Fokker-Planck score learning: efficient free-energy estimation under periodic boundary conditions
Accurate free-energy estimation is essential in molecular simulation, yet the periodic boundary conditions (PBC) commonly used in computer simulations have rarely been explicitly exploited. Equilibrium methods such as umbrella sampling, metadynamics, and adaptive biasing force require extensive samp...
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| Main Authors: | , |
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| Format: | Article (Journal) |
| Language: | English |
| Published: |
13 November 2025
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| In: |
The journal of physical chemistry. B, Biophysics, biomaterials, liquids, and soft matter
Year: 2025, Volume: 129, Issue: 45, Pages: 11780-11790 |
| ISSN: | 1520-5207 |
| DOI: | 10.1021/acs.jpcb.5c04579 |
| Online Access: | Verlag, lizenzpflichtig, Volltext: https://doi.org/10.1021/acs.jpcb.5c04579
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| Author Notes: | Daniel Nagel and Tristan Bereau |
| Summary: | Accurate free-energy estimation is essential in molecular simulation, yet the periodic boundary conditions (PBC) commonly used in computer simulations have rarely been explicitly exploited. Equilibrium methods such as umbrella sampling, metadynamics, and adaptive biasing force require extensive sampling, while nonequilibrium pulling with Jarzynski’s equality suffers from poor convergence due to exponential averaging. Here, we introduce a physics-informed, score-based diffusion framework: by mapping PBC simulations onto a Brownian particle in a periodic potential, we derive the Fokker-Planck steady-state score that directly encodes free-energy gradients. A neural network is trained on nonequilibrium trajectories to learn this score, providing a principled scheme to efficiently reconstruct the potential of mean force. On benchmark periodic potentials and small-molecule membrane permeation, our method is up to 1 order of magnitude more efficient than umbrella sampling. |
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| Item Description: | Online veröffentlicht: 30. Oktober 2025 Gesehen am 01.12.2025 |
| Physical Description: | Online Resource |
| ISSN: | 1520-5207 |
| DOI: | 10.1021/acs.jpcb.5c04579 |