Automatic Method for Identifying Reaction Coordinates in Complex Systems

Cited by (400)

Items 201–300 of 400

1. Permutationally Invariant Networks for Enhanced Sampling (PINES): Discovery of Multimolecular and Solvent-Inclusive Collective Variables
   Nicholas S. M. Herringer, Siva Dasetty, Diya Gandhi, Junhee Lee, Andrew L. Ferguson · 2023 · Journal of Chemical Theory and Computation
2. Contour forward flux sampling: Sampling rare events along multiple collective variables
   Ryan S. DeFever, Sapna Sarupria · 2019 · The Journal of Chemical Physics
3. Distinct dissociation kinetics between ion pairs: Solvent-coordinate free-energy landscape analysis
   Yoshiteru Yonetani · 2015 · The Journal of Chemical Physics
4. An exploration of machine learning models for the determination of reaction coordinates associated with conformational transitions
   Nawavi Naleem, Charlles R. A. Abreu, Krzysztof Warmuz, Muchen Tong, Serdal Kırmızıaltın, Mark E. Tuckerman · 2023 · The Journal of Chemical Physics
5. Data-Driven Path Collective Variables
   Arthur France‐Lanord, Hadrien Vroylandt, Mathieu Salanne, Benjamin Rotenberg, Antonino Marco Saitta, Fabio Pietrucci · 2024 · Journal of Chemical Theory and Computation
6. Dynamical Reweighting for Biased Rare Event Simulations
   Bettina G. Keller, Peter G. Bolhuis · 2024 · Annual Review of Physical Chemistry
7. Molecular recognition of DNA by ligands: Roughness and complexity of the free energy profile
   Wenwei Zheng, Attilio Vittorio Vargiu, Mary A. Rohrdanz, Paolo Carloni, Cecilia Clementi · 2013 · The Journal of Chemical Physics
8. Competitive reaction pathways in vibrationally induced photodissociation of H 2 SO 4
   Juvenal Yosa, Tibor Zs. Nagy, Markus Meuwly · 2014 · Physical Chemistry Chemical Physics
9. Point Cloud Discretization of Fokker--Planck Operators for Committor Functions
   Rongjie Lai, Jianfeng Lu · 2018 · Multiscale Modeling and Simulation
10. Building Markov state models with solvent dynamics
    Gu, Chen, Chang, Huang-Wei, Maibaum, Lutz, Pande, Vijay S, Carlsson, Gunnar E, Guibas, Leonidas J · 2013 · BMC Bioinformatics
11. Experiments and Comprehensive Simulations of the Formation of a Helical Turn
    Gouri S. Jas, Wendy A. Hegefeld, Peter Májek, Krzysztof Kuczera, Ron Elber · 2012 · The Journal of Physical Chemistry B
12. Optimal Reaction Coordinates and Kinetic Rates from the Projected Dynamics of Transition Paths.
    Line Mouaffac, Karen Palacio-Rodríguez, F. Pietrucci · 2023 · Journal of Chemical Theory and Computation
13. Extracting Physically Intuitive Reaction Coordinates from Transition Networks of a β-Sheet Miniprotein
    Bo Qi, Stefanie Muff, Amedeo Caflisch, Aaron R. Dinner · 2010 · The Journal of Physical Chemistry B
14. Minimizing memory as an objective for coarse-graining
    Nicholas Guttenberg, James F. Dama, Marissa G. Saunders, Gregory A. Voth, Jonathan Weare, Aaron R. Dinner · 2013 · The Journal of Chemical Physics
15. The dynamics of the conformational changes in the hexopyranose ring: a transition path sampling approach
    Wojciech Płaziński, Mateusz Drach · 2014 · RSC Advances
16. Simulating the Kinetics and Thermodynamics of Transitions via Forward Flux/Umbrella Sampling
    Ernesto E. Borrero, Fernando A. Escobedo · 2009 · The Journal of Physical Chemistry B
17. On the role of chemical detail in simulating protein folding kinetics
    Young Min Rhee, Vijay S. Pande · 2005 · Chemical Physics
18. Machine learning of slow collective variables and enhanced sampling via spatial techniques
    Tuğçe Gökdemir, Jakub Rydzewski · 2025 · Chemical Physics Reviews
19. Uncertainty in a Markov state model with missing states and rates: Application to a room temperature kinetic model obtained using high temperature molecular dynamics
    Abhijit Chatterjee, Swati Bhattacharya · 2015 · The Journal of Chemical Physics
20. Decomposition of energy and free energy changes by following the flow of work along reaction path.
    K. Haas, J. Chu · 2009 · Journal of Chemical Physics
21. Transition path sampling for discrete master equations with absorbing states
    Nathan Eidelson, Baron Peters · 2012 · The Journal of Chemical Physics
22. Dynamics in the Active Site of β-Secretase: A Network Analysis of Atomistic Simulations
    Sabyashachi Mishra, Amedeo Caflisch · 2011 · Biochemistry
23. A Rigorous Method for Identifying a One-Dimensional Reaction Coordinate in Complex Molecules
    Shanshan Wu, Huiyu Li, Ao Ma · 2022 · Journal of Chemical Theory and Computation
24. Exploring the Mechanisms of Reactions in Solution from Transition Path Sampling Molecular Dynamics Simulations
    Dirk Zahn · 2005 · Journal of Chemical Theory and Computation
25. Multidimensional minimum-work control of a 2D Ising model.
    Miranda D. Louwerse, David A. Sivak · 2022 · Journal of Chemical Physics
26. Manifold learning in atomistic simulations: a conceptual review
    Jakub Rydzewski, Ming Chen, Ómar Valsson · 2023 · Machine Learning Science and Technology
27. DNA-Binding Kinetics Determines the Mechanism of Noise-Induced Switching in Gene Networks
    Margaret J. Tse, Brian K. Chu, Mahua Roy, Elizabeth L. Read · 2015 · Biophysical Journal
28. Exploring chemical reactivity of complex systems with path‐based coordinates: Role of the distance metric
    Kirill Zinovjev, Iñaki Tuñón · 2014 · Journal of Computational Chemistry
29. Accelerated Nucleation Due to Trace Additives: A Fluctuating Coverage Model
    Geoffrey G. Poon, Baron Peters · 2015 · The Journal of Physical Chemistry B
30. A Simple and Accurate Method To Calculate Free Energy Profiles and Reaction Rates from Restrained Molecular Simulations of Diffusive Processes
    Victor Ovchinnikov, Kwangho Nam, Martin Karplus · 2016 · The Journal of Physical Chemistry B
31. Dynamic colloidal assembly pathways via low dimensional models
    Yuguang Yang, Raghuram Thyagarajan, David M. Ford, Michael A. Bevan · 2016 · The Journal of Chemical Physics
32. Integrated Hamiltonian Sampling: A Simple and Versatile Method for Free Energy Simulations and Conformational Sampling
    Toshifumi Mori, Robert J. Hamers, Joel A. Pedersen, Qiang Cui · 2014 · The Journal of Physical Chemistry B
33. Rich Dynamics Underlying Solution Reactions Revealed by Sampling and Data Mining of Reactive Trajectories
    Jun Zhang, Zhen Zhang, Yi Yang, Sirui Liu, Lijiang Yang, Yi Qin Gao · 2017 · ACS Central Science
34. Kinetic energy flows in activated dynamics of biomolecules
    Huiyu Li, Ao Ma · 2020 · The Journal of Chemical Physics
35. Accounting for the kinetics in order parameter analysis: lessons from theoretical models and a disordered peptide.
    Ganna Berezovska, D. Prada-Gracia, Stefano Mostarda, F. Rao · 2012 · Journal of Chemical Physics
36. Generalized essential energy space random walks to more effectively accelerate solute sampling in aqueous environment
    Chao Lv, Lianqing Zheng, Wei Yuan Yang · 2012 · The Journal of Chemical Physics
37. A benchmark for reaction coordinates in the transition path ensemble
    Wenjin Li, Ao Ma · 2016 · The Journal of Chemical Physics
38. Recovery of Protein Folding Funnels from Single-Molecule Time Series by Delay Embeddings and Manifold Learning
    Jiang Wang, Andrew L. Ferguson · 2018 · The Journal of Physical Chemistry B
39. Identifying mechanistically distinct pathways in kinetic transition networks
    Daniel Sharpe, David J. Wales · 2019 · The Journal of Chemical Physics
40. Hierarchical phenomena in multicomponent liquids: simulation methods, analysis, chemistry
    Michael J. Servis, Ernesto Martínez-Baez, Aurora E. Clark · 2020 · Physical Chemistry Chemical Physics
41. Rearrangement of Dewar Benzene Derivatives Studied by DFT
    Martin Dračínský, Obis Castaño, Martin Kotora, Petr Bouř · 2010 · The Journal of Organic Chemistry
42. Sequential Water and Headgroup Merger: Membrane Poration Paths and Energetics from MD Simulations
    Greg Bubnis, Helmut Grubmüller · 2020 · Biophysical Journal
43. Enhanced sampling of protein conformational changes via true reaction coordinates from energy relaxation
    Huiyu Li, Ao Ma · 2025 · Nature Communications
44. Dynamics of activation in the voltage-sensing domain of Ciona intestinalis phosphatase Ci-VSP
    Spencer C. Guo, Rong Shen, Benoı̂t Roux, Aaron R. Dinner · 2024 · Nature Communications
45. S-shooting: a Bennett–Chandler-like method for the computation of rate constants from committor trajectories
    Georg Menzl, Andreas Singraber, Christoph Dellago A · 2016 · Faraday Discussions
46. Efficient and exact sampling of transition path ensembles on Markovian networks
    Daniel Sharpe, David J. Wales · 2020 · The Journal of Chemical Physics
47. Exact Topology of the Dynamic Probability Surface of an Activated Process by Persistent Homology
    Farid Manuchehrfar, Huiyu Li, Wei Tian, Ao Ma, Jie Liang · 2021 · The Journal of Physical Chemistry B
48. Steady-state nucleation rate and flux of composite nucleus at saddle point
    Masao Iwamatsu · 2012 · The Journal of Chemical Physics
49. CATBOSS: Cluster Analysis of Trajectories Based on Segment Splitting
    Jovan Damjanovic, James M. Murphy, Yu‐Shan Lin · 2021 · Journal of Chemical Information and Modeling
50. Inexact iterative numerical linear algebra for neural network-based spectral estimation and rare-event prediction.
    J. Strahan, Spencer C. Guo, Chatipat Lorpaiboon, A. Dinner, J. Weare · 2023 · Journal of Chemical Physics
51. Reducing the cost of evaluating the committor by a fitting procedure
    Wenjin Li, Ao Ma · 2015 · The Journal of Chemical Physics
52. Atomistic Simulations for Reactions and Vibrational Spectroscopy in the Era of Machine Learning─ Quo Vadis?
    Markus Meuwly · 2022 · The Journal of Physical Chemistry B
53. Reactive Coarse-Grained Molecular Dynamics
    Thomas P. Dannenhoffer-Lafage, Gregory A. Voth · 2020 · Journal of Chemical Theory and Computation
54. Artificial Intelligence Resolves Kinetic Pathways of Magnesium Binding to RNA
    Jan Neumann, Nadine Schwierz · 2022 · Journal of Chemical Theory and Computation
55. Implications of Alternative Substrate Binding Modes for Catalysis by Uracil-DNA Glycosylase: An Apparent Discrepancy Resolved
    Ao Ma, Jie Hu, Martin Karplus, Aaron R. Dinner · 2006 · Biochemistry
56. A maximum caliber approach for continuum path ensembles
    P. Bolhuis, Z. F. Brotzakis, M. Vendruscolo · 2021 · European Physical Journal B : Condensed Matter Physics
57. Bézier curve string method for the study of rare events in complex chemical systems
    Michael A. Bellucci, Bernhardt L. Trout · 2014 · The Journal of Chemical Physics
58. Sampling reactive regions in phase space by following the minimum dynamic path
    Oliver T. Unke, Sebastian Brickel, Markus Meuwly · 2019 · The Journal of Chemical Physics
59. The use of a generalized born model for the analysis of protein conformational transitions: A comparative study with explicit solvent simulations for chemotaxis Y protein (CheY)
    Mark S. Formaneck, Qiang Cui · 2006 · Journal of Computational Chemistry
60. Analyzing Multimodal Probability Measures with Autoencoders
    Tony Lelièvre A, Thomas Pigeon, Gabriel Stoltz, Zhang Wei · 2024 · The Journal of Physical Chemistry B
61. Quantifying Rare Events in Stochastic Reaction-Diffusion Dynamics Using Tensor Networks
    Schuyler B. Nicholson, Todd R. Gingrich · 2023 · Physical Review X
62. How is Membrane Permeation of Small Ionizable Molecules Affected by Protonation Kinetics?
    Jonathan J. Harris, Christophe J. Chipot, Benoı̂t Roux · 2024 · The Journal of Physical Chemistry B
63. Using pretrained graph neural networks with token mixers as geometric featurizers for conformational dynamics
    Zihan Pengmei, Chatipat Lorpaiboon, Spencer C. Guo, J. Weare, Aaron R. Dinner · 2024 · Journal of Chemical Physics
64. Divided Saddle Theory: A New Idea for Rate Constant Calculation
    János Daru, András Stirling · 2014 · Journal of Chemical Theory and Computation
65. Rock climbing: A local-global algorithm to compute minimum energy and minimum free energy pathways
    Clark Templeton, Serena H. Chen, Arman Fathizadeh, Ron Elber · 2017 · The Journal of Chemical Physics
66. Supervised learning and the finite-temperature string method for computing committor functions and reaction rates
    Muhammad Risyad Hasyim, Clay H. Batton, Kranthi Kiran Mandadapu · 2022 · The Journal of Chemical Physics
67. Computing transition path theory quantities with trajectory stratification
    Bodhi P. Vani, Jonathan Weare, Aaron R. Dinner · 2022 · The Journal of Chemical Physics
68. Variational deep learning of equilibrium transition path ensembles
    Aditya Narayan Singh, David T. Limmer · 2023 · The Journal of Chemical Physics
69. Water pulls the strings in hydrophobic polymer collapse
    Gerhard Hummer · 2007 · Proceedings of the National Academy of Sciences
70. Critical length of a one-dimensional nucleus
    Mark N. Joswiak, Michael F. Doherty, Baron Peters · 2016 · The Journal of Chemical Physics
71. Dissecting the Dynamics during Enzyme Catalysis: A Case Study of Pin1 Peptidyl-Prolyl Isomerase
    Toshifumi Mori, Shinji Saito · 2020 · Journal of Chemical Theory and Computation
72. Generation of initial trajectories for transition path sampling of chemical reactions with ab initio molecular dynamics
    Christopher N. Rowley, Tom K. Woo · 2007 · The Journal of Chemical Physics
73. Peptide Isomerization is Suppressed at the Air–Water Interface
    Aditya Narayan Singh, David T. Limmer · 2022 · The Journal of Physical Chemistry Letters
74. Machine learning for molecular simulations of crystal nucleation and growth
    Sapna Sarupria, Steven W. Hall, Jutta Rogal · 2022 · MRS Bulletin
75. Value of Temporal Information When Analyzing Reaction Coordinates
    Piao Ma, Ron Elber, Dmitrii E. Makarov · 2020 · Journal of Chemical Theory and Computation
76. Memory kernel minimization-based neural networks for discovering slow collective variables of biomolecular dynamics
    Bojun Liu, Siqin Cao, Jordan G. Boysen, Mingyi Xue, Xuhui Huang · 2025 · Nature Computational Science
77. Dimension reduction of noisy interacting systems
    Niccolò Zagli, Grigorios A. Pavliotis, Valerio Lucarini, Alexander Alecio · 2023 · Physical Review Research
78. Simple Physics and Integrators Accurately Reproduce Mercury Instability Statistics
    Dorian S. Abbot, David M. Hernandez, Sam Hadden, Robert J. Webber, Georgios P. Afentakis, Jonathan Weare · 2023 · The Astrophysical Journal
79. Effective data-driven collective variables for free energy calculations from metadynamics of paths
    Lukas Müllender, Andrea Rizzi, Michele Parrinello, Paolo Carloni, Davide Mandelli · 2023 · PNAS Nexus
80. Hydrogen bonds vs RMSD: Geometric reaction coordinates for protein folding
    Yannik Kasprzak, J. Rückert, N. Ludolph, Ch. Hübner, Hauke Paulsen · 2025 · The Journal of Chemical Physics
81. Transition state ensemble optimization for reactions of arbitrary complexity
    Kirill Zinovjev, Iñaki Tuñón · 2015 · The Journal of Chemical Physics
82. Good Rates From Bad Coordinates: The Exponential Average Time-dependent Rate Approach
    Nicodemo Mazzaferro, Subarna Sasmal, Pilar Cossio, Glen M. Hocky · 2024 · Journal of Chemical Theory and Computation
83. A new perspective on transition states: χ1 separatrix
    Paul Jay Ledbetter, Cecilia Clementi · 2011 · The Journal of Chemical Physics
84. Employing Artificial Neural Networks to Identify Reaction Coordinates and Pathways for Self-Assembly.
    Jörn H Appeldorn, Simon Lemcke, T. Speck, Arash Nikoubashman · 2022 · Journal of Physical Chemistry B
85. Extending the scope of ‘in silico experiments’: Theoretical approaches for the investigation of reaction mechanisms, nucleation events and phase transitions
    Dirk Zahn, Agnieszka Kawska, Gotthard Seifert, Yuri Grin, Rüdiger Kniep, Stefano Leoni · 2007 · Science and Technology of Advanced Materials
86. Divergence among Local Structure, Dynamics, and Nucleation Outcome in Heterogeneous Nucleation of Close-Packed Crystals
    Tiago S. Domingues, Sarwar Hussain, Amir Haji‐Akbari · 2024 · The Journal of Physical Chemistry Letters
87. Spectral Map for Slow Collective Variables, Markovian Dynamics, and Transition State Ensembles
    Jakub Rydzewski · 2024 · Journal of Chemical Theory and Computation
88. Learning the committor without collective variables
    Sergio Contreras Arredondo, Chenyu Tang, Radu A. Talmazan, Alberto Megías, Cheng Giuseppe Chen, Christophe J. Chipot · 2026 · Nature Computational Science
89. Nonadiabatic transition path sampling
    M. C. Sherman, Steven A. Corcelli · 2016 · The Journal of Chemical Physics
90. Exact reaction coordinates for flap opening in HIV-1 protease
    Shanshan Wu, Huiyu Li, Ao Ma · 2022 · Proceedings of the National Academy of Sciences
91. Estimation of reactive fluxes in gradient stochastic systems using an analogy with electric circuits
    Maria Cameron · 2013 · Journal of Computational Physics
92. Probing reaction channels via reinforcement learning
    Senwei Liang, Aditya Narayan Singh, Yuanran Zhu, David T. Limmer, Chao Yang · 2023 · Machine Learning Science and Technology
93. PyRETIS 3: Conquering rare and slow events without boundaries
    Wouter Vervust, Daniel Tianhou Zhang, An Ghysels, Sander Roet, Titus S. van Erp, Enrico Riccardi · 2024 · Journal of Computational Chemistry
94. Information Thermodynamics of the Transition-Path Ensemble
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95. Force-Correction Analysis Method for Derivation of Multidimensional Free-Energy Landscapes from Adaptively Biased Replica Simulations
    Fabrizio Marinelli, José D. Faraldo‐Gómez · 2021 · Journal of Chemical Theory and Computation
96. Splitting probabilities as optimal controllers of rare reactive events
    Aditya Narayan Singh, David T. Limmer · 2024 · The Journal of Chemical Physics
97. Simulating Crystallization in a Colloidal System Using State Predictive Information Bottleneck Based Enhanced Sampling.
    Vanessa J Meraz, Ziyue Zou, P. Tiwary · 2024 · Journal of Physical Chemistry B
98. NaCl Dissociation Explored Through Predictive Power Path Sampling Analysis
    Konrad Wilke, Shuxia Tao, Sofı́a Calero, Anders Lervik, Titus S. van Erp · 2025 · Journal of Chemical Theory and Computation
99. The role of fluctuations in the nucleation process
    Yuanpeng Deng, Peilin Kang, Xiang Qun Xu, Hui Li, Michele Parrinello · 2026 · Proceedings of the National Academy of Sciences
100. Comment on “Toward Identification of the Reaction Coordinate Directly from the Transition State Ensemble Using the Kernel PCA Method”
     Baron Peters · 2011 · The Journal of Physical Chemistry B