Literature DB >> 29055297

Rock climbing: A local-global algorithm to compute minimum energy and minimum free energy pathways.

Clark Templeton1, Szu-Hua Chen2, Arman Fathizadeh3, Ron Elber3.   

Abstract

The calculation of minimum energy or minimum free energy paths is an important step in the quantitative and qualitative studies of chemical and physical processes. The computations of these coordinates present a significant challenge and have attracted considerable theoretical and computational interest. Here we present a new local-global approach to study reaction coordinates, based on a gradual optimization of an action. Like other global algorithms, it provides a path between known reactants and products, but it uses a local algorithm to extend the current path in small steps. The local-global approach does not require an initial guess to the path, a major challenge for global pathway finders. Finally, it provides an exact answer (the steepest descent path) at the end of the calculations. Numerical examples are provided for the Mueller potential and for a conformational transition in a solvated ring system.

Year:  2017        PMID: 29055297      PMCID: PMC5565490          DOI: 10.1063/1.4986298

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  18 in total

1.  Scalable molecular dynamics with NAMD.

Authors:  James C Phillips; Rosemary Braun; Wei Wang; James Gumbart; Emad Tajkhorshid; Elizabeth Villa; Christophe Chipot; Robert D Skeel; Laxmikant Kalé; Klaus Schulten
Journal:  J Comput Chem       Date:  2005-12       Impact factor: 3.376

2.  Equilibrium free energies from nonequilibrium metadynamics.

Authors:  Giovanni Bussi; Alessandro Laio; Michele Parrinello
Journal:  Phys Rev Lett       Date:  2006-03-07       Impact factor: 9.161

3.  String method in collective variables: minimum free energy paths and isocommittor surfaces.

Authors:  Luca Maragliano; Alexander Fischer; Eric Vanden-Eijnden; Giovanni Ciccotti
Journal:  J Chem Phys       Date:  2006-07-14       Impact factor: 3.488

4.  Dominant pathways in protein folding.

Authors:  P Faccioli; M Sega; F Pederiva; H Orland
Journal:  Phys Rev Lett       Date:  2006-09-06       Impact factor: 9.161

5.  Finding transition pathways using the string method with swarms of trajectories.

Authors:  Albert C Pan; Deniz Sezer; Benoît Roux
Journal:  J Phys Chem B       Date:  2008-02-22       Impact factor: 2.991

6.  Transition-path theory and path-finding algorithms for the study of rare events.

Authors:  Weinan E; Eric Vanden-Eijnden
Journal:  Annu Rev Phys Chem       Date:  2010       Impact factor: 12.703

7.  Analyzing milestoning networks for molecular kinetics: definitions, algorithms, and examples.

Authors:  Shruthi Viswanath; Steven M Kreuzer; Alfredo E Cardenas; Ron Elber
Journal:  J Chem Phys       Date:  2013-11-07       Impact factor: 3.488

8.  Implementation of Accelerated Molecular Dynamics in NAMD.

Authors:  Yi Wang; Christopher B Harrison; Klaus Schulten; J Andrew McCammon
Journal:  Comput Sci Discov       Date:  2011

9.  Targeted molecular dynamics: a new approach for searching pathways of conformational transitions.

Authors:  J Schlitter; M Engels; P Krüger
Journal:  J Mol Graph       Date:  1994-06

10.  How conformational dynamics of DNA polymerase select correct substrates: experiments and simulations.

Authors:  Serdal Kirmizialtin; Virginia Nguyen; Kenneth A Johnson; Ron Elber
Journal:  Structure       Date:  2012-04-03       Impact factor: 5.006

View more
  3 in total

1.  Molecular Dynamics-Based Thermodynamic and Kinetic Characterization of Membrane Protein Conformational Transitions.

Authors:  Dylan Ogden; Mahmoud Moradi
Journal:  Methods Mol Biol       Date:  2021

2.  Defect-Assisted Permeation Through a Phospholipid Membrane: Experimental and Computational Study of the Peptide WKW.

Authors:  Arman Fathizadeh; Molly Kogan; Cari M Anderson; Lauren J Webb; Ron Elber
Journal:  J Phys Chem B       Date:  2019-07-26       Impact factor: 2.991

3.  The transition between active and inactive conformations of Abl kinase studied by rock climbing and Milestoning.

Authors:  Brajesh Narayan; Arman Fathizadeh; Clark Templeton; Peng He; Shima Arasteh; Ron Elber; Nicolae-Viorel Buchete; Ron M Levy
Journal:  Biochim Biophys Acta Gen Subj       Date:  2019-12-27       Impact factor: 3.770

  3 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.