Biomolecular Dynamics @ Uni Freiburg

Biomolecular energy flow

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 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.

Scaling Rules for Energy Transport

We examine vibrational energy flow in dehydrated and hydrated villin headpiece subdomain HP36 by master equation simulations. Transition rates used in the simulations are obtained from communica- tion maps calculated for HP36. In addition to energy flow along the main chain, we identify pathways for energy transport in HP36 via hydrogen bonding between residues quite far in sequence space. The results of the master equation simulations compare well with all-atom non-equilibrium simulations to about 1 ps following initial excitation of the protein, and quite well at long times, though for some residues we observe deviations between the master equation and all-atom simulations at intermediate times from about 1–10 ps. Those deviations are less noticeable for hydrated than dehydrated HP36 due to energy flow into the water.
Scaling Rules for Vibrational Energy Transport in Globular Proteins S. Buchenberg, D. M. Leitner, and G. Stock J. Phys. Chem. Lett. 7, 25 (2016)

Energy transport through a peptide helix

Nonequilibrium molecular dynamics simulation of the energy transport through a peptide helix, P. H. Nguyen, S. M. Park, and G. Stock, J. Chem. Phys.132, 025102 (2010)
Energy Transport in Peptide Helices, V. Botan, E. Backus, R. Pfister, A. Moretto, M. Crisma, C. Toniolo, P. H. Nguyen, G. Stock, and P. Hamm, Proc. Nat. Acad. Sci. (USA) 104, 12749-12754 (2007)

Vibrational cooling

Molecular dynamics simulation of cooling: Heat transfer from a photoexcited peptide to the solvent, S. M. Park, P. H. Nguyen, and G. Stock, J. Chem. Phys. 131, 184503 (2009)

Vibrational energy distribution

Classical simulation of quantum energy flow in biomolecules, G. Stock, Phys. Rev. Lett. 102, 118301 (2009)
Dynamic treatment of vibrational energy relaxation in heterogeneous and fluctuating environment, H. Fujisaki, and G. Stock, J. Chem. Phys. 129, 134110 (2008)

Energy flow and function

Energy flow and long-range correlation in guanine-binding riboswitch: A non equilibrium molecular dynamics study, P. H. Nguyen, P. Derreumaux, and G. Stock, J. Phys. Chem. B 113, 9340 (2009)