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.
Computation of transit times using the milestoning method with applications to polymer translocation
Rent:
Rent this article for
USD
10.1063/1.4817200
/content/aip/journal/jcp/139/6/10.1063/1.4817200
http://aip.metastore.ingenta.com/content/aip/journal/jcp/139/6/10.1063/1.4817200
View: Figures

Figures

Image of FIG. 1.
FIG. 1.

A schematic diagram of a trajectory that passes from the reactants region of the conformation space to the products. The blue line represents the trajectory while it is fluctuating between the reactants and the transition region. The red line represents the transition path whose time duration gives a sample of the transit time, whereas the complete trajectory would be a sample of the first passage time.

Image of FIG. 2.
FIG. 2.

A schematic diagram of a trajectory that passes from reactant surface (milestone 1, ), to product surface (milestone 4, ). The trajectory starts on , at the phase space point represented by the filled black circle. The transit time for the transition from milestone 1 to 2 is denoted , and is given by the time duration of the blue path—i.e., the time interval between last crossing the reactant surface (at the filled square) and arriving at milestone 2. The time for the trajectory to then carry on to without returning to the , τ, is given by the red part of the path, and together + τ gives a sample of the transit time of the reaction.

Image of FIG. 3.
FIG. 3.

A homopolymer translocating through a narrow pore. In MFPT calculations, a reflecting boundary is imposed on monomer 1 (dashed line).

Image of FIG. 4.
FIG. 4.

(a) The MTT and (b) MLT plotted as a function of chain length, . The straight lines are least squares fits of the 5 milestone M1TM data to functions of the form () ∝ .

Image of FIG. 5.
FIG. 5.

A schematic diagram of a trajectory that takes a transition path from milestone 1 to 4. Here the milestones are ordered by the reaction coordinate () and milestones 2 and 3 are further broken up into MCM states (the quadrants of each milestone). The reactant (product) surface is taken to coincide with milestone 1(4). The blue path represents a A → β one-step transition path, which starts on the reactant surface and carries on to cluster β on milestone 2 without re-crossing the reactant surface. The duration of this path is denoted . The green path, on the other hand, is an example of a failed one step transition path, as it returns to the reactant surface before making a transition to a state in the transition region. The time τ for the trajectory in β to carry onto the product surface B (milestone 4) without returning to the reactant surface is given by the red segment of the path, and together + τ gives a sample of the transit time of the reaction.

Loading

Article metrics loading...

/content/aip/journal/jcp/139/6/10.1063/1.4817200
2013-08-08
2014-04-16
Loading

Full text loading...

This is a required field
Please enter a valid email address
752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Computation of transit times using the milestoning method with applications to polymer translocation
http://aip.metastore.ingenta.com/content/aip/journal/jcp/139/6/10.1063/1.4817200
10.1063/1.4817200
SEARCH_EXPAND_ITEM