Nanotechnology Now

Our NanoNews Digest Sponsors

Heifer International

Wikipedia Affiliate Button


DHgate

Home > Press > SDSC Team Develops Multi-scale Simulation Software for Chemistry Research: SDSC’s Trestles and Gordon supercomputers used in development and validation

The journal cover shows a calcium ion coordinating to aspartate, a model for proteins in aqueous solution used by the authors to demonstrate features of the software. The multi-scale QM/MM equations governing the implementation are visible on the surface that extends to the horizon.
The journal cover shows a calcium ion coordinating to aspartate, a model for proteins in aqueous solution used by the authors to demonstrate features of the software. The multi-scale QM/MM equations governing the implementation are visible on the surface that extends to the horizon.

Abstract:
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.

SDSC Team Develops Multi-scale Simulation Software for Chemistry Research: SDSC’s Trestles and Gordon supercomputers used in development and validation

San Diego, CA | Posted on February 19th, 2014

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.

####

For more information, please click here

Contacts:
Jan Zverina
858-534-5111


Secondary media contact:
Warren R. Froelich
858 822-3622,

Copyright © University of California - San Diego

If you have a comment, please Contact us.

Issuers of news releases, not 7th Wave, Inc. or Nanotechnology Now, are solely responsible for the accuracy of the content.

Bookmark:
Delicious Digg Newsvine Google Yahoo Reddit Magnoliacom Furl Facebook

Related Links

Download paper:

Walker Molecular Dynamics Lab:

San Diego Supercomputer Center (SDSC):

UC San Diego:

Related News Press

News and information

'Lasers rewired': Scientists find a new way to make nanowire lasers: Berkeley Lab, UC Berkeley scientists adapt next-gen solar cell materials for a different purpose February 12th, 2016

Breaking cell barriers with retractable protein nanoneedles: Adapting a bacterial structure, Wyss Institute researchers develop protein actuators that can mechanically puncture cells February 12th, 2016

Replacement of Toxic Antibacterial Agents Possible by Biocompatible Polymeric Nanocomposites February 12th, 2016

Properties of Polymeric Nanofibers Optimized to Treat Damaged Body Tissues February 12th, 2016

Chemistry

Chemical cages: New technique advances synthetic biology February 10th, 2016

Graphene decharging and molecular shielding February 8th, 2016

Scientists take key step toward custom-made nanoscale chemical factories: Berkeley Lab researchers part of team that creates new function in tiny protein shell structures February 6th, 2016

Discovery of the specific properties of graphite-based carbon materials February 6th, 2016

Software

Researchers from the California NanoSystems Institute at UCLA have created a new technique that greatly enhances digital microscopy images January 27th, 2016

Digital Surf launches revolutionary SEM image colorization January 26th, 2016

Materials scientists at FAU reconstruct turbine material atom by atom in computer simulations January 19th, 2016

NanoOK: Quality Control for portable, rapid, low-cost DNA sequencing December 21st, 2015

Nanomedicine

Breaking cell barriers with retractable protein nanoneedles: Adapting a bacterial structure, Wyss Institute researchers develop protein actuators that can mechanically puncture cells February 12th, 2016

Replacement of Toxic Antibacterial Agents Possible by Biocompatible Polymeric Nanocomposites February 12th, 2016

Properties of Polymeric Nanofibers Optimized to Treat Damaged Body Tissues February 12th, 2016

SLAC X-ray laser turns crystal imperfections into better images of important biomolecules: New method could remove major obstacles to studying structures of complex biological machines February 11th, 2016

Discoveries

'Lasers rewired': Scientists find a new way to make nanowire lasers: Berkeley Lab, UC Berkeley scientists adapt next-gen solar cell materials for a different purpose February 12th, 2016

Breaking cell barriers with retractable protein nanoneedles: Adapting a bacterial structure, Wyss Institute researchers develop protein actuators that can mechanically puncture cells February 12th, 2016

Replacement of Toxic Antibacterial Agents Possible by Biocompatible Polymeric Nanocomposites February 12th, 2016

Properties of Polymeric Nanofibers Optimized to Treat Damaged Body Tissues February 12th, 2016

Announcements

Graphene leans on glass to advance electronics: Scientists' use of common glass to optimize graphene's electronic properties could improve technologies from flat screens to solar cells February 12th, 2016

Breaking cell barriers with retractable protein nanoneedles: Adapting a bacterial structure, Wyss Institute researchers develop protein actuators that can mechanically puncture cells February 12th, 2016

Replacement of Toxic Antibacterial Agents Possible by Biocompatible Polymeric Nanocomposites February 12th, 2016

Properties of Polymeric Nanofibers Optimized to Treat Damaged Body Tissues February 12th, 2016

Interviews/Book Reviews/Essays/Reports/Podcasts/Journals/White papers

'Lasers rewired': Scientists find a new way to make nanowire lasers: Berkeley Lab, UC Berkeley scientists adapt next-gen solar cell materials for a different purpose February 12th, 2016

Breaking cell barriers with retractable protein nanoneedles: Adapting a bacterial structure, Wyss Institute researchers develop protein actuators that can mechanically puncture cells February 12th, 2016

Replacement of Toxic Antibacterial Agents Possible by Biocompatible Polymeric Nanocomposites February 12th, 2016

Properties of Polymeric Nanofibers Optimized to Treat Damaged Body Tissues February 12th, 2016

Energy

Graphene leans on glass to advance electronics: Scientists' use of common glass to optimize graphene's electronic properties could improve technologies from flat screens to solar cells February 12th, 2016

'Lasers rewired': Scientists find a new way to make nanowire lasers: Berkeley Lab, UC Berkeley scientists adapt next-gen solar cell materials for a different purpose February 12th, 2016

New thin film transistor may lead to flexible devices: Researchers engineer an electronics first, opening door to flexible electronics February 10th, 2016

Canadian physicists discover new properties of superconductivity February 8th, 2016

Quantum nanoscience

Nanoscale cavity strongly links quantum particles: Single photons can quickly modify individual electrons embedded in a semiconductor chip and vice versa February 8th, 2016

The iron stepping stones to better wearable tech without semiconductors February 8th, 2016

Spin dynamics in an atomically thin semi-conductor February 1st, 2016

New record in nanoelectronics at ultralow temperatures January 28th, 2016

NanoNews-Digest
The latest news from around the world, FREE





  Premium Products
NanoNews-Custom
Only the news you want to read!
 Learn More
NanoTech-Transfer
University Technology Transfer & Patents
 Learn More
NanoStrategies
Full-service, expert consulting
 Learn More











ASP
Nanotechnology Now Featured Books




NNN

The Hunger Project







Car Brands
Buy website traffic