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

Chemistry

March 2016; 6th Int'l Conference on Nanostructures in Iran July 29th, 2015

News and information

March 2016; 6th Int'l Conference on Nanostructures in Iran July 29th, 2015

Non-Enzyme Sensor Determines Level of Blood Sugar July 29th, 2015

Flexible Future of Point-of-Care Disease Diagnostic July 29th, 2015

Meet the high-performance single-molecule diode: Major milestone in molecular electronics scored by Berkeley Lab and Columbia University team July 29th, 2015

Software

AIS Introduces Industry 4.0 Ready, Industrial Controls and Factory Automation HMI Touch-Panels, for Easy Visual, Control and Monitoring in Discrete and Process Automation Industries June 15th, 2015

New JEOL E-Beam Lithography System to Enhance Quantum NanoFab Capabilities May 6th, 2015

Time Dependant Spectroscopy of Microscopic Samples: CRAIC TimePro™ software is used with CRAIC Technologies microspectrometers to measure the kinetic UV-visible-NIR, Raman and fluorescence spectra of microscopic sample areas May 2nd, 2015

Lifeboat Foundation launches Interactive Friendly AI April 6th, 2015

Nanomedicine

March 2016; 6th Int'l Conference on Nanostructures in Iran July 29th, 2015

Non-Enzyme Sensor Determines Level of Blood Sugar July 29th, 2015

Flexible Future of Point-of-Care Disease Diagnostic July 29th, 2015

Stretching the limits on conducting wires July 25th, 2015

Discoveries

Non-Enzyme Sensor Determines Level of Blood Sugar July 29th, 2015

Flexible Future of Point-of-Care Disease Diagnostic July 29th, 2015

Meet the high-performance single-molecule diode: Major milestone in molecular electronics scored by Berkeley Lab and Columbia University team July 29th, 2015

Detecting small metallic contaminants in food via magnetization: A practical metallic-contaminant detecting system using three high-Tc RF superconducting quantum interference devices (SQUIDs) July 29th, 2015

Announcements

Non-Enzyme Sensor Determines Level of Blood Sugar July 29th, 2015

Flexible Future of Point-of-Care Disease Diagnostic July 29th, 2015

Meet the high-performance single-molecule diode: Major milestone in molecular electronics scored by Berkeley Lab and Columbia University team July 29th, 2015

Detecting small metallic contaminants in food via magnetization: A practical metallic-contaminant detecting system using three high-Tc RF superconducting quantum interference devices (SQUIDs) July 29th, 2015

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

Non-Enzyme Sensor Determines Level of Blood Sugar July 29th, 2015

Flexible Future of Point-of-Care Disease Diagnostic July 29th, 2015

Meet the high-performance single-molecule diode: Major milestone in molecular electronics scored by Berkeley Lab and Columbia University team July 29th, 2015

Detecting small metallic contaminants in food via magnetization: A practical metallic-contaminant detecting system using three high-Tc RF superconducting quantum interference devices (SQUIDs) July 29th, 2015

Energy

March 2016; 6th Int'l Conference on Nanostructures in Iran July 29th, 2015

Smaller, faster, cheaper: A new type of modulator for the future of data transmission July 27th, 2015

Reshaping the solar spectrum to turn light to electricity: UC Riverside researchers find a way to use the infrared region of the sun's spectrum to make solar cells more efficient July 27th, 2015

Industrial Nanotech, Inc. Provides Update on PCAOB Audited Financials July 27th, 2015

Quantum nanoscience

Detecting small metallic contaminants in food via magnetization: A practical metallic-contaminant detecting system using three high-Tc RF superconducting quantum interference devices (SQUIDs) July 29th, 2015

Drawing a line between quantum and classical world: Bell's Inequality fails as a test of the boundary July 21st, 2015

World first: Significant development in the understanding of macroscopic quantum behavior: Researchers from Polytechnique Montréal and Imperial College London demonstrate the wavelike quantum behavior of a polariton condensate on a macroscopic scale and at room temperature July 14th, 2015

The quantum physics of artificial light harvesting: How molecular vibrations make photosynthesis efficient July 13th, 2015

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