Thermodynamic integration network approach to ion transport through protein channels: Perspectives and limits
Sign Up to like & getrecommendations! Published in 2018 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.25615
Abstract: We present a molecular dynamics simulation study of alkali metal cation transport through the double‐helical and the head‐to‐head conformers of the gramicidin ion channel. Our approach is based on a thermodynamic integration network, which consists… read more here.
Keywords: head; thermodynamic integration; network; transport ... See more keywords
Resampling method for reliability-based design optimization based on thermodynamic integration and parallel tempering
Sign Up to like & getrecommendations! Published in 2021 at "Mechanical Systems and Signal Processing"
DOI: 10.1016/j.ymssp.2021.107630
Abstract: Abstract In this paper, a fully decoupled simulation method is proposed for reliability-based design optimization (RBDO) based on thermodynamic integration and parallel tempering (TIPT). We show that the failure probability function and its gradient can… read more here.
Keywords: optimization; method; thermodynamic integration; based thermodynamic ... See more keywords
Alchemical Free-Energy Calculations by Multiple-Replica λ-Dynamics: The Conveyor Belt Thermodynamic Integration Scheme.
Sign Up to like & getrecommendations! Published in 2019 at "Journal of chemical theory and computation"
DOI: 10.1021/acs.jctc.8b00782
Abstract: A new method is proposed to calculate alchemical free-energy differences based on molecular dynamics (MD) simulations, called the conveyor belt thermodynamic integration (CBTI) scheme. As in thermodynamic integration (TI), K replicas of the system are… read more here.
Keywords: thermodynamic integration; energy; scheme; free energy ... See more keywords