Transfer-Learning-Based Coarse-Graining Method for Simple Fluids: Toward Deep Inverse Liquid-State Theory

The Journal of Physical Chemistry Letters
Alireza Moradzadeh, N R Aluru

Abstract

Machine learning is an attractive paradigm to circumvent difficulties associated with the development and optimization of force-field parameters. In this study, a deep neural network (DNN) is used to study the inverse problem of the liquid-state theory, in particular, to obtain the relation between the radial distribution function (RDF) and the Lennard-Jones (LJ) potential parameters at various thermodynamic states. Using molecular dynamics (MD), many observables, including RDF, are determined once the interatomic potential is specified. However, the inverse problem (parametrization of the potential for a specific RDF) is not straightforward. Here we present a framework integrating DNN with big data from 1.5 TB of MD trajectories with a cumulative simulation time of 52 μs for 26 000 distinct systems to predict LJ potential parameters. Our results show that DNN is successful not only in the parametrization of the atomic LJ liquids but also in parametrizing the LJ potential for coarse-grained models of simple multiatom molecules.

References

Aug 20, 2003·Journal of Computational Chemistry·Dirk ReithFlorian Müller-Plathe
Aug 25, 2004·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Yiping Tang, Jianzhong Wu
Aug 16, 2006·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Guillaume GalliéroFrançois Montel
Mar 31, 2007·The Journal of Physical Chemistry. B·W G NoidGregory A Voth
Dec 3, 2008·The Journal of Chemical Physics·M Scott Shell
Mar 5, 2009·Physical Review Letters·Hendrik Hansen-Goos, Klaus Mecke
Sep 28, 2010·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Aviel Chaimovich, M Scott Shell
Sep 28, 2010·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Marco D'Alessandro, Francesco Cilloco
Mar 10, 2011·The Journal of Chemical Physics·Aviel Chaimovich, M Scott Shell
Dec 21, 2011·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Marco D'Alessandro
May 29, 2015·Nature·Yann LeCunGeoffrey Hinton
Nov 14, 2015·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·S KrumscheidS Kalliadasis
Dec 13, 2011·Journal of Chemical Theory and Computation·Alpeshkumar K MaldeAlan E Mark
Nov 26, 2015·Advances and Applications in Bioinformatics and Chemistry : AABC·Adam HospitalJosep L Gelpí
Feb 12, 2017·Science·Giuseppe Carleo, Matthias Troyer
Mar 9, 2017·Journal of Computational Chemistry·Garrett B GohAbhinav Vishnu
Nov 11, 2017·Journal of Chemical Theory and Computation·Martin StroetAlan E Mark
Dec 16, 2017·Science Advances·Albert P BartókMichele Ceriotti
Mar 14, 2018·ACS Central Science·Rafael Gómez-BombarelliAlán Aspuru-Guzik
Mar 24, 2018·Molecular Pharmaceutics·Evgeny PutinAlex Zhavoronkov
May 12, 2018·Journal of Chemical Theory and Computation·Alireza MoradzadehNarayana R Aluru
May 19, 2018·The Journal of Physical Chemistry Letters·Hao Wang, Weitao Yang
Jul 20, 2018·The Journal of Physical Chemistry Letters·Karteek K BejagamSanket A Deshmukh
Jul 25, 2018·The Journal of Chemical Physics·Linfeng ZhangWeinan E
Jan 5, 2019·Physical Review Letters·Tristan Bereau, Joseph F Rudzinski

❮ Previous
Next ❯

Citations

Sep 17, 2020·The Journal of Chemical Physics·Galen T CravenSergei Tretiak
Jul 10, 2020·The Journal of Chemical Physics·Clemens Rauer, Tristan Bereau
Oct 3, 2020·The Journal of Chemical Physics·Haina WangSalvatore Torquato
Jun 3, 2021·International Journal of Molecular Sciences·Xiaoyong Cao, Pu Tian
Jul 10, 2021·The Journal of Chemical Physics·A Moradzadeh, N R Aluru
Nov 19, 2019·The Journal of Physical Chemistry Letters·Alireza Moradzadeh, Narayana R Aluru
May 7, 2020·The Journal of Physical Chemistry Letters·Galen T CravenSergei Tretiak
Nov 6, 2020·The Journal of Physical Chemistry Letters·Oleg V Prezhdo
Nov 20, 2019·Journal of Chemical Information and Modeling·Christian NowakFernando A Escobedo

❮ 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.