Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

SDSC Team Develops Multi-scale Simulation Software for Chemistry Research

20.02.2014
SDSC’s Trestles and Gordon supercomputers used in development and validation

Researchers at the San Diego Supercomputer Center at the University of California, San Diego, have developed software that greatly expands the types of multi-scale QM/MM (mixed quantum and molecular mechanical) simulations of complex chemical systems that scientists can use to design new drugs, better chemicals, or improved enzymes for biofuels production.

A paper outlining the research, titled ‘An Extensible Interface for QM/MM Molecular Dynamics Simulations with AMBER’ and conducted by members of the Walker Molecular Dynamics Lab (WMD) at SDSC, was featured on the cover of the January 15th issue of the Journal of Computational Chemistry.

Multi-scale QM/MM computational methods are crucial to advancing the understanding and solution to problems in the chemical sciences, ranging from drug design to renewable energies. This has been recognized with the award of the 2013 Nobel Prize in chemistry for the development of multi-scale models of complex chemical systems.

In QM/MM simulations, an accurate but computationally complex and thus time-consuming quantum mechanical model is used to identify important features of the electronic structure of a chemically relevant region. This is required, for example, to describe photo-physical processes or chemical reactions in the active site of enzymes. Effects of the surrounding environment are then included with a computationally less complex classical MM model.

“QM/MM simulations are computationally very demanding compared to purely classical MM simulations,” said Ross C. Walker, an SDSC research professor and adjunct associate professor in UC San Diego's Department of Chemistry and Biochemistry. “Access to SDSC's Trestles and Gordon supercomputers and their fast turnaround times were essential to our work. We ran a large amount of jobs to test and validate our implementation at various stages, as well as a large-scale simulation to demonstrate a practical application.”

“Our software enables QM/MM simulations with a variety of advanced quantum mechanical models, and by integrating it with the popular AMBER molecular simulation package, which is used by hundreds of academic and industrial research labs, we can reach a very large user base”, said lead author Andreas W. Goetz, a research scientist with SDSC and expert in multi-scale modeling. “We’re looking forward to many exciting applications that will help scientists in computational chemistry and biophysics understand and predict the behavior of molecular systems at a fundamental level.”

Authors of the new study include SDSC's Goetz and Walker as well as Matthew A. Clark, who developed part of the software during his internship with Walker and Goetz, as part of SDSC’s Research Experience for High School Students (REHS) program and later as an undergraduate research intern in the WMD lab.

Media Contact

Jan Zverina, 858-534-5111, jzverina@sdsc.edu
Secondary media contact:
Warren R. Froelich, 858 822-3622, froelich@sdsc.edu

Jan Zverina | EurekAlert!
Further information:
http://www.sdsc.edu

More articles from Life Sciences:

nachricht Protein Shake-Up
27.03.2015 | Oak Ridge National Laboratory

nachricht How did the chicken cross the sea?
27.03.2015 | Michigan State University

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Experiment Provides the Best Look Yet at 'Warm Dense Matter' at Cores of Giant Planets

In an experiment at the Department of Energy's SLAC National Accelerator Laboratory, scientists precisely measured the temperature and structure of aluminum as...

Im Focus: Energy-autonomous and wireless monitoring protects marine gearboxes

The IPH presents a solution at HANNOVER MESSE 2015 to make ship traffic more reliable while decreasing the maintenance costs at the same time. In cooperation with project partners, the research institute from Hannover, Germany, has developed a sensor system which continuously monitors the condition of the marine gearbox, thus preventing breakdowns. Special feature: the monitoring system works wirelessly and energy-autonomously. The required electrical power is generated where it is needed – directly at the sensor.

As well as cars need to be certified regularly (in Germany by the TÜV – Technical Inspection Association), ships need to be inspected – if the powertrain stops...

Im Focus: 3-D satellite, GPS earthquake maps isolate impacts in real time

Method produced by UI researcher could improve reaction time to deadly, expensive quakes

When an earthquake hits, the faster first responders can get to an impacted area, the more likely infrastructure--and lives--can be saved.

Im Focus: Atlantic Ocean overturning found to slow down already today

The Atlantic overturning is one of Earth’s most important heat transport systems, pumping warm water northwards and cold water southwards. Also known as the Gulf Stream system, it is responsible for the mild climate in northwestern Europe. 

Scientists now found evidence for a slowdown of the overturning – multiple lines of observation suggest that in recent decades, the current system has been...

Im Focus: Robot inspects concrete garage floors and bridge roadways for damage

Because they are regularly subjected to heavy vehicle traffic, emissions, moisture and salt, above- and underground parking garages, as well as bridges, frequently experience large areas of corrosion. Most inspection systems to date have only been capable of inspecting smaller surface areas.

From April 13 to April 17 at the Hannover Messe (hall 2, exhibit booth C16), engineers from the Fraunhofer Institute for Nondestructive Testing IZFP will be...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

World Conference On Regenerative Medicine 2015: Registration And Abstract Submission Now Open

25.03.2015 | Event News

University presidents from all over the world meet in Hamburg

19.03.2015 | Event News

10. CeBiTec Symposium zum Big Data-Problem

17.03.2015 | Event News

 
Latest News

Two Most Destructive Termite Species Forming Superswarms in South Florida

27.03.2015 | Agricultural and Forestry Science

ORNL-Led Team Demonstrates Desalination with Nanoporous Graphene Membrane

27.03.2015 | Materials Sciences

Coorong Fish Hedge Their Bets for Survival

27.03.2015 | Ecology, The Environment and Conservation

VideoLinks
B2B-VideoLinks
More VideoLinks >>>