[论文解读] Protein-Water Energy Transfer via Anharmonic Low-Frequency Vibrations

B. Neff, Matthias Heyden|arXiv (Cornell University)|Jan 6, 2026

Spectroscopy and Quantum Chemical Studies被引用 0

一句话总结

论文使用 FRESEAN 模态分析结合全原子分子动力学来解析被溶剂化的蛋白质如何将多余热量散发到水中，揭示两条主要能量转移通道：通过少数低频模态的快速溶剂介导扩散以及来自大量远红外振动的较慢转移。

ABSTRACT

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.

研究动机与目标

• Understand how a solvated protein dissipates surplus thermal energy into surrounding water.
• Identify which collective protein vibrational modes drive efficient energy transfer across the protein–water interface.
• Quantify how energy partitioning among low-frequency versus high-frequency modes affects heat dissipation.
• Develop a framework to analyze non-equilibrium energy transfer and deviations from energy equipartition in proteins.

提出的方法

• Apply FREquency-SElective ANharmonic (FRESEAN) mode analysis to MD trajectories to isolate low-frequency collective DOFs.
• Compute velocity time auto- and cross-correlations to obtain the vibrational density of states (VDoS) and its frequency dependence.
• Diagonalize the frequency-dependent matrix C(ν) to obtain eigenvectors q_i^f describing collective DOFs at frequency f and project velocities onto these DOFs (Eq. 3).
• Define effective temperatures T_{q_i^f} from projected DOF velocities to quantify energy distribution among DOFs.
• Compare equilibrium and steady-state non-equilibrium ensembles to separate fast (diffusive) and slow (far-infrared) energy-transfer pathways.
• Use C(τ=0) to diagonalize DOFs by their average temperatures and analyze their VDoS contributions (Eq. 7).

实验结果

研究问题

• RQ1 Which protein collective DOFs at low frequencies couple efficiently to solvent to dissipate energy?
• RQ2 How do equilibrium and steady-state non-equilibrium energy distributions differ among DOFs across the vibrational spectrum?
• RQ3 Do fast difusive modes and the larger set of far-infrared modes jointly govern overall protein–water energy transfer?
• RQ4 Can deviations from energy equipartition in non-equilibrium simulations be quantified via FRESEAN-derived DOFs?
• RQ5 How do low-frequency, solvent-coupled vibrations compare to high-frequency, poorly coupled vibrations in heat dissipation efficiency?

主要发现

• Steady-state heat dissipation shows reduced VDoS in 0–1000 cm^-1 compared to equilibrium, indicating low-frequency vibrations transfer energy more efficiently to water.
• Low-frequency collective DOFs linked to rigid-body motions and 10–20 cm^-1 resonances exhibit temperatures near the solvent, signaling strong solvent coupling.
• High-frequency vibrations (e.g., O–H stretches around 3700 cm^-1) show increased kinetic energy but transfer energy more slowly due to frequency mismatch with water.
• Energy transfer efficiency arises from a small set of diffusive/low-frequency modes and a larger number of high-frequency modes that collectively contribute despite weaker per-mode coupling.
• The analysis highlights non-ergodicity and reveals a sensitive measure of deviations from energy equipartition via eigenvalue spectra of C(τ=0).
• VDoS integration confirms that the total vibrational energy remains conserved across equilibrium and steady-state, while its distribution among DOFs shifts.