Variational approach to molecular kinetics

Cited by (307)

Items 201–300 of 307

1. Dynamical matrix propagator scheme for large-scale proton dynamics simulations.
   C. Dreßler, G. Kabbe, Martin Brehm, D. Sebastiani · 2020 · Journal of Chemical Physics
2. tgEDMD: Approximation of the Kolmogorov Operator in Tensor Train Format
   Marvin Lücke, F. Nüske · 2021 · Journal of nonlinear science
3. Conformational analysis of replica exchange MD: Temperature-dependent Markov networks for FF amyloid peptides
   Brajesh Narayan, Colm Herbert, Ye Yuan, Brian J. Rodriguez, Bernard R. Brooks, Nicolae‐Viorel Buchete · 2018 · The Journal of Chemical Physics
4. Revealing the conformational dynamics of UDP-GlcNAc recognition by O-GlcNAc transferase via Markov state model
   Jiaqi Tian, Xin Wen Dong, Tianshuo Wu, Pengbo Wen, Xin Liu, Mengying Zhang, Xiaoli An, Danfeng Shi · 2023 · International Journal of Biological Macromolecules
5. Error Bounds for Dynamical Spectral Estimation
   R. Webber, E. Thiede, Douglas Dow, A. Dinner, J. Weare · 2020 · SIAM Journal on Mathematics of Data Science
6. FSATOOL: A useful tool to do the conformational sampling and trajectory analysis work for biomolecules
   Hao-Miao Zhang, Qian-Kun Gong, Hao-Zhe Zhang, Chang-Jun Chen · 2019 · Journal of Computational Chemistry
7. 7 Data-driven methods for reduced-order modeling
   S. Brunton, J. Kutz · 2020 · Snapshot-Based Methods and Algorithms
8. Analyzing the Long Time-Scale Dynamics of Uremic Toxins Bound to Sudlow Site II in Human Serum Albumin
   James Ludwig, Josh K. Smith, Jim Pfaendtner · 2021 · The Journal of Physical Chemistry B
9. Sparsity and Compressed Sensing
   Steven L. Brunton, J. Nathan Kutz · 2019 · Cambridge University Press eBooks
10. Diffusion Monte Carlo study on temporal evolution of entropy and free energy in nonequilibrium processes.
    Shigenori Tanaka · 2016 · Journal of Chemical Physics
11. Maximizing Kinetic Information Gain of Markov State Models for Optimal Design of Spectroscopy Experiments
    Shriyaa Mittal, Diwakar Shukla · 2018 · The Journal of Physical Chemistry B
12. Variability of SST through Koopman modes
    Antonio Navarra, J. Tribbia, Stefan Klus, Paula Lorenzo-Sánchez · 2024 · Journal of Climate
13. Single-cell morphodynamical trajectories enable prediction of gene expression accompanying cell state change
    Jeremy Copperman, Ian C. McLean, Sean M. Gross, Jalim Singh, Vaibhav Murthy, Young Hwan Chang, Alexander E. Davies, Daniel M. Zuckerman, Laura M. Heiser · 2026 · Cell Systems
14. Reduced Order Models (ROMs)
    Steven L. Brunton, J. Nathan Kutz · 2019 · Cambridge University Press eBooks
15. Fast Functionalization with High Performance in the Autonomous Information Engine
    Zhiyu Cao, Ruicheng Bao, Jiming Zheng, Zhonghuai Hou · 2022 · The Journal of Physical Chemistry Letters
16. Exploring non-equilibrium molecular dynamics of mobile protons in the solid acid CsH2PO4 at the micrometer and microsecond scale.
    C. Dreßler, G. Kabbe, Martin Brehm, D. Sebastiani · 2020 · Journal of Chemical Physics
17. Linear Control Theory
    Steven L. Brunton, J. Nathan Kutz · 2019 · Cambridge University Press eBooks
18. Markov State Models of Protein–Protein Encounters
    Simon Olsson · 2022 · Wiley eBooks
19. AMUSET-TICA: A Tensor-Based Approach for Identifying Slow Collective Variables in Biomolecular Dynamics
    Siqin Cao, Feliks Nüske, Bojun Liu, Micheline B. Soley, Xuhui Huang · 2025 · Journal of Chemical Theory and Computation
20. Characterizing Structural and Kinetic Ensembles of Intrinsically Disordered Proteins Using Writhe
    2025
21. Imaging Metastable States and Transitions in Proteins by Trajectory Map.
    Chuan-Biao Zhang, Jin Yu, Xin Zhou · 2017 · Journal of Physical Chemistry B
22. Integration of machine learning with computational structural biology of plants
    Jiming Chen, Diwakar Shukla · 2022 · Biochemical Journal
23. Assessing transition rates as functions of environmental variables
    Luca Donati, Marcus Weber · 2022 · The Journal of Chemical Physics
24. Improved estimation for energy dissipation in biochemical oscillations
    Zhiyu Cao, Zhonghuai Hou · 2022 · The Journal of Chemical Physics
25. Unbiased molecular dynamics for the direct determination of catalytic reaction times: Paving the way beyond transition state theory
    Thomas Pigeon, Manuel Corral Valero, Pascal Raybaud · 2026 · Journal of Catalysis
26. Unbiasing Enhanced Sampling on a High-Dimensional Free Energy Surface with a Deep Generative Model
    Yikai Liu, Tushar K. Ghosh, Guang Lin, Ming Chen · 2024 · The Journal of Physical Chemistry Letters
27. Enhanced sampling based on slow variables of trajectory mapping
    Chuanbiao Zhang, Fangfu Ye, Ming Li, Xin Zhou · 2018 · Science China Physics Mechanics and Astronomy
28. Structural characterization of codon 129 polymorphism in prion peptide segments (PrP127-132) using the Markov State Models.
    Wycliffe Omwansu, Robinson Musembi, S. Derese · 2024 · Journal of Molecular Graphics and Modelling
29. Exploring substrate binding in the extracellular vestibule of MhsT by atomistic simulations and Markov models
    Ara M. Abramyan, M. Quick, Cathy Xue, J. Javitch, Lei Shi · 2018 · Journal of Chemical Information and Modeling
30. Computation of temperature-dependent dissociation rates of metastable protein–ligand complexes
    Natalia Ernst, K. Fackeldey, Andrea Volkamer, O. Opatz, Marcus Weber · 2019 · Molecular Simulation
31. Maximum margin clustering for state decomposition of metastable systems
    Hao Wu · 2013 · Neurocomputing
32. RevGraphVAMP: A protein molecular simulation analysis model combining graph convolutional neural networks and physical constraints
    Ying Huang, Huiling Zhang, Zhenli Lin, Yanjie Wei, Wenhui Xi · 2024 · Methods
33. Kinetics of Molecular Diffusion and Self-Assembly: Glycine on Cu{110}
    Judith B. Rommel, David J. Wales · 2017 · The Journal of Physical Chemistry C
34. Identifying signatures of proteolytic stability and monomeric propensity in O-glycosylated insulin using molecular simulation
    Wei-Tse Hsu, Dominique A. Ramirez, Tarek Sammakia, Zhongping Tan, Michael R. Shirts · 2022 · Journal of Computer-Aided Molecular Design
35. Markov State Models in Drug Design
    Bettina G. Keller, Stevan Aleksić, Luca Donati · 2018 · Methods and principles in medicinal chemistry
36. Reaction Coordinates are Optimal Channels of Energy Flow
    Ao Ma, Huiyung Li · 2024 · Annual review of physical chemistry (Print)
37. Advancements in characterization of protein dynamics with machine learning
    Mohammad Madani, Anna Tarakanova · 2026 · npj Soft Matter
38. Balanced Models for Control
    Steven L. Brunton, J. Nathan Kutz · 2019 · Cambridge University Press eBooks
39. Screening Fast-Mode Motion in Collective Variable Discovery for Biochemical Processes.
    Donghui Shao, Zhiteng Zhang, Xuyang Liu, Hao-Hao Fu, Xue-Guang Shao, Wen-Sheng Cai · 2024 · Journal of Chemical Theory and Computation
40. Applications of enhanced sampling methods to biomolecular self-assembly: a review
    Mason Hooten, Het Patel, Yiwei Shao, Rishabh Kumar Singh, Meenakshi Dutt · 2025 · Journal of Physics Condensed Matter
41. Elucidating Mechanisms of Molecular Recognition Between Human Argonaute and miRNA Using Computational Approaches
    Hanlun Jiang, Lizhe Zhu, Amélie Héliou, Xin Gao, Julie Bernauer, Xuhui Huang · 2016 · Methods in molecular biology
42. Collective variables between large-scale states in turbulent convection
    P. Maity, Andreas Bittracher, P. Koltai, J. Schumacher · 2023 · Physical Review Research
43. Find slow dynamic modes via analyzing molecular dynamics simulation trajectories
    Chuan-Biao Zhang, Xin Zhou · 2020 · Chinese Physics B
44. Data-Driven Dynamical Systems
    Steven L. Brunton, J. Nathan Kutz · 2019 · Cambridge University Press eBooks
45. Advances in Molecular Simulation
    Matteo Aldeghi, P. Biggin · 2017 · Elsevier eBooks
46. AMOEBA Polarizable Molecular Dynamics Simulations of Guanine Quadruplexes: From the c-Kit Proto-Oncogene to HIV-1
    Dina El Ahdab, Louis Lagardère, Zeina Hobaika, Théo Jaffrelot Inizan, Frédéric Célerse, Nohad Gresh, Richard G. Maroun, Jean‐Philip Piquemal · 2025 · Journal of Chemical Information and Modeling
47. Conformational dynamics of peptide substrate recognition in polypeptide N-acetylgalactosaminyltransferase 2: Markov state models reveal the anchoring and stabilizing determinants.
    Danfeng Shi, En-Hui Lv, Wenhua Li, Q.-Y. Xia, Hong-Wei Du, Jiaqi Tian · 2025 · International Journal of Biological Macromolecules
48. Revealing the Atomistic Mechanism of Rare Events in Molecular Dynamics.
    Jakob J. Kresse, A. Sikorski, V. Sunkara, Surahit Chewle, M. Weber · 2025 · Journal of Chemical Theory and Computation
49. Markov state models from hierarchical density-based assignment
    Ion Mitxelena, Xabier López, David De Sancho · 2021 · The Journal of Chemical Physics
50. Conformational Fluctuations in β2-Microglubulin Using Markov State Modeling and Molecular Dynamics.
    M. Ghorbani, B. Brooks, Jeffery B. Klauda · 2023 · Journal of Physical Chemistry B
51. Transition state searching for complex biomolecules: Algorithms and machine learning
    Jianyu Yang, Kun Xi, Lizhe Zhu · 2023 · Acta Physica Sinica
52. Implementation of Girsanov Reweighting in OpenMM and Deeptime
    Joana-Lysiane Schäfer, Bettina G. Keller · 2024 · The Journal of Physical Chemistry B
53. Existence and uniqueness of solutions of the Koopman–von Neumann equation on bounded domains
    Marian Stengl, Patrick Gelß, Stefan Klus, Sebastian Pokutta · 2024 · Journal of Physics A Mathematical and Theoretical
54. Toward Grid-Based Models for Molecular Association
    Hana Zupan, Bettina G. Keller · 2025 · Journal of Chemical Theory and Computation
55. On Finding Optimal Collective Variables for Complex Systems by Minimizing the Deviation between Effective and Full Dynamics
    Wei Zhang, Christof Schütte · 2025 · Multiscale Modeling and Simulation
56. Clustering and Classification
    Steven L. Brunton, J. Nathan Kutz · 2019 · Cambridge University Press eBooks
57. Machine Learning in Molecular Dynamics Simulations of Biomolecular Systems
    Christopher Kolloff, Simon Olsson · 2023 · Elsevier eBooks
58. Toward a structural identification of metastable molecular conformations.
    Simon Lemcke, Jörn H Appeldorn, Michael Wand, T. Speck · 2023 · Journal of Chemical Physics
59. Data-Driven Control
    Steven L. Brunton, J. Nathan Kutz · 2019 · Cambridge University Press eBooks
60. Modelling Intrinsically Disordered Protein Dynamics as Networks of Transient Secondary Structure
    Hannah K. Wayment-Steele, Carlos Xavier Hernández, V. Pande · 2018 · bioRxiv
61. Nonparametric Bayesian inference for meta-stable conformational dynamics
    Lukas Köhs, Kerri Kukovetz, Oliver Rauh, Heinz Koeppl · 2022 · Physical Biology
62. Understanding the Fast-Triggering Unfolding Dynamics of FK-11 upon Photoexcitation of Azobenzene
    Tiantian Xu, Yongfang Li, Xin Gao, Lu Zhang · 2024 · The Journal of Physical Chemistry Letters
63. Tutorial on Molecular Latent Space Simulators (LSSs): Spatially and Temporally Continuous Data-Driven Surrogate Dynamical Models of Molecular Systems.
    Michael S. Jones, Kirill Shmilovich, Andrew L. Ferguson · 2024 · Journal of Physical Chemistry A
64. Collective Variables and Facilitated Conformational Opening during Translocation of Human Mitochondrial RNA Polymerase (POLRMT) from Atomic Simulations.
    Shannon J. McElhenney, Jin Yu · 2025 · Journal of Chemical Theory and Computation
65. Molecular Understanding of Free-Energy Landscapes
    Marcello Sega, Matteo Salvalaglio · 2026 · Annual Review of Chemical and Biomolecular Engineering
66. Advanced sampling methods to study complex biomolecular systems
    Han Kurt, Ameni Ben Abdeljaoued, Lina Kheflet, Elisa Frezza, Attilio Vittorio Vargiu · 2026 · Elsevier eBooks
67. Investigating causality between principal components in protein dynamics
    Debarshi Banerjee, Ali A. Hassanali, Alessandro Laio · 2026 · The Journal of Chemical Physics
68. Unsupervised random forests for interpretable representation analysis of protein conformational landscapes
    Mohammad Sahil, N. Ahalawat, Jagannath Mondal · 2026 · Patterns
69. Deep learning for structure-preserving universal stable Koopman-inspired embeddings for nonlinear canonical Hamiltonian dynamics
    P. Goyal, Süleyman Yıldız, P. Benner · 2023 · Machine Learning: Science and Technology
70. Coarse-Graining Self-Assembly by the Stochastic Landscape Method
    Michael Faran, Gili Bisker · 2025 · Journal of Chemical Theory and Computation
71. A Bayesian nonparametric model for spectral estimation of metastable systems
    Hao Wu · 2014
72. Regression and Model Selection
    Steven L. Brunton, J. Nathan Kutz · 2019 · Cambridge University Press eBooks
73. Maximum Margin Clustering for State Decomposition of Metastable Systems
    Hao Wu · 2014 · arXiv (Cornell University)
74. Analyzing high-dimensional time-series data using kernel transfer operator eigenfunctions
    Stefan Klus, Sebastian Peitz, Ingmar Schuster · 2018 · arXiv (Cornell University)
75. Machine learning approaches for analyzing and enhancing molecular dynamics simulations
    Yihang Wang, João Marcelo Lamim Ribeiro, Pratyush Tiwary · 2019 · arXiv (Cornell University)
76. SARS-CoV-2 RdRp Follows Asynchronous Translocation Pathway for Viral Transcription and Replication
    Xiaowei Wang, Yuan Yao, Xin Gao, Lu Zhang · 2022 · ChemRxiv
77. Unbiased learning of protein conformational representation via unsupervised random forest
    Mohammad Sahil, Navjeet Ahalawat, Jagannath Mondal · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
78. Trendbericht Theoretische Chemie 2017: Moleküle in Bewegung
    Bettina G. Keller · 2018 · Nachrichten aus der Chemie
79. Modeling a recurrent, hidden dynamical system using energy minimization and kernel density estimates
    Trevor K. Karn, Steven Petrone, Christopher H. Griffin · 2019 · Physical review. E
80. Fluorescence quenching in 2-aminopurine-labeled model DNA systems
    Jacob M. Remington · 2019 · Montana State University ScholarWorks (Montana State University)
81. Interpolation for Parametric ROMs
    Steven L. Brunton, J. Nathan Kutz · 2019 · Cambridge University Press eBooks
82. Bibliography
    2019 · Cambridge University Press eBooks
83. Preface
    Steven L. Brunton, J. Nathan Kutz · 2019 · Cambridge University Press eBooks
84. Glossary
    Steven L. Brunton, J. Nathan Kutz · 2019 · Cambridge University Press eBooks
85. Models of Nanosystems and Methods of Their Investigation, Connected with Orthogonal Splines
    Victor L. Leontiev · 2022 · Lecture notes in mechanical engineering
86. Faculty Opinions recommendation of Predicting the Conformational Variability of Abl Tyrosine Kinase using Molecular Dynamics Simulations and Markov State Models.
    Piotr Setny · 2019 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
87. Index
    Steven L. Brunton, J. Nathan Kutz · 2019 · Cambridge University Press eBooks
88. Estimation of binding free energies with Monte Carlo atomistic simulations and enhanced sampling
    Joan F. Gilabert · 2020
89. Unraveling the Structural Facets of Prp127-132 Polymorphic Variants Using Combined Molecular Dynamics/Markov Modeling
    Wycliffe Omwansu, Robinson Juma Musembi, Solomon Derese · 2024 · SSRN Electronic Journal
90. Learning Allosteric Interactions in Gα Proteins from Molecular Dynamics Simulations
    Yi‐Ping Yu, Maohua Yang, Wenning Wang · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
91. Computational Analysis of the Fully Activated Orexin Receptor 2 across Various Thermodynamic Ensembles with Surface Tension Monitoring and Markov State Modeling.
    R. Doležal · 2025 · Journal of Physical Chemistry B
92. An iterative and automatic collective variable optimization scheme via unsupervised feature selection with CUR matrix decomposition
    Yunsong Fu, Ye Mei, Chungen Liu · 2025 · The Journal of Chemical Physics
93. Upper-Order TICA and Fractional Non-Markovian Process to Model Anomalous Dynamic Regimes
    Arnaldo Rapallo · 2025 · Journal of Chemical Theory and Computation
94. Robust state recognition and multi-scale dynamic mode decomposition of PIV flow fields
    Zihao Wang, Guiyong Zhang, Tiezhi Sun, Huakun Huang, Yichen Jiang, Haitao Li, Yuguo Pei · 2025 · SSRN Electronic Journal
95. Microsecond Dynamics of the Pyrophosphate Ion Release in SARS-CoV-2 RNA Polymerase
    Tiantian Xu, Lin Yang, Xinzhou Xu, Bu-Yu Zhang, Xin Gao, Toyotaka Ishibashi, Peng Gong, Peter Pak‐Hang Cheung, Lu Zhang · 2026 · JACS Au
96. Accurate and robust analysis of molecular kinetics with random features
    Hauke Sprink, Yanchen Zhu, Antonia S. J. S. Mey, Feliks Nüske · 2026 · The Journal of Chemical Physics
97. Analyse de systèmes complexes par dynamique moléculaire polarisable, vers une conception rationnelle de médicaments : des quadruplexes de Guanine au SARS-CoV-2
    Dina El Ahdab · 2021
98. Photoswitchable fluorescence hysteresis based on multichromophoric architectures
    Yang Zhou · 2022
99. Machine Learning Methods for Molecular Dynamic Simulations
    Zineb Belkacemi · 2022 · theses.fr (ABES)
100. Adaptive tensor train metadynamics for high-dimensional free energy exploration
     Nils E. Strand, Siyao Yang, Y. Khoo, Aaron R. Dinner · 2026 · Journal of Chemical Theory and Computation