Navigation Links
How computers push on the molecules they simulate
Date:1/3/2013

ng only a single degree of freedom, and found that when they ignored the shadow work, the calculations were systematically biased. But when they accounted for the shadow work, accurate calculations could be recovered.

"Next we looked at systems with hundreds or thousands of simple molecules," says Sivak. Using models of water molecules in a box, they simulated the state of the system over time, starting from a given thermal energy but with no "pushing" from outside. "We wanted to know how far the water simulation would be pushed by the shadow work alone."

The result confirmed that even in the absence of an explicit driving force, the finite-time-step Langevin dynamics simulation acted by itself as a driving nonequilibrium process. Systematic errors resulted from failing to separate this shadow work from the actual "protocol work" that they explicitly modeled in their simulations. For the first time, Sivak and his colleagues were able to quantify the magnitude of the deviations in various test systems.

Such simulation errors can be reduced in several ways, for example by dividing the evolution of the system into ever-finer time steps, because the shadow work is larger when the discrete time steps are larger. But doing so increases the computational expense.

The better approach is to use a correction factor that isolates the shadow work from the physically meaningful work, says Sivak. "We can apply results from our calculation in a meaningful way to characterize the error and correct for it, separating the physically realistic aspects of the simulation from the artifacts of the computer method."


'/>"/>

Contact: Paul Preuss
paul_preuss@lbl.gov
510-486-6249
DOE/Lawrence Berkeley National Laboratory
Source:Eurekalert  

Page: 1 2 3

Related biology news :

1. 2 NASA visualizations selected for computers graphics showcase
2. Computers can predict effects of HIV policies
3. Computers taught to ID regulating gene sequences
4. Iowa State, Ames Lab researchers invent new tool to study single biological molecules
5. New model gives hands-on help for learning the secrets of molecules
6. Weighing molecules 1 at a time
7. Nano-velcro clasps heavy metal molecules in its grips
8. Researchers develop new stamping process to pattern biomolecules at high resolution
9. A class of RNA molecules protects germ cells from damage, Penn vet researchers show
10. Dance of water molecules turns fire-colored beetles into antifreeze artists
Post Your Comments:
*Name:
*Comment:
*Email:
Related Image:
How computers push on the molecules they simulate
(Date:12/22/2014)... Conn. , Dec. 22, 2014  NXT-ID, Inc. (NASDAQ: ... biometric authentication company focused on the growing mobile commerce market, ... Apollo Robbins for the 2015 International CES debut ... Apollo Robbins will be at the NXT-ID booth January ...
(Date:12/19/2014)... , Dec. 18, 2014 Research and Markets ... "Micro Market Monitor: North America Perimeter Security Systems Market" ... The North American perimeter security market is ... to 2019. Although the U.S. market holds a larger share ...
(Date:12/17/2014)... , Dec. 15, 2014 The Defense Logistics Agency ... detect and prevent counterfeit microcircuits from entering into its ... an in-house microcircuit anti-counterfeit initiative dubbed DNA marking. The ... increasing their reliability throughout the supply chain. The new ...
Breaking Biology News(10 mins):NXT-ID Hires Master Pickpocket and Security Consultant Apollo Robbins for Wocket Smart Wallet CES 2015 Debut 2NXT-ID Hires Master Pickpocket and Security Consultant Apollo Robbins for Wocket Smart Wallet CES 2015 Debut 3NXT-ID Hires Master Pickpocket and Security Consultant Apollo Robbins for Wocket Smart Wallet CES 2015 Debut 4Micro Market Monitor: North America Perimeter Security Systems Market (Intrusion Detection Sensor, Video Surveillance, Communication/Alarm and Notification, Access Control System) 2Micro Market Monitor: North America Perimeter Security Systems Market (Intrusion Detection Sensor, Video Surveillance, Communication/Alarm and Notification, Access Control System) 3Defense Logistics Agency Launches DNA Marking Capability to Strengthen Microcircuit Supply Chain 2Defense Logistics Agency Launches DNA Marking Capability to Strengthen Microcircuit Supply Chain 3
... other medicines inside soil microbes and other natural sources is ... than 50 percent of today,s prescription drugs. This new era ... Chemical & Engineering News , the weekly newsmagazine of ... editor, points out that natural products are the source of ...
... genomes provide useful medical information beyond what current newborn ... question are being funded by the Eunice Kennedy Shriver ... and the National Human Genome Research Institute (NHGRI), both ... $5 million to four grantees have been made in ...
... controlled study of science faculty at minority-serving institutions ... increased the number of peer-reviewed research publications, the ... professional and curricular activities of those who participated ... The study, published today in the journal, ...
Cached Biology News:NIH program explores the use of genomic sequencing in newborn healthcare 2NIH program explores the use of genomic sequencing in newborn healthcare 3NIH program explores the use of genomic sequencing in newborn healthcare 4Outside mentoring support for science faculty at minority-serving institutions pays off 2Outside mentoring support for science faculty at minority-serving institutions pays off 3Outside mentoring support for science faculty at minority-serving institutions pays off 4
(Date:1/22/2015)... Jan. 22, 2015  Transwestern | RBJ today announces the firm ... space for Shire a leading biopharmaceutical company, at Two Ledgemont ... RBJ,s Robert Richards , president, and Brian Cohen ... the entire five-floor building at 95 Hayden Ave. ...
(Date:1/22/2015)... Pipette.com has added the Eppendorf ... portfolio of Eppendorf products. , The Eppendorf Centrifuge 5424/5424 ... 5424/5424 R and receive the following:, , ... or Eppendorf Reference 2 ,     3 Free ...
(Date:1/22/2015)... January 22, 2015 Diagenode, Inc., ... as the Bioruptor® and complete solutions for epigenetics ... chromatin immunoprecipitation, alleviating the need for manual processing. ... needed for ChIP of histones or transcription factors ...
(Date:1/22/2015)... N.J. , Jan. 22, 2015  Derma Sciences, ... regeneration company focused on advanced wound care, announces ... placental tissues, have been added to the Premier, ... increases the opportunity for the AMNIOEXCEL® and AMNIOMATRIX® ...
Breaking Biology Technology:Transwestern?RBJ Advises Shire in 202,000 SF Lease, Creating Boston's Largest Suburban Biotech Campus 2Eppendorf Announces Promotional Bundle Which Includes: Eppendorf Centrifuge 5424, 3-Pack of Pipettes, and Tips - Available Now at Pipette.com 2Diagenode Launches Unique Semi-Automated Solution for Chromatin Immunoprecipitation 2Derma Sciences Expands Access of its AMNIOTIC TISSUE Product Line with New Premier, Inc. Agreement 2Derma Sciences Expands Access of its AMNIOTIC TISSUE Product Line with New Premier, Inc. Agreement 3Derma Sciences Expands Access of its AMNIOTIC TISSUE Product Line with New Premier, Inc. Agreement 4Derma Sciences Expands Access of its AMNIOTIC TISSUE Product Line with New Premier, Inc. Agreement 5
... 17, 2011 Hadasit Bio-Holdings, Ltd. - (OTCBB: HADSY), ... on intellectual property developed by the Hadassah University Hospital, ... company Enlivex Therapeutics (92% owned by Hadasit Bio) has ... in its Phase I / II clinical trial using ...
... ReportsnReports   announces ... Recovery Solutions, Electric Vehicle, Telemedicine, NFC PoS Terminal, 3D ... Technoavio / Infiniti Research has recently ... Priced differently based on the market and geography researched, ...
... Institute for Biotechnology) and Ghent University have shown that ... rheumatoid arthritis, an often-crippling inflammation of the joints that ... the underlying molecular mechanism of the disease was largely ... , the researchers demonstrate that a cell-specific defect in ...
Cached Biology Technology:Clinical Developments at Enlivex Therapeutics - a Hadasit Bio-Holdings Portfolio Company 2Clinical Developments at Enlivex Therapeutics - a Hadasit Bio-Holdings Portfolio Company 3Clinical Developments at Enlivex Therapeutics - a Hadasit Bio-Holdings Portfolio Company 4ReportsnReports - Global Hospital Information Systems, Mobile Health Applications, Electric Vehicle Market Research Reports 2ReportsnReports - Global Hospital Information Systems, Mobile Health Applications, Electric Vehicle Market Research Reports 3ReportsnReports - Global Hospital Information Systems, Mobile Health Applications, Electric Vehicle Market Research Reports 4ReportsnReports - Global Hospital Information Systems, Mobile Health Applications, Electric Vehicle Market Research Reports 5Defect in A20 gene expression causes rheumatoid arthritis 2
... gene in baculoviral expression vector, transfection ... purification of ten clones, generation of ... clone, protein expression and tag purification ... yield and timeline: 1-4 mg of ...
... Synthesis Service provides you with ... knockdown any gene. We offer ... pairs with terminal dT nucleotides), ... lengths of your choice. Each ...
EDG-1 Western blot control Source: Cell Lysate Application: Western Blotting Control...
Hybridization cassette for one slide...
Biology Products: