Nanotechnology Now

Our NanoNews Digest Sponsors

Heifer International

Wikipedia Affiliate Button

Home > Press > SDSC Team Develops Multi-scale Simulation Software for Chemistry Research: SDSCs 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: SDSCs 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

Information storage with a nanoscale twist: Discovery of a novel rotational force inside magnetic vortices makes it easier to design ultrahigh capacity disk drives March 28th, 2017

ATTOPSEMI Technology Joins FDXcelerator Program to Deliver Advanced Non-Volatile Memory IP to GLOBALFOUNDRIES 22 FDX Technology Platform: Leading-edge I-fuse brings higher reliability, smaller cell size and ease of programmability for consumer, automotive, and IoT applications March 27th, 2017

Leti and HORIBA Scientific to Host Webinar on Ultrafast Characterization Tool: Plasma Profiling Time-of-Flight Mass Spectrometer Tool Cuts Optimization Time In Layer Deposition and Fabrication of Wide Range of Applications March 27th, 2017

Laser activated gold pyramids could deliver drugs, DNA into cells without harm: Microstructures create temporary pores in cells March 27th, 2017

Chemistry

Promising results obtained with a new electrocatalyst that reduces the need for platinum: Researchers from Aalto University have succeeded in manufacturing electrocatalysts used for storing electric energy with one-hundredth of the amount of platinum that is usually needed March 24th, 2017

Researchers develop groundbreaking process for creating ultra-selective separation membranes: Discovery could greatly improve energy-efficiency of separation and purification processes in the chemical and petrochemical industries March 15th, 2017

Optical fingerprint can reveal pollutants in the air: Researchers at Chalmers University of Technology have proposed a new, sophisticated method of detecting molecules with sensors based on ultra-thin nanomaterials March 15th, 2017

Triboelectric Nanogenerators Boost Mass Spectrometry Performance March 1st, 2017

Molecular phenomenon discovered by advanced NMR facility: Cutting edge technology has shown a molecule self-assembling into different forms when passing between solution state to solid state, and back again - a curious phenomenon in science - says research by the University of Wa February 22nd, 2017

Software

Leti to Release Versatile SensiNact IoT Platform for Open-Source Development: Middleware Collects, Aggregates and Secures Scripting of Data From Multiple Devices via Virtually Any IoT Communication Protocol March 14th, 2017

Nanomechanics Inc. Continues Growth in Revenue and Market Penetration: Leading nanoindentation company reports continued growth in revenues and distribution channels on national and international scales December 27th, 2016

Nanomedicine

Laser activated gold pyramids could deliver drugs, DNA into cells without harm: Microstructures create temporary pores in cells March 27th, 2017

Researchers make flexible glass for tiny medical devices: Glass can bend over and over again on a nanoscale March 27th, 2017

Cryo-electron microscopy achieves unprecedented resolution using new computational methods March 25th, 2017

Nanobiotix: The Independent Data Monitoring Committee Recommends the Continuation of the Ongoing Phase II/III Trial of NBTXR3 in Soft Tissue Sarcoma March 23rd, 2017

Discoveries

Information storage with a nanoscale twist: Discovery of a novel rotational force inside magnetic vortices makes it easier to design ultrahigh capacity disk drives March 28th, 2017

A big leap toward tinier lines: Self-assembly technique could lead to long-awaited, simple method for making smaller microchip patterns March 27th, 2017

Laser activated gold pyramids could deliver drugs, DNA into cells without harm: Microstructures create temporary pores in cells March 27th, 2017

Researchers make flexible glass for tiny medical devices: Glass can bend over and over again on a nanoscale March 27th, 2017

Announcements

Information storage with a nanoscale twist: Discovery of a novel rotational force inside magnetic vortices makes it easier to design ultrahigh capacity disk drives March 28th, 2017

ATTOPSEMI Technology Joins FDXcelerator Program to Deliver Advanced Non-Volatile Memory IP to GLOBALFOUNDRIES 22 FDX Technology Platform: Leading-edge I-fuse brings higher reliability, smaller cell size and ease of programmability for consumer, automotive, and IoT applications March 27th, 2017

Leti and HORIBA Scientific to Host Webinar on Ultrafast Characterization Tool: Plasma Profiling Time-of-Flight Mass Spectrometer Tool Cuts Optimization Time In Layer Deposition and Fabrication of Wide Range of Applications March 27th, 2017

Laser activated gold pyramids could deliver drugs, DNA into cells without harm: Microstructures create temporary pores in cells March 27th, 2017

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

Information storage with a nanoscale twist: Discovery of a novel rotational force inside magnetic vortices makes it easier to design ultrahigh capacity disk drives March 28th, 2017

A big leap toward tinier lines: Self-assembly technique could lead to long-awaited, simple method for making smaller microchip patterns March 27th, 2017

Laser activated gold pyramids could deliver drugs, DNA into cells without harm: Microstructures create temporary pores in cells March 27th, 2017

Researchers make flexible glass for tiny medical devices: Glass can bend over and over again on a nanoscale March 27th, 2017

Energy

Argon is not the 'dope' for metallic hydrogen March 24th, 2017

Rice U. refines filters for greener natural gas: New study defines best materials for carbon capture, methane selectivity March 23rd, 2017

Artificial photosynthesis steps into the light: Rice University lab turns transition metals into practical catalyst for solar, other applications March 23rd, 2017

Researchers develop groundbreaking process for creating ultra-selective separation membranes: Discovery could greatly improve energy-efficiency of separation and purification processes in the chemical and petrochemical industries March 15th, 2017

Quantum nanoscience

The speed limit for intra-chip communications in microprocessors of the future January 23rd, 2017

First experimental proof of a 70 year old physics theory: First observation of magnetic phase transition in 2-D materials, as predicted by the Nobel winner Onsager in 1943 January 6th, 2017

Quantum simulation technique yields topological soliton state in SSH model January 3rd, 2017

Diamonds are technologists' best friends: Researchers from the Lomonosov Moscow State University have grown needle- and thread-like diamonds and studied their useful properties December 30th, 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