Sentence examples for extensive replica exchange from inspiring English sources
We carried out extensive replica exchange molecular dynamics simulations on 1BBL in explicit solvent to address this controversy and provide a microscopic picture of its folding thermodynamics.
In this study, we performed an extensive replica exchange with flexible tempering (REFT) molecular dynamics simulation of the ternary replicating complex of the archaeal family B DNA polymerase from the thermophile Thermococcus gorgonarius, right before the chemical step.
Extensive replica exchange Monte Carlo folding and unfolding simulations in implicit solvent with capped and uncapped termini failed to converge to any consistent cluster of structures, suggesting that the fragment remains largely unstructured in solution under the conditions considered.
ASyncRE is written in Python following a modular design conducive to extensions to various replica exchange schemes and molecular dynamics engines.
Here, we have performed extensive atomistic replica-exchange molecular dynamics simulations of the solvated wild-type (WT), A2V, and A2T Aβ1–42 monomers.
Parallel replica exchange sampling is an extended ensemble technique often used to accelerate the exploration of the conformational ensemble of atomistic molecular simulations of chemical systems.
A wide variety of methods are used to address the need to sample the extensive conformational space explored by IDPs/IDRs, including molecular dynamics methods, often enhanced by approaches such as replica exchange and related methods [ 106, 107], and Monte Carlo sampling methods [ 108, 109].
Modified Monte Carlo methods are presented in the context of protein design and sequence sampling: Monte Carlo with replica exchange (MCREM) and biased Monte Carlo with replica exchange (BMCREM).
This umbrella-sampling replica exchange molecular dynamics method performs a replica exchange molecular dynamics simulation along peptide association reaction coordinates using umbrella restraints.
This problem has led to the development of many improved replica exchange methods.
Moreover, our proposed non-blocking replica exchange reduces communication overhead in pair-wise process replica exchanges by allowing the process reaching the replica exchange point to leap-ahead while waiting for the other one to reach the common replica exchange point.
