Nanotechnology, Alternate Energy and Virtual Screening…oh my!

March 9th, 2010 by Lalitha Subramanian, PhD

It was indeed very pleasant to visit the Stanford campus last week; I had a chance to see familiar faces, as well as new ones, amongst the attendees at the workshop, “Bridging the Gap Between Theory and Experiment: Which Theoretical Approaches Are Best Suited To Solve Real Problems In Nanotechnology and Biology”

There were several invited talks on semiconductors and catalyst nano particles, apart from my talk on alternate energy.  Many of the speakers discussed the suitability of a particular simulation approach for the study of specific applications, while others discussed the most recent state-of-the-art theoretical advances to tackle real problems at several timescales.  It is particularly challenging when simulations are to be used not just for gaining insights into a system but to be a predictive tool as well as for virtual screening.  While virtual screening is a well-studied art in the world of small molecule drug discovery, this is only now gaining traction in the materials world.

For further inight into virtual screening in materials, check out George Fitzgerald’s webinar on High-throughput Quantum Chemistry and Virtual Screening for Lithium Ion Battery Electrolyte Materials, next Wednesday, March 16.

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Calling DFT to Order

February 15th, 2010 by George Fitzgerald, PhD

One of the most interesting developments in density functional theory (DFT) in recent years is the emergence of the so-called “Order-N” methods. What’s that mean? Quantum chemists and physicists classify the computational cost of a method by how rapidly it scales with the number of electrons (or the number of molecular orbitals.) This can get into a real jargon of computational chemistry, but here are some examples:   

ONETEP gets its speed by using localized molecular orbitals (MOs). Top: a conventional MO is spatially delocalized, hence it interacts with many other MOs. Bottom: localized MOs do not interacte, hence less computational effort is required to evaluate matrix elements.

 Consider the N4 case as an example. This means that if you double the size of the system that you’re modeling, say from a single amino acid to a DNA base pair, the cost  (i.e., CPU time) goes up by roughly 16x. That makes many of these approaches prohibitive for systems with a large number of atoms. The good news is that it doesn’t really need to cost this much. The atomic orbitals that constitute the molecular orbitals have finite ranges, so clever implementations can hold down the scaling. The holy grail is to develop methods that scale as N1 or N, hence the expression “Order-N” or “linear scaling.” Using such a method, doubling the size of the system simply doubles the amount of CPU time.   

My favorite Order-N method is ONETEP (not surprising, considering that it’s distributed by Accelrys). As explained in their publications, this approach uses orbitals that can be spatially localized more than conventional molecular orbitals to achieve its speed. As a result of localization, there’s a lot of sparsity in the DFT calculation, meaning a lot of terms go to zero and don’t need to be evaluated. Consequently, it’s possible to perform DFT calculations on systems with 1000s of atoms. Because of its ability to treat system of this size, it’s ideally suited for nanotechnology applications. Some recent examples include silicon nanorods (Si766H462) or building quasicrystals (Penrose tiles) with 10,5-coronene.  

Why bring this up now? CECAM (Centre Euopéen de Calcul Atomique et Moléculaire) is hosting a workshop on linear-scaling DFT with ONETEP April 13-16 in Cambridge, UK. This is a chance for experienced modelers and newcomers to learn from the expert. Plus they’ll have access to the Cambridge Darwin supercomputer cluster, so attendees will have fun running some really big calculations. What kind of materials would you want to study if you had access to this sort of technology?

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Materials and Energy: A Maturing Relationship

February 11th, 2010 by Gerhard Goldbeck-Wood, PhD

After simple combustion, and the nuclear option, the relationship between materials and energy is as topical as ever. Taking a new turn in the 21st century the couple have matured into exploring more subtle ways to relate to each other. What am I talking about? Well, there are so many ways in which materials affect energy and energy is affected by materials, i.e. energy generation, storage, conservation and the efficient use of energy. In all of these, insights at the atomistic and quantum level help us to design cleaner energy sources, and find less wasteful ways of using energy. To find out more on how modelling supports the discovery and understanding of new materials for fuel cells and batteries, please check out the Materials Studio 5.0 Webinar Series.  Following the recent webinar on fuel cell catalysts (for which you can still access the recording), we have two more webinars scheduled on the topic:

February 17th, 2pm GMT/6am PST: Atomic-Scale Insights into Materials for Clean Energy. The webinar will be given by Prof Saiful Islam from University of Bath, who is a renowned expert in the field: check out the interviews, podcasts and publications.

March 16th, 3pm GMT/8am PDT:  High-throughput Quantum Chemistry and Virtual Screening for Lithium Ion Battery Electrolyte Materials . George Fitzgerald will include results from a collaboration with Mitsubishi Chemical Inc which was also published in The Journal of Power Sources.

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Theory and Experiment in “Step” on Semiconductors

February 8th, 2010 by George Fitzgerald, PhD

A recent news article by the University of Texas at Dallas (UTD)  highlighted recent joint work by the Department of Materials Science and Engineering and Accelrys on critical surface reactions of Silicon. The research points the way to ”improve semiconductor devices’ performance in health care and solar power applications in particular.”

Who cares? Anybody who uses chips, solar cells, or any other device containing semiconductors (in other words, all of us.)  

Insertion of Nitrogen atom is predicted to occur preferentially at the step edge of Si(111)

 How does the latest research help? A typical semiconductor device consists of a metal oxide semiconductor layer (e.g., HfO2) deposited on a silicon substrate. As explained by co-author Dr. Mat Halls, formation of an SiO2interlayer between the silicon substrate and metal oxide can decrease semiconductor performance. One approach to solving this is to introduce a nitride barrier to prevent the growth of interfacial SiO2. The ability to introduce such heteroatoms into the topmost layers of Si affords additional opportunities to tune the surface properties by enhancing chemical reactivity at these sites to form functional surfaces. But how do you get the nitrogen to stick to the surface?     

In the latest research, published in Nature Materials, used infra-red spectroscopy  to explore the possible formation mechanisms of nitride on silicon surfaces terminated by hydrogen. Calculations using density functional theory (DFT) demonstrated how stepped edges are important to formation of the nitride layers. The reaction mechanism on the stepped surface provides a means of controlling the reaction. As the authors wrote: “The ability to control the reaction … enables the realization of applications … including sensing, electrical and thermal transport, and molecular computing.” This is a beautiful demonstration of the complementarity of theory and experiment. One can deal with facts, but requires interpretation. The other provides detailed explanations at the atomic level, but sometime requires an anchor to the “real world.” Together they can do more. Wouldn’t it be great if all viewpoints could be reconciled this well?

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DFT Redux

January 14th, 2010 by George Fitzgerald, PhD

I thought I’d start the year with an easy blog, simply following up on my earlier ramblings of 25 October 2009: DFT Goes (Even More) Mainstream. In that article I discussed the success of Density FunctionalTheory (DFT) and used the annual number of publications as a metric. The numbers show that publications grew by over 25% per annum, but the results for 2009 were naturally incomplete.

Happily the trend continued through 2009 for a total of 4621 DFT references in ACS Journals. Here are a few of my favorite publications, thought not all are drawn from the ACS citations. Yes, of course, these use Accelrys DFT packages, but they are still pretty cool articles:

Let me and my readers know what you think are the most interesting DFT articles from 2009.

†Strictly speaking, this was not QSAR, Quantitative Structure-Activity Relationship, because they didn’t actually base predictions on the structure. I use the term here more generally to refer to relationships that predict complex properites like catalytic activity, on the basis of simpler properties, like workfunction.

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“Fueling” the Discovery of New and Alternative Materials

January 6th, 2010 by Accelrys Team

Materials Studio Webinar Series Part V: Exploring New Fuel Cell Materials

There is increasing pressure to deliver lighter, more efficient and less expensive materials more frequently and faster than ever before. Fortunately, the integration of Materials Studio applications such as CASTEP and the Pipeline Pilot platform opens a range of possibilities for the discovery of new materials.

The experts at Accelrys have developed a new framework that screens complex systems and properties across numerous materials and applications. This system is currently being applied to fuel cell catalysts to find alternatives to costly materials such as platinum. Dr. Jacob Gavartin and Dr. Gerhard Goldbeck-Wood will discuss this approach and its application in detail during next week’s webinar:

Exploring New Fuel Cell Materials: High Throughput Calculations and Data Analysis with Materials Studio 5.0 and Pipeline Pilot
January 13, 8am PST / 4pm GMT

Register today!

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Materials Studio 5.0: A particle-ular challenge

December 11th, 2009 by Stephen Todd, PhD

In the last of the series of my blogs on Materials Studio 5.0 functionality, I will be writing about new functionality in the mesoscale area. Back in Materials Studio 4.4, we developed a new module called Mesocite. Mesocite is a module for doing coarse-grained molecular dynamics where the elementary particle is a bead. In coarse-grained molecular dynamics, a bead typically represents several heavy atoms. This has advantages over classical molecular dynamics such as Forcite Plus as you can access longer time and length scales.

In Materials Studio 5.0, we added the capability to do Dissipative Particle Dynamics (DPD) to Mesocite. DPD is a very coarse-grained dynamics approach where the bead can represent many atoms or even molecules. We already have a module which can do DPD in Materials Studio but this has limited ability to be extended. By developing the new DPD in Mesocite, we could take advantage of the underlying MatServer environment to easily extend DPD to run in parallel and work with MaterialsScript amongst other things.

One issue we faced is that the legacy DPD tool works in reduced units whereas MatServer requires physical units. The use of reduced units is fairly standard in DPD however it makes it more difficult to relate the results back to experimentalists. Therefore, we thought that switching to physical units would be a good idea. However, there were still questions as to how customers would work with a DPD in physical units. We asked a small focus group of customers very early in the release as to how they would like to parameterize DPD calculations. All agreed that getting the results in physical units was preferable but they still wanted to set up the calculations in reduced units as they have lots of historical data they want to re-use. So, we have a new user interface which allows setup in either reduced or physical units but then converts to physical units for the calculation!

When a new piece of functionality is added to Materials Studio, I like to add a tutorial on how to apply the software, what sort of values customers should use, and how to get the most out of the software. For the new DPD functionality, I looked at several papers before settling on an application by Groot and Rabone looking at the effect of non-ionic surfactants on membrane properties. This interested me as it demonstrates the strength of mesoscale in looking at varying concentrations of different components and seeing the effect on morphology. I also realized that I could use some of the Mesocite analysis to really analyze the system for properties such as concentration profiles and examining the diffusivity of the beads across the membrane. This mapped really well to the original results and produced what I hope is an interesting tutorial.

There was another reason I chose this paper too – Groot and Rabone also looked at the effect of strain on the membrane. This wasn’t possible with the old DPD module but, using some MaterialsScript, I could strain the system and then calculate the surface tension. As I like to dabble with MaterialsScript, the lure of this was irresistible and the script I made is available from the Accelrys Community website.

One minor issue was that the system sizes and relative amounts were not clear from the paper. Luckily there are several ex-Unilever people at Accelrys, so one of my colleagues, Dr Neil Spenley, contacted one of the authors, Dr Robert D. Groot. I was also lucky that Dr Groot obviously hordes his old research work and, a day later, I had the original DPD input file in my hands!

The results from the strain calculations also show the same trends as those reported by Groot and Rabone so I was pretty happy with this work.

So that wraps up my blogs on Materials Studio 5.0. I hope to have given you an insight into some of the processes that go into making a new version of Materials Studio.

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Falling towards MRS

November 25th, 2009 by Accelrys Team

As we make our way to the MRS Fall Meeting at the John B. Hynes Convention Center in Boston, MA from November 30 to December 4, we find ourselves looking forward to the many wonderful things in store for us; not the least of which is the opportunity to visit such a great city.

We  eagerly anticipate the plenary session on Monday as Andre Geim from the University of Manchester, UK will present “an overview of [his] work on graphene, concentrating on its fascinating electronic and optical properties, and speculating about future applications.”

At the exhibit in booth #508, Accelrys materials modeling experts will showcase the new features and enhancements found in Materials Studio 5.0.

On Wednesday, December 2 at 12:00 pm, Dr. George Fitzgerald of Accelrys will host a luncheon workshop, “Data Pipelining and Workflow Management for Materials Science Applications,” that will demonstrate how to combine materials modeling with workflow management tools to improve productivity. The workshop will present examples in polymers, catalysts, and nanotechnology. To register, please visit: http://webrsvp.mrs.org/rsvp.aspx?meeting_id=55

We hope to see you there!

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Life Without Oxygen

November 16th, 2009 by Max Petersen, Ph.D.

During my Ph.D. defense I joined untold legions of candidates that had to regurgitate on the same question: “How would life have evolved on a planet were carbon was replaced by silicon?” The depth of knowledge – that silicon and carbon have different number of electrons – might be considered pinnacles of academic higher education, but to make an impact on real world applications you might have to mix things up a bit, like throwing an “…and if there was no oxygen…” into the equation.

The question of “silicon based life” – or semiconductor technology to be mundane – has suffered lately of an acute case of excess oxygen. SiO2, the gate dielectric of choice of our forefathers, is today often nothing more than a pure nuisance. Mechanisms to avoid the toxic effects of oxygen have recently been discussed by researchers at Rutgers, University of Texas, and our very own colleague, Mat Halls. In a Nature Materials article, the authors demonstrate mechanisms for growing ultra-thin nitride layers on Si(111) substrates. These layers act as an effective barrier for oxygen diffusion and therefore avoid formation of SiO2 oxide layers in silicon substrates. For people outside of the field it should be noted that these pesky oxide layers were the showstoppers for many low-k dielectrics efforts which are essential to further device integration.

A schematic of how life without oxygen might have evolved - explanations see text.

A schematic of how life without oxygen might have evolved - explanations see text.

Fascinating enough, the growth of these films is initiated by decoration of dihydride stepedges. Mat was able not only to map out the entire reaction pathway using DMol3, but also to compute vibrational frequencies of all intermediates that could directly be linked to the experiments via IR spectroscopy. At low temperatures, these decorations can be stabilized and can provide the starting point for functionalization with potential applications in sensing, electrical and thermal transport, and molecular computing.

The experimental technique used to grow these films is called “atomic layer deposition” in which controlled reactions saturate a substrate with a single species which can then be alternated with other reactions to produce films with unprecedented uniformity and quality. This might sound like a big hoop to jump through just to keep oxygen out of a silicon substrate, but who knows what obstacles scientists struggle with on planets without oxygen, particularly when it comes to developing novel gate dielectrics, such as ZrO, HfO, and Al2O3.

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Theory Meets Industry In Nagoya

November 12th, 2009 by George Fitzgerald, PhD

I’ve enjoyed 2 days so far in Nagoya attending the “Theory Meets Industry” conference. There is some amazing work going on by both developers of computational methods and those who apply them. We’ve heard from developers like Bernard Delley and his recent work onTDDFT in DMol3, which will enable excited state calculations and UV spectra. We’ve also heard from Georg Kresse about his recent work on the Random Phase Approximation (RPA),which offers a way to improve not just DFT band gaps but total energies, as well.

There’s been an emphasis in alternative energy from the industrial participants. Applications are really diverse:

  • Rradiation damage in reactor containment materials by Christophe Domain of EDF
  • Improved solar cells by Royji Asahi of Toyota Central R&D Labs
  • Fischer-Tropsch catalysis by Werner Janse van Rensburg of Sasol Technologies
  • Hydrogen storage materials by Pascal Raybaud of IFP

This list also reflects the true international spirit of the conference.

I’ve also heard some interesting new approaches to doing calculations fast while not sacrificing accuracy. Gabor Csanyi of Cambridge University presented his Gaussian Approximation Potentials (GAP), an alternative to force fields that spans more of the potential energy surface. And Isao Tanaka of Kyoto University showed how he uses an improved Cluster Expansion method to study phase transitions. Keep your eye on these methods for future developments.

Today I make my own small contribution by presenting my work on high-throughput computation. Look for details on that in a future blog.

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