Stochastic Neural Network Approach for Learning High-Dimensional Free Energy Surfaces

Physical Review Letters
Elia SchneiderMark E Tuckerman

Abstract

The generation of free energy landscapes corresponding to conformational equilibria in complex molecular systems remains a significant computational challenge. Adding to this challenge is the need to represent, store, and manipulate the often high-dimensional surfaces that result from rare-event sampling approaches employed to compute them. In this Letter, we propose the use of artificial neural networks as a solution to these issues. Using specific examples, we discuss network training using enhanced-sampling methods and the use of the networks in the calculation of ensemble averages.

References

Jul 1, 1985·Physical Review. B, Condensed Matter·A N ZismanS M Stishov
Nov 3, 2001·Physical Review Letters·A B BelonoshkoB Johansson
Sep 25, 2002·Proceedings of the National Academy of Sciences of the United States of America·Alessandro Laio, Michele Parrinello
Mar 1, 2005·IEEE Transactions on Neural Networks·Silvia Ferrari, Robert F Stengel
Feb 1, 2008·Physical Review Letters·Alessandro BarducciMichele Parrinello
Apr 25, 2008·The Journal of Chemical Physics·D Quigley, P M Rodger
Sep 28, 2010·Physical Review Letters·M Bonomi, M Parrinello
Sep 30, 2010·Proceedings of the National Academy of Sciences of the United States of America·Gareth A TribelloMichele Parrinello
Jul 30, 2011·Physical Review Letters·Tang-Qing Yu, Mark E Tuckerman
Jul 4, 2012·Journal of Chemical Theory and Computation·Kyle A BeauchampVijay S Pande
Jul 19, 2012·The Journal of Chemical Physics·Ming ChenMark E Tuckerman
Nov 5, 2013·The Journal of Chemical Physics·Philipp Geiger, Christoph Dellago
Mar 14, 2014·The Journal of Physical Chemistry. B·Alexandar T TzanovMark E Tuckerman
Apr 30, 1998·The Journal of Physical Chemistry. B·A D MacKerellM Karplus
Sep 23, 2014·The Journal of Chemical Physics·Lilia V NedialkovaGerhard Hummer
Mar 5, 2015·Proceedings of the National Academy of Sciences of the United States of America·Ming ChenMark E Tuckerman
Aug 12, 2014·Journal of Chemical Theory and Computation·Michel A Cuendet, Mark E Tuckerman
Sep 9, 2014·Journal of Chemical Theory and Computation·Thomas StecherGábor Csányi
Aug 4, 2016·Acta Crystallographica Section B, Structural Science, Crystal Engineering and Materials·Anthony M ReillyColin R Groom
Sep 7, 2016·Journal of Chemical Theory and Computation·Letif MonesGábor Csányi
Jun 22, 2017·Proceedings of the National Academy of Sciences of the United States of America·Eliodoro ChiavazzoIoannis G Kevrekidis

❮ Previous
Next ❯

Citations

Mar 17, 2018·The Journal of Chemical Physics·Hythem Sidky, Jonathan K Whitmer
Sep 5, 2020·International Journal of Molecular Sciences·Raudah LazimSun Choi
Sep 17, 2018·The Journal of Chemical Physics·Daniel P Zaleski, Kirill Prozument
Apr 9, 2018·The Journal of Chemical Physics·Ashley Z GuoJuan J de Pablo
Jul 25, 2018·The Journal of Chemical Physics·Linfeng ZhangWeinan E
Jun 17, 2019·The Journal of Chemical Physics·Jakub Rydzewski, Omar Valsson
Apr 22, 2019·The Journal of Chemical Physics·Michele Ceriotti
Feb 25, 2020·Annual Review of Physical Chemistry·Frank NoéCecilia Clementi
Sep 3, 2020·The Journal of Chemical Physics·Paul SinzMatthew Hirn
Jul 2, 2018·The Journal of Chemical Physics·Christoph Wehmeyer, Frank Noé
Sep 10, 2018·The Journal of Chemical Physics·Navjeet Ahalawat, Jagannath Mondal
Apr 2, 2018·The Journal of Chemical Physics·Linfeng ZhangWeinan E
Apr 3, 2019·Physical Review. E·Sajal Kumar Giri, Himangshu Prabal Goswami
Jan 11, 2020·Physical Review Letters·Jutta RogalMark E Tuckerman
Oct 18, 2020·Nature Communications·Mihail BogojeskiKieron Burke
Nov 11, 2020·The Journal of Chemical Physics·Jun ZhangYi Qin Gao
Apr 22, 2021·The Journal of Physical Chemistry. a·Atreyee BanerjeeDavid J Wales
May 5, 2021·Chemical Reviews·Aldo GlielmoAlessandro Laio
Jul 10, 2021·The Journal of Chemical Physics·A Moradzadeh, N R Aluru
Jul 20, 2018·The Journal of Physical Chemistry Letters·Karteek K BejagamSanket A Deshmukh
May 10, 2020·Journal of Chemical Theory and Computation·Yuki Mitsuta, Yasuteru Shigeta
Mar 27, 2019·Journal of Chemical Theory and Computation·Riccardo CapelliMichele Parrinello
Jun 5, 2020·Journal of Chemical Theory and Computation·Michael R Shirts, Andrew L Ferguson
Nov 5, 2020·The Journal of Physical Chemistry. B·Xinqiang Ding, Bin Zhang
Nov 10, 2017·Journal of Chemical Theory and Computation·Tobias Lemke, Christine Peter
Mar 26, 2020·Journal of Chemical Theory and Computation·Dube Dheeraj PrakashchandJagannath Mondal
Aug 3, 2019·The Journal of Physical Chemistry. a·Lin ShenWei-Hai Fang
May 30, 2019·ACS Central Science·Jiang WangCecilia Clementi
Aug 14, 2020·The Journal of Physical Chemistry. a·Jun ZhangYi Qin Gao
Jul 10, 2021·The Journal of Chemical Physics·Xingcheng LinBin Zhang
Oct 28, 2021·The Journal of Physical Chemistry Letters·Maxim SecorSharon Hammes-Schiffer

❮ 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.