Inertial stochastic dynamics. II. Influence of inertia on slow kinetic processes of supercoiled DNA
Journal of Chemical Physics, ISSN: 0021-9606, Vol: 112, Issue: 17, Page: 7323-7338
2000
- 24Citations
- 28Captures
Metric Options: Counts1 Year3 YearSelecting the 1-year or 3-year option will change the metrics count to percentiles, illustrating how an article or review compares to other articles or reviews within the selected time period in the same journal. Selecting the 1-year option compares the metrics against other articles/reviews that were also published in the same calendar year. Selecting the 3-year option compares the metrics against other articles/reviews that were also published in the same calendar year plus the two years prior.
Example: if you select the 1-year option for an article published in 2019 and a metric category shows 90%, that means that the article or review is performing better than 90% of the other articles/reviews published in that journal in 2019. If you select the 3-year option for the same article published in 2019 and the metric category shows 90%, that means that the article or review is performing better than 90% of the other articles/reviews published in that journal in 2019, 2018 and 2017.
Citation Benchmarking is provided by Scopus and SciVal and is different from the metrics context provided by PlumX Metrics.
Example: if you select the 1-year option for an article published in 2019 and a metric category shows 90%, that means that the article or review is performing better than 90% of the other articles/reviews published in that journal in 2019. If you select the 3-year option for the same article published in 2019 and the metric category shows 90%, that means that the article or review is performing better than 90% of the other articles/reviews published in that journal in 2019, 2018 and 2017.
Citation Benchmarking is provided by Scopus and SciVal and is different from the metrics context provided by PlumX Metrics.
Article Description
We apply our new algorithms presented in the companion paper (LTID: long-time-step inertial dynamics, IBD: inertial Brownian dynamics) for mass-dependent Langevin dynamics (LD) with hydrodynamics, as well as the standard Brownian dynamical (BD) propagator, to study the thermal fluctuations of supercoiled DNA minicircles. Our DNA model accounts for twisting, bending, and salt-screened electrostatic interactions. Though inertial relaxation times are on the order of picoseconds, much slower kinetic processes are affected by the Brownian (noninertial) approximation typically employed. By comparing results of LTID and IBD to those generated using the standard (BD) algorithm, we find that the equilibrium fluctuations in writhing number, Wr, and radius of gyration, R, are influenced by mass-dependent terms. The autocorrelation functions for these quantities differ between the BD simulations and the inertial LD simulations by as much as 10%. In contrast, when the nonequilibrium process of relaxation from a perturbed state is examined, all methods (inertial and diffusive) yield similar results with no detectable statistical differences between the mean folding pathways. Thus, while the evolution of an ensemble toward equilibrium is equally well described by the inertial and the noninertial methods, thermal fluctuations are influenced by inertia. Examination of such equilibrium fluctuations in a biologically relevant macroscopic property - namely the two-site intermolecular distance-reveals mass-dependent behavior: The rate of juxtaposition of linearly distant sites along a 1500-base pair DNA plasmid, occurring over time scales of milliseconds and longer, is increased by about 8% when results from IBD are compared to those from BD. Since inertial modes that decay on the picosecond time scale in the absence of thermal forces exert an influence on slower fluctuations in macroscopic properties, we advocate that IBD be used for generating long-time trajectories of supercoiled DNA systems. IBD is a practical alternative since it requires modest computational overhead with respect to the standard BD method. © 2000 American Institute of Physics.
Bibliographic Details
Provide Feedback
Have ideas for a new metric? Would you like to see something else here?Let us know