Energy transport through molecular systems has recently received considerable interest,
in particular, due to its importance for molecular electronics and the functioning of
biological systems. In experiment, energy is usually induced into the molecule by
photoexcitation of a chromophore or by pumping a localized infrared vibration.
This triggers an cascade of dynamical processes including
- the femtosecond vibrational energy redistribution from localized high-frequency modes to delocalized low-frequency modes,
- transport of energy through the molecule, and
- the cooling the molecules due to heat transfer to the solvent.
To study these processes in biomolecules such as peptides, proteins, and RNA, we combine
quantum-classical techniques well-known from the description of gas phase reactions with
biomolecular force fields typically used in all-atom molecular dynamics simulations.
This leads to nonequilibrium molecular dynamics simulations, which mimic the laser
excitation of the molecules by nonequilibrium phase-space initial condition for the solute
and the solvent atoms. To understand the quantum effects involved, we furthermore perform
classical and quantum-mechanical perturbation theory. The results are discussed in the
light of recent time-resolved infrared experiments.
Master equation model to predict energy transport pathways in proteins
Recent time-resolved experiments and accompanying molecular dynamics simulations allow us to monitor the flow of vibrational energy in biomolecules. As a simple means to describe these experimental and simulated data, Buchenberg et al. [J. Phys. Chem. Lett. 7, 25 (2016)] suggested a master equation model that accounts for the energy transport from an initially excited residue to some target residue. The transfer rates of the model were obtained from two scaling rules, which account for the energy transport through the backbone and via tertiary contacts, respectively, and were parameterized using simulation data of a small α-helical protein at low temperatures. To extend the applicability of the model to general proteins at room temperature, here a new parameterization is presented, which is based on extensive nonequilibrium molecular dynamics simulations of a number of model systems. With typical transfer times of 0.5–1 ps between adjacent residues, backbone transport represents the fastest channel of energy flow. It is well described by a diffusive-type scaling rule, which requires only an overall backbone diffusion coefficient and interatom distances as input. Contact transport, e.g., via hydrogen bonds, is considerably slower (6–30 ps) at room temperature. A new scaling rule depending on the inverse square contact distance is suggested, which is shown to successfully describe the energy transport in the allosteric protein PDZ3. Since both scaling rules require only the structure of the considered system, the model provides a simple and general means to predict energy transport in proteins. To identify the pathways of energy transport, Monte Carlo Markov chain simulations are performed, which highlight the competition between backbone and contact transport channels.