Sampling diffusive transition paths

PDF Version Also Available for Download.

Description

We address the problem of sampling double-ended diffusive paths. The ensemble of paths is expressed using a symmetric version of the Onsager-Machlup formula, which only requires evaluation of the force field and which, upon direct time discretization, gives rise to a symmetric integrator that is accurate to second order. Efficiently sampling this ensemble requires avoiding the well-known stiffness problem associated with sampling infinitesimal Brownian increments of the path, as well as a different type of stiffness associated with sampling the coarse features of long paths. The fine-features sampling stiffness is eliminated with the use of the fast sampling algorithm (FSA), ... continued below

Physical Description

12

Creation Information

F. Miller III, Thomas & Predescu, Cristian October 12, 2006.

Context

This article is part of the collection entitled: Office of Scientific & Technical Information Technical Reports and was provided by UNT Libraries Government Documents Department to Digital Library, a digital repository hosted by the UNT Libraries. More information about this article can be viewed below.

Who

People and organizations associated with either the creation of this article or its content.

Publisher

Provided By

UNT Libraries Government Documents Department

Serving as both a federal and a state depository library, the UNT Libraries Government Documents Department maintains millions of items in a variety of formats. The department is a member of the FDLP Content Partnerships Program and an Affiliated Archive of the National Archives.

Contact Us

What

Descriptive information to help identify this article. Follow the links below to find similar items on the Digital Library.

Description

We address the problem of sampling double-ended diffusive paths. The ensemble of paths is expressed using a symmetric version of the Onsager-Machlup formula, which only requires evaluation of the force field and which, upon direct time discretization, gives rise to a symmetric integrator that is accurate to second order. Efficiently sampling this ensemble requires avoiding the well-known stiffness problem associated with sampling infinitesimal Brownian increments of the path, as well as a different type of stiffness associated with sampling the coarse features of long paths. The fine-features sampling stiffness is eliminated with the use of the fast sampling algorithm (FSA), and the coarse-feature sampling stiffness is avoided by introducing the sliding and sampling (S&S) algorithm. A key feature of the S&S algorithm is that it enables massively parallel computers to sample diffusive trajectories that are long in time. We use the algorithm to sample the transition path ensemble for the structural interconversion of the 38-atom Lennard-Jones cluster at low temperature.

Physical Description

12

Source

  • Journal Name: THE JOURNAL OF CHEMICAL PHYSICS

Language

Item Type

Identifier

Unique identifying numbers for this article in the Digital Library or other systems.

  • Report No.: LBNL-1725E
  • Grant Number: DE-AC02-05CH11231
  • Office of Scientific & Technical Information Report Number: 951186
  • Archival Resource Key: ark:/67531/metadc934905

Collections

This article is part of the following collection of related materials.

Office of Scientific & Technical Information Technical Reports

Reports, articles and other documents harvested from the Office of Scientific and Technical Information.

Office of Scientific and Technical Information (OSTI) is the Department of Energy (DOE) office that collects, preserves, and disseminates DOE-sponsored research and development (R&D) results that are the outcomes of R&D projects or other funded activities at DOE labs and facilities nationwide and grantees at universities and other institutions.

What responsibilities do I have when using this article?

When

Dates and time periods associated with this article.

Creation Date

  • October 12, 2006

Added to The UNT Digital Library

  • Nov. 13, 2016, 7:26 p.m.

Description Last Updated

  • Nov. 18, 2016, 3:21 p.m.

Usage Statistics

When was this article last used?

Congratulations! It looks like you are the first person to view this item online.

Interact With This Article

Here are some suggestions for what to do next.

Start Reading

PDF Version Also Available for Download.

International Image Interoperability Framework

IIF Logo

We support the IIIF Presentation API

F. Miller III, Thomas & Predescu, Cristian. Sampling diffusive transition paths, article, October 12, 2006; Berkeley, California. (digital.library.unt.edu/ark:/67531/metadc934905/: accessed September 18, 2018), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.