1December 2007

PoweringDISCOVERIES!

A Publication Of The Institute Of High Performance Computing MITA (P) No. 159/07/2007

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7VOLUME 2 ISSUE 4

The libraries and book stores of today are stocked with books from historical fiction to high fantasy. We live in a time where there is an unprecedented variety of literature to capture the imagination of its readers.

Here at IHPC, we believe in fostering the interest of our students in science and technology through outreach activities. Come January, we will embark on a pilot project to schools. Called “Science Chronicles – A Literary Quest”, it is a science fiction writing competition open to all students in Singapore between the ages of 15 – 18. The aim is to foster a new breed of scientific thinkers and writers who can apply their knowledge of science with the art of imaginative literary creation.

Budding science writers will be given free reign to pen their literary creations. They will be judged on their originality, ideas expressed, creative use of interesting setting and notably, with some aspect of science in their storyline. Hence, it is not just for those who are interested in computers, technology, mathematics and science, but also for those who love literature, writing stories and would like

to stretch the limit of their imaginations on science and technology. The past has shown that what is science fiction today could be the norm and reality of tomorrow.

A workshop will be organised for these students to learn more about science and science fiction as a literary genre. They will learn about the impact of science on society, such as how many of the electronic devices we take for granted today were inspired from the imagination of visionary writers. Invited speakers will also share their personal experience and inspiration from their reading of science fiction.

F o r m o r e i n f o r m a t i o n a b o u t S c i e n c e C h r o n i c l e s , l o g o n t o www.science-chronicles.com or email crystal@ihpc.a-star.edu.sg. The competition will be launched in January 2008 and results will be announced in June 2008. Attractive cash prizes await the winners and their schools.

So turn your imagination into reality through words and let others draw inspiration!

Science Chronicles – A Literary Quest Powering Imagination to Reality – fostering a new breed of scientific thinkers and writers

Compliments of the season

3Outreach

IHPC-Science Mentorship

Programme 2007

6Research

Mechanical Behaviour of Nanowires

12In The News

Dr Raj. Thampuran awarded Public Service Medal at

National Day Awards 2007

2 December 2007

EventBy Rick GOH Siow Monggohsm@ihpc.a-star.edu.sg

By Kevin VERAGOOveragoo@ihpc.a-star.edu.sg

By Freddy CHUA Chong Tatchuact@ihpc.a-star.edu.sg

Gelato ICE Conference 2007

The Gelato ICE: Itanium Conference & Expo is the world’s only conference dedicated to Linux on the Intel Itanium architecture. This event is organised by the Gelato Federation which is the global technical community dedicated to advancing Linux on the Intel Itanium platform through collaboration, education and leadership. Held this year on 1st

and 2nd October, the organisers chose Singapore again as the venue for the conference as they recognised the strong Itanium processor adoption rate in the

Asia-Pacific region. Of course, another compelling reason was that Dr. Mark K. Smith – the managing director of Gelato Federation – was impressed with the clean and new facilities available at the Biopolis when Gelato ICE was held there in 2006.

The Gelato ICE programme committee had put together a series of technical presentations that addressed the current high-performance computing issues and collaborative project solutions that catered specifically for Linux on Itanium. Speakers include international researchers covering topics such as compilers, grid, multicore, parallel computing, performance analysis, reliability, scalability and virtualisation.

Mr Kevin Veragoo, from the Advanced Comput ing (AC) programme, gave a p r e s e n t a t i o n o n I H P C a n d h ighl ighted var ious act iv i t ies such a s t h e I H P C o p e n - s o u rc e p a g e (http://software.ihpc.a-star.edu.sg/software.html) as well as IHPC’s move to its future home in Fusionopolis.

Dr Rick Goh, another researcher from the AC programme, also touched on one of his collaborative projects with NTU - “Resource-eff icient Adaptive Parallelism Framework for Multicore and Multiprocessor Systems”.In addition to talks, there was also a poster presentation in the reception area of the conference, allowing for ample opportunities to interact with other international researchers from USA, UK as well as Europe.

Contrary to hearsay that Itanium is a dead or dying technology, the situation could not be further from the truth. About 70% of top global MNCs are choosing Itanium for their mission critical applications. One reason is because Itanium processors are able to recover/correct up to 2-bit errors in applications. This platform puts high

emphasis on RAS – Reliability, Availability and Serviceability – which according to a survey, are what enterprises list as their high priorities, along with performance and scalability.

For the HPC market, Itanium is unique for its ability to scale both processor and addressable-memory in a single system image. Itanium2 processors also have variable TLB page-size from 4kB to 4GB. Currently dualcore Itanium processors (codename Montecito) are available. On Intel’s roadmap, quadcore (Tukwila) will be made available in 2008 and multicores (Poulson) in 2010.

The conference was considered a success, with many of the attendees from IHPC as well as researchers from diverse parts of the globe, coming together to benefit from the multiple tutorials on the various parallel computing techniques and tools.

IHPC was represented by researchers from the AC programme and A*CRC (Computational Resource Centre) staff at the conference.

Participants enjoying their conference dinner.

Dr Rick Goh from the AC programme giving his presentation on Parallel Computing.

IHPC’s booth.

3December 2007

Outreach Science Mentorship Programme (SMP) @ IHPCBy Corporate Comms

comms@ihpc.a-star.edu.sg

The SMP is a collaborative outreach activity orgranised by the Gifted Education Branch of the Ministry of Education. Targeted at students in the Integrated Programme, the various schools will send teams of 3 students to be attached to a selected institution, where one (or two) mentors will guide them through a project from planning to completion.

The selection stage is also an intricate process that requires the students to write in and convince the mentors that they have what it takes to see the project through to fruition. The mentors will then select the group with the most potential, if there is more than one group of students vying for the project.

For IHPC-SMP 2007, 3 students from Nanyang Girls’ School – Fong Jiayi, Go Shiyu and Wu Jing Jing - were attached at the institute for a period of six months. Below is an account of their research experiences as well as their interactions with their mentors, Dr Chee Chin Yi (Large-scale Complex Systems programme) and Mr Chong Chiet Sing (Advanced Computing programme):

CONVERTING 3D MEDICAL IMAGES INTO NUMERICAL MODELSOur ProjectOur project focused on the creation of a finite element human spine model with the use of the MRI scans of a body and the program, MIMICS as a tool to help us segment out the human spinal bones, giving us a 3D model of the human spine to perform analysis on.

In the project, we used the software called Finite Element Modelling (FEM) which helped us to study the human spinal impact tolerances and how the spine reacts under a certain amount of stress.

The MIMICS program links numerous scanned images to the Finite Element Ana lys is (FEA) which ext racts the

geometry from these images and creates a 3 dimensional model. FEA uses a complex system of points called nodes. These nodes will then make a grid called a mesh.

The mesh produced is programmed to have material and structural properties, which will demarcate how the structure or model will react to certain stress or loading conditions. The nodes of the structure are assigned at a certain density throughout the material depending on the stress levels of a particular area.

Vibrational analysis was also done on our spinal model and the tests done included random vibrations, shock and impact. Lastly, we let the super computers run a series of computational procedures involving applied forces and determining the material properties of the spinal bone, which includes the values of the bone’s density, Young modulus and Poisson’s Ratio. Such a structural analysis allows the determination of the effects such as strains, stresses and deformations that are caused by applying structural loads such as force, pressure and gravity.

We were exposed to an in-depth study of the human spinal impact tolerances and managed to learn a great deal about the various computing programmes and systems which we would not have had the chance to learn about if not for this Science Mentorship Programme. This experience has been a most enriching one for us, not forgetting about the invaluable lessons which taught us the importance of working well in a team.

Our Mentors Our mentors, Dr Chee Chin Yi and Mr. Chong Chiet Sing, played important roles through helping and guiding us, providing clear instructions throughout our time of internship with IHPC. Under their guidance, we were able to carry out the project smoothly and even manage to have much fun at the same time Their care and patience to us have been much appreciated and we would not have come this far without their support.

In the first part of the project, where we had to create the 3D spinal model, Mr Chong always took time to check on our progress. He would try his best to help us in every way possible such as providing us with websites where we could acquire more research materials and knowledge to aid us in our project.

Dr Chee was both a friend and mentor. He often joked with us, making the whole

project much more enjoyable. We were deeply touched by his relentless support for us at all times and we could see that he truly believed that we had the potential to do well.

Like the old saying goes, nothing is easy. Through the course of doing this Science Mentorship Programme, we encountered many ups and downs, with many difficulties along the way. The most pressing concern was time constraints. As we all had our own busy schedules, it was a mean feat to be able to meet up together as a complete team for all the sessions to work on the project. Due to the clash of enrichment lessons and CCA sessions, we had to learn to split up the workload among the group members. At most times, only 2 of us instead of the whole group would be present at IHPC to do the project. Thus, sometimes this may have led to a lack of communication among the group members.

Another problem which we encountered was our inability to grasp the concepts and pr inc ip les of the subject at a comfortable pace. Most of what we learnt from working on the project were brand new theories introduced to us, such as FEA and MIMICS. We had never come across these concepts before and thus it was rather hard for us at first to be able to understand the working theories behind these programs. However, through the continual process of trial-and-error, coupled with Dr Chee’s patient explanations, we were finally able to grasp the concepts and make good use of them for our project.

Best Oral Presentation for Group Category The Nanyang Girls’ School team did IHPC proud by receiving the Best Oral Presentation award on 15th September at Singapore Polytechnic. Well done, girls!

Dr Chee Chin Yi with the students and teacher from

Nanyang Girls’ School.

From left - Fong Jiayi, Wu Jing Jing and Go Shiyu (Nanyang Girls’ School).

4 December 2007

Outreach

Research into the area of Silicon Photonics is a new avenue that had picked up over the recent years. Under the research thrust of the Engineering Software and Applications (ESA) programme at IHPC, this specialised study into the field of optics holds a great deal of potential in modern devices such as optical fiber communications, silicon waver chips and CD/DVD/Blue-ray entertainment consoles. With this in mind, the latest topic of discussion for the Seminar Series was on Photonics. Aptly titled ‘See the Light’ and held on the 23rd August at the A*STAR main auditorium in Biopolis, the invited speakers were presented with an opportunity to enlighten the students on the cutting-edge technological benefits that can be reaped from this area of scientific research.

Dr Desmond Lim from the Defense Science Organisation (DSO) National Laboratories started things off with his presentation entitled ‘Microwave Photonics’. Dr Lim introduced Microwave Photonics as a merger of microwave electronics and photonics and touched on the var ious appl icat ions of the technology in transmission, processing and miniaturisation. Focusing on the area of miniturisation, Dr Lim pointed out the example of a typical computer processor chip, which is no bigger than an adult-sized finger nail, containing over 300 million microprocessor transistors.

Dr Aaron Danner from the National University of Singapore, spoke on the topic of Photonic Crystals. He pointed out that the field of photonic crystals and the use of nano-scale structures to control photons, displays potentially revolutionary control of the flow of photons and hence quantum information. He also predicted that to be able to refine and develop this technology which enables photon

generat ion, storage, entanglement, and state teleportation could herald an unprecedented era of quantum computing in which a new parallelism would become available under which currently impossible problems would become tractable. A slew of potential applications in the area of photonic crystal include miniturised dense multi-channel optical components such as add-drop filters and tunable micro-cavity lasers.

Dr Jason Png, IHPC’s resident researcher took to the podium next with his talk on ‘Devices in Silicon Photonics’. Dr Png gave an overview of the latest state-of-the-art component research in photonics. In particular, a number of optical devices using the silicon material, including modulators, chromatic dispersion compensators, and 1D photonic bandgap crystals were discussed. He also further touched on the critical issues of waveguide design for single mode and polarisation performances.

The seminar was rounded off with Dr Lim Soon Thor’s presentation on ‘Silicon Photonics-From Micron to Nano’. Dr Lim expanded on Dr Png’s presentation by expounding on the differences in the physical nature behind dielectric, planar and rib waveguides. By adopting a variation of the three different waveguides, Dr Lim explained how researchers are moving from the micro-scale to the nano-scale in terms of their findings. However, an adverse effect of moving into smaller waveguide dimensions would result in increased difficulty in maintaining single-mode operations whilst simultaneously designing for polarisation independence. This is one of the current problems that are plaguing researchers today.

For the 270 students that attended the session, the talks provided a closer look at the growing world of modern

technology and how Silicon Photonics plays a major role in the development of future devices that might be used by everyday people. The students also gained valuable insight into the Silicon Photonics research direction undertaken by the ESA programme which, in turn, is aided by the supercomputing resources available at IHPC.

By Corporate Comms comms@ihpc.a-star.edu.sg

IHPC Seminar Series: Photonics – See the Light

Dr Aaron Danner (middle) explaining about Photonic Crystals to a student.

IHPC’s Dr Lim Soon Thor (left) speaking more about Silicon Photonics to students after his presentation.

Students and participants of the seminar having a stretch after a long session of presentations.

Dr Desmond Lim from DSO National Labs.

5December 2007

ResearchBy Adrian KOH Soo Jin kohsj@ihpc.a-star.edu.sg

Background Information and MotivationMetallic nanomaterials have generated immense interest within the scientific research community due to the excellent electrical, magnetic, optical and thermal properties displayed by nanometallics at size scales smaller than 100 nm. The transitional group of cubic close-packed (CCP) metals–elements found between groups 9 and 11 of the periodic table–was discovered to possess excellent ductility, toughness and resistance to corrosion. The unique combination of these excellent physical properties allowed transitional CCP nanometals to be deployed in harsh physical, chemical and biological environments.

Amongst these transitional CCP metals, platinum (Pt) and gold (Au) nanometals stood out. Pt has a relatively higher ductility, corrosion resistance and reactivity as compared to other CCP metals. In addition to that, it possesses good biocompatibility, which makes it an ideal candidate for biomedical applications. Hence, Pt nanomaterials were commonly used for the fabrication of opto-electronic devices, catalysis, atomic force microscope (AFM) tips, nano-electro-mechanical systems (NEMS) and biosensors. Bulk Au is known to possess excellent conductivity. Nanometallic Au with characteristics sizes smaller than 2 nm was discovered to be virtually electrical resistance-free, approaching the unit quantum conductance in the limiting case of a single, monatomic Au nanowire chain. These Au atomic chains were found to be very stable, which enabled them to be fabricated and employed as ultrahigh-density nano-electronic circuits. Based on these desirable properties, Pt and Au nanometals displayed great potential to be fabricated and used to a broad range of scientific applications and thus, both metals formed the focus of the investigations of this article.

Research ObjectivesFrom a pragmatic viewpoint, the electrical, magnetic and optical properties of nanometals would naturally generate a deal interest for researchers, as these properties have more direct and imminent applicability. As such, for the past decade or so, a lot of attention was focused on investigating these physical properties, both via laboratory experiment and computational simulations. These studies established the applicability of nanometals –in particular, one-dimensional metallic nanowires–in extreme physical (electrical nano-arrays, NEMS), chemical (catalysis) and biological (drug delivery, retinal implants) environments. The often-neglected mechanical properties thus became a point of contention as it is a necessity to understand how the metallic nanowires deform and respond to these harsh environments, so as to maintain their applicability. Research seeks to investigate the mechanical response of Pt and Au nanowires, subjected to a broad strain rate spectrum (from quasi-static to supersonic), which revealed interesting and novel static and dynamic properties in these nanowires.

Modelling and Simulation ResultsA series of computational studies on the static and dynamic mechanical responses of Pt and Au nanowires with characteristic sizes ranging between 1.4 nm and 7.0nm were conducted. Molecular dynamics (MD) simulation was used for all studies. The many-body Sutton-Chen (SC) potential was adopted. The SC potential form was formulated from first-principles generalisation for metallic d-bonds, which captures the density-dependent atomic interactions (or many-body interactions) in a vivid manner. As such, the (111) surface reconstruction observed in CCP structures were well-described by the SC potential, and the elastic constants and bulk mechanical properties of typical FCC metals predicted by the potential falls within a deviation of 10% from the experimental values. The simplicity of the SC potential allows simulations to be performed in an efficient manner, based on the MPI-parallelised open-source MD code – DL_POLY. The original program only enables equilibrium MD (EMD) to be performed. The program has been modified to enable non-equilibrium MD (NEMD) to be performed for mechanically and thermally-perturbed systems.

Fig. 1 - Atomic diagrams for Pt and Au nanowire, with atoms at their original fcc lattice positions. White atoms denote Pt atoms, yellow atoms denote Au atoms, brown atoms denote the fixed atomic layers, cyan atoms denote surface atoms and pink atoms denote corner atoms. (a) 2.0 nm x 4.0 nm (890 atoms); (b) 4.0 nm x 8.0 nm (6 660 atoms); (c) 6.0 nm x 12.0 nm (22 000 atoms). Diagrams alongside the nanowires indicate the respective longitudinal cross-sections.

Mechanical Behaviour of Nanowires

6 December 2007

Fig. 1 shows the atomic models of the MD simulations. Non-periodic boundary conditions were applied in all three Cartesian directions, creating all-round free surfaces. The nanowires were first subjected to thermal equilibration at 300K, allowing the atoms to settle into their stable positions. This process was known as thermodynamic relaxation, which allows the program to detect undesirable atomic configurations. The nanowires were then stretched by displacing the top and bottom fixed atomic planes at a constant stretch velocity. The stretch velocities between the quasi-static 1.0 m s-1 and the supersonic 1200 m s-1 were studied, which revealed three distinct deformation modes for metallic nanowires namely, the quasi-static, crystalline-ordered deformation (for stretch velocities between 1.0 m s-1 and 10 m s-1), the transitional mixed-mode deformation (for stretch velocities between 10 m s-1 and 100 m s-1), and the amorphous disordered deformation (for stretch velocities above 100 m s-1), resulting in the observation of “strain-induced melting” in metallic nanowires.

Simulations showed that, due to the absence of defects, single-crystalline metallic nanowires could achieve tensile strength in the giga-pascal region (109 N/m2) under static loading. They undergo quasi-periodic stress-strain cycles, display superplastic behaviour after first yield, and rupturing at more than 50% strain with the formation of atomic-scale substructures nearing rupture, as shown in Fig. 2. The Young’s modulus and Poisson ratio of the nanowires were not significantly different from the bulk properties. The nanowires were observed to undergo phase transformation at room temperature under sufficiently high strain rates. The ordered FCC crystalline structure of the nanowire was phase-transformed into a disordered amorphous structure. This curious phenomenon is unique only at nanoscale as the fusion of enthalpy (i.e. the amount of energy required to hold the atoms together) is greatly reduced. This reduced enthalpy of fusion allowed the energy supplied by a sufficiently high strain rate (> 100 m s-1), to physically break the metallic bonds and send the originally ordered structure into disarray. This would not have been possible for bulk materials with a very much higher enthalpy of fusion. From Fig. 3, it could be seen that the kinetic energy per atom exceeded the enthalpy of fusion for nanowires subjected to the high strain rate of 480 m s-1, resulting in obvious phase transformation as illustrated in Fig. 4 --Nanowires could therefore be “mechanically-melted” at room temperature and, from Fig. 4, it was discovered that the melting is localised, and the location of the melted region could be easily controlled by varying the strain rate. The amorphous structure could then be stretched to two times more its original length (>100% strain), displaying both exceptional strength and superplasticity. “Strain-induced melting” is a neat way to produce nano-metallic glasses, due to advantages such as localisation and controllability.

It has been further discovered that the strain wave propagation speed is size-dependent, which was observed to be much faster than that predicted from the continuum 1D wave propagation equation. This was attributed to the significant proportion of surface atoms in nanowires with characteristic sizes smaller than 4.0 nm, resulting in the presence of inherent surface stresses. The enhancement in wave propagation speed was found to follow a second-order relationship with the surface stresses.

Conclusion and Future Studies

Fig. 2 - Stress-strain response of small Pt nanowires with diameter 1.4 nm.

Fig. 3 - Mechanism behind “strain-induced melting” of metallic nanowires.

7December 2007

Conclusion and Future StudiesA series of computational studies were conducted to investigate the static and dynamic mechanical responses of Pt and Au nanowires. Several key observations could be highlighted. Firstly, the metallic nanowire deforms in three dominant modes – the crystalline-ordered for low strain rates, mixed-mode for moderate strain rates and amorphous-disordered for high strain rates. Secondly, nanowires could be “mechanically melted” at room temperature due to its reduced enthalpy of fusion, leading to a neater and simpler way to melt nanomaterials. Thirdly, the melting due to dynamic straining is localised, and could be accurately predicted by the one-dimensional wave propagation equation, indicating that the location of the melt could be well-controlled. Finally, the strain wave propagation speed in a metallic nanowire is size-dependent, and is much faster than

that predicted from the continuum wave equation for nanowires with characteristic sizes smaller than 4.0 nm. Observations revealed novel and interesting mechanical properties for metallic nanowires, indicating the promise of metallic nanowires to be deployed in a broad range of physical applications. Subsequent studies will be extended to investigate the mechanical and thermal behaviour of other metallic nanowire systems like nanoring, nanospring and nanochain. Fragmentation of nanowires, due to Rayleigh instability, was observed during gradual heating of the atomic system. It would be interesting to observe if such phenomenon do occur in nanorings, and two-dimensional nanosystems like nanoshells and nanosheets (Fig. 5).

Fig. 4 - Evolution from mixed-mode deformation to amorphous-disordered deformation over a spectrum of strain rates, indicating highly localized necks.

Fig. 5 - Future studies on (a) Melting of nanorings; (b) Deformation of nanosprings and nanochains; (c) Melting of nanoshells; (d) Melting of nanosheets

8 December 2007

ResearchBy YONG Kian Soonyongks@ihpc.a-star.edu.sg

Interactions of Pentacene with Si(111)-7x7 Si(111)-7x7 is a chemically rich semiconductor surface due to the different reactive sites at the center and corner adatoms and the rest atoms. These surface atoms contain unpaired electrons which form chemical bonds readily with various incoming molecules. Fig. 1 shows the locations of the adatoms and rest atoms within a single surface unit cell with the corresponding scanning tunneling microscopy (STM) image. STM is a surface analytical tool that is capable of producing atomically-resolved images containing convoluting topographic and electronic structures of the surface. Apparently, only the twelve adatoms within a unit cell are visible in the STM image as the rest atoms are spatially lower than the adatoms to be detected by the STM tip. Furthermore, each unit cell on the surface comprises of an unfaulted and a faulted half, as regards to the stacking sequence of the top few layers of atoms.

The understanding of the reaction of Si(111)-7x7 with pentacene (Fig. 2), an important molecule in organic electronics, contributes to the development of silicon-based organic-inorganic hybrid devices. In order to achieve an atomistic understanding of the reaction, investigation using techniques that offer atomic scale information, such as STM, is imperative. Additionally, theoretical simulation and modelling helps to verify and to explain the experimental results.

Fig. 3a shows three STM images of Si(111)-7x7 with adsorbed pentacene, which correspond to three types of binding configurations of the molecules on the surface. The three configurations are labelled as type ‘A’, ‘B’, and ‘C’ binding modes in Fig. 3a(i)-(iii) respectively. Type ‘A’ configuration comprises of a pair of bright spots that straddle across the faulted and unfaulted halves of the unit cell. Additionally, the two bright spots are located at specific positions relative to each other and close to the adatoms. In contrast, pentacene in type ‘B’ configuration appears as a dark feature in the STM image as shown in Fig. 3a(ii). This dark feature occupies only one half of the 7x7 unit cell and systematically replaces neighboring centre adatoms pair. Similarly, pentacene in type ‘C’ configuration also appears as a dark feature, but it straddles across the faulted and unfaulted halves of the unit cell as displayed in Fig. 3a(iii). Specifically, this dark feature results in the simultaneous disappearance of a centre adatom on one half and a corner adatom on the other half of the unit cell.

Fig. 2 – A pentacene molecule with some of its dimensions (in unit of angstrom) shown.

Fig. 3 – (a) STM images and (b) schematic diagrams showing the configurations of pentacene on a Si(111)-7 x 7 unit cell for type (i) ‘A’, (ii) ‘B’, and (iii) ‘C’ binding modes.

Fig. 1 - (a) Single unit cell of Si(111)-7 x 7 showing the locations of the center adatoms (red), corner adatoms (blue), and rest atoms (orange). (b) STM image of Si(111)-7 x 7. Within the unit cell (outlined rhombus), the twelve bright spots correspond to the adatom positions.

9December 2007

The structures of pentacene in the different binding configurations on Si(111)-7x7 can be elucidated by studying their orientations with respect to the underlying Si atoms as well as by comparing the dimensions between the surface Si atoms and the pentacene C atoms. The unique locations of the two bright spots in the STM image for configuration ‘A’ suggest the involvement of the two adatoms, where the two bright spots are closely located at, in bonding pentacene to the substrate. Having a separation of 13.84 Å, these two particular adatoms can only react with the two farthest carbon atoms in pentacene (C-7 and C-14 in Figure 2), which are separated by a distance of 12.32 Å. The binding configuration is shown in Figure 3b(i), where the pentacene molecule is snuggly fitted within three adatoms and one rest atom on the substrate.

Going by similar analysis, the configuration of pentacene in type ‘B’ and ‘C’ binding modes can be elucidated and are shown in Figure 3b(ii) and (iii), respectively. Pentacene in configuration ‘B’ comprises of four covalent bonds that are formed between the two opposite C in ring I as well as ring IV and two neighboring pairs of centre adatom-rest atom. Configuration ‘C’, on the other hand, involves the terminal bridging of pentacene between two oppositely oriented adatom-rest atom pairs that span across the faulted and unfaulted halves of a unit cell. Furthermore, pentacene in configuration ‘C’ was found to be present in the lowest proportion among the various binding modes.

Theoretical calculations were performed to model the different configurations of pentacene on Si(111)-7x7. Clusters having a single pentacene molecule bonded to the corresponding adsorption sites on Si(111)-7x7 were built and allowed to relax to give rise to the structures as shown in Figure 4. Apparently, pentacene in the various binding modes adopt almost flat-lying configurations on the surface. Furthermore, pentacene in configuration ‘C’ (Figure 4c) is twisted due to the orientation of the two reacted adatom-rest atom pairs as well as the height difference between the adatom and the rest atom. Hence, the lower number of type ‘C’ configuration may partly be justified by kinetic factor.

Though no data is available for conclusions to be made regarding the influence of kinetic factor, it is intuitive that the activation barrier for the production of type ‘C’ species is relatively high. This can be attributed to the energy required for the extensive breaking of the p bonds within pentacene to form the twisted structure so as to fulfill the prior geometric requirement for pentacene to bind to the surface in this configuration.

The STM images of the three binding configurations were also simulated and are shown in Figure 5. Figures 5a(i)-(iii) show the experimental images for configurations ‘A’, ‘B’, and ‘C’ and the corresponding simulated images are shown in Figures 5b(i)-(iii). For configuration ‘A’, a number of spots having very high intensity are apparent in the simulated image whereas two large bright spots are observed in the experimental image. The discrepancy between the experimental and theoretical results may be accounted for by the method that was used in the simulation, which neglects the actual geometry of the STM tip. In contrast, the spots in the simulated images for configurations ‘B’ and ‘C’ are much dimmer as compared to the Si. Such relative brightness intensities agree with the corresponding experimental STM images, where dark features are observed at the regions where the pentacene molecules are located.

Fig. 4 – Optimised structures for pentacene binding configurations (a) ‘A’, (b) ‘B’, and (c) ‘C’ on Si(111)-7x7. Each cluster has the following notation: ball-and-stick: pentacene, yellow lines: unfaulted half, green lines: faulted half, red spheres: adatoms, orange spheres: rest atoms. The schematic diagram on the left of each cluster shows the attachment position of the pentacene molecule within a unit cell.

Fig. 5 – (a) Experimental and (b) corresponding simulated STM images of pentacene in binding configurations (i) ‘A’, (ii) ‘B’, and (iii) ‘C’ on Si(111)-7x7.

10 December 2007

Research

In this post genomic era, when the sequence of the human genome as well as that of many other organisms have already been completed, the next phase of research will focus on analysing and making sense of the vast amount of information at hand.

While the blueprint of our body may be known, an understanding of how the individual components actually work in tandem to produce life is only beginning to emerge. Much resources has been invested to identify genes, proteins and their corresponding functions, and to translate this knowledge into treatment for diseases. In particular, an area that has received constant attention is cell communication, which plays a central role in the function and behaviour of cells and tissues. Throughout their lifetime, cells need to interpret and respond to signals from the external environment in order to survive, grow, move and even die. In this aspect, biochemical reactions and metabolic pathways are the most common means by which cells communicate. These, however, do not represent the whole picture and there is, in fact, a mechanical aspect to cell signalling.

Mechanotransduction is the process by which external mechanical stimuli are converted into biochemical signals. Essentially all organisms are sensitive to physical forces at various different levels, from the smallest cell to tissues and organs. It is these forces that regulate a wide array of physiological processes, such as the formation of bone and wound healing. Failure or deregulation in the response mechanism often leads to some form of deficiencies or diseases.

At the cell level, the cytoskeleton and extracellular matrix (ECM) regulate cellular signal transduction. Besides providing structural support to the cell, the cytoskeleton and ECM also relay external mechanical forces into the inner cell and alter its biochemical properties, thereby initiating a change in behaviour.

Role of Cytoskeleton in Cell Communication

By WONG Sum Thaiwongst@ihpc.a-star.edu.sg

The cytoskeleton of a cell. Actin filaments are shown in red, microtubules in green, and the nuclei are in blue.

11December 2007

Within a cell, the cytoskeleton primarily consists of three types of protein fibers – microfilaments, microtubules and intermediate filaments, arranged in a networked structure. Each type of fibers has a different composition and structural organisation. Microfilaments are two-stranded helical polymers of the protein actin and appear as flexible structures with a diameter of 5-9 nm. They are distributed throughout the cell and determine the shape of the cell surface. Microtubules are long, hollow cylinders of the protein tubulin. With a larger diameter of 25nm, they are more rigid than microfilaments. They have one end attached to the centrosome (required for cell division) and determine the positions of organelles and direct intracellular transport. Intermediate filaments are ropelike fibers with a diameter of 10nm. They are made from a large family of intermediate filament proteins and serve to provide mechanical strength and resistance to shear stress. The function of the cytoskeleton is dependent on these filaments, which are interconnected through linkage to each other and other cellular components.

Unlike the cytoskeleton, the ECM is found in between the cells and is composed of a variety of proteins and complex sugars, secreted locally by surrounding cells and arranged into an organised meshwork. Cells attached to the ECM through many different types of adhesion points, of which the largest and most well-studied is the focal adhesion (FA). These structures consist of a large number of structural and signaling proteins. For all adhesion points, a specific transmembrane protein known as integrin binds to the external ECM. By recruiting other cytoskeletal proteins, which binds to the intracellular microfilaments, integrin anchors the cytoskeleton to the ECM and provides a means for bidirectional communication across the cell membrane.

The cellular response to mechanical forces is coupled to the internal organisation of the cytoskeleton as well as to adhesion to the surrounding ECM. Through applying or removing an external load on a cell and restructuring its cytoskeleton and the adjacent ECM, the cell is able to transduce the changes in mechanical environment into different biochemical reactions within itself. It has been shown that cells can even activate different genes and thus synthesise different proteins simply by modifying their shapes. One possible explanation for this phenomenon is that the enzymes and other molecules are physically immobilised on the cytoskeleton, and changing the conformation of the cytoskeleton could affect the biochemical interactions and hence alter the resultant singalling pathways.

In conclusion, the study of mechanotransduction has shown that the cytoskeleton of the cell has provided an alternative means for cell communication. With further research and development of new tools, there is a possibility that mechanical force may turn out to be the most effective means to control cellular behaviour and ultimately the fate of the cell. From the medical perspective, this approach also has the potential to lead to new treatments in areas such as cancer therapy and tissue engineering.

References[1] Orr A. W., Helmke B. P., Blackman B. R. & Schwartz M. A. (2006).

Mechanisms of Mechanotransduction, Developmental Cell 10, pp. 11-20

[2] Chen C. S., Tan J. & Tien J. (2004). Mechanotransduction at Cell-Matrix and Cell-Cell Contacts, Annu. Rev. Biomed. Eng. 6, pp. 275-302

[3] Alberts B., Johnson A., Lewis J., Raff M., Roberts K., Walter P. (2002). The Cytoskeleton, Molecular Biology of the Cell, pp. 907-982

Organisation of Actin filaments, Microtubules, and Intermediate filaments within a cell.

12 December 2007

Editorial TeamJerry LimJoanne TanDaryl Yap

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In The NewsBy Corporate Commscomms@ihpc.a-star.edu.sg

Dr Raj. Thampuran awarded Public Administration Medal at National Day Awards 2007

Congratulations to Dr Li Er Ping, Programme Manager of the Engineering Software and Applications (ESA) programme on his elevated status to an IEEE fellow! The announcement was made on 16th November 2007 and the formal award presentation ceremony will be held in USA in 2008. Dr Li’s position will be effective on 1st January 2008 with the following citation:

For contributions to electromagnetic modelling and simulation in high speed electronics

An IEEE Fellow is the highest grade of membership in the organisation, and every year only a select group of recipients are awarded this prestigious honour. The grade of Fellow recognises exceptional distinction in the profession and is conferred only by invitation by the Board of Directors.

Dr Li Er Ping elevated to Institute of Electrical and Electronics Engineers (IEEE) Fellow

Congratulations to Dr Raj. Thampuran, Executive Director of IHPC, on being conferred the Public Administration Medal (Bronze) at the National Day Awards 2007! The Medal was presented to Dr Thampuran by His Excellency, the President of Singapore, Mr S R Nathan on 26th November 2007 at Suntec Convention Centre. It is awarded in recognition of efficiency and competency of all outstanding Singaporean public officers.

Throughout his service with A*STAR, Dr Thampuran has carried out his duties to the highest standards. As Director

of A*STAR’s Science and Engineering Research Council, Dr Thampuran was responsible for overseeing the Chemicals and Biological Sciences Portfolio and the research and development infrastructure.

As Executive Director of the Institute of High Performance Computing, one of A*STAR’s 14 research institutes, he formulated and developed the plan to re-shape and reposition IHPC as a leader in its field.

Congratulations to Dr Thampuran once again!