Literature DB >> 18999998

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

Weinan E1, Eric Vanden-Eijnden.   

Abstract

Transition-path theory is a theoretical framework for describing rare events in complex systems. It can also be used as a starting point for developing efficient numerical algorithms for analyzing such rare events. Here we review the basic components of transition-path theory and path-finding algorithms. We also discuss connections with the classical transition-state theory.

Year:  2010        PMID: 18999998     DOI: 10.1146/annurev.physchem.040808.090412

Source DB:  PubMed          Journal:  Annu Rev Phys Chem        ISSN: 0066-426X            Impact factor:   12.703


  95 in total

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2.  Investigating reaction pathways in rare events simulations of antibiotics diffusion through protein channels.

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3.  Markov state modeling and dynamical coarse-graining via discrete relaxation path sampling.

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4.  Rotational diffusion affects the dynamical self-assembly pathways of patchy particles.

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Journal:  Proc Natl Acad Sci U S A       Date:  2015-11-30       Impact factor: 11.205

5.  Network representation of conformational transitions between hidden intermediates of Rd-apocytochrome b562.

Authors:  Mojie Duan; Hanzhong Liu; Minghai Li; Shuanghong Huo
Journal:  J Chem Phys       Date:  2015-10-07       Impact factor: 3.488

6.  Perspective: Computer simulations of long time dynamics.

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Review 7.  Machine Learning Force Fields and Coarse-Grained Variables in Molecular Dynamics: Application to Materials and Biological Systems.

Authors:  Paraskevi Gkeka; Gabriel Stoltz; Amir Barati Farimani; Zineb Belkacemi; Michele Ceriotti; John D Chodera; Aaron R Dinner; Andrew L Ferguson; Jean-Bernard Maillet; Hervé Minoux; Christine Peter; Fabio Pietrucci; Ana Silveira; Alexandre Tkatchenko; Zofia Trstanova; Rafal Wiewiora; Tony Lelièvre
Journal:  J Chem Theory Comput       Date:  2020-07-16       Impact factor: 6.006

8.  Graph representation of protein free energy landscape.

Authors:  Minghai Li; Mojie Duan; Jue Fan; Li Han; Shuanghong Huo
Journal:  J Chem Phys       Date:  2013-11-14       Impact factor: 3.488

9.  Thermodynamically reversible paths of the first fusion intermediate reveal an important role for membrane anchors of fusion proteins.

Authors:  Yuliya G Smirnova; Herre Jelger Risselada; Marcus Müller
Journal:  Proc Natl Acad Sci U S A       Date:  2019-01-30       Impact factor: 11.205

10.  QM/MM free energy simulations: recent progress and challenges.

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Journal:  Mol Simul       Date:  2016-07-05       Impact factor: 2.178

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