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Baseline Comparisons of Complementary Sampling Methods for Assembly Driven by Short-Ranged Pair Potentials toward Fast and Flexible Hybridization

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  • Aysegul Ozkan, University of Florida
  • ,
  • Meera Sitharam, University of Florida
  • ,
  • Jose C. Flores-Canales
  • ,
  • Rahul Prabhu, University of Florida
  • ,
  • Maria Kurnikova, Carnegie Mellon University

This work measures baseline sampling characteristics that highlight fundamental differences between sampling methods for assembly driven by short-ranged pair potentials. Such granular comparison is essential for fast, flexible, and accurate hybridization of complementary methods. Besides sampling speed, efficiency, and accuracy of uniform grid coverage, other sampling characteristics measured are (i) accuracy of covering narrow low energy regions that have low effective dimension (ii) ability to localize sampling to specific basins, and (iii) flexibility in sampling distributions. As a proof of concept, we compare a recently developed geometric methodology EASAL (Efficient Atlasing and Search of Assembly Landscapes) and the traditional Monte Carlo (MC) method for sampling the energy landscape of two assembling trans-membrane helices, driven by short-range pair potentials. By measuring the above-mentioned sampling characteristics, we demonstrate that EASAL provides localized and accurate coverage of crucial regions of the energy landscape of low effective dimension, under flexible sampling distributions, with much fewer samples and computational resources than MC sampling. EASAL's empirically validated theoretical guarantees permit credible extrapolation of these measurements and comparisons to arbitrary number and size of assembling units. Promising avenues for hybridizing the complementary advantages of the two methods are discussed.

OriginalsprogEngelsk
TidsskriftJournal of Chemical Theory and Computation
Vol/bind17
Nummer3
Sider (fra-til)1967-1987
Antal sider21
ISSN1549-9618
DOI
StatusUdgivet - mar. 2021

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