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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