Protein-Water Energy Transfer via Anharmonic Low-Frequency Vibrations
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arXiv
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| Format: | Preprint |
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2026
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| _version_ | 1866917186430304256 |
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| author | Neff, Brandon Heyden, Matthias |
| author_facet | Neff, Brandon Heyden, Matthias |
| contents | Heat dissipation is ubiquitous in living systems, which constantly convert distinct forms of energy into each other. The transport of thermal energy in liquids and even within proteins is well understood but kinetic energy transfer across a heterogeneous molecular boundary provides additional challenges. Here, we use atomistic molecular dynamics simulations under steady-state conditions to analyze how a protein dissipates surplus thermal energy into the surrounding solvent. We specifically focus on collective degrees of freedom that govern the dynamics of the system from the diffusive regime to mid-infrared frequencies. Using a fully anharmonic analysis of molecular vibrations, we analyzed their vibrational spectra, temperatures, and heat transport efficiencies. We find that the most efficient energy transfer mechanisms are associated with solvent-mediated friction. However, this mechanism only applies to a small number of degrees of freedom of a protein. Instead, less efficient vibrational energy transfer in the far-infrared dominates heat transfer overall due to a large number of vibrations in this frequency range. A notable by-product of this work is a highly sensitive measure of deviations from energy equi-partition in equilibrium systems, which can be used to analyze non-ergodic properties. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2601_02699 |
| institution | arXiv |
| publishDate | 2026 |
| record_format | arxiv |
| spellingShingle | Protein-Water Energy Transfer via Anharmonic Low-Frequency Vibrations Neff, Brandon Heyden, Matthias Soft Condensed Matter Statistical Mechanics Heat dissipation is ubiquitous in living systems, which constantly convert distinct forms of energy into each other. The transport of thermal energy in liquids and even within proteins is well understood but kinetic energy transfer across a heterogeneous molecular boundary provides additional challenges. Here, we use atomistic molecular dynamics simulations under steady-state conditions to analyze how a protein dissipates surplus thermal energy into the surrounding solvent. We specifically focus on collective degrees of freedom that govern the dynamics of the system from the diffusive regime to mid-infrared frequencies. Using a fully anharmonic analysis of molecular vibrations, we analyzed their vibrational spectra, temperatures, and heat transport efficiencies. We find that the most efficient energy transfer mechanisms are associated with solvent-mediated friction. However, this mechanism only applies to a small number of degrees of freedom of a protein. Instead, less efficient vibrational energy transfer in the far-infrared dominates heat transfer overall due to a large number of vibrations in this frequency range. A notable by-product of this work is a highly sensitive measure of deviations from energy equi-partition in equilibrium systems, which can be used to analyze non-ergodic properties. |
| title | Protein-Water Energy Transfer via Anharmonic Low-Frequency Vibrations |
| topic | Soft Condensed Matter Statistical Mechanics |
| url | https://arxiv.org/abs/2601.02699 |