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© Structural Dynamics Of Macromolecules
The structure of a bacterial analog of the nicotinic receptor (one color per subunit) inserted into the cell membrane (grey and orange). A representation of the volume accessible to ions is shown in yellow.
Publication : The Journal of chemical physics

Ab initio sampling of transition paths by conditioned Langevin dynamics

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in The Journal of chemical physics - 21 Oct 2017

Delarue M, Koehl P, Orland H

Link to Pubmed [PMID] – 29055326

J Chem Phys 2017 Oct;147(15):152703

We propose a novel stochastic method to generate Brownian paths conditioned to start at an initial point and end at a given final point during a fixed time t under a given potential U(x). These paths are sampled with a probability given by the overdamped Langevin dynamics. We show that these paths can be exactly generated by a local stochastic partial differential equation. This equation cannot be solved in general but we present several approximations that are valid either in the low temperature regime or in the presence of barrier crossing. We show that this method warrants the generation of statistically independent transition paths. It is computationally very efficient. We illustrate the method first on two simple potentials, the two-dimensional Mueller potential and the Mexican hat potential, and then on the multi-dimensional problem of conformational transitions in proteins using the “Mixed Elastic Network Model” as a benchmark.

https://www.ncbi.nlm.nih.gov/pubmed/29055326