1887
banner image
No data available.
Please log in to see this content.
You have no subscription access to this content.
No metrics data to plot.
The attempt to load metrics for this article has failed.
The attempt to plot a graph for these metrics has failed.
Simulating rare events in equilibrium or nonequilibrium stochastic systems
Rent:
Rent this article for
USD
10.1063/1.2140273
/content/aip/journal/jcp/124/2/10.1063/1.2140273
http://aip.metastore.ingenta.com/content/aip/journal/jcp/124/2/10.1063/1.2140273

Figures

Image of FIG. 1.
FIG. 1.

Schematic illustration of the definition of regions and and the interfaces (here, ). Three transition paths are shown.

Image of FIG. 2.
FIG. 2.

The first (a) and second (b) stages of the FFS method. The distribution of points at the interfaces depends on the history of the paths, as illustrated by the dashed lines in (b). The circles are members of the collection of points at the interfaces .

Image of FIG. 3.
FIG. 3.

Schematic illustration of the extraction of the transition path ensemble from the FFS procedure. All partial paths that reach the subsequent interface are shown. Partial paths that do not contribute to the TPE are shown by dotted lines. The solid lines correspond to the TPE; the width of the line indicates the weight of the contribution of a particular partial path to the TPE.

Image of FIG. 4.
FIG. 4.

A schematic view of the generation of a branched path (thick lines) using the branched growth sampling method. The simulation run in the basin is shown by a dotted line. Trial runs which fail to reach are shown by thin lines. The generation of the initial point for the next path is also shown.

Image of FIG. 5.
FIG. 5.

A schematic view of the generation of a transition path using the Rosenbluth sampling method. The simulation run in the basin is shown by a dotted line. The transition path is shown by bold lines. Trial runs which do not form part of the transition path are shown by thin lines. The generation of the next starting point at is also illustrated.

Image of FIG. 6.
FIG. 6.

Two transition paths generated by the Rosenbluth method. The bottom path must be reweighted by a factor of 9 relative to the top path.

Image of FIG. 7.
FIG. 7.

Reaction scheme for the genetic switch. Proteins A and B can dimerize and bind to the DNA at the operator site, . When is bound to , is not produced, and when is bound to , is not produced. Both proteins are degraded in the monomer form. Forward and backward rate constants and are identical for A and B.

Image of FIG. 8.
FIG. 8.

as a function of time (in units of ) for a typical simulation run.

Image of FIG. 9.
FIG. 9.

(a) An illustration of the polymer simulation. (b) A “zoomed in” view, showing the three regions used to define , in Eq. (13).

Image of FIG. 10.
FIG. 10.

(a) as a function of time (in units of ) for a typical brute-force simulation run.

Image of FIG. 11.
FIG. 11.

Illustration of the division of a path into partial paths. (a) A path which begins in and reaches . Points 2–6 belong to the partial path , points 7–17 to , and points 18–42 to . (b) A path which begins and ends in . Partial paths are coded as follows: open circles, squares, and triangles.

Tables

Generic image for table
Table I.

Path sampling and brute-force (BF) results for , , and . The brute-force result is obtained by fitting as described in the text. is the approximate number of simulation steps performed in obtaining the result in the table.

Generic image for table
Table II.

Path sampling and brute-force results for , , and . Units of and are . The brute-force result is obtained by fitting as described in the text. The errors represent the standard error in the mean of a series of independent estimates. is the approximate number of simulation steps performed in arriving at the result given in the table.

Generic image for table
Table III.

Path sampling and brute-force results for , and , for the polymer translocation problem with the altered parameter set. Units of and are . The errors represent the standard error in the mean of a series of independent estimates. is the approximate number of simulation steps performed in arriving at the result given in the table.

Generic image for table
Table IV.

FFS and brute-force results for , , and , for the polymer translocation problem of Sec. IV B, with pruning probability at all interfaces. Units of and are . The errors represent the standard error in the mean of a series of independent estimates. is the approximate number of simulation steps performed in arriving at the result given in the table

Loading

Article metrics loading...

/content/aip/journal/jcp/124/2/10.1063/1.2140273
2006-01-10
2014-04-20
Loading

Full text loading...

This is a required field
Please enter a valid email address
752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Simulating rare events in equilibrium or nonequilibrium stochastic systems
http://aip.metastore.ingenta.com/content/aip/journal/jcp/124/2/10.1063/1.2140273
10.1063/1.2140273
SEARCH_EXPAND_ITEM