Realistic Transition Paths for Large Biomolecular Systems: A Langevin Bridge Approach
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arXiv
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| Autori principali: | , , |
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| Natura: | Preprint |
| Pubblicazione: |
2025
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| _version_ | 1866917116466167808 |
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| author | Koehl, Patrice Delarue, Marc Orland, Henri |
| author_facet | Koehl, Patrice Delarue, Marc Orland, Henri |
| contents | We introduce a computational framework for generating realistic transition paths between distinct conformations of large bio-molecular systems. The method is built on a stochastic integro-differential formulation derived from the Langevin bridge formalism, which constrains molecular trajectories to reach a prescribed final state within a finite time and yields an efficient low-temperature approximation of the exact bridge equation. To obtain physically meaningful protein transitions, we couple this formulation to a new coarse-grained potential combining a Go-like term that preserves native backbone geometry with a Rouse-type elastic energy term from polymer physics; we refer to the resulting approach as SIDE. We evaluate SIDE on several proteins undergoing large-scale conformational changes and compare its performance with established methods such as MinActionPath and EBDIMS. SIDE generates smooth, low-energy trajectories that maintain molecular geometry and frequently recover experimentally supported intermediate states. Although challenges remain for highly complex motions-largely due to the simplified coarse-grained potential-our results demonstrate that SIDE offers a powerful and computationally efficient strategy for modeling bio-molecular conformational transitions. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2512_01903 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Realistic Transition Paths for Large Biomolecular Systems: A Langevin Bridge Approach Koehl, Patrice Delarue, Marc Orland, Henri Biomolecules Biological Physics We introduce a computational framework for generating realistic transition paths between distinct conformations of large bio-molecular systems. The method is built on a stochastic integro-differential formulation derived from the Langevin bridge formalism, which constrains molecular trajectories to reach a prescribed final state within a finite time and yields an efficient low-temperature approximation of the exact bridge equation. To obtain physically meaningful protein transitions, we couple this formulation to a new coarse-grained potential combining a Go-like term that preserves native backbone geometry with a Rouse-type elastic energy term from polymer physics; we refer to the resulting approach as SIDE. We evaluate SIDE on several proteins undergoing large-scale conformational changes and compare its performance with established methods such as MinActionPath and EBDIMS. SIDE generates smooth, low-energy trajectories that maintain molecular geometry and frequently recover experimentally supported intermediate states. Although challenges remain for highly complex motions-largely due to the simplified coarse-grained potential-our results demonstrate that SIDE offers a powerful and computationally efficient strategy for modeling bio-molecular conformational transitions. |
| title | Realistic Transition Paths for Large Biomolecular Systems: A Langevin Bridge Approach |
| topic | Biomolecules Biological Physics |
| url | https://arxiv.org/abs/2512.01903 |