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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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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Ohayou, Nagoya

November 5th, 2009 by George Fitzgerald, PhD

What would entice me to spend 12 hours squeezed into a 757? How about terrific sushi, good company, and great science. The 3rd Theory Meets Industry International Workshop will be held November 11-13 in Nagoya, Japan. As you can read on their website:

The purpose of the current workshop is to exchange ideas at the cutting edge of first principles calculations, particularly their application to real-world problems.
Nagoya Castle, build in 1612, is one of the most famous sight seeing spots in Nagoya. Image courtesy of Wikipedia, http://en.wikipedia.org/wiki/Nagoya

Nagoya Castle, built in 1612. Courtesy of Wikipedia, http://en.wikipedia.org/wiki/Nagoya

This is truly a meeting of both developers of modeling applications and industrial practitioners. Rivalries are put aside and scientists discuss what’s being developed and what needs to be developed.

 

Theoretical chemists such as Bernard Delley (Paul Scherrer Institute) and Georg Kresse (University of Vienna) will be in attendance. And scientists from around the world – quite literally – will present their applications of modeling. The list includes applications to energy harvesting, alloys, Fischer-Tropsch catalysis, and oxide semiconductors – to name just a few. For a complete list download the programme.

Stay tuned for more info. In so far as jetlag allows, I’ll post updates by blog and twitter during the meeting.

では、また (See you)

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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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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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