Markov state models based on milestoning

Cited by (227)

Items 101–200 of 227

1. Adaptive resolution simulation in equilibrium and beyond
   Han Wang, A. Agarwal · 2014 · The European Physical Journal Special Topics
2. An adaptive weighted ensemble procedure for efficient computation of free energies and first passage rates
   Divesh Bhatt, İvet Bahar · 2012 · The Journal of Chemical Physics
3. Coiled-coil response to mechanical force: global stability and local cracking.
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4. Toward a Benchmark for Markov State Models: The Folding of HP35
   Daniel Nagel, Sofia Sartore, Gerhard Stock · 2023 · The Journal of Physical Chemistry Letters
5. 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
6. Computing reaction rates in bio-molecular systems using discrete macro-states
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7. The molecular basis for the pH-dependent calcium affinity of the pattern recognition receptor langerin
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8. Hyperbolic periodic orbits in nongradient systems and small-noise-induced metastable transitions
   Molei Tao · 2017 · Physica D Nonlinear Phenomena
9. Long-time methods for molecular dynamics simulations: Markov State Models and Milestoning
   Brajesh Narayan, Ye Yuan, Arman Fathizadeh, Ron Elber, Nicolae‐Viorel Buchete · 2020 · Progress in molecular biology and translational science
10. Finding Dominant Structures of Nonreversible Markov Processes
    N. D. Conrad, Marcus Weber, C. Schütte · 2016 · Multiscale Modeling & simulation
11. Extracting the diffusion tensor from molecular dynamics simulation with Milestoning.
    M. Mugnai, R. Elber · 2015 · Journal of Chemical Physics
12. Connecting the conformational behavior of cyclic octadepsipeptides with their ionophoric property and membrane permeability
    Thomas Stadelmann, Govindan Subramanian, Sanjay Menon, Chad E. Townsend, R. Scott Lokey, Marc‐Olivier Ebert, Sereina Riniker · 2020 · Organic & Biomolecular Chemistry
13. Approximating selected non-dominant timescales by Markov state models
    Sarich, Marco, Schütte, Christof · 2012 · Communications in Mathematical Sciences
14. On the removal of initial state bias from simulation data.
    Marco Bacci, A. Caflisch, A. Vitalis · 2019 · Journal of Chemical Physics
15. Set-free Markov state model building.
    Marcus Weber, K. Fackeldey, C. Schütte · 2017 · Journal of Chemical Physics
16. A new class of enhanced kinetic sampling methods for building Markov state models
    Arti Bhoutekar, Susmita Ghosh, Swati Bhattacharya, Abhijit Chatterjee · 2017 · The Journal of Chemical Physics
17. SAPPHIRE-based clustering.
    F. Cocina, A. Vitalis, A. Caflisch · 2020 · Journal of Chemical Theory and Computation
18. Modularity revisited: A novel dynamics-based concept for decomposing complex networks
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19. Optimized Markov state models for metastable systems
    Enrico Guarnera, Eric Vanden-Eijnden · 2016 · The Journal of Chemical Physics
20. Efficient and exact sampling of transition path ensembles on Markovian networks
    Daniel Sharpe, David J. Wales · 2020 · The Journal of Chemical Physics
21. Modeling non-Markovian data using Markov state and Langevin models
    Benjamin Lickert, Gerhard Stock · 2020 · The Journal of Chemical Physics
22. Perspective: Time irreversibility in systems observed at coarse resolution
    Cai Dieball, Aljaž Godec · 2025 · The Journal of Chemical Physics
23. Simulations of thermodynamics and kinetics on rough energy landscapes with milestoning
    Juan M. Bello‐Rivas, Ron Elber · 2015 · Journal of Computational Chemistry
24. Agent-based modeling: Population limits and large timescales
    Jan-Hendrik Niemann, Stefanie Winkelmann, Sarah Wolf, Christof Schütte · 2021 · Chaos An Interdisciplinary Journal of Nonlinear Science
25. Excess and loss of entropy production for different levels of coarse graining.
    Pierpaolo Bilotto, L. Caprini, A. Vulpiani · 2021 · Physical Review E
26. 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
27. Projected metastable Markov processes and their estimation with observable operator models
    Hao Wu, Jan-Hendrik Prinz, Frank Noé · 2015 · The Journal of Chemical Physics
28. Reliable Approximation of Long Relaxation Timescales in Molecular Dynamics
    Wei Zhang, C. Schütte · 2017 · Entropy
29. Non-equilibrium Markov state modeling of periodically driven biomolecules.
    F. Knoch, T. Speck · 2019 · Journal of Chemical Physics
30. Diffusion maps embedding and transition matrix analysis of the large-scale flow structure in turbulent Rayleigh–Bénard convection
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31. Leveraging Bayesian analysis to improve accuracy of approximate models
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32. Metastability, spectrum, and eigencurrents of the Lennard-Jones-38 network
    Maria Cameron · 2014 · The Journal of Chemical Physics
33. Machine Learning of committor functions for predicting high impact climate events
    Dario Lucente, Freddy Bouchet, Corentin Herbert · 2020
34. Markov state modeling and dynamical coarse-graining via discrete relaxation path sampling
    Boris Fačkovec, Eric Vanden‐Eijnden, David J. Wales · 2015 · The Journal of Chemical Physics
35. Fast Atomistic Molecular Dynamics Simulations from Essential Dynamics Samplings
    Oliver Carrillo, Charles A. Laughton, Modesto Orozco · 2012 · Journal of Chemical Theory and Computation
36. Progress in deep Markov state modeling: Coarse graining and experimental data restraints
    Andreas Mardt, Frank Noé · 2021 · The Journal of Chemical Physics
37. Neural potentials of proteins extrapolate beyond training data
    Geemi P. Wellawatte, Glen M. Hocky, Andrew D. White · 2023 · The Journal of Chemical Physics
38. Identification of Mutational Hot Spots for Substrate Diffusion: Application to Myoglobin
    David De Sancho, Adam Kubas, Po-Hung Wang, Jochen Blumberger, Robert B. Best · 2015 · Journal of Chemical Theory and Computation
39. Milestoning with coarse memory
    Alexander T. Hawk · 2013 · The Journal of Chemical Physics
40. Markov Model Theory
    Marco Sarich, Jan-Hendrik Prinz, Christof Schütte · 2013 · Advances in experimental medicine and biology
41. Time-Dependent Markov State Models for Single Molecule Force Spectroscopy
    Susmita Ghosh, Abhijit Chatterjee, Swati Bhattacharya · 2017 · Journal of Chemical Theory and Computation
42. Kinetics analysis of ubiquitin local fluctuations with Markov state modeling of the LE4PD normal modes
    Eric R. Beyerle, Marina Guenza · 2019 · The Journal of Chemical Physics
43. 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
44. Data-driven efficient solvers for Langevin dynamics on manifold in high dimensions
    Yuan Gao, Jiang Liu, Nan Wu · 2020 · Applied and Computational Harmonic Analysis
45. Bayesian Mechanistic Inference, Statistical Mechanics, and a New Era for Monte Carlo
    Daniel M. Zuckerman, August George · 2024 · Journal of Chemical Theory and Computation
46. Efficiently sampling conformations and pathways using the concurrent adaptive sampling (CAS) algorithm
    Surl-Hee Ahn, Jay W. Grate, Eric Darve · 2017 · The Journal of Chemical Physics
47. Volume-scaled common nearest neighbor clustering algorithm with free-energy hierarchy
    Weiß, Gregor, Benjamin Ries, Shuzhe Wang, Sereina Riniker · 2021 · arXiv (Cornell University)
48. Aggregation dynamics of charged peptides in water: Effect of salt concentration
    Susmita Ghosh, T Devanand, Upayan Baul, Satyavani Vemparala · 2019 · The Journal of Chemical Physics
49. Dynamical matrix propagator scheme for large-scale proton dynamics simulations.
    C. Dreßler, G. Kabbe, Martin Brehm, D. Sebastiani · 2020 · Journal of Chemical Physics
50. A probabilistic algorithm for aggregating vastly undersampled large Markov chains
    Andreas Bittracher, C. Schütte · 2021 · Physica A: Statistical Mechanics and its Applications
51. Analysis of molecular dynamics simulations of 10-residue peptide, chignolin, using statistical mechanics: Relaxation mode analysis and three-dimensional reference interaction site model theory
    Yutaka Maruyama, Hiroshi Takano, Ayori Mitsutake · 2019 · Biophysics and Physicobiology
52. Modeling the effect of codon translation rates on co-translational protein folding mechanisms of arbitrary complexity
    Luca Caniparoli, Edward P. O’Brien · 2015 · The Journal of Chemical Physics
53. Multiple Length and Time-scale Approaches in Materials Modeling
    Likun Tan · 2017 · Advances in Materials
54. Mathematical Foundations of Accelerated Molecular Dynamics Methods
    Tony Lelièvre A · 2018 · Springer eBooks
55. Adaptive spectral clustering with application to tripeptide conformation analysis.
    Fiete Haack, K. Fackeldey, S. Röblitz, O. Scharkoi, Marcus Weber, B. Schmidt · 2013 · Journal of Chemical Physics
56. A sparse Markov chain approximation of LQ-type stochastic control problems
    Ralf Banisch, C. Hartmann · 2016 · Mathematical Control and Related Fields
57. A Step-by-Step Guide on How to Construct Quasi-Markov State Models to Study Functional Conformational Changes of Biological Macromolecules
    Andrew Kai-hei Yik, Yunrui Qiu, Ilona Christy Unarta, Siqin Cao, Xuhui Huang · 2023
58. gen.parRep: A first implementation of the Generalized Parallel Replica dynamics for the long time simulation of metastable biochemical systems
    Florent Hédin, Tony Lelièvre A · 2019 · Computer Physics Communications
59. Hierarchical Markov State Model Building to Describe Molecular Processes
    David K. Wolfe, Joseph R. Persichetti, Ajeet K. Sharma, Phillip S. Hudson, H. Lee Woodcock, Edward P. O’Brien · 2020 · Journal of Chemical Theory and Computation
60. Energy-based clustering: Fast and robust clustering of data with known likelihood functions
    Moritz Thürlemann, Sereina Riniker · 2023 · The Journal of Chemical Physics
61. Spectral analysis and clustering of large stochastic networks. Application to the Lennard-Jones-75 cluster
    Maria Cameron, Tingyue Gan · 2016 · Molecular Simulation
62. Learning Good State and Action Representations via Tensor Decomposition
    Chengzhuo Ni, Anru R. Zhang, Yaqi Duan, Mengdi Wang · 2021 · IEEE International Symposium on Information Theory (ISIT)
63. ScMiles2: A Script to Conduct and Analyze Milestoning Trajectories for Long Time Dynamics
    Alfredo E. Cárdenas, Allison Hunter, Hao Wang, Ron Elber · 2022 · Journal of Chemical Theory and Computation
64. 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
65. Markov State Models of Protein–Protein Encounters
    Simon Olsson · 2022 · Wiley eBooks
66. Non-Markov models of single-molecule dynamics from information-theoretical analysis of trajectories
    Kevin Song, Raymond Park, Atanu Das, Dmitrii E. Makarov, Etienne Vouga · 2023 · The Journal of Chemical Physics
67. Exploring Configuration Space and Path Space of Biomolecules Using Enhanced Sampling Techniques—Searching for Mechanism and Kinetics of Biomolecular Functions
    Fujisaki, Hiroshi, Moritsugu, Kei, Matsunaga, Yasuhiro · 2018 · International Journal of Molecular Sciences
68. Sterically driven current reversal in a molecular motor model
    Alex Albaugh, Geyao Gu, Todd R. Gingrich · 2023 · Proceedings of the National Academy of Sciences
69. A Mathematical Theory of Optimal Milestoning (with a Detour via Exact Milestoning)
    Ling Lin, Jian-Feng Lu, E. Vanden-Eijnden · 2016 · Communications on Pure and Applied Mathematics
70. Violation of Local Detailed Balance Despite a Clear Time-Scale Separation
    David Hartich, Aljaž Godec · 2021 · arXiv (Cornell University)
71. Precisely controlled colloids: a playground for path-wise non-equilibrium physics
    Cai Dieball, Yasamin Mohebi Satalsari, Angel B. Zuccolotto-Bernez, Stefan U. Egelhaaf, Manuel Alejandro Escobedo-Sanchez, Aljaž Godec · 2025 · Soft Matter
72. MasterMSM: A Package for Constructing Master Equation Models of Molecular Dynamics
    de Sancho, David, Aguirre, Anne · 2019 · Journal of Chemical Information and Modeling
73. Petrov–Galerkin methods for the construction of non-Markovian dynamics preserving nonlocal statistics
    Huan Lei, Xiantao Li · 2021 · The Journal of Chemical Physics
74. Meshless discretization of LQ-type stochastic control problems
    Ralf Banisch, C. Hartmann · 2013 · arXiv (Cornell University)
75. Markov State Models in Drug Design
    Bettina G. Keller, Stevan Aleksić, Luca Donati · 2018 · Methods and principles in medicinal chemistry
76. Multi-Level DBSCAN: A Hierarchical Density-Based Clustering Method for Analyzing Molecular Dynamics Simulation Trajectories
    Song Liu, Siqin Cao, Michael Suarez, Eshani C. Goonetillek, Xuhui Huang · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
77. Markov-Type State Models to Describe Non-Markovian Dynamics
    Sofia Sartore, Franziska Teichmann, Gerhard Stock · 2025 · Journal of Chemical Theory and Computation
78. SM-TCN: Multi-Resolution Sparse Convolution Network for Efficient High-Dimensional Time Series Forecast
    Ziyou Guo, Yan Sun, Tieru Wu · 2025 · Sensors
79. Waiting Time Distributions in Hybrid Models of Motor–Bead Assays: A Concept and Tool for Inference
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80. Diffusion over barriers
    Baron Peters · 2017 · Elsevier eBooks
81. The Master Equation Approach to Problems in Chemical and Biological Physics
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82. Pseudo generators of spatial transfer operators
    Andreas Bittracher, Péter Koltai, Oliver Junge · 2014 · arXiv (Cornell University)
83. CommonNNClustering─A Python Package for Generic Common-Nearest-Neighbor Clustering
    Jan-Oliver Kapp-Joswig, Bettina G. Keller · 2023 · Journal of Chemical Information and Modeling
84. Markov state models from hierarchical density-based assignment
    Ion Mitxelena, Xabier López, David De Sancho · 2021 · The Journal of Chemical Physics
85. Conformational Dynamics in Corynebacterium glutamicum Diaminopimelate Epimerase: Insights from Ligand Parameterization, Atomistic Simulation, and Markov State Modeling
    Sunita Muduli, Soumyajit Karmakar, Sabyashachi Mishra · 2024 · Journal of Chemical Information and Modeling
86. Implementation of Girsanov Reweighting in OpenMM and Deeptime
    Joana-Lysiane Schäfer, Bettina G. Keller · 2024 · The Journal of Physical Chemistry B
87. Toward Grid-Based Models for Molecular Association
    Hana Zupan, Bettina G. Keller · 2025 · Journal of Chemical Theory and Computation
88. An iterative aggregation and disaggregation method for the steady state solution of large scale continuous systems
    Katja Biswas · 2015 · Computer Physics Communications
89. A variation on the Donsker–Varadhan inequality for the principal eigenvalue
    Jianfeng Lu, Stefan Steinerberger · 2017 · Proceedings of the Royal Society A Mathematical Physical and Engineering Sciences
90. Discrete stochastic variables
    Baron Peters · 2017 · Elsevier eBooks
91. Computing the Minimal Rebinding Effect for NonReversible Processes
    Susanne Röhl, Marcus Weber, Konstantin Fackeldey · 2021 · Multiscale Modeling and Simulation
92. Non-Markov-Type Analysis and Diffusion Map Analysis for Molecular Dynamics Trajectory of Chignolin at a High Temperature
    H. Fujisaki, H. Suetani, L. Maragliano, A. Mitsutake · 2022 · Life
93. GRadient Adaptive Decomposition (GRAD) Method: Optimized Refinement Along Macrostate Borders in Markov State Models
    Pablo Romano, Marina Guenza · 2017 · Journal of Chemical Information and Modeling
94. Discrete state model of a self-aggregating colloidal system with directional interactions
    Salman Fariz Navas, Sabine H. L. Klapp · 2024 · The Journal of Chemical Physics
95. Building multiscale Markov state models by systematic mapping of temporal communities
    Nir Nitskansky, Kessem Clein, Barak Raveh · 2025 · Bioinform.
96. Deep Learning for Protein Modeling: From Single Structure to Bound Complex and Thermodynamic Ensemble, With a Focus on Architectural Design
    Daniele Angioletti, Matteo Carli, Marco Nobile, Vittorio Limongelli · 2026 · Wiley Interdisciplinary Reviews Computational Molecular Science
97. Finding metastabilities in reversible Markov chains based on incomplete sampling
    K. Fackeldey, A. Niknejad, Marcus Weber · 2017 · Special Matrices
98. A Markov state modeling analysis of sliding dynamics of a 2D model.
    M. Teruzzi, F. Pellegrini, A. Laio, E. Tosatti · 2017 · Journal of Chemical Physics
99. Simulation of the T-jump triggered unfolding and thermal unfolding vibrational spectroscopy related to polypeptides conformation fluctuation
    Xian Chen, Tianmin Wu, Zhe‐Ning Chen, Tan Jin, Wei Zhuang, Yisong Zheng · 2017 · Science China Chemistry
100. Determination of Kinetics and Thermodynamics of Biomolecular Processes with Trajectory Fragments
     Alfredo E. Cárdenas · 2018 · Springer series on bio- and neurosystems