Automatic Method for Identifying Reaction Coordinates in Complex Systems

Cited by (400)

Items 101–200 of 400

1. Learning reaction coordinates via cross-entropy minimization: Application to alanine dipeptide
   Yusuke Mori, Kei-ichi Okazaki, Toshifumi Mori, Kang Kim, Nobuyuki Matubayasi · 2020 · The Journal of Chemical Physics
2. Accelerating All-Atom Simulations and Gaining Mechanistic Understanding of Biophysical Systems through State Predictive Information Bottleneck
   Shams Mehdi, Dedi Wang, Shashank Pant, Pratyush Tiwary · 2022 · Journal of Chemical Theory and Computation
3. Pathways to self-organization: Crystallization via nucleation and growth
   Swetlana Jungblut, Christoph Dellago · 2016 · The European Physical Journal E
4. Molecular Understanding of Homogeneous Nucleation of CO2 Hydrates Using Transition Path Sampling
   A. Arjun, Peter G. Bolhuis · 2020 · The Journal of Physical Chemistry B
5. A Machine-Driven Hunt for Global Reaction Coordinates of Azobenzene Photoisomerization
   Pedram Tavadze, Guillermo Avendaño-Franco, Pengju Ren, Xiaodong Wen, Yongwang Li, James P. Lewis · 2017 · Journal of the American Chemical Society
6. Transition Manifolds of Complex Metastable Systems
   Andreas Bittracher, P. Koltai, Stefan Klus, Ralf Banisch, M. Dellnitz, C. Schütte · 2017 · Journal of nonlinear science
7. Inertial likelihood maximization for reaction coordinates with high transmission coefficients
   Baron Peters · 2012 · Chemical Physics Letters
8. Evidence for a Size Dependent Nucleation Mechanism in Solid State Polymorph Transformations
   Gregg T. Beckham, Baron Peters, Bernhardt L. Trout · 2008 · The Journal of Physical Chemistry B
9. OneOPES, a Combined Enhanced Sampling Method to Rule Them All
   Valerio Rizzi, Simone Aureli, Narjes Ansari, F. Gervasio · 2023 · bioRxiv
10. BayesWHAM: A Bayesian approach for free energy estimation, reweighting, and uncertainty quantification in the weighted histogram analysis method
    Andrew L. Ferguson · 2017 · Journal of Computational Chemistry
11. Using Markov Models to Simulate Electron Spin Resonance Spectra from Molecular Dynamics Trajectories
    Deniz Sezer, Jack H. Freed, Benoı̂t Roux · 2008 · The Journal of Physical Chemistry B
12. Common Features of Extraordinary Rate Theories
    Baron Peters · 2015 · The Journal of Physical Chemistry B
13. Calculating Iso-Committor Surfaces as Optimal Reaction Coordinates with Milestoning
    Ron Elber, Juan M. Bello‐Rivas, Piao Ma, Alfredo E. Cárdenas, Arman Fathizadeh · 2017 · Entropy
14. An extended autoencoder model for reaction coordinate discovery in rare event molecular dynamics datasets
    M. Frassek, A. Arjun, Peter G. Bolhuis · 2021 · The Journal of Chemical Physics
15. Characterization of a Dynamic String Method for the Construction of Transition Pathways in Molecular Reactions
    Margaret E. Johnson, Gerhard Hummer · 2012 · The Journal of Physical Chemistry B
16. Minimum free energy pathways and free energy profiles for conformational transitions based on atomistic molecular dynamics simulations.
    A. van der Vaart, M. Karplus · 2007 · Journal of Chemical Physics
17. Enhanced Sampling in the Age of Machine Learning: Algorithms and Applications
    Kai Zhu, Enrico Trizio, Jintu Zhang, Renling Hu, Linlong Jiang, Tingjun Hou, Luigi Bonati · 2025 · Chemical Reviews
18. Splitting Probabilities as a Test of Reaction Coordinate Choice in Single-Molecule Experiments
    John D. Chodera, Vijay S. Pande · 2011 · Physical Review Letters
19. Interplay of non-Markov and internal friction effects in the barrier crossing kinetics of biopolymers: Insights from an analytically solvable model
    Dmitrii E. Makarov · 2013 · The Journal of Chemical Physics
20. Is Protein Folding Sub-Diffusive?
    Sergei V. Krivov · 2010 · PLoS Computational Biology
21. Nucleation mechanism of clathrate hydrates of water-soluble guest molecules
    Ryan S. DeFever, Sapna Sarupria · 2017 · The Journal of Chemical Physics
22. Protein Dynamics and Enzymatic Chemical Barrier Passage
    Dimitri Antoniou, Steven D. Schwartz · 2011 · The Journal of Physical Chemistry B
23. Optimal reaction coordinates
    Polina V. Banushkina, Sergei V. Krivov · 2016 · Wiley Interdisciplinary Reviews Computational Molecular Science
24. Interpretable embeddings from molecular simulations using Gaussian mixture variational autoencoders
    Yasemin Bozkurt Varolgüneş, Tristan Bereau, J. F. Rudzinski · 2019 · Machine Learning: Science and Technology
25. Multitask Machine Learning of Collective Variables for Enhanced Sampling of Rare Events
    Lixin Sun, Jonathan Vandermause, Simon Batzner, Yu Yang Xie, David Clark, Wei Chen, Boris Kozinsky · 2022 · Journal of Chemical Theory and Computation
26. Transition Path Theory
    Eric Vanden‐Eijnden · 2013 · Advances in experimental medicine and biology
27. Free energy for protein folding from nonequilibrium simulations using the Jarzynski equality
    Daniel K. West, Peter D. Olmsted, Emanuele Paci · 2006 · The Journal of Chemical Physics
28. Discovering Collective Variables of Molecular Transitions via Genetic Algorithms and Neural Networks
    F. Hooft, Alberto Pérez de Alba Ortíz, B. Ensing · 2021 · Journal of Chemical Theory and Computation
29. Explaining reaction coordinates of alanine dipeptide isomerization obtained from deep neural networks using Explainable Artificial Intelligence (XAI)
    Takuma Kikutsuji, Yusuke Mori, Kei-ichi Okazaki, Toshifumi Mori, Kang Kim, Nobuyuki Matubayasi · 2022 · The Journal of Chemical Physics
30. Toward Identification of the Reaction Coordinate Directly from the Transition State Ensemble Using the Kernel PCA Method
    Dimitri Antoniou, Steven D. Schwartz · 2011 · The Journal of Physical Chemistry B
31. Order-disorder transition in Co-Pt nanoparticles: Coexistence, transition states, and finite-size effects
    F. Calvo, C. Mottet · 2011 · Physical Review B
32. String Method for Calculation of Minimum Free-Energy Paths in Cartesian Space in Freely Tumbling Systems
    Davide Branduardi, José D. Faraldo‐Gómez · 2013 · Journal of Chemical Theory and Computation
33. The stochastic separatrix and the reaction coordinate for complex systems
    Dimitri Antoniou, Steven D. Schwartz · 2009 · The Journal of Chemical Physics
34. Comparison between Mean Forces and Swarms-of-Trajectories String Methods
    L. Maragliano, B. Roux, E. Vanden-Eijnden · 2014 · Journal of Chemical Theory and Computation
35. Deep reinforcement learning of transition states
    Jun Zhang, Yao-Kun Lei, Zhen Zhang, Xu Han, Maodong Li, Yi Yang, Yi Yang, Yi Qin Gao · 2021 · Physical Chemistry Chemical Physics
36. Reaction coordinates in complex systems-a perspective
    Jutta Rogal · 2021 · The European Physical Journal B
37. Thermodynamics-inspired explanations of artificial intelligence
    Shams Mehdi, Pratyush Tiwary · 2024 · Nature Communications
38. Efficient Computation, Sensitivity, and Error Analysis of Committor Probabilities for Complex Dynamical Processes
    Jan-Hendrik Prinz, M. Held, Jeremy C. Smith, Frank Noé · 2011 · Multiscale Modeling & simulation
39. Dynamic coupling between coordinates in a model for biomolecular isomerization
    Ao Ma, Ambarish Nag, Aaron R. Dinner · 2006 · The Journal of Chemical Physics
40. Hopping of Water in a Glassy Polymer Studied via Transition Path Sampling and Likelihood Maximization
    Li Xi, Manas Shah, Bernhardt L. Trout · 2013 · The Journal of Physical Chemistry B
41. Long-timescale predictions from short-trajectory data: A benchmark analysis of the trp-cage miniprotein
    J. Strahan, Adam Antoszewski, Chatipat Lorpaiboon, B. P. Vani, J. Weare, A. Dinner · 2020 · Journal of Chemical Theory and Computation
42. Kinetics and reaction coordinate for the isomerization of alanine dipeptide by a forward flux sampling protocol
    Camilo Velez‐Vega, Ernesto E. Borrero, Fernando A. Escobedo · 2009 · The Journal of Chemical Physics
43. Machine learning of single molecule free energy surfaces and the impact of chemistry and environment upon structure and dynamics
    Mansbach, Rachael A., Ferguson, Andrew L. · 2015 · The Journal of Chemical Physics
44. Essential energy space random walk via energy space metadynamics method to accelerate molecular dynamics simulations
    Hongzhi Li, Donghong Min, Yusong Liu, Wei Yuan Yang · 2007 · The Journal of Chemical Physics
45. Landmark diffusion maps (L-dMaps): Accelerated manifold learning out-of-sample extension
    Andrew W. Long, Andrew L. Ferguson · 2017 · Applied and Computational Harmonic Analysis
46. Multiscale Reweighted Stochastic Embedding: Deep Learning of Collective Variables for Enhanced Sampling
    Jakub Rydzewski, Ómar Valsson · 2021 · The Journal of Physical Chemistry A
47. Computer Simulations of Homogeneous Nucleation of Benzene from the Melt
    Manas Shah, Erik E. Santiso, Bernhardt L. Trout · 2011 · The Journal of Physical Chemistry B
48. Delineation of Folding Pathways of a β-Sheet Miniprotein
    Zheng, Wenwei, Qi, Bo, Rohrdanz, Mary A., Caflisch, Amedeo, Dinner, Aaron R., Clementi, Cecilia · 2011 · The Journal of Physical Chemistry B
49. Nonlinear intrinsic variables and state reconstruction in multiscale simulations
    Carmeline J. Dsilva, Ronen Talmon, Neta Rabin, Ronald R. Coifman, Ioannis G. Kevrekidis · 2013 · The Journal of Chemical Physics
50. Optimising reaction coordinates for crystallisation by tuning the crystallinity definition
    Swetlana Jungblut, Andreas Singraber, Christoph Dellago A · 2013 · Molecular Physics
51. Reaction mechanism and reaction coordinates from the viewpoint of energy flow
    Wenjin Li, Ao Ma · 2016 · The Journal of Chemical Physics
52. Driving and characterizing nucleation of urea and glycine polymorphs in water
    Ziyue Zou, E. Beyerle, Sun-Ting Tsai, P. Tiwary · 2022 · Proceedings of the National Academy of Sciences of the United States of America
53. Bias annealing: A method for obtaining transition paths de novo
    Jie Hu, Ao Ma, Aaron R. Dinner · 2006 · The Journal of Chemical Physics
54. Nonlinear machine learning in simulations of soft and biological materials
    Jiang Wang, Andrew L. Ferguson · 2017 · Molecular Simulation
55. Transition path sampling of protein conformational changes
    Jarek Juraszek, Jocelyne Vreede, Peter G. Bolhuis · 2011 · Chemical Physics
56. Identification of the protein folding transition state from molecular dynamics trajectories
    Stefanie Muff, Amedeo Caflisch · 2009 · The Journal of Chemical Physics
57. Variational Identification of Markovian Transition States
    Linda Martini, Adam Kells, Roberto Covino, Gerhard Hummer, Nicolae‐Viorel Buchete, Edina Rosta · 2017 · Physical Review X
58. Solvent Viscosity Dependence of the Protein Folding Dynamics
    Young Min Rhee, Vijay S. Pande · 2008 · The Journal of Physical Chemistry B
59. Molecular Mechanism of Acid-Catalyzed Hydrolysis of Peptide Bonds Using a Model Compound
    Bin Pan, Margaret Speed Ricci · 2010 · The Journal of Physical Chemistry B
60. SGOOP-d: Estimating Kinetic Distances and Reaction Coordinate Dimensionality for Rare Event Systems from Biased/Unbiased Simulations.
    Sun-Ting Tsai, Zachary Smith, P. Tiwary · 2021 · Journal of Chemical Theory and Computation
61. Modelling proteins: Conformational sampling and reconstruction of folding kinetics
    Konstantin V. Klenin, Birgit Strodel, David J. Wales, Wolfgang Wenzel · 2010 · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics
62. Numerical Construction of the pfold (Committor) Reaction Coordinate for a Markov Process
    Sergei V. Krivov · 2011 · The Journal of Physical Chemistry B
63. Analyzing Complex Reaction Mechanisms Using Path Sampling
    Titus S. van Erp, Mahmoud Moqadam, Enrico Riccardi, Anders Lervik · 2016 · Journal of Chemical Theory and Computation
64. The role of memory-dependent friction and solvent viscosity in isomerization kinetics in viscogenic media
    Benjamin A. Dalton, Henrik Kiefer, Roland R. Netz · 2024 · Nature Communications
65. Kinetics and mechanism of the unfolding native-to-loop transition of Trp-cage in explicit solvent via optimized forward flux sampling simulations
    Camilo Velez‐Vega, Ernesto E. Borrero, Fernando A. Escobedo · 2010 · The Journal of Chemical Physics
66. Dynamical coring of Markov state models
    Daniel Nagel, Anna Weber, Benjamin Lickert, Gerhard Stock · 2019 · The Journal of Chemical Physics
67. How wet should be the reaction coordinate for ligand unbinding?
    P. Tiwary, B. Berne · 2016 · Journal of Chemical Physics
68. Committor-Consistent Variational String Method
    Ziwei He, C. Chipot, Benoı T. Roux · 2022 · Journal of Physical Chemistry Letters
69. Maximum Flux Transition Paths of Conformational Change
    Ruijun Zhao, Juanfang Shen, Robert D. Skeel · 2010 · Journal of Chemical Theory and Computation
70. Calculation of free energy landscapes: A histogram reweighted metadynamics approach
    Jens Smiatek, Andreas Heuer · 2011 · Journal of Computational Chemistry
71. Coupling Protein Dynamics with Proton Transport in Human Carbonic Anhydrase II
    Srabani Taraphder, C. Mark Maupin, Jessica M. J. Swanson, Gregory A. Voth · 2016 · The Journal of Physical Chemistry B
72. Protein Dynamics and the Enzymatic Reaction Coordinate
    Steven D. Schwartz · 2013 · Topics in current chemistry
73. An Explicit Consideration of Desolvation is Critical to Binding Free Energy Calculations of Charged Molecules at Ionic Surfaces
    Toshifumi Mori, Robert J. Hamers, Joel A. Pedersen, Qiang Cui · 2013 · Journal of Chemical Theory and Computation
74. Estimating diffusivity along a reaction coordinate in the high friction limit: Insights on pulse times in laser-induced nucleation
    Brandon C. Knott, Nathan Duff, Michael F. Doherty, Baron Peters · 2009 · The Journal of Chemical Physics
75. Everything everywhere all at once: a probability-based enhanced sampling approach to rare events
    Enrico Trizio, Pei‐Lin Kang, Michele Parrinello · 2025 · Nature Computational Science
76. On the coupling between slow diffusion transport and barrier crossing in nucleation
    Baron Peters · 2011 · The Journal of Chemical Physics
77. Peptide Permeation across a Phosphocholine Membrane: An Atomically Detailed Mechanism Determined through Simulations and Supported by Experimentation
    Alfredo E. Cárdenas, Chad I. Drexler, Rachel Nechushtai, Ron Mittler, Assaf Friedler, Lauren J. Webb, Ron Elber · 2022 · The Journal of Physical Chemistry B
78. p(TP|q) peak maximization: Necessary but not sufficient for reaction coordinate accuracy
    Baron Peters · 2010 · Chemical Physics Letters
79. Recovering Kinetics from a Simplified Protein Folding Model Using Replica Exchange Simulations: A Kinetic Network and Effective Stochastic Dynamics
    Weihua Zheng, Michael Andrec, Emilio Gallicchio, Ronald M. Levy · 2009 · The Journal of Physical Chemistry B
80. A Review of Nano and Microscale Heat Transfer: An Experimental and Molecular Dynamics Perspective
    Samyabrata Chatterjee, Paras, Han Hu, Monojit Chakraborty · 2023 · Processes
81. Riemann metric approach to optimal sampling of multidimensional free-energy landscapes
    Viveca Lindahl, Jack Lidmar, Berk Hess · 2018 · Physical review. E
82. Protein Function Analysis through Machine Learning
    Chris Avery, John Patterson, Tyler J. Grear, Theodore D. Frater, Donald J. Jacobs · 2022 · Biomolecules
83. Reaction Coordinates for Conformational Transitions Using Linear Discriminant Analysis on Positions
    Subarna Sasmal, Martin McCullagh, Glen M. Hocky · 2023 · Journal of Chemical Theory and Computation
84. Reaction Coordinate, Free Energy, and Rate of Intramolecular Proton Transfer in Human Carbonic Anhydrase II
    Sanjib Paul, Tanmoy Kumar Paul, Srabani Taraphder · 2018 · The Journal of Physical Chemistry B
85. Predicting efficacy of drug-carrier nanoparticle designs for cancer treatment: a machine learning-based solution
    Md Raisul Kibria, R. Akbar, Poonam Nidadavolu, O. Havryliuk, Sébastien Lafond, Sepinoud Azimi · 2023 · Scientific Reports
86. Predicting rare events using neural networks and short-trajectory data
    John Strahan, Justin M Finkel, Aaron R. Dinner, Jonathan Weare · 2023 · Journal of Computational Physics
87. Transition-State Theory, Dynamics, and Narrow Time Scale Separation in the Rate-Promoting Vibrations Model of Enzyme Catalysis
    Baron Peters · 2010 · Journal of Chemical Theory and Computation
88. Nonparametric variational optimization of reaction coordinates
    Polina V. Banushkina, Sergei V. Krivov · 2015 · The Journal of Chemical Physics
89. A Molecular Mechanism of Hydrolysis of Peptide Bonds at Neutral pH Using a Model Compound
    Bin Pan, Margaret Speed Ricci, Bernhardt L. Trout · 2011 · The Journal of Physical Chemistry B
90. Maximum flux transition paths of conformational change
    Ruijun Zhao, Juanfang Shen, Robert D. Skeel · 2016
91. Deep learning path-like collective variable for enhanced sampling molecular dynamics.
    Thorben Fröhlking, L. Bonati, Valerio Rizzi, F. Gervasio · 2024 · Journal of Chemical Physics
92. Ion Permeation through a Phospholipid Membrane: Transition State, Path Splitting, and Calculation of Permeability
    Arman Fathizadeh, Ron Elber · 2018 · Journal of Chemical Theory and Computation
93. Recent advances in describing and driving crystal nucleation using machine learning and artificial intelligence
    Eric R. Beyerle, Ziyue Zou, Pratyush Tiwary · 2023 · Current Opinion in Solid State and Materials Science
94. Automatic Selection of Order Parameters in the Analysis of Large Scale Molecular Dynamics Simulations
    M. M. Sultan, G. Kiss, D. Shukla, V. Pande · 2014 · Journal of Chemical Theory and Computation
95. The dynamics of peptide-water interactions in dialanine: An ultrafast amide I 2D IR and computational spectroscopy study
    Chi-Jui Feng, Andrei Tokmakoff · 2017 · The Journal of Chemical Physics
96. Hidden Conformation Events in DNA Base Extrusions: A Generalized-Ensemble Path Optimization and Equilibrium Simulation Study
    Liaoran Cao, Chao Lv, Wei Yuan Yang · 2013 · Journal of Chemical Theory and Computation
97. Nonlinear machine learning and design of reconfigurable digital colloids
    Andrew Long, Carolyn L. Phillips, Eric Jankowski, Andrew L. Ferguson · 2016 · Soft Matter
98. Investigations of α-helix↔β-sheet transition pathways in a miniprotein using the finite-temperature string method.
    V. Ovchinnikov, M. Karplus · 2014 · Journal of Chemical Physics
99. Competing Reaction Mechanisms of Peptide Bond Formation in Water Revealed by Deep Potential Molecular Dynamics and Path Sampling
    Rolf David, Iñaki Tuñón, Damien Laage · 2024 · Journal of the American Chemical Society
100. Analysis of the Free-Energy Surface of Proteins from Reversible Folding Simulations
     Lucy R. Allen, Sergei V. Krivov, Emanuele Paci · 2009 · PLoS Computational Biology