Obtaining reaction coordinates by likelihood maximization

Cited by (417)

Items 101–200 of 417

1. Common Features of Extraordinary Rate Theories
   Baron Peters · 2015 · The Journal of Physical Chemistry B
2. 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
3. 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
4. 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
5. Mechanism of the electroneutral sodium/proton antiporter PaNhaP from transition-path shooting
   Kei-ichi Okazaki, David Wöhlert, Judith Warnau, Hendrik Jung, Özkan Yıldız, Werner Kühlbrandt, Gerhard Hummer · 2019 · Nature Communications
6. Kinetic pathways of water exchange in the first hydration shell of magnesium
   Schwierz, Nadine · 2020 · The Journal of Chemical Physics
7. 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
8. α-helix to β-hairpin transition of human amylin monomer.
   Sadanand Singh, Chi-Cheng Chiu, A. S. Reddy, J. D. de Pablo · 2013 · Journal of Chemical Physics
9. Commute Maps: Separating Slowly Mixing Molecular Configurations for Kinetic Modeling
   Frank Noé, Ralf Banisch, Cecilia Clementi · 2016 · Journal of Chemical Theory and Computation
10. Nonclassical pathways of crystallization in colloidal systems
    John Russo, Hajime Tanaka · 2016 · MRS Bulletin
11. Phase space and collective variable based simulation methods for studies of rare events
    Sanjib Paul, Nisanth N. Nair, Harish Vashisth · 2019 · Molecular Simulation
12. Optimal reaction coordinates
    Polina V. Banushkina, Sergei V. Krivov · 2016 · Wiley Interdisciplinary Reviews Computational Molecular Science
13. Nucleation mechanism of clathrate hydrates of water-soluble guest molecules
    Ryan S. DeFever, Sapna Sarupria · 2017 · The Journal of Chemical Physics
14. Protein Dynamics and Enzymatic Chemical Barrier Passage
    Dimitri Antoniou, Steven D. Schwartz · 2011 · The Journal of Physical Chemistry B
15. 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
16. Non-Markovian out-of-equilibrium dynamics: A general numerical procedure to construct time-dependent memory kernels for coarse-grained observables
    Hugues Meyer, Philipp Pelagejcev, Tanja Schilling · 2020 · Europhysics Letters (EPL)
17. String Method with Swarms-of-Trajectories, Mean Drifts, Lag Time, and Committor
    Benoı̂t Roux · 2021 · The Journal of Physical Chemistry A
18. Kinetics of Ligand-Protein Dissociation from All-Atom Simulations: Are We There Yet?
    João Marcelo Lamim Ribeiro, Sun-Ting Tsai, Debabrata Pramanik, Yihang Wang, P. Tiwary · 2018 · Biochemistry
19. 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
20. Optimizing transition interface sampling simulations
    Ernesto E. Borrero, Marcus Weinwurm, Christoph Dellago A · 2011 · The Journal of Chemical Physics
21. 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
22. Cis-to-Trans Isomerization of Azobenzene Derivatives Studied with Transition Path Sampling and Quantum Mechanical/Molecular Mechanical Molecular Dynamics
    Anja Muždalo, Peter Saalfrank, Jocelyne Vreede, Mark Santer · 2018 · Journal of Chemical Theory and Computation
23. 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
24. Order-disorder transition in Co-Pt nanoparticles: Coexistence, transition states, and finite-size effects
    F. Calvo, C. Mottet · 2011 · Physical Review B
25. Collective Variable-Based Enhanced Sampling: From Human Learning to Machine Learning.
    Hao-Hao Fu, H. Bian, Xue-Guang Shao, Wen-Sheng Cai · 2024 · Journal of Physical Chemistry Letters
26. The stochastic separatrix and the reaction coordinate for complex systems
    Dimitri Antoniou, Steven D. Schwartz · 2009 · The Journal of Chemical Physics
27. Harnessing atomistic simulations to predict the rate at which dislocations overcome obstacles
    S. Saroukhani, Linh Nguyen, K.W.K. Leung, Chandra Veer Singh, Derek H. Warner · 2016 · Journal of the Mechanics and Physics of Solids
28. OpenPathSampling: A Python Framework for Path Sampling Simulations. 2. Building and Customizing Path Ensembles and Sample Schemes
    David W. H. Swenson, Jan-Hendrik Prinz, Frank Noé, John D. Chodera, Peter G. Bolhuis · 2018 · Journal of Chemical Theory and Computation
29. Nucleation pathway and kinetics of phase-separating active Brownian particles
    David Richard, Hartmut Löwen, Thomas Speck · 2016 · Soft Matter
30. Reaction coordinates in complex systems-a perspective
    Jutta Rogal · 2021 · The European Physical Journal B
31. Accelerated Simulations of Molecular Systems through Learning of Effective Dynamics
    Pantelis Rafail Vlachas, Julija Zavadlav, Matej Praprotnik, Petros Koumoutsakos · 2021 · Journal of Chemical Theory and Computation
32. 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
33. 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
34. Shape and area fluctuation effects on nucleation theory
    Santi Prestipino, Alessandro Laio, Erio Tosatti · 2014 · The Journal of Chemical Physics
35. Elucidating the Locking Mechanism of Peptides onto Growing Amyloid Fibrils through Transition Path Sampling
    Marieke Schor, Jocelyne Vreede, Peter G. Bolhuis · 2012 · Biophysical Journal
36. Multi-dimensional spectral gap optimization of order parameters (SGOOP) through conditional probability factorization
    Zachary Smith, Debabrata Pramanik, Sun-Ting Tsai, Pratyush Tiwary · 2018 · The Journal of Chemical Physics
37. 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
38. 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
39. 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
40. Optimising reaction coordinates for crystallisation by tuning the crystallinity definition
    Swetlana Jungblut, Andreas Singraber, Christoph Dellago A · 2013 · Molecular Physics
41. A Local Order Parameter-Based Method for Simulation of Free Energy Barriers in Crystal Nucleation
    Hossein Eslami, Neda Khanjari, Florian Müller‐Plathe · 2017 · Journal of Chemical Theory and Computation
42. Reaction mechanism and reaction coordinates from the viewpoint of energy flow
    Wenjin Li, Ao Ma · 2016 · The Journal of Chemical Physics
43. 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
44. Who's on base? Revealing the catalytic mechanism of inverting family 6 glycoside hydrolases
    Heather B. Mayes, Brandon C. Knott, Michael F. Crowley, Linda J. Broadbelt, Jerry Ståhlberg, Gregg T. Beckham · 2016 · Chemical Science
45. Reaction coordinates and transition states in enzymatic catalysis
    Kirill Zinovjev, Iñaki Tuñón · 2017 · Wiley Interdisciplinary Reviews Computational Molecular Science
46. Transition path sampling of protein conformational changes
    Jarek Juraszek, Jocelyne Vreede, Peter G. Bolhuis · 2011 · Chemical Physics
47. Localized Orientational Order Chaperones the Nucleation of Rotator Phases in Hard Polyhedral Particles
    Vikram Thapar, Fernando A. Escobedo · 2014 · Physical Review Letters
48. Nonlinear machine learning in simulations of soft and biological materials
    Jiang Wang, Andrew L. Ferguson · 2017 · Molecular Simulation
49. Variational Identification of Markovian Transition States
    Linda Martini, Adam Kells, Roberto Covino, Gerhard Hummer, Nicolae‐Viorel Buchete, Edina Rosta · 2017 · Physical Review X
50. A one-way shooting algorithm for transition path sampling of asymmetric barriers
    Z. Faidon Brotzakis, Peter G. Bolhuis · 2016 · The Journal of Chemical Physics
51. Numerical Construction of the pfold (Committor) Reaction Coordinate for a Markov Process
    Sergei V. Krivov · 2011 · The Journal of Physical Chemistry B
52. Analyzing Complex Reaction Mechanisms Using Path Sampling
    Titus S. van Erp, Mahmoud Moqadam, Enrico Riccardi, Anders Lervik · 2016 · Journal of Chemical Theory and Computation
53. Investigating dislocation motion through a field of solutes with atomistic simulations and reaction rate theory
    S. Saroukhani, Derek H. Warner · 2017 · Acta Materialia
54. Nested Transition Path Sampling
    Peter G. Bolhuis, Gábor Cśanyi · 2018 · Physical Review Letters
55. 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
56. Protein Folding Free Energy Landscape along the Committor - the Optimal Folding Coordinate
    Sergei V. Krivov · 2018 · Journal of Chemical Theory and Computation
57. Identification of kinetic order parameters for non-equilibrium dynamics
    Fabian Paul, Hao Wu, Maximilian Vossel, Bert L. de Groot, Frank Noé · 2019 · The Journal of Chemical Physics
58. How wet should be the reaction coordinate for ligand unbinding?
    P. Tiwary, B. Berne · 2016 · Journal of Chemical Physics
59. Committor-Consistent Variational String Method
    Ziwei He, C. Chipot, Benoı T. Roux · 2022 · Journal of Physical Chemistry Letters
60. 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
61. 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
62. Protein Dynamics and the Enzymatic Reaction Coordinate
    Steven D. Schwartz · 2013 · Topics in current chemistry
63. Reaction Coordinate for Ice Crystallization on a Soft Surface
    Laura Lupi, Rebecca Hanscam, Yuqing Qiu, Valeria Molinero · 2017 · The Journal of Physical Chemistry Letters
64. 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
65. On the coupling between slow diffusion transport and barrier crossing in nucleation
    Baron Peters · 2011 · The Journal of Chemical Physics
66. Effects of a Mutation on the Folding Mechanism of a β-Hairpin
    Jarek Juraszek, Peter G. Bolhuis · 2009 · The Journal of Physical Chemistry B
67. How to quantify and avoid finite size effects in computational studies of crystal nucleation: The case of heterogeneous ice nucleation
    Sarwar Hussain, Amir Haji‐Akbari · 2021 · The Journal of Chemical Physics
68. p(TP|q) peak maximization: Necessary but not sufficient for reaction coordinate accuracy
    Baron Peters · 2010 · Chemical Physics Letters
69. Reaction coordinates and rate constants for liquid droplet nucleation: Quantifying the interplay between driving force and memory
    Sun-Ting Tsai, Zachary Smith, Pratyush Tiwary · 2019 · The Journal of Chemical Physics
70. 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
71. The hydrolysis mechanism of a GH45 cellulase and its potential relation to lytic transglycosylase and expansin function
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72. Transition-State Theory, Dynamics, and Narrow Time Scale Separation in the Rate-Promoting Vibrations Model of Enzyme Catalysis
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73. Nonparametric variational optimization of reaction coordinates
    Polina V. Banushkina, Sergei V. Krivov · 2015 · The Journal of Chemical Physics
74. 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
75. On the Relation Between Projections of the Reweighted Path Ensemble
    Peter G. Bolhuis, Wolfgang Lechner · 2011 · Journal of Statistical Physics
76. Dynamics and Kinetics Study of “In-Water” Chemical Reactions by Enhanced Sampling of Reactive Trajectories
    Jun Zhang, Yi Yang, Lijiang Yang, Yi Qin Gao · 2015 · The Journal of Physical Chemistry B
77. Ensemble of Transition State Structures for the Cis−Trans Isomerization of N-Methylacetamide
    Yves A. Mantz, Davide Branduardi, Giovanni Bussi, Michele Parrinello · 2009 · The Journal of Physical Chemistry B
78. Simultaneous estimation of free energies and rates using forward flux sampling and mean first passage times
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79. Nonlinear machine learning and design of reconfigurable digital colloids
    Andrew Long, Carolyn L. Phillips, Eric Jankowski, Andrew L. Ferguson · 2016 · Soft Matter
80. 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
81. Derivation of an exact, nonequilibrium framework for nucleation: Nucleation is a priori neither diffusive nor Markovian
    Anja Kuhnhold, Hugues Meyer, Graziano Amati, Philipp Pelagejcev, Tanja Schilling · 2019 · Physical review. E
82. Breakage of Hydrophobic Contacts Limits the Rate of Passive Lipid Exchange between Membranes
    Julia R. Rogers, Phillip L. Geissler · 2020 · The Journal of Physical Chemistry B
83. The water-catalyzed mechanism of the ring-opening reaction of glucose
    Wojciech Płaziński, Anita Płazińska, Mateusz Drach · 2015 · Physical Chemistry Chemical Physics
84. Nucleus-size pinning for determination of nucleation free-energy barriers and nucleus geometry
    Abhishek Kumar Sharma, Fernando A. Escobedo · 2018 · The Journal of Chemical Physics
85. 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
86. Maximum Likelihood Analysis of Reaction Coordinates during Solidification in Ni
    Grisell Díaz Leines, Jutta Rogal · 2018 · The Journal of Physical Chemistry B
87. Contour forward flux sampling: Sampling rare events along multiple collective variables
    Ryan S. DeFever, Sapna Sarupria · 2019 · The Journal of Chemical Physics
88. An exploration of machine learning models for the determination of reaction coordinates associated with conformational transitions
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89. Point Cloud Discretization of Fokker--Planck Operators for Committor Functions
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90. Experiments and Comprehensive Simulations of the Formation of a Helical Turn
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91. Identification of a multi-dimensional reaction coordinate for crystal nucleation in Ni3Al
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92. QM/MM Simulations of Enzymatic Hydrolysis of Cellulose: Probing the Viability of an Endocyclic Mechanism for an Inverting Cellulase
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93. Practical guide to replica exchange transition interface sampling and forward flux sampling
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94. Optimal Reaction Coordinates and Kinetic Rates from the Projected Dynamics of Transition Paths.
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95. Short-Time Infrequent Metadynamics for Improved Kinetics Inference
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96. Folding mechanism of a polymer chain with short-range attractions
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97. Extracting Physically Intuitive Reaction Coordinates from Transition Networks of a β-Sheet Miniprotein
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98. The dynamics of the conformational changes in the hexopyranose ring: a transition path sampling approach
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99. Coordination Dynamics of Zinc Triggers the Rate Determining Proton Transfer in Human Carbonic Anhydrase II
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100. Transition Path Sampling Study of the Feruloyl Esterase Mechanism
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