Spectroscopy: Where Theory Meets the Real World

February 23rd, 2010 by George Fitzgerald, PhD

One of the most successful uses of quantum mechanical modeling methods is to predict spectra. These methods are capable of yielding good predictions of UV/Visible, NMR, Infrared, Raman, THz, and EELS (electron energy loss spectroscopy) to name just a few. Spectroscopy (according to Wikipedia) is the “study of the interaction between radiation and matter as a function of wavelength … or frequency.” How does this help chemists? We can use the spectra to determine the structure of new molecules or materials; to determine the composition of mixtures; or to follow the course of a chemical reaction in situ. How does modeling help with this? In a number of ways, but I’ll cover just 2.

One way modeling comes into play is by working with experimental results to remove ambiguities. When a chemist is trying the determine the structure of a new material, he or she takes a spectrum, or two, or three. His or her knowledge of the ingredients together with the spectra gives a pretty good idea what the chemical or crystal structure is. In a lot of cases the data are sufficient only  to narrow this down to 3-4 possible structures. Molecular modeling resolve this ambiguity by predicting the spectrum of each possibility; the spectrum that matches the experimental one presumably corresponds to the “right” one. Modeling is even more valuable when investigating defect structures like this work on Mg2.5VMoO8.

Another use is telling where experimentalists to look for the spectral peaks of a new compound. This can be especially important when trying to detect the spectra of new, novel, or poorly characterized materials. Experimental terahertz (THz) spectroscopy, for example, examines the spectral range of 3-120 cm-1, and can be used for detection and identification for a wide assortment of compounds including explosives like HMX. It’s a lot safer to investigate these materials by modeling than in the lab.

A recent blog by Dr. Damian Allishighlights the importance of doing the simulations correctly. (By the way, Damian, congrats on getting to page 1000.) A lot of work for the past 40-odd years has gone into predicting spectra of isolated – or gas phase – molecules. But materials like HMX are crystalline, and calculations on the isolated molecules make for poor comparison with crystals. The recent work underscores how important it is to simulate crystals using crystals. And it’s not just for THz spectra. Recent work on NMR leads to the same conclusion. A couple of programs can do this. Damian’s blog focuses on DMol3 and Crystal06, but we should also mention CASTEP and Gaussian as other applications capable of predicting a wide variety of properties for solids.

Let’s keep modeling – but be careful out there: short cuts will lead to poor results, and molecular modeling will end up taking the rap for user error.

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Making Sense of the Cloud for Science: Part 1 continued

February 22nd, 2010 by Conrad Agramont

I last left you with a list of terms and examples surrounding the term “cloud computing;” now it’s time for a little context.  Utility Computing, such as Amazon Web Services (AWS) Elastic Cloud Computing (EC2) provides a customer with the ability to spin up new machines on-demand.  From the customer side, you don’t care what machine it’s on but you do get to define the type of resources you want to consume such as CPU cores and Memory.  So far this sounds just like Hosting, right?  Correct!  What’s different is that you don’t have to sign a long term contract for that resource AND you’re not tied to that actual hardware since in the background it’s really just a Virtual Machine.  Now this is where it gets interesting.  Hosting has been around for a while, but since Server Virtualization technologies such as Microsoft Hyper-V and VMware vSphere has become mature, it enables the flexibility and architectures of Cloud Computing.  And since this Server Virtualization is available to Enterprises, this is where you hear the term “Private Cloud” being add to the Enterprise mix.

Now let me quickly tackle a common question.  “What’s the difference between Amazon Web Services, Microsoft Azure, and Salesforce?  Aren’t they all the same?”  First off, this is a great question, but it’s really comparing apples, oranges, and tomatoes.  Yes, those are all fruits but each provide something very different to the consumer.  Where Clouds are different than fruit is that you can layer some of the clouds to deliver a service.  Remember that AWS is a Utility.  Microsoft Azure is a resource targeted towards developers.  Developers are different than IT and therefore have different requirements.  They like to write applications that typically consume some data and provide a User Interface.  They don’t want to be bothered with patch management, monitoring systems, deployment of servers, etc.  Microsoft Azure abstracts this from the developer.  They instead write to the “Fabric” of the Cloud Computing platform that Microsoft manages, which allows the developer focus on what they do best.  Finally, with Salesforce.com it’s even further abstracted.  You still have developers that can write applications based on Salesforce.com, but the developer is given even more constraints on what they can develop and how it can be implemented.

OK, enough of the Cloud Tutorial, but hopefully you have an understanding that there are many different types of clouds and how they can be used.  Are there challenges to adoption? You bet!  But there are always challenges when adopting technology.  While the above was about the technology, there are a number of business issues, concerns and questions that need to be addressed as well.  In the case of many organizations, one of the biggest hurdles is around securing and transporting of the data.

In the coming weeks, we’ll provide an update on our roadmap for leveraging, supporting, and providing guidance on using Cloud Computing and Virtualization technologies.  Accelrys has already been moving forward to partner with a number of Cloud vendors, Service Providers, and third-party software vendors to ensure our customer have the power of choice, delivery models, and a clear path to leverage Accelrys products in the cloud.

If you’re in any stage of interest, planning, evaluating, or deploying Accelrys products or other scientific applications in the Cloud, we’d love to hear from you!  As the leading provider of Scientific Informatics Solutions, we’re interested in supporting our customers no matter where there environment is – at home or in the cloud.  Visit our forums to continue the discussion: http://accelrys.org/

In the next part of this blog series, I’ll focus on the Business Issues found with leveraging the cloud.

To view all Conrad’s Cloud Series posts, please visit: http://blog.accelrys.com/author/conrad/

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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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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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Science, Fens and (No) Mountains

December 8th, 2009 by Gerhard Engel, PhD

I love the Alps: French, German, Swiss, Italian, Austrian, Slovenian, whatever. I take my family there every summer. They’ve got what Cambridge, England lacks.  You know: rocks, glaciers, waterfalls, lakes, meadows, cows, Strudel, Schnitzel, the lot.

So why exactly do I live and work in one of the flattest areas of the UK, a city just south of an area  of former swampland that the natives lovingly call “The Fens?”

It’s a long story really, a story of science  and adventure initially, but I suppose I ended up here because Cambridge is both the seat of a world-famous university and a European innovation hub that benefits from the ready availability of smart people and a prestigious address. That, and the absence of valleys, turned a wet piece of English countryside into Europe’s “Silicon Fen.”

No wonder then that at some point, around  1990, a Cambridge University spinoff called Cambridge Molecular Design became one of the precursors of Accelrys and evolved into what is now our European Headquarters.

I had an opportunity to reminisce about Accelrys’ roots and connections with Cambridge on the occasion of a recent meeting with the CEO of Cambridge Network, Matt Schofield. Cambridge Network provides many invaluable services to the Silicon Fen community. It helps employers find the right employees, it organizes and helps companies host outstanding events , runs special interest groups, and it offers a range of member benefits and business development opportunities for its members. In short, it offers tools and information that bring the Cambridge community together.

Accelrys has deep roots within this community.  Some of our flagship Materials Science products such as CASTEP and ONETEP originated here and are being continuously enhanced by teams of researchers at Cambridge University and their collaborators, and we benefit from many other fruitful  partnerships such as the one with Cambridge Crystallographic Data Centre. Several Accelrys scientists, myself included, learned their trade as part of thriving university departments such as the Cavendish Laboratory. Many of our customers benefit from the close geographical proximity that the Silicon Fen provides; and several of our partners have a presence in Cambridge and surrounding areas.

But at the same time, the Cambridge Network meeting reminded me that even more could be done to join efforts with Cambridge companies and university departments. Globalization is wonderful, but nothing beats partners next door. So we’ll continue to look to for Silicon Fen collaborations. Which is easy thanks to Cambridge Network, and because there’s not a single mountain obstructing our view …

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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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Taking a Deep Dive into the Sea of Spectroscopy

November 24th, 2009 by Accelrys Team

Materials Studio Webinar Series Part IV: Spectroscopy Methods in CASTEP

Over the last few weeks we’ve been providing insight into the numerous new functionalities and enhancements included in the latest version of Materials Studio. In our next webinar, Dr. Stewart Clark from the University of Durham and Dr. Keith Refson from the Science and Technology Facilities Council will dive deeper into the spectroscopy methods available in CASTEP. With Materials Studio 5.0, released last month, you can now predict Raman frequencies and intensities for solid-state materials and molecules. Raman is frequently used as a tool for probing the chemistry of in situ experiments. It is valuable since it can characterize both a solid substrate and molecular fragments. The ability to predict Raman spectra for these systems will aid experimentalists in interpreting the spectra and understanding the chemistry of these systems in detail.

Next week’s presenters are part of the CASTEP Developers Group that we have worked very closely with over the years. Read their praises from our own Product Manager, Stephen Todd. In this one-hour webinar they will provide background theory on spectroscopy, demonstrate how to do calculations in CASTEP and share results.

Raman study publication available: Our guest presenters, in collaboration with Accelrys staff, recently completed a study on the Raman spectra functionality in CASTEP. This paper is available for download through the Journal of Physics, free for a limited time. Download the Paper.

Join this team of experts on Dec 2nd at 8am PST / 4pm GMT as they share their insights and methodologies and answer your questions. Don’t miss this webinar: Register today!

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Materials Studio 5.0: “Packed” Full of Enhancements for Polymer Scientists

November 17th, 2009 by Accelrys Team

Materials Studio Webinar Series: Part III

This week’s webinar will focus on numerous Materials Studio 5.0 modules with enhancements of interest to Polymer Scientists. For example, the Amorphous Cell tool has new functionality such as the “Packing” task that allows you to pack molecules into a cell of any shape, into cells already containing a structure or into isosurfaces, such as the interior of a nanotube, to build complex structured systems. Also, exposure through MaterialsScript enables full automation of polymer workflows. Equally, the new DPD functionality in Mesocite extends the mesoscale modeling functionality to a new series of properties.

Join us on November 18th at 8am PST / 4pm GMT for Materials Studio 5.0: Use Cases for Polymer Scientists and get an in-depth overview of these new tools and example applications. Register today!

To view upcoming webinars in the series, please visit: http://accelrys.com/events/webinars/materials-studio-50.

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