Featured Research

from universities, journals, and other organizations

Catching molecular motion at just the right time: Theorists overcome loss of entropy and friction in computational simulations

Date:
September 21, 2011
Source:
University of Oregon
Summary:
Researchers have devised a mathematically rich analytic approach to account for often-missing thermodynamic and molecular parameters in molecular dynamic simulations. The new approach returns atomistic-level data into the time frame of the macroscopic world.

Marina G. Guenza and Ivan Lyubimov of the University of Oregon have developed a mathematical formula that returns pivotal information into course-grain simulations.
Credit: University of Oregon

University of Oregon researchers have devised a mathematically rich analytic approach to account for often-missing thermodynamic and molecular parameters in molecular dynamic simulations.

The new approach, which returns atomistic-level data into the time frame of the macroscopic world, is detailed in a paper appearing online ahead of regular publication in the journal Physical Review E. The method is all about timing, says Marina G. Guenza, professor of theoretical physical chemistry, and may help reduce trial-and-error experimentation required in manufacturing when such information is missing.

Molecular dynamic simulations are indispensable tools -- a natural partner of experiments and theory -- that help scientists understand the properties of new materials and processes by providing a view at the resolution of atoms. Simulations expedite the development of new materials by showing how those with a specific atomistic structure behave in various conditions, for example when they are strained or frozen.

Simulations of polymers and biological systems have been used since the 1990s. That effort has focused on the short-time motion of macromolecules described in atomistic detail, which, in addition to plastics and glasses, also applies to DNA and proteins, Guenza said.

However, modelers remove critical pieces of information, such as atom-level activity, to scale back simulations to cover only generic components and access longer times in an accessible simulation run. This technique provides helpful but incomplete data about behavioral responses, Guenza said. Simulations in which atomistic information is withheld are called coarse-grained models.

"These are big molecules," she said. "They move slowly. It is difficult to set up a simulation where the atomistic definition is included and still be able to see things happen on the long time scale, which can be really important. Coarse-graining allows one to simulate macromolecules for longer time, but, because some information is eliminated, the motion measured is unrealistically fast."

Entropy -- a loss of thermodynamic energy -- and surface friction are lost in these simulations, she said. Simulations at the atomistic level depict motion occurring in femtoseconds. (A femtosecond is a millionth of a nanosecond; a nanosecond, a billionth of a second.)

To understand what happens in macroscopic systems, you have to look at movement over longer periods of time -- over seconds, says Ivan Lyubimov, a UO doctoral student in chemistry and lead author. "When you try to simulate a second's worth of information at the atomistic level, with all the details included, it might take one or two years for the computer to run the simulation, and you'd still have errors due to numerical algorithms," he said.

Guenza and Lyubimov looked at simulations where thousands of macromolecules of polyethelene are represented as interacting soft particle, i.e. a coarse-grained model, and applied an original theory that refocuses the information missing in the simulations.

Guenza -- a member of the UO's Institute of Theoretical Science, Materials Science Institute and Institute of Molecular Biology -- and Lyubimov first detailed the basics of their theoretical formula in 2010 in the Journal of Chemical Physics.

Their "first-principle" approach looks at the loss of energy, due to the change in entropy, caused by the coarse-graining of the molecule in simulations. Coarse-graining also affects the surface of molecules in simulation, so the formalism accounts for the loss of friction as well.

"We were able to show that if you run your simulation with less detail, we can correct for these factors, and you'll produce the correct motion -- the dynamics -- of the real system," Guenza said. "We have done a lot of tests with different experiments and simulations, and our method works pretty well. No one else has been able to do this with a theoretical solution."

The method, the authors wrote, is different from others currently in use, because it is analytical rather than numerical. It removes the need for separate, time-consuming atomistic simulations to account for missing information obtained from coarse-grained simulations.

"Parameters can be varied for different systems, depending on the molecule size, density and temperature," Lyubimov said. "You can make realistic predictions for the type of material you want to study, at much less expense. You don't have to know all of the details, but you do need a certain number of parameters based on the chemical structure that you want to study."

The National Science Foundation supported the research.


Story Source:

The above story is based on materials provided by University of Oregon. Note: Materials may be edited for content and length.


Journal Reference:

  1. I. Lyubimov, M. Guenza. First-principle approach to rescale the dynamics of simulated coarse-grained macromolecular liquids. Physical Review E, 2011; 84 (3) DOI: 10.1103/PhysRevE.84.031801

Cite This Page:

University of Oregon. "Catching molecular motion at just the right time: Theorists overcome loss of entropy and friction in computational simulations." ScienceDaily. ScienceDaily, 21 September 2011. <www.sciencedaily.com/releases/2011/09/110921093608.htm>.
University of Oregon. (2011, September 21). Catching molecular motion at just the right time: Theorists overcome loss of entropy and friction in computational simulations. ScienceDaily. Retrieved July 24, 2014 from www.sciencedaily.com/releases/2011/09/110921093608.htm
University of Oregon. "Catching molecular motion at just the right time: Theorists overcome loss of entropy and friction in computational simulations." ScienceDaily. www.sciencedaily.com/releases/2011/09/110921093608.htm (accessed July 24, 2014).

Share This




More Computers & Math News

Thursday, July 24, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Bill Gates: Health, Agriculture Key to Africa's Development

Bill Gates: Health, Agriculture Key to Africa's Development

AFP (July 24, 2014) Health and agriculture development are key if African countries are to overcome poverty and grow, US software billionaire Bill Gates said Thursday, as he received an honourary degree in Ethiopia. Duration: 00:36 Video provided by AFP
Powered by NewsLook.com
Creative Makeovers for Ugly Cellphone Towers

Creative Makeovers for Ugly Cellphone Towers

AP (July 24, 2014) Mobile phone companies and communities across the country are going to new lengths to disguise those unsightly cellphone towers. From a church bell tower to a flagpole, even a pencil, some towers are trying to make a point. (July 24) Video provided by AP
Powered by NewsLook.com
Robot Parking Valet Creates Stress-Free Travel

Robot Parking Valet Creates Stress-Free Travel

AP (July 23, 2014) 'Ray' the robotic parking valet at Dusseldorf Airport in Germany lets travelers to avoid the hassle of finding a parking spot before heading to the check-in desk. (July 23) Video provided by AP
Powered by NewsLook.com
Facebook Earnings Put Smile on Investors Faces

Facebook Earnings Put Smile on Investors Faces

Reuters - Business Video Online (July 23, 2014) Facebook earnings beat forecasts- with revenue climbing 61 percent. Bobbi Rebell reports. Video provided by Reuters
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:
from the past week

In Other News

... from NewsDaily.com

Science News

    Health News

      Environment News

        Technology News



          Save/Print:
          Share:

          Free Subscriptions


          Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

          Get Social & Mobile


          Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

          Have Feedback?


          Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
          Mobile: iPhone Android Web
          Follow: Facebook Twitter Google+
          Subscribe: RSS Feeds Email Newsletters
          Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins