Free Energy Computations: A Mathematical Perspective

Cited by (253)

Items 101–200 of 253

1. Role of sessile disconnection dipoles in shear-coupled grain boundary migration
   Melvyn Larranaga, F. Mompiou, Marc Legros, Nicolas Combe · 2020 · Physical Review Materials
2. Parametrizing coarse grained models for molecular systems at equilibrium
   Evangelia Kalligiannaki, Antonis Chazirakis, Anastasios Tsourtis, Markos A. Katsoulakis, Petr Plecháč, Vagelis Harmandaris · 2016 · The European Physical Journal Special Topics
3. Ab Initio Phase Diagram of Gold in Extreme Conditions
   P. Richard, Aloïs Castellano, Romuald Béjaud, Lucas Baguet, J. Bouchet, Grégory Geneste, François Bottin A · 2023 · Physical Review Letters
4. Moment Conditions and Bayesian Non-Parametrics
   Luke Bornn, Neil Shephard, Reza Solgi · 2018 · Journal of the Royal Statistical Society Series B (Statistical Methodology)
5. Simulating Coulomb and Log-Gases with Hybrid Monte Carlo Algorithms
   Djalil Chafaï, Grégoire Ferré · 2018 · Journal of Statistical Physics
6. Order Conditions for Sampling the Invariant Measure of Ergodic Stochastic Differential Equations on Manifolds
   Adrien Laurent, Gilles Vilmart · 2021 · Foundations of Computational Mathematics
7. Computing Surface Reaction Rates by Adaptive Multilevel Splitting Combined with Machine Learning and Ab Initio Molecular Dynamics
   Thomas Pigeon, Gabriel Stoltz, Manuel Corral Valero, Ani Anciaux‐Sedrakian, Maxime Moreaud, Tony Lelièvre A, Pascal Raybaud · 2023 · Journal of Chemical Theory and Computation
8. Data-Efficient Generation of Protein Conformational Ensembles with Backbone-to-Side-Chain Transformers
   Shriram Chennakesavalu, Grant M. Rotskoff · 2024 · The Journal of Physical Chemistry B
9. Error Analysis of Kernel EDMD for Prediction and Control in the Koopman Framework
   Friedrich Philipp, Manuel Schaller, Karl Worthmann, Sebastian Peitz, Feliks Nüske · 2025 · Journal of Nonlinear Science
10. Harnessing fluctuations to discover dissipative evolution equations
    Xiaoguai Li, Nicolas Dirr, Peter Embacher, Johannes Zimmer, Celia Reina · 2019 · Journal of the Mechanics and Physics of Solids
11. Ergodic SDEs on submanifolds and related numerical sampling schemes
    Wei Zhang · 2019 · ESAIM Mathematical Modelling and Numerical Analysis
12. Quantifying Energetic and Entropic Pathways in Molecular Systems
    Eric R. Beyerle, Shams Mehdi, Pratyush Tiwary · 2022 · The Journal of Physical Chemistry B
13. A b initio canonical sampling based on variational inference
    Aloïs Castellano, François Bottin A, Johann Bouchet, Antoine Levitt, Gabriel Stoltz · 2022 · Physical review. B./Physical review. B
14. Self-healing umbrella sampling: convergence and efficiency
    Gersende Fort, Benjamin Jourdain A, Tony Lelièvre A, Gabriel Stoltz · 2015 · Statistics and Computing
15. GEOMETRIC LANGEVIN EQUATIONS ON SUBMANIFOLDS AND APPLICATIONS TO THE STOCHASTIC MELT-SPINNING PROCESS OF NONWOVENS AND BIOLOGY
    MARTIN GROTHAUS, PATRIK STILGENBAUER · 2012 · Stochastics and Dynamics
16. Hypoelliptic multiscale Langevin diffusions: large deviations, invariant measures and small mass asymptotics
    Wenqing Hu, Konstantinos Spiliopoulos · 2017 · Electronic Journal of Probability
17. Essential Considerations for Free Energy Calculations of RNA–Small Molecule Complexes: Lessons from the Theophylline-Binding RNA Aptamer
    Ali Rasouli, Frank C. Pickard, Sreyoshi Sur, Alan M. Grossfield, Mehtap Işık · 2024 · Journal of Chemical Information and Modeling
18. On particle Gibbs samplers
    Pierre Del Moral, Robert Kohn, Frédéric Patras · 2016 · Annales de l Institut Henri Poincaré Probabilités et Statistiques
19. Error estimates on ergodic properties of discretized Feynman–Kac semigroups
    Grégoire Ferré, Gabriel Stoltz · 2019 · Numerische Mathematik
20. A duality formula and a particle Gibbs sampler for continuous time Feynman-Kac measures on path spaces
    Marc Arnaudon, Pierre Del Moral · 2020 · Electronic Journal of Probability
21. Multiple projection Markov chain Monte Carlo algorithms on submanifolds
    Tony Lelièvre A, Gabriel Stoltz, Zhang Wei · 2022 · IMA Journal of Numerical Analysis
22. The Fokker–Planck Equation
    Grigorios A. Pavliotis · 2014 · Texts in applied mathematics
23. Anharmonic thermo-elasticity of tungsten from accelerated Bayesian adaptive biasing force calculations with data-driven force fields
    Anruo Zhong, Clovis Lapointe, Alexandra M. Goryaeva, Jacopo Baima, Manuel Athènes, Mihai‐Cosmin Marinica · 2023 · Physical Review Materials
24. Analyzing Multimodal Probability Measures with Autoencoders
    Tony Lelièvre A, Thomas Pigeon, Gabriel Stoltz, Zhang Wei · 2024 · The Journal of Physical Chemistry B
25. Some Remarks on Free Energy and Coarse-Graining
    Frédéric Legoll, Tony Lelièvre A · 2011 · Lecture notes in computational science and engineering
26. Feynman-Kac Particle Integration with Geometric Interacting Jumps
    Pierre Del Moral, Pierre E. Jacob, Anthony Lee, Lawrence M. Murray, Gareth William Peters · 2013 · Stochastic Analysis and Applications
27. Partitioning a macroscopic system into independent subsystems
    Luigi Delle Site, Giovanni Ciccotti, Carsten Hartmann · 2017 · Journal of Statistical Mechanics Theory and Experiment
28. Cumulant GAN
    Yannis Pantazis, Dipjyoti Paul, Michail Fasoulakis, Yannis Stylianou, Markos A. Katsoulakis · 2022 · IEEE Transactions on Neural Networks and Learning Systems
29. Longtime convergence of the temperature-accelerated molecular dynamics method
    Gabriel Stoltz, Eric Vanden-Eijnden · 2018 · Nonlinearity
30. Machine learning surrogate models for strain-dependent vibrational properties and migration rates of point defects
    Clovis Lapointe, Thomas D. Swinburne, Laurent Proville, Charlotte Becquart, Normand Mousseau, Mihai‐Cosmin Marinica · 2022 · Physical Review Materials
31. LANGEVIN MOLECULAR DYNAMICS DERIVED FROM EHRENFEST DYNAMICS
    Anders Szepessy · 2011 · Mathematical Models and Methods in Applied Sciences
32. Thermodynamics of DNA: sensitizer recognition. Characterizing binding motifs with all-atom simulations
    Hugo Gattuso, Elise E. Dumont, Christophe J. Chipot, Antonio Monari, François Dehez · 2016 · Physical Chemistry Chemical Physics
33. Accelerated convergence to equilibrium and reduced asymptotic variance for Langevin dynamics using Stratonovich perturbations
    Assyr Abdulle A, Grigorios A. Pavliotis, Gilles Vilmart · 2019 · Comptes Rendus Mathématique
34. A new boundary driven NEMD scheme for heat and particle diffusion in binary mixtures
    Clark Templeton, Ron Elber, Mauro Ferrario, Giovanni Ciccotti · 2021 · Molecular Physics
35. Jarzynski’s Equality, Fluctuation Theorems, and Variance Reduction: Mathematical Analysis and Numerical Algorithms
    Carsten Hartmann, Christof Schütte, Wei Zhang · 2019 · Journal of Statistical Physics
36. Optimal friction matrix for underdamped Langevin sampling
    Martin Chak, Nikolas Kantas, Tony Lelièvre A, Grigorios A. Pavliotis · 2023 · ESAIM Mathematical Modelling and Numerical Analysis
37. Accurate calculation of absolute free energy of binding for SHP2 allosteric inhibitors using free energy perturbation
    Li Liang, Haichun Liu, Guomeng Xing, Chenglong Deng, Yi Hua, Rui Gu, Tao Lu, Yadong Chen, Yanmin Zhang · 2022 · Physical Chemistry Chemical Physics
38. Quantum Rényi entropy by optimal thermodynamic integration paths
    Miha Srdinšek, Michele Casula, Rodolphe Vuilleumier · 2022 · Physical Review Research
39. Reversible and non-reversible Markov chain Monte Carlo algorithms for reservoir simulation problems
    Paul Dobson, И.В. Фурсов, Gabriel J. Lord, Michela Ottobre · 2020 · Computational Geosciences
40. Quasi-stationary distribution for the Langevin process in cylindrical domains, part II: overdamped limit
    Mouad Ramil · 2022 · Electronic Journal of Probability
41. Nonasymptotic Bounds for Suboptimal Importance Sampling
    Carsten Hartmann, Lorenz Richter · 2024 · SIAM/ASA Journal on Uncertainty Quantification
42. OGRe: Optimal Grid Refinement Protocol for Accurate Free Energy Surfaces and Its Application in Proton Hopping in Zeolites and 2D COF Stacking
    Borgmans, Sander, Rogge, Sven M. J., Vanduyfhuys, Louis, Van Speybroeck, Veronique · 2023 · Journal of Chemical Theory and Computation
43. Convergence is not correctness: context-dependent performance of enhanced-sampling methods across biological complexity
    Christopher Kang, Cheng Giuseppe Chen, Chenyu Tang, Sergio Contreras Arredondo, Mengchen Zhou, Haohao Fu, Lan Yang, James C. Gumbart, Ashkan Fakharzadeh, Mahmoud Moradi et al. · 2026 · Nature Communications
44. Mathematical Foundations of Accelerated Molecular Dynamics Methods
    Tony Lelièvre A · 2018 · Springer eBooks
45. Anharmonic free energy of lattice vibrations in fcc crystals from a mean-field bond
    Thomas D. Swinburne, Jan Janßen, Mira Todorova, Gideon Simpson, Petr Plecháč, Mitchell Luskin, Jörg Neugebauer · 2020 · Physical review. B./Physical review. B
46. Thermodynamically Optimized Machine-Learned Reaction Coordinates for Hydrophobic Ligand Dissociation
    Eric R. Beyerle, Pratyush Tiwary · 2024 · The Journal of Physical Chemistry B
47. Stochastic disks that roll
    Miranda C. Holmes-Cerfon · 2016 · Physical review. E
48. Thermal Fluctuations of Singular Bar-Joint Mechanisms
    Mannattil, Manu, Schwarz, J. M., Santangelo, Christian D. · 2022 · Physical Review Letters
49. Combining Fast Exploration with Accurate Reweighting in the OPES-eABF Hybrid Sampling Method
    Andreas Hulm, Robert P. Schiller, Christian Ochsenfeld · 2025 · Journal of Chemical Theory and Computation
50. Kinetically Consistent Coarse Graining Using Kernel-Based Extended Dynamic Mode Decomposition
    Vahid Nateghi, F. Nüske · 2024 · Journal of Chemical Theory and Computation
51. Coarse-Graining and Forecasting Atomic Material Simulations with Descriptors
    Thomas D. Swinburne · 2023 · Physical Review Letters
52. Buckets Instead of Umbrellas for Enhanced Sampling and Free Energy Calculations
    Ramsha Javed, Anji Babu Kapakayala, Nisanth N. Nair · 2024 · Journal of Chemical Theory and Computation
53. Reducing exit-times of diffusions with repulsive interactions
    Paul-Éric Chaudru de Raynal, Manh Hong Duong, Pierre Monmarché, Milica Tomašević, Julian Tugaut · 2023 · ESAIM Probability and Statistics
54. Computational Error Estimates for Born–Oppenheimer Molecular Dynamics with Nearly Crossing Potential Surfaces
    Christian Bayer, Håkon Hoel, Ashraful Kadir, Petr Plecháč, Mattias Sandberg, Anders Szepessy · 2015 · Applied Mathematics Research eXpress
55. Spin-diffusions and diffusive molecular dynamics
    Brittan Farmer, Mitchell Luskin, Petr Plecháč, Gideon Simpson · 2017 · Modelling and Simulation in Materials Science and Engineering
56. Normalizing constants of log-concave densities
    Nicolas Brosse, Alain Durmus, Éric Moulines · 2018 · Electronic Journal of Statistics
57. An ergodic theorem for the weighted ensemble method
    David Aristoff · 2022 · Journal of Applied Probability
58. Fixing the Flux: A Dual Approach to Computing Transport Coefficients
    Noé Blassel, Gabriel Stoltz · 2024 · Journal of Statistical Physics
59. Variational time reversal for free-energy estimation in nonequilibrium steady states
    Jorge L. Rosa-Raíces, David T. Limmer · 2024 · Physical review. E
60. Ambient space formulations and statistical mechanics of holonomically constrained Langevin systems
    Jessika Walter, Carsten Hartmann, John H. Maddocks · 2011 · The European Physical Journal Special Topics
61. Convergence and Efficiency of Adaptive Importance Sampling Techniques with Partial Biasing
    Gersende Fort, Benjamin Jourdain A, Tony Lelièvre A, Gabriel Stoltz · 2018 · Journal of Statistical Physics
62. Large deviations of empirical measures of diffusions in weighted topologies
    Grégoire Ferré, Gabriel Stoltz · 2020 · Electronic Journal of Probability
63. Using a Coarse-Grained Modeling Framework to Identify Oligomeric Motifs with Tunable Secondary Structure
    Christopher C. Walker, Garrett A. Meek, Theodore L. Fobe, Michael R. Shirts · 2021 · Journal of Chemical Theory and Computation
64. Extending the Regime of Linear Response with Synthetic Forcings
    Renato Spacek, Gabriel Stoltz · 2023 · Multiscale Modeling and Simulation
65. Estimation for stochastic damping Hamiltonian systems under partial observation. III. Diffusion term
    Patrick Cattiaux, José R. León, Clémentine Prieur · 2016 · The Annals of Applied Probability
66. Analysis of an Adaptive Biasing Force method based on self-interacting dynamics
    Michel Benaı̈m, Charles-Édouard Bréhier, Pierre Monmarché · 2020 · Electronic Journal of Probability
67. Pseudo generators for under-resolved molecular dynamics
    Andreas Bittracher, Carsten Hartmann, Oliver Junge, P. Koltai · 2015 · The European Physical Journal Special Topics
68. Measuring the Irreversibility of Numerical Schemes for Reversible Stochastic Differential Equations
    Markos Katsoulakis, Yannis Pantazis, Luc Rey-Bellet · 2013 · ESAIM Mathematical Modelling and Numerical Analysis
69. Mobility Estimation for Langevin Dynamics Using Control Variates
    Grigorios A. Pavliotis, Gabriel Stoltz, Urbain Vaes · 2023 · Multiscale Modeling and Simulation
70. On Sampling Minimum Energy Path
    Mouad Ramil, Caroline Boudier, Alexandra M. Goryaeva, Mihai‐Cosmin Marinica, Jean‐Bernard Maillet · 2022 · Journal of Chemical Theory and Computation
71. Microstructure and Oxidation Behavior of Cobalt Diffusional Coating Fabricated on AISI 429 Stainless Steel
    Hadi Ebrahimifar · 2019 · Oxidation of Metals
72. Convergence of adaptive biasing potential methods for diffusions
    Michel Benaı̈m, Charles-Édouard Bréhier · 2016 · Comptes Rendus Mathématique
73. Unveiling the Underlying Mechanism for Compression and Decompression Strokes of a Molecular Engine
    Peng Liu, Christophe J. Chipot, Wensheng Cai, Xueguang Shao · 2014 · The Journal of Physical Chemistry C
74. Measuring the Irreversibility of Numerical Schemes for Reversible Stochastic Differential Equations
    Markos A. Katsoulakis, Yannis Pantazis, Luc Rey-Bellet · 2012 · ACMAC's PrePrint Repository (Archimedes Center for Modeling, Analysis and Computation)
75. Consistency of a likelihood estimator for stochastic damping Hamiltonian systems. Totally observed data
    José Rafael León, Luis-Ángel Rodríguez, Roberto Ruggiero · 2018 · ESAIM Probability and Statistics
76. Coupled Quantum Harmonic Oscillators and Feynman–Kac path integrals for Linear Diffusive Particles
    Pierre Del Moral, Emma Horton · 2023 · Communications in Mathematical Physics
77. Enhanced conformational exploration of protein loops using a global parameterization of the backbone geometry
    2023
78. Accelerated Bayesian Imaging by Relaxed Proximal-Point Langevin Sampling
    Teresa Klatzer, Paul Dobson, Yoann Altmann, Marcelo Pereyra, Jesús María Sanz-Serna, Konstantinos C. Zygalakis · 2024 · SIAM Journal on Imaging Sciences
79. Temperature–energy-space sampling molecular dynamics: deterministic and single-replica method utilizing continuous temperature system
    Ikuo Fukuda, Kei Moritsugu · 2020 · Journal of Physics A Mathematical and Theoretical
80. Midpoint projection algorithm for stochastic differential equations on manifolds
    Ria Rushin Joseph, Jesse van Rhijn, P. D. Drummond · 2023 · Physical review. E
81. Error estimates of the backward Euler–Maruyama method for multi-valued stochastic differential equations
    Monika Eisenmann, Mihály Kovács, Raphael Kruse, Stig Larsson · 2021 · BIT Numerical Mathematics
82. Density estimation via binless multidimensional integration
    Matteo Carli, Álex Rodríguez, Alessandro Laio, Aldo Glielmo · 2025 · Machine Learning Science and Technology
83. The String Method with Swarms of Trajectories: A Tutorial for Free-Energy Calculations Along a Zero-Drift Pathway
    Chenyu Tang, Haochuan Chen, Emad Tajkhorshid, Benoı̂t Roux, Christophe J. Chipot · 2025 · The Journal of Physical Chemistry B
84. Anomalous self-diffusion in tungsten and molybdenum: Exonerating the di-vacancy contribution and the key role of interatomic interaction
    Clovis Lapointe, Anruo Zhong, Thomas D. Swinburne, Fabien Bruneval, Manuel Athènes, Mihai‐Cosmin Marinica · 2025 · Physical Review Materials
85. Asymptotic Analysis for the Generalized Langevin Equation with Singular Potentials
    Manh Hong Duong, Hung Dang Nguyen · 2024 · Journal of Nonlinear Science
86. Reflection coupling for unadjusted generalized Hamiltonian Monte Carlo in the nonconvex stochastic gradient case
    Martin Chak, Pierre Monmarché · 2025 · IMA Journal of Numerical Analysis
87. A duality formula for Feynman–Kac path particle models
    Pierre Del Moral, Robert Kohn, Frédéric Patras · 2015 · Comptes Rendus Mathématique
88. An overlook on statistical inference issues for stochastic damping hamiltonian systems under the fluctuation-dissipation condition
    Patrick Cattiaux, José Rafael León, A. A. Pineda Centeno, Clémentine Prieur · 2016 · Statistics
89. The Vlasov-Fokker-Planck equation in non-convex landscapes: convergence to equilibrium
    Manh Hong Duong, Julian Tugaut · 2018 · Electronic Communications in Probability
90. Hopf algebra structures for the backward error analysis of ergodic stochastic differential equations
    Eugen Bronasco, Adrien Laurent · 2026 · Numerische Mathematik
91. 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
92. Combined error estimates for local fluctuations of SPDEs
    Christian Kuehn, Patrick Kürschner · 2020 · Advances in Computational Mathematics
93. The method of stochastic characteristics for linear second-order hypoelliptic equations
    Juraj Földes, David P. Herzog · 2023 · Probability Surveys
94. Numerics with coordinate transforms for efficient Brownian dynamics simulations
    Dominic Phillips, Benedict Leimkuhler, Charles Matthews · 2024 · Molecular Physics
95. A Uniformly Accurate Scheme for the Numerical Integration of Penalized Langevin Dynamics
    Adrien Laurent · 2022 · SIAM Journal on Scientific Computing
96. Computation of Free Energy Differences
    Gabriel Stoltz · 2015 · Springer eBooks
97. Applications to Real Size Biological Systems
    Christophe J. Chipot · 2015 · Springer eBooks
98. Calculating Free-Energy Differences Using an Average Force: A Tutorial for Adaptive Biasing Force Simulations
    Radu A. Talmazan, Haohao Fu, Mengchen Zhou, Jérôme Hénin, James C. Gumbart, Christophe J. Chipot · 2025 · The Journal of Physical Chemistry B
99. Spectral analysis of a semiclassical random walk associated to a general confining potential
    Thomas Normand · 2025 · Annales de la faculté des sciences de Toulouse Mathématiques
100. Free-Energy Calculations of Biomolecular Processes: Methods Development, Benchmarking, and Applications
     Zoe Cournia, Christophe J. Chipot · 2026 · The Journal of Physical Chemistry B