Literature DB >> 23030145

Path finding on high-dimensional free energy landscapes.

Grisell Díaz Leines1, Bernd Ensing.   

Abstract

We present a method for determining the average transition path and the free energy along this path in the space of selected collective variables. The formalism is based upon a history-dependent bias along a flexible path variable within the metadynamics framework but with a trivial scaling of the cost with the number of collective variables. Controlling the sampling of the orthogonal modes recovers the average path and the minimum free energy path as the limiting cases. The method is applied to resolve the path and the free energy of a conformational transition in alanine dipeptide.

Entities:  

Year:  2012        PMID: 23030145     DOI: 10.1103/PhysRevLett.109.020601

Source DB:  PubMed          Journal:  Phys Rev Lett        ISSN: 0031-9007            Impact factor:   9.161


  11 in total

1.  Free Energy Landscape and Conformational Kinetics of Hoogsteen Base Pairing in DNA vs. RNA.

Authors:  Dhiman Ray; Ioan Andricioaei
Journal:  Biophys J       Date:  2020-09-02       Impact factor: 4.033

2.  Scalable molecular dynamics on CPU and GPU architectures with NAMD.

Authors:  James C Phillips; David J Hardy; Julio D C Maia; John E Stone; João V Ribeiro; Rafael C Bernardi; Ronak Buch; Giacomo Fiorin; Jérôme Hénin; Wei Jiang; Ryan McGreevy; Marcelo C R Melo; Brian K Radak; Robert D Skeel; Abhishek Singharoy; Yi Wang; Benoît Roux; Aleksei Aksimentiev; Zaida Luthey-Schulten; Laxmikant V Kalé; Klaus Schulten; Christophe Chipot; Emad Tajkhorshid
Journal:  J Chem Phys       Date:  2020-07-28       Impact factor: 3.488

3.  ATP dependent NS3 helicase interaction with RNA: insights from molecular simulations.

Authors:  Andrea Pérez-Villa; Maria Darvas; Giovanni Bussi
Journal:  Nucleic Acids Res       Date:  2015-09-10       Impact factor: 16.971

4.  A Companion Guide to the String Method with Swarms of Trajectories: Characterization, Performance, and Pitfalls.

Authors:  Haochuan Chen; Dylan Ogden; Shashank Pant; Wensheng Cai; Emad Tajkhorshid; Mahmoud Moradi; Benoît Roux; Christophe Chipot
Journal:  J Chem Theory Comput       Date:  2022-02-09       Impact factor: 6.006

5.  String method for calculation of minimum free-energy paths in Cartesian space in freely-tumbling systems.

Authors:  Davide Branduardi; José D Faraldo-Gómez
Journal:  J Chem Theory Comput       Date:  2013-09-10       Impact factor: 6.006

Review 6.  Frontiers in Multiscale Modeling of Photoreceptor Proteins.

Authors:  Maria-Andrea Mroginski; Suliman Adam; Gil S Amoyal; Avishai Barnoy; Ana-Nicoleta Bondar; Veniamin A Borin; Jonathan R Church; Tatiana Domratcheva; Bernd Ensing; Francesca Fanelli; Nicolas Ferré; Ofer Filiba; Laura Pedraza-González; Ronald González; Cristina E González-Espinoza; Rajiv K Kar; Lukas Kemmler; Seung Soo Kim; Jacob Kongsted; Anna I Krylov; Yigal Lahav; Michalis Lazaratos; Qays NasserEddin; Isabelle Navizet; Alexander Nemukhin; Massimo Olivucci; Jógvan Magnus Haugaard Olsen; Alberto Pérez de Alba Ortíz; Elisa Pieri; Aditya G Rao; Young Min Rhee; Niccolò Ricardi; Saumik Sen; Ilia A Solov'yov; Luca De Vico; Tomasz A Wesolowski; Christian Wiebeler; Xuchun Yang; Igor Schapiro
Journal:  Photochem Photobiol       Date:  2021-02-13       Impact factor: 3.521

7.  Fast exploration of an optimal path on the multidimensional free energy surface.

Authors:  Changjun Chen
Journal:  PLoS One       Date:  2017-05-18       Impact factor: 3.240

8.  Closer Look at Inverse Electron Demand Diels-Alder and Nucleophilic Addition Reactions on s-Tetrazines Using Enhanced Sampling Methods.

Authors:  Rangsiman Ketkaew; Fabrizio Creazzo; Sandra Luber
Journal:  Top Catal       Date:  2021-10-23       Impact factor: 2.910

9.  The HAMP signal relay domain adopts multiple conformational states through collective piston and tilt motions.

Authors:  Lizhe Zhu; Peter G Bolhuis; Jocelyne Vreede
Journal:  PLoS Comput Biol       Date:  2013-02-28       Impact factor: 4.475

10.  Computational Recipe for Efficient Description of Large-Scale Conformational Changes in Biomolecular Systems.

Authors:  Mahmoud Moradi; Emad Tajkhorshid
Journal:  J Chem Theory Comput       Date:  2014-06-03       Impact factor: 6.006

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