Literature DB >> 17678132

Reaction rate calculation by parallel path swapping.

Titus S van Erp1.   

Abstract

The efficiency of path sampling simulations can be improved considerably using the approach of path swapping. For this purpose, we devise a new algorithmic procedure based on the transition interface sampling technique. In the same spirit of parallel tempering, paths between different ensembles are swapped, but the role of temperature is here played by the interface position. We test the method on the denaturation transition of DNA using the Peyrard-Bishop-Dauxois model. We find that the new algorithm gives a reduction of the computational cost by a factor of 20.

Year:  2007        PMID: 17678132     DOI: 10.1103/PhysRevLett.98.268301

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


  8 in total

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Authors:  Weina Du; Peter G Bolhuis
Journal:  Biophys J       Date:  2015-01-20       Impact factor: 4.033

2.  The role of multivalency in the association kinetics of patchy particle complexes.

Authors:  Arthur C Newton; Jan Groenewold; Willem K Kegel; Peter G Bolhuis
Journal:  J Chem Phys       Date:  2017-06-21       Impact factor: 3.488

3.  Molecular mechanism for cavitation in water under tension.

Authors:  Georg Menzl; Miguel A Gonzalez; Philipp Geiger; Frédéric Caupin; José L F Abascal; Chantal Valeriani; Christoph Dellago
Journal:  Proc Natl Acad Sci U S A       Date:  2016-11-01       Impact factor: 11.205

4.  Local initiation conditions for water autoionization.

Authors:  Mahmoud Moqadam; Anders Lervik; Enrico Riccardi; Vishwesh Venkatraman; Bjørn Kåre Alsberg; Titus S van Erp
Journal:  Proc Natl Acad Sci U S A       Date:  2018-04-30       Impact factor: 11.205

5.  Predicting the mechanism and rate of H-NS binding to AT-rich DNA.

Authors:  Enrico Riccardi; Eva C van Mastbergen; William Wiley Navarre; Jocelyne Vreede
Journal:  PLoS Comput Biol       Date:  2019-03-07       Impact factor: 4.475

6.  OpenPathSampling: A Python Framework for Path Sampling Simulations. 2. Building and Customizing Path Ensembles and Sample Schemes.

Authors:  David W H Swenson; Jan-Hendrik Prinz; Frank Noe; John D Chodera; Peter G Bolhuis
Journal:  J Chem Theory Comput       Date:  2018-12-31       Impact factor: 6.006

7.  OpenPathSampling: A Python Framework for Path Sampling Simulations. 1. Basics.

Authors:  David W H Swenson; Jan-Hendrik Prinz; Frank Noe; John D Chodera; Peter G Bolhuis
Journal:  J Chem Theory Comput       Date:  2018-12-31       Impact factor: 6.006

8.  Rate Prediction for Homogeneous Nucleation of Methane Hydrate at Moderate Supersaturation Using Transition Interface Sampling.

Authors:  A Arjun; P G Bolhuis
Journal:  J Phys Chem B       Date:  2020-09-08       Impact factor: 2.991

  8 in total

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