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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The Power to Deliver– Prof. Robert Langer to Kick Off Accelrys UGM

February 12th, 2010 by Gerhard Goldbeck-Wood, PhD

I am really excited that Prof Robert Langer is going to join the Accelrys UGM in Boston to deliver a plenary address. Though he probably needs no introduction, Langer received the Charles Stark Draper Prize, considered the equivalent of the Nobel Prize for engineers and the 2008 Millennium Prize, the world’s largest technology prize. Check out a recent video, to hear more about his own journey which took him from a Chemical Engineering degree to the forefront of medical research on delivery systems and tissue engineering.

As the UGM sets out to discuss the latest advances in materials and pharmaceuticals research, Prof Langer brings it all together. Drugs on their own are powerful, but putting them simply into pills seems a bit like a powerful engine in a car without a steering wheel. Langer has pioneered ways in which materials, especially polymers can be used to steer their delivery to much greater effect in curing disease. With the development of nanotechnology over the last decade, the sophistication of the drug and the material can work more and more together, and I really look forward to the materials and life science interaction at the UGM.

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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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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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Take the leap: Materials Studio 5.0

October 16th, 2009 by Gerhard Goldbeck-Wood, PhD

Just back from the EUGM and Nanotech Consortium Meeting, a week of lively discussions (and foosball matches ;-) and of course our announcement of the release of Materials Studio 5.0. It’s been great finally to talk about and demo all the new features, which we are all so excited about. Getting the requests in for shipment of the new version already … well, it won’t be long.

You can read more about Materials Studio 5.0 at a high level in our Press Release, or in more detail in our ‘What’s New’ document. Perhaps you have read the ‘Transforming Materials Modeling’ tag line in there: imagine the discussions we’ve had about that: “Is it really?” “What is transforming…” and so on. But honestly it is what we are aiming to do with Materials Studio, and there are many things in the 5.0 release that make a real difference.

My take right now from the discussions at the Consortium and User Group Meetings is that the efficiency you gain because of the integration and flexibility this new release provides is quite a step change. The new Amorphous Cell for example got some wows from Materials Science and Life Science folks alike. It’s really a kind of universal structure builder. Want to build a nanocomposite, for example with nanotubes and polymers around them: not a problem. And perhaps there is some small molecule inside the tube: easy.  And what about a protein soaked in a solution: consider it done!

For the second ‘transforming’ example, for me it’s Kinetix, the new Kinetic Monte Carlo module we built for the Nanotech Consortium. I alluded to Kinetic Monte Carlo development earlier, and thanks to a great collaboration with Tonek Jansen and Johan Lukkien from TU Eindhoven, you can now simulate processes such as a Fuel Cell cathode reaction in Materials Studio, over real time scales of minutes. Considering we start at femtoseconds, that’s quite a leap anyway.

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Overlaps and Crossovers at the European User Group Meeting

August 11th, 2009 by Gerhard Goldbeck-Wood, PhD

We announced the European User Group meeting a few days ago. Check out the UGM webpages, and especially the themes.  I am excited that we’ll have users from all product and application areas together, including:

• Materials Studio

• Discovery Studio and Platform

• Training sessions and the lot.

We’re in different tracks, but I expect to see some interesting overlaps/crossovers.  For example, we’ll discuss the high throughput methods in materials to the platform, along with what we can learn from the collaborative environments and custom solutions in the Discovery Studio field for other areas such as Materials.

Also, I’ll be hosting the Annual meeting of the Nanotech Consortium on the Tuesday/Wednesday of that week, where we’ll discuss the latest, especially in the field of kinetic modelling of reactions. Take a look at my previous post on that subject.

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Driven by Multiscale Simulation: from Carbon atoms to car engines

July 14th, 2009 by Gerhard Goldbeck-Wood, PhD

Multiscale has been a buzzword for such a long time now, most of us must be genuinely tired of it. Nevertheless, when you see actual applications, and the fruits of a lot of hard work come together, I find it still exciting.

A great example I encountered last week is the work by Prof Markus Kraft and his group at Cambridge University’s Chemical Engineering Department. He was over at our Cambridge office for an Accelrys Science and Technology Seminar, talking about soot particles, the black stuff of course that’s actually used to good effect in dyes, and that engineers try and avoid in combustion engines.

The formation of these nano-particles is really and truly a multiscale process. Kraft’s research team starts the long multiscale journey at the quantum level, using DMol3 in Materials Studio to calculate transition states for oxidation reactions of polycyclic aromatic hydrocarbons (PCAH)

This information then enters into rate constant calculations, which then in turn go into Kinetic Monte Carlo simulations (see some cool and funny examples). With KMC you can see the PCAH structures grow. They are then analysed to give input to a population balance model for particles at the next scale, finally entering into engine models.

You can obviously read up the whole story much better in the Kraft group publications. The point here is that it’s a great example of how the different simulation tools through the scales fit together to solve a complex engineering problem.

Developing such a multiscale toolset is what the Nanotechnology Consortium is all about. Already its 14 Members access a module (also tested at Markus Kraft’s lab), to determine rate constants on the basis of transition state calculations. The tool was developed by Struan Robertson, Accelrys’ Simulations group manager. Incidentally he’s just got another great publication out on the topic: “Detailed balance in multiple-well chemical reactions” with guys from Sandia, Argonne, Leeds and Oxford. Great stuff about how you get a handle on calculating rate constants for complex reactions such as in combustion and atmospheric chemistry.

Transition state calculations themselves become more realistic as a result of another Consortium development, i.e. hybrid QM/MM calculations with MS QMERA, based on the well-known ChemShell environment.

In many cases, a detailed understanding of reactive processes, especially at interfaces, is required. The challenge is that quantum methods can only provide a very limited range of dynamics, while forcefield methods cannot adaequately describe reactions.

So we got together with Prof Frauenheim’s group at Bremen University and collaborators to integrate DFTB+ into the Materials Studio toolset .

Last not least of course there is Kinetic Monte Carlo. As in the work by Kraft I described above, KMC really makes the leap in scale, especially time scale, and connects the ‘science into engineering’ world. The Nanotech Consortium is moving forward in this field as well. Watch this space for more on Kinetic Monte Carlo in the Accelrys toolset.

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