DMol3 – Electronic structure calculations of diamond-like semiconductors

March 17th, 2010 by Accelrys Team

Offering insight from the perspective of a user, Accelrys is please to host a posting written by guest blogger Matthew Srnec, who will be presenting a poster of his work during the American Chemical Society (ACS) Conference next week, in San Francisco.

“As an undergraduate in chemistry, I was very fortunate to participate in a Research Experience for Undergraduates at Duquesne University in the summer of 2009.  Under the advising of Dr. Jennifer Aitken of the Department of Chemistry and Biochemistry, a computational research project was outlined for me regarding various materials that Dr. Aitken and her graduate students were studying.  I was introduced to Accelry’s DMol3 module in Materials Studio and was instructed to learn the intricacies of this program and apply it to the diamond-like semiconductors that Dr. Aitken’s lab was interested in.  Throughout my ten weeks at Duquesne, I found Accelrys’ DMol3 program extremely user friendly.  Their “help” feature aided immensely in performing the desired calculations and positive feedback was provided from their helpdesk when I came across any problems with my calculations.  At the conclusion of my research experience, tremendous progress was made using the DMol3 module with regard to diamond-like semiconductor calculations.

The success of these calculations has given me the opportunity to present the aforementioned research at the American Chemical Society Conference in San Francisco on March 22nd, 2010.  This presentation will take place during the Undergraduate Research Poster Session in the Division of Chemical Education.  I encourage anyone interested in learning more about this research and my experiences with Accelrys’ DMol3 module to visit my poster (#596) between 12:00-3:00 PM for an overview of my work.  I am delighted to have this opportunity and look forward to seeing you in San Francisco!”

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Sustainability: Part 1

March 16th, 2010 by Michael Doyle, PhD

Recently I have been flying a lot; its sort of an occupational hazard of being a field scientist during the winter months. Anyway, on one of the flights I was reading an article about the Exxon initiative in green algae based bio-plastics and feedstocks. This brought my mind back to the concept of sustainability and its myriad facets in chemical, pharmaceutical and materials sciences. Sustainability in terms of energy usage and cost of synthesis. Sustainability in terms of sourcing and raw materials and bio processing or germline design and breeding.  Even sustainability in terms of our education. These features fall into a common framework of technology and planning for the future, or using some of the perception and benefits of technology to guide our steps forward.

I remembered my initial feelings as a young scientist working in a refinery. I was overawed by the complexity and size of the cracking, reforming, fractionating, stripping and converting columns and reactors in the refinery and plant. I was there setting up a modelling and near remote sensor, (infra-red) process control system, to help optimize plant throughput and quality using chemical and process optimization, but that is another story.

Anyway, one day after climbing up and down the towers, I was discussing the plant with my manager and he asked me a question. “What is the most interesting or amazing thing about a chemical plant?”  I replied about the size, intricacy and complexity. He said in his view “no;” in his view it was the fact that you could never see, touch or smell the product, unless there was a vent over, or some sort of failure “bad thing” in the process. He continued the comparison; think of a car production line, there you can see all the product as it moves down the line with new wheels and engines being attached. In a chemical plant you cannot see anything of the complex changes that are performed on the materials as they flow through the reactors, stripping columns and condensers. In hind sight, this is a green or sustainable comment.  My view a few years on is that the chemical industry, and yes there have been some very few mistakes, is an amazing industry where very little of the product is exposed to the environment and all the complex and myriad transformations are performed in carefully protected containers. This in terms of efficiency, complexity and microscale materials engineering is a stunning achievement. Now other aspects of sustainability are the fate of the products that come out of these processes, the use of precious energy and fossil fuel reserves in these processes and the impact these materials have on people and their lives.

It is interesting to also note that one of the larger areas of sustainable research is in the pharmaceutical area. Here, there is significant research and development activity in the area of sustainable synthesis, which we will explore later, in Part 2 of this post.  Stay tuned!

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Spring forward to the ACS Conference

March 15th, 2010 by Accelrys Team

Join us at the ACS Spring 2010 Conference, held at Moscone Center in San Francisco on March 21-25, 2010.  At booth #1008, Accelrys will be showcasing the latest developments in Pipeline Pilot, Discovery Studio and Materials Studio.

We have a variety of talks, workshops and posters planned for the conference, including:

TALKS
* High-throughout quantum chemistry and virtual screening for materials solutions
* CAESAR II: The combination of direct geometry method and CAESAR algorithm for super fast conformational search
* Fast and accurate computational approach to protein ionization: Combining the generalized Born model with an iterative mobile cluster method

WORKSHOPS                                                                                                                                                                                                                                                                                                                                                                   * High-Throughput Computational Methods for Materials Discovery and Optimization
* Staying Ahead Of Your Medicinal Chemistry Project Data

POSTER                                                                                                                                                                                                                                                                                                                                                                              * Electronic structure calculations of diamond-like semiconductors

For more information, and to register for the workshops, go to http://accelrys.com/events/conferences/conference-pages/acs-spring-2010.html

If you’d like to learn about the ACS conference on Twitter and see Accelrys’ live tweets, follow #ACS_SF.

 We look forward to seeing you in San Francisco!

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Discover New Materials for Batteries Through Modeling

March 12th, 2010 by Accelrys Team

In the 21st century, materials and energy are more topical than ever before. Insights at the atomistic and quantum level help us to design cleaner energy sources, and find less wasteful ways of using energy. Join us on March 16th as Dr. George Fitzgerald presents “High-throughput Quantum Chemistry and Virtual Screening for Lithium Ion Battery Electrolyte Materials.”

Register to learn:

  • How modeling can support the discovery of components to enhance the performance of lithium ion battery formulations
  • How to use Materials Studio components in Pipeline Pilot to analyze and screen a materials structure library for Li-Ion battery additives
  • Results from a collaboration with Mitsubishi Chemical Inc which was also published in The Journal of Power Sources

This presentation is part of our ongoing webinar series that showcases how Accelrys products and services are transforming materials research. You can download related archived presentations in this series or register for future webinars.

We look forward to sharing our insights with you throughout this webinar series.

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Making Sense of the Cloud for Science:Part 3

March 11th, 2010 by Conrad Agramont

Cloud and Managed Services

In the first part of this series, we discussed the basic collection of cloud offerings and what type of value they provide to IT, Developers, and Customers.  The second part explained some of the Business Issues when leveraging the cloud from with your Enterprise environment.  In this post, we’ll focus more on the various services models that are associated with the Cloud.

Even within an ASP, there will be a range of providers.  Let’s take Accelrys Pipeline Pilot (PP) for example.  It’s a product that provides rich data-flow capabilities and has a specialty in science computing.   Today, most customers deploy PP on-premise by either the Research & Development (R&D) Information Technology (IT) department or by a group of scientists.  PP makes using and managing the platform in either of these scenarios extremely easy, yet powerfully scalable.  Regardless of how easy it is to manage PP, there are other concerns one must have when managing any platform or application.  This includes maintenance, backup and recovery, security, data management, etc.  Not to mention supporting an ever growing user base also looking to leverage Pipeline Pilot.  This could result in time being taken away from your main business driver: Science!

Taking the step to move your basic deployment into the “Cloud,” such as Amazon Web Service (AWS), is an interesting first start.  Now you don’t have to worry about the Operation System and everything underneath it (e.g. hardware, cooling, power, etc.), but you’re still left with everything else.  This is where Application Service Providers (ASP) comes into play.  An ASP can come in different packages.  For one, the ASP could actually be a group internally to your business. OK, so they’re not “really” an ASP, but they could function as one as they provide the service for a given cost and they’re not directly tied to your organization.  Hey, could this be Corporate IT?  Sure, or perhaps another scientific group within your business offering their investment to another team and doing cross charging to offset the costs.  And by the way, doing this in the cloud to remove the burden and cost from IT to manage it.  Perhaps this scenario has too many moving parts for your fancy.  I’ll move on.

A more traditional ASP manages the application and perhaps even provides application level support.  Taking Pipeline Pilot as an example again, providing application support really comes in two flavors.  The first is supporting the application platform and tools themselves; for instance, if you’re writing a protocol (a set of tasks in a data pipeline) or running an application built on PP.  The other is more focused on the science itself and relating it to the product.  While there may be many that could help with the PP Platform, Infrastructure, and even the tools, it’s a big leap to also support the science.  The key here for you is, when shopping for a cloud vendor or ASP take a look at the breath of services you’ll get from them and anticipate your need for science, application, and infrastructure support.  Not to mention the difference in cloud infrastructure that requires a Message Passing Interface (MPI) infrastructure (more on that later).

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/

To view all Conrad’s Cloud Series posts, please click here.

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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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How many modelers?

March 8th, 2010 by Gerhard Goldbeck-Wood, PhD

How many of “us” are out there? I mean how many people doing modeling and simulation? I’d really like to know, ideally broken down by discipline, such as Materials Science vs Life Science, and quantum, classical and mesoscale.

Alas, there are preciously few statistics on that, so when I read in the Monthly Update (Feb 2010) of the Psi-k network that they conducted a study on size of the ab initio simulation community, it got my immediate attention.

Representing a network of people from the quantum mechanics field, Peter Dederichs, Volker Heine and colleagues Phivos Mavropoulos and Dirk Tunger from Research Center Jülich searched publications by keywords such as ‘ab initio’, and made sure not to double-count authors. In fact they tend to underestimate by assuming people with the same surname and first initial are the same. As Prof Dederichs, the chair of the network tells me, checks were also made to ensure that papers from completely different fields are not included. Also they estimate that their keyword range underestimates the number of papers by about 10%. Of course there are those that didn’t publish a paper in 2008, the year for which the study was done. Moreover, Dederichs says, there are those who published papers which don’t have proper keywords like “ab initio” or “first principles” in the abstract or title, so they are not found in the search. All of that is likely to compensate for counting co-authors that are not actually modelers.

All in all, they come up with about 23,000 people! And the number of publications in the field indicates a linear rise year on year.

That’s quite a lot more than they expected, and I agree. The global distribution was also surprising, with about 11,000 in Europe, about 5,600 in America, and 5,700 in East Asia (China, Japan, Korea, Taiwan and Singapore). That’s a lot of QM guys, especially here in Europe. Now, there will be a response from the US on that one I guess?

I wonder how many classical modelers there are. I’d hazard a guess that the number of classical modelers is about half those in the QM community, at least in the Materials Science field. Assuming that the mesoscale modeling community is quite small, that would make for a total of at least 30,000 modelers worldwide.

What is your view, or informed opinion? Anybody else knows about or has done some studies? I am going to open up a poll in the right sidebar on the number of people involved in quantum, classical and mesoscale modeling in total. It would be great to hear also how you came up with your selection.

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Making Sense of the Cloud for Science:Part 2

February 26th, 2010 by Conrad Agramont

Business Issues in the Cloud

In the first part of this series, we discussed the basic collection of cloud offerings and what type of value they provide to IT, Developers, and Customers.  In this post, we’ll focus more on the business issues when leveraging the cloud.

One of the biggest hurdles leveraging Cloud Services is around securing and transporting of the data.  There’s no single answer or solution to resolve these issues, and there is no shortage of webinars, papers, conferences, etc. that focus on this so I don’t think I need to dig into that (just yet).  But what’s important to recognize is that all of the Cloud vendors, security experts, and network providers are working to both provide an answer that meets your business and technical requirements but also earns your trust.  The best way to get over that hump is to learn more and try it out.

First try the cloud on non-critical but impactful tasks.  Then start to increase your usage of critical data, connect directly to internal data, and perform tasks that provide real business value.  This isn’t an original approach since it’s pretty much the typically evaluation or Proof of Concept (POC), but that’s exactly the point!  Driving a project like this is more than just technology based, as you’ll most likely involve many people within your organization, such as Legal, Finance, IT, and Security in order to plan and complete the project.  There will be lots of concerns from these various groups, many reasonable and some that just requires lots of education.  So make sure you invest in educating them on the basics of the Cloud first.  This will make the rest of the process much smoother, but not easier.

Second, you’ll need to consider network bandwidth usage and data storage costs.  All of the cloud vendors have some sort of fee when uploading, downloading, and storing your data.  When you first look at this, its penny’s per GB, but when dealing with large data volumes and data transactions (e.g. Read and Writing across the network) those costs can get pretty high.  So your first thought will be that cloud pricing is extremely high, but what you may not be factoring in is all the things the cloud vendor is doing for you that’s beyond just the price of the disk, network, cooling, and power.  The cloud vendors typically offer a high SLA, so that includes data replication, de-duplication, resiliency, continuity, and more.  And not to mention the staff, planning, and operations to make all of that happen.  If you compared that to your own infrastructure and added that to your internal per-GB cost of storage, you’ll most likely see that the Cloud is more affordable but that assumes your meeting the same level of SLA and process as the Cloud vendors which most are not.  That said, there are some applications and data that may not be a good fit for many of the cloud vendors because of the special nature of the application, massive data size with high volume transactions, high throughput requirements, legal requirements, and more.  But this is starting to be the exception versus the rule.

Many organizations are making the leap of putting their most trusted data into the cloud, and some are doing it without realizing the significance. Email and Sales force automation having been leading the charge in hosted applications and Software as a Service (SaaS) deployments.  Now think of it this way, if you can store all of your communications and customer records on the cloud, why can’t you do more?  By businesses taking this leap, they start to build trust in external parties maintaining and operating their business critical services.  In a recent report by Goldman Sachs, they note that customers see a “shift towards cloud unstoppable”.  http://news.cnet.com/8301-13846_3-10453066-62.html The trend towards cloud services and applications won’t be a complete rip and replace, business will look to the cloud as an extension of their overall enterprise architecture and infrastructure.

When comparing the many Cloud/IaaS vendors in the market today, it’s already moving towards mass commodity price points and common functionality.  And that’s great if you want to take a piece of existing traditional on-premise software and simply deploy it to the cloud.  What you have to look out for are pitfalls in the software license, security, deployment architectures, and the fact that you’re still responsible for managing that software in the “Cloud”.  So the next layer to look for is a Services vendor that can deliver you the application.  This can at times come from the vendor directly or through partner network supported by the vendor.  Each has their own value proposition and differences in how flexible they can be delivering additional custom services.   Again, this type of application + service model isn’t new as the Application Service Provider (ASP) model has been around for years.  What’s new is that these ASP’s can still provide lots of value and cost reduction to the customer but now leveraging computing and storage that provided by a “Cloud” offering (e.g. AWS).

In the next part of this blog series, we’ll focus more on the various services models that will be available to customers based on a cloud version of Pipeline Pilot.

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

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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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