Variationally Optimized Free-Energy Flooding for Rate Calculation

Physical Review Letters
James McCartyMichele Parrinello

Abstract

We propose a new method to obtain kinetic properties of infrequent events from molecular dynamics simulation. The procedure employs a recently introduced variational approach [Valsson and Parrinello, Phys. Rev. Lett. 113, 090601 (2014)] to construct a bias potential as a function of several collective variables that is designed to flood the associated free energy surface up to a predefined level. The resulting bias potential effectively accelerates transitions between metastable free energy minima while ensuring bias-free transition states, thus allowing accurate kinetic rates to be obtained. We test the method on a few illustrative systems for which we obtain an order of magnitude improvement in efficiency relative to previous approaches and several orders of magnitude relative to unbiased molecular dynamics. We expect an even larger improvement in more complex systems. This and the ability of the variational approach to deal efficiently with a large number of collective variables will greatly enhance the scope of these calculations. This work is a vindication of the potential that the variational principle has if applied in innovative ways.

References

Dec 1, 1994·Journal of Computer-aided Molecular Design·T HuberW F van Gunsteren
Sep 1, 1995·Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics·H Grubmüller
Apr 6, 2001·Physical Review Letters·F Wang, D P Landau
Feb 28, 2002·Physical Review Letters·Ulrich H E Hansmann, Luc T Wille
Apr 25, 2002·Annual Review of Physical Chemistry·Peter G BolhuisPhillip L Geissler
Sep 25, 2002·Proceedings of the National Academy of Sciences of the United States of America·Alessandro Laio, Michele Parrinello
Apr 30, 2004·Journal of Computational Chemistry·Junmei WangDavid A Case
Jul 23, 2004·The Journal of Chemical Physics·Anton K Faradjian, Ron Elber
Jul 23, 2004·The Journal of Chemical Physics·Donald HamelbergJ Andrew McCammon
Feb 7, 2006·Journal of Molecular Graphics & Modelling·Junmei WangDavid A Case
Jan 11, 2007·The Journal of Chemical Physics·Giovanni BussiMichele Parrinello
Mar 17, 2009·The Journal of Physical Chemistry. B·Paul MaragakisMartin Karplus
Dec 31, 2009·Journal of the American Chemical Society·Luca MaraglianoEric Vanden-Eijnden
Mar 10, 2011·The Journal of Chemical Physics·Aviel Chaimovich, M Scott Shell
May 10, 2011·The Journal of Chemical Physics·Jan-Hendrik PrinzFrank Noé
Jan 31, 2014·Physical Review Letters·Pratyush Tiwary, Michele Parrinello
Feb 25, 2014·The Journal of Chemical Physics·Matthias U BohnerJohannes Kästner
Mar 4, 2014·Nature Communications·Diwakar ShuklaVijay S Pande
Sep 13, 2014·Physical Review Letters·Omar Valsson, Michele Parrinello
Jan 24, 2015·The Journal of Chemical Physics·François SicardManoel Manghi
Aug 19, 2015·The Journal of Physical Chemistry Letters·Julian Schneider, Karsten Reuter
Nov 18, 2015·Journal of Chemical Theory and Computation·Omar Valsson, Michele Parrinello
Apr 8, 2014·Journal of Chemical Theory and Computation·Matteo SalvalaglioMichele Parrinello
Jan 1, 2008·Journal of Chemical Theory and Computation·Berk Hess

❮ Previous
Next ❯

Citations

Jan 21, 2016·Proceedings of the National Academy of Sciences of the United States of America·Patrick ShafferMichele Parrinello
Apr 9, 2016·Journal of Chemical Theory and Computation·James McCartyMichele Parrinello
Mar 17, 2016·Annual Review of Physical Chemistry·Omar ValssonMichele Parrinello
Jan 11, 2017·The Journal of Physical Chemistry Letters·GiovanniMaria PicciniMichele Parrinello
Oct 19, 2016·Faraday Discussions·Pablo M PiaggiMichele Parrinello
Aug 17, 2019·Proceedings of the National Academy of Sciences of the United States of America·Luigi BonatiMichele Parrinello
Sep 24, 2020·The Journal of Chemical Physics·Kristof M BalErik C Neyts
Mar 16, 2017·Proceedings of the National Academy of Sciences of the United States of America·Michele InvernizziMichele Parrinello
Aug 24, 2018·The Journal of Chemical Physics·João Marcelo Lamim RibeiroPratyush Tiwary
Aug 24, 2018·The Journal of Chemical Physics·Yong WangKresten Lindorff-Larsen
Mar 27, 2019·Journal of Chemical Theory and Computation·Riccardo CapelliMichele Parrinello
Dec 15, 2018·Biochemistry·João Marcelo Lamim RibeiroPratyush Tiwary
Sep 15, 2017·The Journal of Physical Chemistry Letters·Ferruccio PalazzesiMichele Parrinello
Jun 28, 2019·The Journal of Physical Chemistry Letters·GiovanniMaria Piccini, Michele Parrinello
Jun 9, 2020·The Journal of Physical Chemistry Letters·Jayashrita Debnath, Michele Parrinello
Oct 5, 2017·Journal of Chemical Theory and Computation·Bradley M Dickson
May 2, 2018·Journal of Chemical Theory and Computation·Yi Isaac Yang, Michele Parrinello

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Physical Review Letters
Pratyush Tiwary, Michele Parrinello
Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
Yanier CrespoAlessandro Laio
The Journal of Physical Chemistry. B
Wenwei ZhengCecilia Clementi
© 2021 Meta ULC. All rights reserved