We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small computer cluster reactions as complex as protein folding, using sta
te of the art all-atom force fields in explicit solvent. We test this method against molecular dynamics (MD) simulations of the folding of an alpha- and a beta-protein performed with the same all-atom force field on the Anton supercomputer. We find that our approach yields results consistent with those of MD simulations, at a computational cost orders of magnitude smaller.
We introduce an atomistic approach to the dissipative quantum dynamics of charged or neutral excitations propagating through macromolecular systems. Using the Feynman-Vernon path integral formalism, we analytically trace out from the density matrix t
he atomic coordinates and the heat bath degrees of freedom. This way we obtain an effective field theory which describes the real-time evolution of the quantum excitation and is fully consistent with the fluctuation-dissipation relation. The main advantage of the field-theoretic approach is that it allows to avoid using the Keldysh contour formulation. This simplification makes it straightforward to derive Feynman diagrams to analytically compute the effects of the interaction of the propagating quantum excitation with the heat bath and with the molecular atomic vibrations. For illustration purposes, we apply this formalism to investigate the loss of quantum coherence of holes propagating through a poly(3-alkylthiophene) polymer
The dominant reaction pathway (DRP) is a rigorous framework to microscopically compute the most probable trajectories, in non-equilibrium transitions. In the low-temperature regime, such dominant pathways encode the information about the reaction mec
hanism and can be used to estimate non-equilibrium averages of arbitrary observables. On the other hand, at sufficiently high temperatures, the stochastic fluctuations around the dominant paths become important and have to be taken into account. In this work, we develop a technique to systematically include the effects of such stochastic fluctuations, to order k_B T. This method is used to compute the probability for a transition to take place through a specific reaction channel and to evaluate the reaction rate.
