locating characteristic potential-energy minima of liquids, E.Holmstrom,N. Bock, Travis B. Peery, R. Lizarraga, G. De Lorenzi-Venneri, Eric D.Chisolm, and Duane C. Wallace PHYSICAL REVIEW E 80, 051111 (2009).

[37] First Principle Calculations of Core-Level Binding Energy and Auger kinetic EnergyShifts in Metallic Solids, Weine Olovsson, Tobias Marten, Erik Holmstrom, BorjeJohansson, Igor A. Abrikosov, Journal of Electron Spectroscopy and Related Phenome-na 178-179, Trends in X-ray Photoelectron Spectroscopy of solids (theory, techniquesand applications), 88-99 (2009).

[38] Quantitative local environment characterization in amorphous oxides, A. Amezaga, E.Holmstrom, R. Lizarraga, E. Menendez-Proupin, P. Bartolo-Perez, and P. Giannozzi,Phys. Rev. B 81, 014210 (2010).

[39] Core-level shift analysis of amorphous CdTeOx materials, R. Lizarraga, E. Holmstrom,A. Amezaga, N. Bock , T. Peery, E. Menendez-Proupin, and P. Giannozzi, J. Mater.Sci. 45, 5071-5076 (2010).

[40] Iron porphyrins attached to single-walled carbon nanotubes: Electronic and dynamicalproperties from ab initio calculations, I. Ruiz Tagle, W. Orellana, Physical Review B82, 115406 (2010).

[41] Characterization of spin-state tuning in thermally annealed semiconductor quantumdot, E. Margapoti, Fabrizio M. Alves, V. Lopez-Richard, C. Destefani, G. E. Marques,E. Menendez-Proupin, Fanyao Qu, S. Mahapatra, K. Brunner, and C. Bougerol , Phys.Rev. B 82, 205318 (2010).

[42] Approximate quantum mechanical method for describing excitations and related pro-perties of finite single-walled carbon nanotubes, A. L. Montero , M. E. Fuentes, E.Menendez-Proupin, W. Orellana, C. F. Bunge, L. A. Montero, and J. M. Garcıa de laVega, Phys. Rev. B 81, 235409 (2010).

[43] Las Palmeras Molecular Dynamics: A flexible and modular molecylar dynamics code, S.Davis, C. Loyola, F. Gonzalez, and J. Peralta, Computational Physics Communication181 2126-2139 (2010).

[44] Onset of failure in argon by the effect of a shockwave: A molecular dynamics study,Claudia Loyola, Sergio Davis, Joaquın Peralta, and Gonzalo Gutierrez, ComputationalMaterials Science 49, 582-587 (2010).

[45] Computer simulation study of amorphous compounds: structural and vibrational pro-perties, G. Gutierrez, E. Menendez-Proupin, C. Loyola, J. Peralta, and S. Davis, J.Mater. Sci. 45, 5124-5134 (2010).

[46] Atomistic study of vibrational properties of gamma-Al2O3, C. Loyola, E. Menendez-Proupin, and G. Gutierrez, J. Mater. Sci. 45, 5094-5100, (2010).

[47] Efficient Spin Injection Through Exchange Coupling at Organic Semiconduc-tor/Ferromagnet Heterojunctions, Yiqiang Zhan, Erik Holmstrom, Raquel Lizarraga,Olle Eriksson, Xianjie Liu, Fenghong Li, Elin Carlegrim, Sven Stafstrom, Mats Fahl-man, Advanced Materials 22, 1626-1630 (2010)

[48] Theoretical studies of the incommensurate magnetic structure of a heavy fermion sys-tem: CeRhIn5, Torbjorn Bjorkman, Raquel Lizarraga, Fredrik Bultmark, Olle Eriksson,John M. Wills, Anders Bergman, Per H. Andersson, and Lars Nordstrom, Phys. Rev.B 81, 094433 (2010).

[49] Computational Study of the Interactions between Guanine Derivatives and Cyclin-Dependent Kinase 2 (CDK2) by CoMFA and QM/MM, Julio Caballero, Jans Alzate,Journal Of Chemical Information And Modeling 50, 110-122 (2010)

[50] Structural and dynamical properties of the Cu46Zr54 alloy in crystalline, amorphousand liquid state: a molecular dynamic study, C. Valencia-Balvın, C. Loyola, J. Osorioand G. Gutierrez. Physica B 405, 4970-4977 (2010).

[51] Distributed Structures Underlie Gating Differences between the K-in Channel KAT1and the K-out Channel SKOR, Riedelsberger J, Sharma T, Gonzalez W, GajdanowiczP, Morales-Navarro SE, Garcia-Mata C, Mueller-Roeber B, Gonzalez-Nilo FD, BlattMR, Dreyer I, MOLECULAR PLANT 3 (1), 236-245 (2010)

[52] Gating of a pH-Sensitive K-2P Potassium Channel by an Electrostatic Effect of BasicSensor Residues on the Selectivity Filter, Zuniga L, Marquez V, Gonzalez-Nilo FD,Chipot C, Cid LP, Sepulveda FV, Niemeyer MI, PLOS ONE 6 (1) Article Number:e16141 (2011).

[53] Nanoinformatics: an emerging area of information technology at the intersection of bio-informatics, computational chemistry and nanobiotechnology, Gonzalez-Nilo F, Perez-Acle T, Guinez-Molinos S, Geraldo DA, Sandoval C, Yevenes A, Santos LS, Laurie VF,Mendoza H, Cachau RE, BIOLOGICAL RESEARCH 44 (1), 43-51 (2011)

[54] Supramolecular complexes of quantum dots and a polyamidoamine (PAMAM)-folatederivative for molecular imaging of cancer cells, Geraldo DA, Duran-Lara EF, AguayoD, Cachau RE, Tapia J, Esparza R, Yacaman MJ, Gonzalez-Nilo FD, Santos LS,ANALYTICAL AND BIOANALYTICAL CHEMISTRY 400 (2), 483-492 (2011)

[55] Nitrogen/Gold Codoping of TiO (101) Anatase Surface. A Theoretical Study Basedon DFT Calculations Yanaris Ortega, Norge Cruz Hernandez, Eduardo Menendez-Proupin, Jesus Graciani and Javier Fdez. Sanz, accepted to Physical Chemistry Che-mical Physics (PCCP).

[56] Computer simulation of elastic constants of hydroxyapatite and fluorapatite, E.Menendez-Proupin, S. Cervantes-Rodriguez, R. Osorio-Pulgar, M. Franco-Cisterna, H.Camacho-Montes, and M. E. Fuentes, accepted to Journal of the Mechanical Behaviorof Biomedical Materials.

Non-ISI papers

[57] Convective instability of viscoelastic ferrofluid, D. Laroze, J. Martinez-Mardones , AIPConference Proceeding 913, 9 (2007).

[58] Dynamical behaviour of two Interacting Dipoles, C. Cortes, P. Vargas, G.Gutierrez,and D. Laroze Journal of Physics: Conference Series 134, 012016 (2008).

Papers, submitted

[59] Structural transformation of amorphous Al2O3 under pressure: a molecular dynamicsstudy , G.Gutierrez, submitted PRB.

[60] Structural, elastic, vibrational, and electronic properties of amorphous Al2O3 from ab-initio calculations, S. Davis and G. Gutierrez, submitted to J. Chemical Physics.

[61] Thermal stability and dynamical properties of Ti3SiC2 (0001) at high temperatures:First-principles calculations, Walter Orellana and Gonzalo Gutierrez, submitted toActa Materialia.

VIII. DISSEMINATION AND KNOWLEDGE TRANSFER AC-TIVITIES

Schools, workshops, courses, and lectures organized by the Anillo

[1] Workshop de Simulacion Molecular: Energıa Libre. Profesor invitado Dr. ChristopheChipot, CNRS/Nancy-Francia. Con ma de 45 participantes, se discutio sobre metodos yherramientas computacionales avanzadas para la evaluacion de energıa libre en sistemascomplejos. Talca, 19-21 Nov. 2007.

[2] VI Encuentro de Modelos Fısicos y Matematicos en Ingenierıa EMFIMIN 2007.Noviembre 15-16, 2007, Santiago, Chile.

[3] Curso de postgrado Fısica Cuantica Aplicada a la Ciencia de Materiales. Facultadde Ciencias, Universidad de Chile, impartido por G. Gutierrez, E. Menendez y W.Orellana. Asistieron 10 alumnos, cuatro estudiantes del proyecto. March-July 2007.

[4] Latinamerican School in Computational Materials Science (seehttp://www.gnm.cl/school/ ). This activity, organized by the Anillo researchersE. Menendez and W. Orellana with S. Scandolo (ICTP), P. Gianozzi (Democritos/U.Udine) and S. Cozzini (Democritos/Sissa). It was a joint effort of our Anillo Project,two chilean universities (U. de Chile and UNAB), the Italian National SimulationCenter, and the UNESCO International Centre for Theoretical Physics of Trieste. Theactivity consisted on a course in High Performance Computing, and advanced works-hop, and a tutorial course on the ab initio simulation package Quantum-ESPRESSO.In total, the activity lasted two weeks, and received 54 student participants, 30 fromChile and 24 from Argentina, Brazil, Peru, Colombia, Mexico, and Uruguay. Alsoattended 15 foreign and 6 national advanced scientists that acted as speakers andprofessors. This activity marked an important step in terms of international contactsand recognition for our group as a regional force in the topic of computationalmaterials science.

[5] Advanced Course on Free Energy Calculations: Theory and Practice Coordinator, Da-nilo Gonzalez. This course was given in the CBSM of the Universidad de Talca, Talca.The course had 45 pedagogic hours, during 5 days period, from December 15 to 19,2008. This course was co-financed by the PhD program in Applied Sciences of theUTalca, by the European Community FP7 ACTION-GRID project (local coordina-tor: Danilo Gonzalez) and by the our Project Anillo ACT/24. This event had theparticipation of 25 PhD students from the Applied Science and Biotechnology PhDprograms of the Universidad de Talca. All the integrants of the Anillo participated.Also professors and students from Universidad de Santiago (USACH), Universidad deChile, Universidad de Valparaıso, Universidad Austral de Valdivia and from PontificiaUniversidad Catolica de Chile were present. During the course, it was discussed advan-ced methods of free energy calculation across a reaction coordinate, utilizing the ABFmethod (Adaptive Biasing Forces). It was also done advanced tutorials of simulationsof molecular dynamics and of molecular visualization using the VMD program.

[6] Physics of proteins. Course given by Dr. C. Camacho, University of Pittsburgh, Physicsof Proteins from 11-14 August 2008, 4.5 hrs., 18 people (PhD student, undergraduateand researchers) attended.

[7] Tutorial course of Quantum-ESPRESSO delivered by E. Menendez, was taught byinvitation of the University of Chihuahua, in Mexico. This course had a duration offive days (25 hours) and was attended by ten scientists and students of several researchinstitutions of the state of Chihuahua. November 2008.

[8] Introductory course on structural bioinformatics and drug design, given by J. Alzate,National University of Rio Cuarto, Rio Cuarto, Argentina. November 24-26, 2008.

[9] Course Shock Waves, Second Semester, July-Dec. 2008. Course was given at Fa-cultad de ciencias, Universidad de Chile. Coordinator Gonzalo Gutierrez, Lectu-rers: L. Moraga, G. Gutierrez, M. Branes. (ver http://fisica.ciencias.uchile.cl/ gon-zalo/?n=Docencia.2008OndChq)

[10] Metodos simplificados para calculos de estructura electronica, Profesor Jorge Kohanoff,de la Queens University Belfast, en el laboratorio de GNM los dıas 18, 20 y 21 deAgosto desde las 14:00 hasta las 17:00 hrs. El curso incluyo un trabajo practico conun programa basado en Tight-binding Molecular Dynamics. Attende by 12 students.

[11] Simposio Y - Computational Modeling and Data Driven Materials Discovery, ICAM09(11th International Conference on Advanced Materials), Rio de Janeiro, 20-25 de Sep-tiembre 2009: Co-chair G. Gutierrez, GNM.

[12] Taller de Modelacion Multifısica mediante Elementos Finitos, 18 dic 2009, Sala 1,Auditorium Albert Einstein Departamento de Fısica de la Facultad de Ciencias (LasPalmeras 3425 Nunoa Santiago) (56) (2) 9787441 Grupo de Nanomateriales, U. deChile.

[13] NanoTaller Python, 12-13 Jan 2009. Basic notion about Python language, given atFacultad de Ciencias by S. Davis, PhD student at KTH, Sweden, and member ofGNM. More than 20 student attended it.

[14] First International Conference on Bioinformatics, organized by the Ibero-AmericanSociety for Bioinformatics (SoIBio) (2010).

[15] Escuela de Simulacion Computacional de dinamica molecular clasica: Las PalmerasMD, 4-8 de Enero de 2010, Facultad de Ciencias, Universidad de Chile, Santiago.More than 20 sudent attended. See http://www.lpmd.cl/school/

[16] In addition, we have supported the Symposium of the Chilean Physical Society andpartially supported the attendance of more than 20 undergraduate student form U.Chile to that event.

Technical Colloquia

[11] D. Laroze, Localizacion en sistemas magneticos extendidos, Departamento de Fısica,Universidad de la Frontera, Temuco, Chile (Nov. 2007).

[12] D.Laroze, Termodinamica y Dinamica en sistemas magneticos, Universidad de Tara-paca, Arica, Chile (Mar. 2008).

[13] E. Menendez, Simulacion de la estructura de vidrios de CdTeOx, Facultad de CienciasFısicas y Matematicas, Universidad de Chile, Santiago, Chile (Mar. 2008); also atFacultad de Ciencias, U. de Chile (Abr. 2008).

[14] G. Gutierrez, Ab-initio calculations in materials, CESMEC, FIU, Miami, (Ene. 2007)

[15] G. Gutierrez, Equilibrio termico en sistemas magneticos, Facultad de Ciencias Fisicasy Matematicas, Universidad de Chile, Santiago, Chile (Jun. 2007)

[16] G. Gutierrez, Simulacion computacional de materiales, Departamento de Fısica, U. deConcepcion (Abril 2008).

[17] G. Gutierrez, Seminars at: Departamento de Fısica, Universidad de Concepcion, April08; Taller Nanociencia, VRID, UChile, April 08; Departamento de Quımica, Facultadde Ciencias, Nov 08; Departamento de Fısica, F. Ciencias Fısicas y Matematicas, U.de Chile, Dic.08.

[18] E. Menendez: Seminars at Universidad de Chile, Universidad de Valencia, Spain, Uni-versidad de Sevilla, Spain.

[19] D. Laroze, Seminars at Instituto de Alta Investigacion, Arica, Chile; Anillo de FisicaNo Lineal , Santiago, Chile.

[20] G.Gutierrez, Charla Simulacion computacional de materiales, Ecuela de Dinamica Mo-lecular, LPMD, Facultad de Ciencias, U. de Chile, Ene. 2010.

Talk to the public at large, high schools, etc.

[21] Charla de difusion Auditorio Abate Molina a Estudiantes de Ensenanza media de laVII Region. Esta actividad permitio explicar, a mas de 600 alumnos seleccionadosde diversos liceos de la VII region, las actividades desarrolladas en nuestro AnilloCientıfico.

[22] E. Menendez, Charla “Puntos cuanticos”, Colegio Latino-Cordillera (9/10/2007), en elmarco de la actividad 1000 cientıficos, 1000 Aulas, del programa EXPLORA.

[23] Actividad de puertas abiertas. Facultad de Ciencias. Universidad de Chile. Presentacionde stand por parte de Anillo ACT-24, Oct. 2007.

[24] G. Gutierrez, Charla Nanotecnologıa, dictada en: Inauguracion del Ciclo de charlascientıficas para estudiantes de Ensenanza media, Direccion de Extension, Facultad deCiencias, U de Chile, 16/05/2007; Liceo Manuel de Salas, Julio 2007; Scuola Italianade Santiago Agosto 2007; Instituto Nacional Octubre 2007.

[25] G. Gutierrez, Charla Transporte de calor en sistemas magneticos: un ejemplo de“spintronica”, II Escuela de Invierno para la divulgacion de la Robotica, Nanotec-nologıa y Neurociencia, UTFSM, Valparaıso, Agosto 2008.

[26] G.Gutierrez, Charla Nanotecnologıa, Colegio Jungenland Schule, Talagante, Nov. 2008.

[27] W. Orellana, Nanomateriales y Nanotecnologıa, Olimpiada Chilena de Fısica, Univer-sidad Andres Bello, (October 2008).

[28] W. Orellana, Nanomateriales y Nanotecnologıa, Colegio Pıa Marta, Estacion Central,(August 2008).

[29] D. Laroze, Estudios de Doctorado en la Universidad de Tarapaca, SOBOFI, La Paz,Bolivia (Nov. 2008).

[30] G.Gutierrez, Charla El juego de los atomos: materiales avanzados, Charla inauguralexposicion Explora-Conicyt, Museo de Historia Natural, Quinta Normal, Julio 2009.

[31] G.Gutierrez, Charla Necesidades energeticas y nanotecnologıa, Instituto Rafael Ariztıa,Quillota, Oct. 2009.

[32] G.Gutierrez, Charla Necesidades energeticas y nanotecnologıa, Semana de la CienciaColegio San Ignacio El Bosque, Nov. 2009.

Press

[29] G. Gutierrez, Radio interview, Radio Universidad de Chile, programa Milenio, 03.Ene.2007.

[30] G. Gutierrez, Radio interview, Radio Universidad de Chile, programa Semaforo Cul-tural, 9 Abril 2007, a G. Gutierrez.

Connection with the productive sector

This year we have been able to develop several initiative in order to establish real linkswith the productive sector of our country. We are very happy with this new branch ofour Anillo, that allows us to do research but also to contribute to the development of ourindustries as well as to create new possibilities for our student and associates. This initiative isin progress and both the group of Universidad de Talca, CBSM (which has been particularlyaggressive in this respect) and the Group of NanoMaterials at Universidad de Chile areworking hard to develop and consolidate the connection to the productive sector.

1. ADJUDICATION OF FONDEF TIC EDU FOR EDUCATION: in the education sec-tor, our group, together with the Bioinformatics group (CBUC) from the UniversidadCatolica, directed by Dr. Tomas Perez-Acle, got the adjudication of the project titled:Collaborative Learning System Based on Grid Infrastructure (SACGRID): Applicationsin Biological Sciences and Biotechnology. This project will be financed by the tender ofProgram Technology of Information and Effective Communications for Education (TICEDU) from the FONDEF program of CONICYT. SACGRID is a 36 months project,with a budget of Ch$ 287.900.000 (US$ 480.000). The working team is formed by inves-tigators of the Foundation Science for the Life (David Holmes and Pablo Rosenblatt),the Universidad de Talca (Danilo Gonzalez and Sergio Guinez) and the UniversidadCatolica (Tomas Perez Acle and Jorge Manzi). Microsoft Chile, HP Chile and CoffeeBusiness participate as strategic partners of SACGRID.

2. CONSULTING IN THE PROJECT Thermophysical properties of the tires used in mi-ning trucks. We have been working in the modeling of truck tires together the companyIICLtda (http://www.iicltda.cl/). This company have close links to the copper miningindustry, and work in several projects with them. We (Prof. G. Gutierrez and L. Moragafrom GNM and a Mathematical Engineer’s student ) developed a model based on theThermodynamic theory of continuous media. The contract with IICLtda was aboutUS$11000.- for four months. The work also included the advice in the experimentalside.

3. APPLICATION TO BASAL PROJECT. A multidisciplinary group, leaded by resear-chers from the Universidad de Talca, and including people from CChen (State NuclearEnergy Agency), U. de Chile (Group of NanoMaterials) among others, , and privatecompanies, got together to postulate to the Basal project, for a total budget of 6.000million pesos (US$ 10.000.000), for a 5 years period. This group was led by Dr. DaniloGonzalez and considered the development of three areas: pulse power physics, nanobio-logy and precision agriculture. Each one of these areas was coordinated in investigationin the areas of food, mining and medicine. This project was provided with the supportof the Institute Fraunhoffer-Germany, NCI-USA, CODELCO, ECOMETALES, Bio-Frutales S.A, SUN Microsystem, among other companies. This project was presentedin January, 2008, shortlisted in February and had a negative response on March 8.

4. ADJUDICATION OF FONDEF NANOFOOD: the CBSM together with the Facultyof Agronomy and the Instituto de Quımica of the Universidad de Talca, postulated aFONDEF project titled: Nanobiology applied to the food industry: Quality assuranceand improved commercial value. For this project, we had the support of FraunhofferInstitute-Germany, BioFrutales SA and SUN Microsystem. This project has as objectiveto implement a system based on nanoparticles for the specific extraction of non-desiredmolecules (e.g.: pesticides) in liquid food, such as wine, oils and fruits juices.

IX. LESSONS LEARNED

The following section can be used in case of available information related to the possibledifficulties, inconveniences or similar issues in the management of the project within the hostinstitution, between CONICYT and the host institution, institution and researchers or anyother combination of participants and activities involved. The idea is to resolve these issueson behalf of better practices in the current and future handling of these initiatives.Information provided in this section must be concise, stating all variables involved and outco-mes. Do not extend further than 2 pages. Indicate the need of confidentiality when required.

The Anillo project allows us to develop research in a medium scale, that would be impos-sible with other kind of grant, like Fondecyt. Even summing our individual Fondecyt grant,we could not afford activities like those international schools we organized, neither the invi-tation to researcher and graduate student to spent some time with us, nor the installation ofthe high performance computer facility we did. These kind of activities are vital in order toenhance the vision and experience to student and researcher, particularly in a country likeChile, which is far away from the scientific capitals. Thus, we consider quite important tocontinue which this initiative, that give the opportunity to small group to do research withoptimal conditions. For group like us, with two or three researcher in each universities, thisgrant are ideal: fondecyt is only individual, and that large grant like Financiamiento Basal orFondap are to big, that you need to include to many different topics. We expect to continuetis initiative, in order to give sustaintability of Anillos like ours, that have consolidate in oneresearch team different groups, like one in Santiago and the other in Talca.

13

X. INDICATORS

The following table corresponds to a selection of general and specific indicators that may or may not apply to the scope of your project. If you require or would like to define indicators particular to your activities and results, please include them at the end of this table. This program is aware that quantitative indicators do not cover most of the actual impact of your activities. Please add up here all outputs resulting from the three-year period.

N° of Main Researchers 3

N° of Associated Researchers 3

F =0 Gender (%) of the main researchers

M =100

F =0

General

Gender (%) of the associated researchers M =100

Nº of ISI publications 56

Nº of non- ISI publications 2

Percentage of publications Co-authored with researchers of the Project 70%

Average impact index of ISI publications 3

Average number of citations per article up to this date 5

N° of international presentations/conferences 47

Scientific production

N° of national presentations/conferences 57

N° of patent applications 0

N° of patents granted 0

N° of licenses and/or material transfer agreements 2

N° of Spin-offs 1 Percentage of the annual funding of the project received from companies 1%

Annual sales volume of the companies involved ?

N° of employees of the companies involved 10

Commercial or other production (only if applies)

Industrial sector of the companies involved Mining

18

Number of undergraduate students 23

Female (%) of undergraduate students 35%

Number of Master’s students 4

Female (%)of Master’s students 0

Number of Ph.D. students 11

Female (%)of Ph.D. students 45%

Number of postdocs participating in the project 4

Female (%)of postdocs 25%

Number of undergraduate theses finished 8

Number of graduate theses finished (Master) 3

Number of graduate theses finished (Ph.D) 3

Percentage of co-tutored theses with external researchers

21%

Human resources training

Percentage of co-tutored theses with researchers of the Project

21%

N° of national collaboration projects 2

N° of international collaboration projects 4

Number of stays/visits to other institutions by students or researchers of the project

8

Number of stays/visits in the project from students or researchers of other centers or projects

24

N° of public or private(not enterprises) involved in the project

24

National and International collaboration

Percentage of publications Co-authored with external researchers

80%

Nº of dissemination/extramural events 28

Nº of times the project appears in mass media 10

Total Nº of attendants to dissemination events 1500

Nº of national academic attendants 300

Nº of international academic attendants 100

Nº of attendants from non-academic sectors 1100

Dissemination and extramural activities

N° of documents, reports, proceedings resulting from dissemination/extramural events or activities

6