efficient sampling of knotting-unknotting pathways for semiflexible gaussian chains

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ID: 182527
2017
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Abstract
We propose a stochastic method to generate exactly the overdamped Langevin dynamics of semi-flexible Gaussian chains, conditioned to evolve between given initial and final conformations in a preassigned time. The initial and final conformations have no restrictions, and hence can be in any knotted state. Our method allows the generation of statistically independent paths in a computationally efficient manner. We show that these conditioned paths can be exactly generated by a set of local stochastic differential equations. The method is used to analyze the transition routes between various knots in crossable filamentous structures, thus mimicking topological reconnections occurring in soft matter systems or those introduced in DNA by topoisomerase enzymes. We find that the average number of crossings, writhe and unknotting number are not necessarily monotonic in time and that more complex topologies than the initial and final ones can be visited along the route.
Reference Key
micheletti2017polymersefficient Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors ;Cristian Micheletti;Henri Orland
Journal Journal of Fluorescence
Year 2017
DOI
10.3390/polym9060196
URL
http://www.mdpi.com/2073-4360/9/6/196
Keywords Keywords not found

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