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Title: Sequential data assimilation for single-molecule FRET photon-counting data

Data assimilation is a statistical method designed to improve the quality of numerical simulations in combination with real observations. Here, we develop a sequential data assimilation method that incorporates one-dimensional time-series data of smFRET (single-molecule Förster resonance energy transfer) photon-counting into conformational ensembles of biomolecules derived from “replicated” molecular dynamics (MD) simulations. A particle filter using a large number of “replicated” MD simulations with a likelihood function for smFRET photon-counting data is employed to screen the conformational ensembles that match the experimental data. We examine the performance of the method using emulated smFRET data and coarse-grained (CG) MD simulations of a dye-labeled polyproline-20. The method estimates the dynamics of the end-to-end distance from smFRET data as well as revealing that of latent conformational variables. The particle filter is also able to correct model parameter dependence in CG MD simulations. We discuss the applicability of the method to real experimental data for conformational dynamics of biomolecules.
Authors:
 [1] ;  [2] ;  [1] ;  [3] ;  [3] ;  [4]
  1. Advanced Institute for Computational Science, RIKEN, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047 (Japan)
  2. Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi, Yokohama 230-0045 (Japan)
  3. (Japan)
  4. (IMDA) 6F, 1-6-5 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047 (Japan)
Publication Date:
OSTI Identifier:
22415930
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Chemical Physics; Journal Volume: 142; Journal Issue: 21; Other Information: (c) 2015 AIP Publishing LLC; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY; COMPUTERIZED SIMULATION; DYES; ENERGY TRANSFER; MOLECULAR DYNAMICS METHOD; MOLECULES; ONE-DIMENSIONAL CALCULATIONS; ORGANIC POLYMERS; PARTICLES; PERFORMANCE; PHOTONS; RESONANCE