Machine learning force fields and coarse-grained variables in molecular dynamics: application to materials and biological systems.
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Fabio Pietrucci | Alexandre Tkatchenko | Andrew L. Ferguson | Michele Ceriotti | Zofia Trstanova | Gabriel Stoltz | Tony Lelievre | Aaron R Dinner | Paraskevi Gkeka | Christine Peter | Amir Barati Farimani | Rafal P. Wiewiora | Jean-Bernard Maillet | Zineb Belkacemi | John Damon Chodera | Andrew L Ferguson | Herve Minoux | Ana Silveira | Rafal Wiewiora | A. Tkatchenko | T. Lelièvre | J. Chodera | A. Ferguson | G. Stoltz | Z. Trstanova | M. Ceriotti | C. Peter | A. Dinner | H. Minoux | P. Gkeka | F. Pietrucci | J. Maillet | A. Barati Farimani | A. Silveira | Zineb Belkacemi | Amir Barati Farimani | Zofia Trstanova
[1] Rongjie Lai,et al. Point Cloud Discretization of Fokker-Planck Operators for Committor Functions , 2017, Multiscale Model. Simul..
[2] Michele Parrinello,et al. Simplifying the representation of complex free-energy landscapes using sketch-map , 2011, Proceedings of the National Academy of Sciences.
[3] Lexing Ying,et al. Solving for high-dimensional committor functions using artificial neural networks , 2018, Research in the Mathematical Sciences.
[4] J. Tenenbaum,et al. A global geometric framework for nonlinear dimensionality reduction. , 2000, Science.
[5] Stefan Klus,et al. Diffusion maps tailored to arbitrary non-degenerate Itô processes , 2017, Applied and Computational Harmonic Analysis.
[6] R. Zwanzig. Nonequilibrium statistical mechanics , 2001, Physics Subject Headings (PhySH).
[7] Mohammad M. Sultan,et al. Variational encoding of complex dynamics. , 2017, Physical review. E.
[8] P. Collet,et al. Quasi-Stationary Distributions: Markov Chains, Diffusions and Dynamical Systems , 2012 .
[9] Cecilia Clementi,et al. Rapid exploration of configuration space with diffusion-map-directed molecular dynamics. , 2013, The journal of physical chemistry. B.
[10] Francesco Luigi Gervasio,et al. From A to B in free energy space. , 2007, The Journal of chemical physics.
[11] P. Deuflhard,et al. Robust Perron cluster analysis in conformation dynamics , 2005 .
[12] Markov Models of Molecular Kinetics. , 2019, The Journal of chemical physics.
[13] Sébastien Maignan,et al. SAR156497, an exquisitely selective inhibitor of aurora kinases. , 2014, Journal of medicinal chemistry.
[14] F. Noé,et al. Collective variables for the study of long-time kinetics from molecular trajectories: theory and methods. , 2017, Current opinion in structural biology.
[15] Kilian Q. Weinberger,et al. Unsupervised Learning of Image Manifolds by Semidefinite Programming , 2004, Proceedings of the 2004 IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 2004. CVPR 2004..
[16] Matthias Scholz,et al. Nonlinear Principal Component Analysis: Neural Network Models and Applications , 2008 .
[17] Marcus Weber,et al. Fuzzy spectral clustering by PCCA+: application to Markov state models and data classification , 2013, Advances in Data Analysis and Classification.
[18] Hao Wu,et al. Data-Driven Model Reduction and Transfer Operator Approximation , 2017, J. Nonlinear Sci..
[19] Hod Lipson,et al. Distilling Free-Form Natural Laws from Experimental Data , 2009, Science.
[20] Clarence W. Rowley,et al. A Data–Driven Approximation of the Koopman Operator: Extending Dynamic Mode Decomposition , 2014, Journal of Nonlinear Science.
[21] Vijay S Pande,et al. Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9. , 2013, Journal of chemical theory and computation.
[22] Wei Chen,et al. Nonlinear Discovery of Slow Molecular Modes using Hierarchical Dynamics Encoders , 2019, The Journal of chemical physics.
[23] I. Mezić. Spectral Properties of Dynamical Systems, Model Reduction and Decompositions , 2005 .
[24] J. Preto,et al. Fast recovery of free energy landscapes via diffusion-map-directed molecular dynamics. , 2014, Physical chemistry chemical physics : PCCP.
[25] D. Donoho,et al. Hessian eigenmaps: Locally linear embedding techniques for high-dimensional data , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[26] Hiroshi Takano,et al. Molecular Dynamics Study of Relaxation Modes of a Single Polymer Chain , 1997 .
[27] Vojtěch Spiwok,et al. Metadynamics in the conformational space nonlinearly dimensionally reduced by Isomap. , 2011, The Journal of chemical physics.
[28] Pierre Comon,et al. Independent component analysis, A new concept? , 1994, Signal Process..
[29] Ann B. Lee,et al. Geometric diffusions as a tool for harmonic analysis and structure definition of data: diffusion maps. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[30] Vijay S. Pande,et al. Modeling Molecular Kinetics with tICA and the Kernel Trick , 2015, Journal of chemical theory and computation.
[31] V. Schramm,et al. Enzymatic transition states, transition-state analogs, dynamics, thermodynamics, and lifetimes. , 2011, Annual review of biochemistry.
[32] Ioannis G Kevrekidis,et al. Intrinsic map dynamics exploration for uncharted effective free-energy landscapes , 2016, Proceedings of the National Academy of Sciences.
[33] Toni Giorgino,et al. Identification of slow molecular order parameters for Markov model construction. , 2013, The Journal of chemical physics.
[34] Ioannis G Kevrekidis,et al. Integrating diffusion maps with umbrella sampling: application to alanine dipeptide. , 2011, The Journal of chemical physics.
[35] M. Kramer. Nonlinear principal component analysis using autoassociative neural networks , 1991 .
[36] Frank Noé,et al. A Variational Approach to Modeling Slow Processes in Stochastic Dynamical Systems , 2012, Multiscale Model. Simul..
[37] Erik H. Thiede,et al. Galerkin approximation of dynamical quantities using trajectory data. , 2018, The Journal of chemical physics.
[38] Zoe Cournia,et al. Investigating the Structure and Dynamics of the PIK3CA Wild-Type and H1047R Oncogenic Mutant , 2014, PLoS Comput. Biol..
[39] Jing Wang,et al. MLLE: Modified Locally Linear Embedding Using Multiple Weights , 2006, NIPS.
[40] Patrick J. F. Groenen,et al. Modern Multidimensional Scaling: Theory and Applications , 2003 .
[41] Hao Wu,et al. VAMPnets for deep learning of molecular kinetics , 2017, Nature Communications.
[42] Lydia E Kavraki,et al. Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction , 2006, Proc. Natl. Acad. Sci. USA.
[43] D. Kern,et al. Dynamic personalities of proteins , 2007, Nature.
[44] Joshua B. Tenenbaum,et al. Global Versus Local Methods in Nonlinear Dimensionality Reduction , 2002, NIPS.
[45] S T Roweis,et al. Nonlinear dimensionality reduction by locally linear embedding. , 2000, Science.
[46] Eric Vanden-Eijnden,et al. On-the-fly free energy parameterization via temperature accelerated molecular dynamics. , 2012, Chemical physics letters.
[47] Amir Barati Farimani,et al. Machine Learning Harnesses Molecular Dynamics to Discover New $\mu$ Opioid Chemotypes , 2018 .
[48] Zhen Yang,et al. A Version of Isomap with Explicit Mapping , 2006, 2006 International Conference on Machine Learning and Cybernetics.
[49] F. Noé,et al. Commute Maps: Separating Slowly Mixing Molecular Configurations for Kinetic Modeling. , 2016, Journal of chemical theory and computation.
[50] Bert L. de Groot,et al. Detection of Functional Modes in Protein Dynamics , 2009, PLoS Comput. Biol..
[51] B. Nadler,et al. Diffusion Maps - a Probabilistic Interpretation for Spectral Embedding and Clustering Algorithms , 2008 .
[52] P. Nguyen,et al. Complexity of free energy landscapes of peptides revealed by nonlinear principal component analysis , 2006, Proteins.
[53] P. Deuflhard,et al. A Direct Approach to Conformational Dynamics Based on Hybrid Monte Carlo , 1999 .
[54] Weinan E,et al. Sampling saddle points on a free energy surface. , 2014, The Journal of chemical physics.
[55] Matteo T Degiacomi,et al. Coupling Molecular Dynamics and Deep Learning to Mine Protein Conformational Space. , 2019, Structure.
[56] M. Maggioni,et al. Determination of reaction coordinates via locally scaled diffusion map. , 2011, The Journal of chemical physics.
[57] Mikhail Belkin,et al. Laplacian Eigenmaps for Dimensionality Reduction and Data Representation , 2003, Neural Computation.
[58] F. Noé,et al. Kinetic distance and kinetic maps from molecular dynamics simulation. , 2015, Journal of chemical theory and computation.
[59] Diwakar Shukla,et al. Reinforcement Learning Based Adaptive Sampling: REAPing Rewards by Exploring Protein Conformational Landscapes. , 2017, The journal of physical chemistry. B.
[60] B. Keller,et al. Girsanov reweighting for metadynamics simulations. , 2018, The Journal of chemical physics.
[61] Jeff A. Bilmes,et al. Deep Canonical Correlation Analysis , 2013, ICML.
[62] F. Takens. Detecting strange attractors in turbulence , 1981 .
[63] Frank Noé,et al. Variational Approach to Molecular Kinetics. , 2014, Journal of chemical theory and computation.
[64] Michele Parrinello,et al. Using sketch-map coordinates to analyze and bias molecular dynamics simulations , 2012, Proceedings of the National Academy of Sciences.
[65] Hiroshi Takano,et al. Relaxation modes in random spin systems , 1995 .
[66] Schuster,et al. Separation of a mixture of independent signals using time delayed correlations. , 1994, Physical review letters.
[67] Amir Barati Farimani,et al. Binding Pathway of Opiates to μ-Opioid Receptors Revealed by Machine Learning , 2018, 1804.08206.
[68] M. Weber,et al. An Automatic Adaptive Importance Sampling Algorithm for Molecular Dynamics in Reaction Coordinates , 2018, SIAM J. Sci. Comput..
[69] Z. Cournia,et al. Exploring a non-ATP pocket for potential allosteric modulation of PI3Kα. , 2015, The journal of physical chemistry. B.
[70] Gerhard Hummer,et al. Position-dependent diffusion coefficients and free energies from Bayesian analysis of equilibrium and replica molecular dynamics simulations , 2005 .
[71] L Donati,et al. Girsanov reweighting for path ensembles and Markov state models. , 2017, The Journal of chemical physics.
[72] Marino Arroyo,et al. Modeling and enhanced sampling of molecular systems with smooth and nonlinear data-driven collective variables. , 2013, The Journal of chemical physics.
[73] I. Kevrekidis,et al. Coarse molecular dynamics of a peptide fragment: Free energy, kinetics, and long-time dynamics computations , 2002, physics/0212108.
[74] Frank Noé,et al. Hierarchical Time-Lagged Independent Component Analysis: Computing Slow Modes and Reaction Coordinates for Large Molecular Systems. , 2016, Journal of chemical theory and computation.
[75] Vijay S. Pande,et al. Everything you wanted to know about Markov State Models but were afraid to ask. , 2010, Methods.
[76] J. Harlim,et al. Variable Bandwidth Diffusion Kernels , 2014, 1406.5064.
[77] Vijay S. Pande,et al. Note: Variational Encoding of Protein Dynamics Benefits from Maximizing Latent Autocorrelation , 2018, The Journal of chemical physics.
[78] Yuelei Sui. Local Tangent Space Alignment , 2013 .
[79] V. Schramm,et al. Enzymatic transition states and transition state analogues. , 2005, Current opinion in structural biology.
[80] Martin Held,et al. Efficient Computation, Sensitivity, and Error Analysis of Committor Probabilities for Complex Dynamical Processes , 2011, Multiscale Model. Simul..