Literature DB >> 32559068

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

Paraskevi Gkeka1, Gabriel Stoltz2,3, Amir Barati Farimani4, Zineb Belkacemi1,2, Michele Ceriotti5, John D Chodera6, Aaron R Dinner7, Andrew L Ferguson8, Jean-Bernard Maillet9, Hervé Minoux10, Christine Peter11, Fabio Pietrucci12, Ana Silveira6, Alexandre Tkatchenko13, Zofia Trstanova14, Rafal Wiewiora6, Tony Lelièvre2,3.   

Abstract

Machine learning encompasses tools and algorithms that are now becoming popular in almost all scientific and technological fields. This is true for molecular dynamics as well, where machine learning offers promises of extracting valuable information from the enormous amounts of data generated by simulation of complex systems. We provide here a review of our current understanding of goals, benefits, and limitations of machine learning techniques for computational studies on atomistic systems, focusing on the construction of empirical force fields from ab initio databases and the determination of reaction coordinates for free energy computation and enhanced sampling.

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Year:  2020        PMID: 32559068      PMCID: PMC8312194          DOI: 10.1021/acs.jctc.0c00355

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  126 in total

1.  The Amber biomolecular simulation programs.

Authors:  David A Case; Thomas E Cheatham; Tom Darden; Holger Gohlke; Ray Luo; Kenneth M Merz; Alexey Onufriev; Carlos Simmerling; Bing Wang; Robert J Woods
Journal:  J Comput Chem       Date:  2005-12       Impact factor: 3.376

2.  Complexity of free energy landscapes of peptides revealed by nonlinear principal component analysis.

Authors:  Phuong H Nguyen
Journal:  Proteins       Date:  2006-12-01

3.  Perspective: Insight into reaction coordinates and dynamics from the potential energy landscape.

Authors:  D J Wales
Journal:  J Chem Phys       Date:  2015-04-07       Impact factor: 3.488

4.  Improving collective variables: The case of crystallization.

Authors:  Yue-Yu Zhang; Haiyang Niu; GiovanniMaria Piccini; Dan Mendels; Michele Parrinello
Journal:  J Chem Phys       Date:  2019-03-07       Impact factor: 3.488

5.  Sampling saddle points on a free energy surface.

Authors:  Amit Samanta; Ming Chen; Tang-Qing Yu; Mark Tuckerman; Weinan E
Journal:  J Chem Phys       Date:  2014-04-28       Impact factor: 3.488

6.  Neural Network Based Prediction of Conformational Free Energies - A New Route toward Coarse-Grained Simulation Models.

Authors:  Tobias Lemke; Christine Peter
Journal:  J Chem Theory Comput       Date:  2017-11-28       Impact factor: 6.006

7.  Machine learning and data science in soft materials engineering.

Authors:  Andrew L Ferguson
Journal:  J Phys Condens Matter       Date:  2018-01-31       Impact factor: 2.333

8.  Markov Models of Molecular Kinetics.

Authors:  Frank Noé; Edina Rosta
Journal:  J Chem Phys       Date:  2019-11-21       Impact factor: 3.488

9.  Equation of State of Fluid Methane from First Principles with Machine Learning Potentials.

Authors:  Max Veit; Sandeep Kumar Jain; Satyanarayana Bonakala; Indranil Rudra; Detlef Hohl; Gábor Csányi
Journal:  J Chem Theory Comput       Date:  2019-03-12       Impact factor: 6.006

10.  End-to-End Differentiable Learning of Protein Structure.

Authors:  Mohammed AlQuraishi
Journal:  Cell Syst       Date:  2019-04-17       Impact factor: 10.304

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  11 in total

Review 1.  Modelling Sorption and Transport of Gases in Polymeric Membranes across Different Scales: A Review.

Authors:  Eleonora Ricci; Matteo Minelli; Maria Grazia De Angelis
Journal:  Membranes (Basel)       Date:  2022-08-31

Review 2.  Bottom-up Coarse-Graining: Principles and Perspectives.

Authors:  Jaehyeok Jin; Alexander J Pak; Aleksander E P Durumeric; Timothy D Loose; Gregory A Voth
Journal:  J Chem Theory Comput       Date:  2022-09-07       Impact factor: 6.578

3.  Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials.

Authors:  Benjamin Pampel; Omar Valsson
Journal:  J Chem Theory Comput       Date:  2022-06-28       Impact factor: 6.578

4.  Protein Flexibility and Dissociation Pathway Differentiation Can Explain Onset of Resistance Mutations in Kinases.

Authors:  Mrinal Shekhar; Zachary Smith; Markus A Seeliger; Pratyush Tiwary
Journal:  Angew Chem Int Ed Engl       Date:  2022-05-19       Impact factor: 16.823

Review 5.  Bottom-Up Coarse-Grained Modeling of DNA.

Authors:  Tiedong Sun; Vishal Minhas; Nikolay Korolev; Alexander Mirzoev; Alexander P Lyubartsev; Lars Nordenskiöld
Journal:  Front Mol Biosci       Date:  2021-03-17

6.  Molecular free energy optimization on a computational graph.

Authors:  Xiaoyong Cao; Pu Tian
Journal:  RSC Adv       Date:  2021-04-06       Impact factor: 3.361

7.  Martini 3 Model of Cellulose Microfibrils: On the Route to Capture Large Conformational Changes of Polysaccharides.

Authors:  Rodrigo A Moreira; Stefan A L Weber; Adolfo B Poma
Journal:  Molecules       Date:  2022-02-01       Impact factor: 4.411

8.  Combining Machine Learning and Computational Chemistry for Predictive Insights Into Chemical Systems.

Authors:  John A Keith; Valentin Vassilev-Galindo; Bingqing Cheng; Stefan Chmiela; Michael Gastegger; Klaus-Robert Müller; Alexandre Tkatchenko
Journal:  Chem Rev       Date:  2021-07-07       Impact factor: 60.622

9.  Deep Learning Approaches to Surrogates for Solving the Diffusion Equation for Mechanistic Real-World Simulations.

Authors:  J Quetzalcóatl Toledo-Marín; Geoffrey Fox; James P Sluka; James A Glazier
Journal:  Front Physiol       Date:  2021-06-24       Impact factor: 4.566

Review 10.  "Dividing and Conquering" and "Caching" in Molecular Modeling.

Authors:  Xiaoyong Cao; Pu Tian
Journal:  Int J Mol Sci       Date:  2021-05-10       Impact factor: 5.923

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