The influence of multi-dimensionality and off-diagonal non-Markovian friction coupling on coarse-grained dynamics
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| Format: | Preprint |
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2025
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| _version_ | 1866908396261736448 |
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| author | Kiefer, Henrik Ayaz, Cihan Dalton, Benjamin A. Netz, Roland R. |
| author_facet | Kiefer, Henrik Ayaz, Cihan Dalton, Benjamin A. Netz, Roland R. |
| contents | Coarse-graining complex molecular systems to lower-dimensional reaction coordinates is a powerful approach for capturing their effective dynamics. The generalized Langevin equation (GLE) provides an exact framework for modeling coarse-grained dynamics, and is particularly useful when non-Markovian effects are significant. While one-dimensional GLE models are commonly used, many systems require multi-dimensional reaction coordinates to account for coupled dynamics. Here, we study the GLE formalism for multi-dimensional reaction coordinates, incorporating a memory matrix to quantify non-Markovian frictional coupling between coordinates, and a multi-dimensional potential. Using the GLE model, in conjunction with a multi-dimensional Markovian embedding scheme, we investigate different systems that are characterized by two-dimensional reaction coordinates, namely the dihedral dynamics of pentane and alanine dipeptide, obtained from molecular dynamics simulations in explicit water. We identify significant off-diagonal friction couplings arising from intramolecular and hydrodynamic interactions. Unlike previous studies, our results highlight the critical role of different terms in the multi-dimensional GLE in accurately capturing key dynamical properties, including mean first-passage times and mean-squared displacements, particularly in systems with coupled non-Markovian coordinates. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2506_05966 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | The influence of multi-dimensionality and off-diagonal non-Markovian friction coupling on coarse-grained dynamics Kiefer, Henrik Ayaz, Cihan Dalton, Benjamin A. Netz, Roland R. Chemical Physics Statistical Mechanics Coarse-graining complex molecular systems to lower-dimensional reaction coordinates is a powerful approach for capturing their effective dynamics. The generalized Langevin equation (GLE) provides an exact framework for modeling coarse-grained dynamics, and is particularly useful when non-Markovian effects are significant. While one-dimensional GLE models are commonly used, many systems require multi-dimensional reaction coordinates to account for coupled dynamics. Here, we study the GLE formalism for multi-dimensional reaction coordinates, incorporating a memory matrix to quantify non-Markovian frictional coupling between coordinates, and a multi-dimensional potential. Using the GLE model, in conjunction with a multi-dimensional Markovian embedding scheme, we investigate different systems that are characterized by two-dimensional reaction coordinates, namely the dihedral dynamics of pentane and alanine dipeptide, obtained from molecular dynamics simulations in explicit water. We identify significant off-diagonal friction couplings arising from intramolecular and hydrodynamic interactions. Unlike previous studies, our results highlight the critical role of different terms in the multi-dimensional GLE in accurately capturing key dynamical properties, including mean first-passage times and mean-squared displacements, particularly in systems with coupled non-Markovian coordinates. |
| title | The influence of multi-dimensionality and off-diagonal non-Markovian friction coupling on coarse-grained dynamics |
| topic | Chemical Physics Statistical Mechanics |
| url | https://arxiv.org/abs/2506.05966 |