Learning free energy landscapes using artificial neural networks

Sidky, Hythem; Whitmer, Jonathan K.

doi:10.1063/1.5018708

Title: Learning free energy landscapes using artificial neural networks

Authors:

Sidky, Hythem ^[1];

^[1]

Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA

Publication Date:: 2018-03-14

Sponsoring Org.:: USDOE

OSTI Identifier:: 1425538

Resource Type:: Publisher's Accepted Manuscript

Journal Name:: Journal of Chemical Physics

Additional Journal Information:: Journal Name: Journal of Chemical Physics Journal Volume: 148 Journal Issue: 10; Journal ID: ISSN 0021-9606

Publisher:: American Institute of Physics

Country of Publication:: United States

Language:: English

Citation Formats


                    Sidky, Hythem, and Whitmer, Jonathan K. Learning free energy landscapes using artificial neural networks.  United States: N. p., 2018. 
Web.  doi:10.1063/1.5018708.

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                    Sidky, Hythem, & Whitmer, Jonathan K. Learning free energy landscapes using artificial neural networks.  United States.  https://doi.org/10.1063/1.5018708

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                    Sidky, Hythem, and Whitmer, Jonathan K. Wed .  
"Learning free energy landscapes using artificial neural networks".  United States.  https://doi.org/10.1063/1.5018708.

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@article{osti_1425538,

  title        = {Learning free energy landscapes using artificial neural networks},

  author       = {Sidky, Hythem and Whitmer, Jonathan K.},

  abstractNote = {},

  doi          = {10.1063/1.5018708},

  journal      = {Journal of Chemical Physics},

  number       = 10,

  volume       = 148,

  place        = {United States},

  year         = {2018},

  month        = {3}

}

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Title: Learning free energy landscapes using artificial neural networks

Citation Formats

Adaptive umbrella sampling: Self-consistent determination of the non-Boltzmann bias journal, January 1987

An adaptive umbrella sampling procedure in conformational analysis using molecular dynamics and its application to glycol journal, November 1992

The Adaptive Biasing Force Method: Everything You Always Wanted To Know but Were Afraid To Ask journal, August 2014

A computer-aided diagnostic system to characterize CT focal liver lesions: design and optimization of a neural network classifier journal, September 2003

Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling journal, February 1977

Free-energy landscape of protein oligomerization from atomistic simulations journal, November 2013

Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations journal, September 1997

Multilayer feedforward networks are universal approximators journal, January 1989

Stochastic Neural Network Approach for Learning High-Dimensional Free Energy Surfaces journal, October 2017

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method journal, January 2008

Basis Function Sampling: A New Paradigm for Material Property Computation journal, November 2014

Bayesian Interpolation journal, May 1992

Flux Tempered Metadynamics journal, September 2011

Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint journal, May 2016

Metadynamics with Adaptive Gaussians journal, June 2012

Extended Adaptive Biasing Force Algorithm. An On-the-Fly Implementation for Accurate Free-Energy Calculations journal, July 2016

Generalized Neural-Network Representation of High-Dimensional Potential-Energy Surfaces journal, April 2007

Measuring liquid crystal elastic constants with free energy perturbations journal, January 2014

THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method journal, October 1992

Molecular Dynamics with On-the-Fly Machine Learning of Quantum-Mechanical Forces journal, March 2015

Simulation studies of the fidelity of biomolecular structure ensemble recreation journal, December 2006

Free Energy Surface Reconstruction from Umbrella Samples Using Gaussian Process Regression journal, August 2014

Sculpting bespoke mountains: Determining free energies with basis expansions journal, July 2015

Variational Approach to Enhanced Sampling and Free Energy Calculations journal, August 2014

Graphite-diamond phase coexistence study employing a neural-network mapping of the ab initio potential energy surface journal, March 2010

Topology, structures, and energy landscapes of human chromosomes journal, April 2015

Forecasting electricity market pricing using artificial neural networks journal, March 2007

Automatic Method for Identifying Reaction Coordinates in Complex Systems † journal, April 2005

Large-scale screening of hypothetical metal–organic frameworks journal, November 2011

A Practical Bayesian Framework for Backpropagation Networks journal, May 1992

Probability Distributions for Complex Systems: Adaptive Umbrella Sampling of the Potential Energy journal, January 1998

Evolutionary Optimization in Quantitative Structure−Activity Relationship: An Application of Genetic Neural Networks journal, January 1996

Escaping free-energy minima journal, September 2002

A boundary correction algorithm for metadynamics in multiple dimensions journal, August 2013

Transition-Tempered Metadynamics: Robust, Convergent Metadynamics via On-the-Fly Transition Barrier Estimation journal, August 2014

Calculating free energies using average force journal, November 2001

Neural Network and Nearest Neighbor Algorithms for Enhancing Sampling of Molecular Dynamics journal, May 2017

Adaptive umbrella sampling: Self-consistent determination of the non-Boltzmann bias
journal, January 1987

An adaptive umbrella sampling procedure in conformational analysis using molecular dynamics and its application to glycol
journal, November 1992

The Adaptive Biasing Force Method: Everything You Always Wanted To Know but Were Afraid To Ask
journal, August 2014

A computer-aided diagnostic system to characterize CT focal liver lesions: design and optimization of a neural network classifier
journal, September 2003

Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
journal, February 1977

Free-energy landscape of protein oligomerization from atomistic simulations
journal, November 2013

Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations
journal, September 1997

Multilayer feedforward networks are universal approximators
journal, January 1989

Stochastic Neural Network Approach for Learning High-Dimensional Free Energy Surfaces
journal, October 2017

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
journal, January 2008

Basis Function Sampling: A New Paradigm for Material Property Computation
journal, November 2014

Bayesian Interpolation
journal, May 1992

Flux Tempered Metadynamics
journal, September 2011

Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint
journal, May 2016

Metadynamics with Adaptive Gaussians
journal, June 2012

Extended Adaptive Biasing Force Algorithm. An On-the-Fly Implementation for Accurate Free-Energy Calculations
journal, July 2016

Generalized Neural-Network Representation of High-Dimensional Potential-Energy Surfaces
journal, April 2007

Measuring liquid crystal elastic constants with free energy perturbations
journal, January 2014

THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method
journal, October 1992

Molecular Dynamics with On-the-Fly Machine Learning of Quantum-Mechanical Forces
journal, March 2015

Simulation studies of the fidelity of biomolecular structure ensemble recreation
journal, December 2006

Free Energy Surface Reconstruction from Umbrella Samples Using Gaussian Process Regression
journal, August 2014

Sculpting bespoke mountains: Determining free energies with basis expansions
journal, July 2015

Variational Approach to Enhanced Sampling and Free Energy Calculations
journal, August 2014

Graphite-diamond phase coexistence study employing a neural-network mapping of the ab initio potential energy surface
journal, March 2010

Topology, structures, and energy landscapes of human chromosomes
journal, April 2015

Forecasting electricity market pricing using artificial neural networks
journal, March 2007

Automatic Method for Identifying Reaction Coordinates in Complex Systems ^†
journal, April 2005

Large-scale screening of hypothetical metal–organic frameworks
journal, November 2011

A Practical Bayesian Framework for Backpropagation Networks
journal, May 1992

Probability Distributions for Complex Systems: Adaptive Umbrella Sampling of the Potential Energy
journal, January 1998

Evolutionary Optimization in Quantitative Structure−Activity Relationship: An Application of Genetic Neural Networks
journal, January 1996

Escaping free-energy minima
journal, September 2002

A boundary correction algorithm for metadynamics in multiple dimensions
journal, August 2013

Transition-Tempered Metadynamics: Robust, Convergent Metadynamics via On-the-Fly Transition Barrier Estimation
journal, August 2014

Calculating free energies using average force
journal, November 2001

Neural Network and Nearest Neighbor Algorithms for Enhancing Sampling of Molecular Dynamics
journal, May 2017