102 research outputs found
Quantum Diffusive Dynamics of Macromolecular Transitions
We study the role of quantum fluctuations of atomic nuclei in the real-time
dynamics of non-equilibrium macro-molecular transitions. To this goal we
introduce an extension of the Dominant Reaction Pathways (DRP) formalism, in
which the quantum corrections to the classical overdamped Langevin dynamics are
rigorously taken into account to order h^2 . We first illustrate our approach
in simple cases, and compare with the results of the instanton theory. Then we
apply our method to study the C7_eq to C7_ax transition of alanine dipeptide.
We find that the inclusion of quantum fluctuations can significantly modify the
reaction mechanism for peptides. For example, the energy difference which is
overcome along the most probable pathway is reduced by as much as 50%.Comment: Final version, to appear in the Journal of Chemical Physic
Ab-initio Dynamics of Rare Thermally Activated Reactions
We introduce a framework to investigate ab-initio the dynamics of rare
thermally activated reactions. The electronic degrees of freedom are described
at the quantum-mechanical level in the Born-Oppenheimer approximation, while
the nuclear degrees of freedom are coupled to a thermal bath, through a
Langevin equation. This method is based on the path integral representation for
the stochastic dynamics and yields the time evolution of both nuclear and
electronic degrees of freedom, along the most probable reaction pathways,
without spending computational time to explore metastable states. This approach
is very efficient and allows to study thermally activated reactions which
cannot be simulated using ab-initio molecular dynamics techniques. As a first
illustrative application, we characterize the dominant pathway in the
cyclobutene to butadiene reaction.Comment: 4 pages, 4 figure
Fluctuations in the Ensemble of Reaction Pathways
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 mechanism 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
Investigating Biological Matter with Theoretical Nuclear Physics Methods
The internal dynamics of strongly interacting systems and that of
biomolecules such as proteins display several important analogies, despite the
huge difference in their characteristic energy and length scales. For example,
in all such systems, collective excitations, cooperative transitions and phase
transitions emerge as the result of the interplay of strong correlations with
quantum or thermal fluctuations. In view of such an observation, some
theoretical methods initially developed in the context of theoretical nuclear
physics have been adapted to investigate the dynamics of biomolecules. In this
talk, we review some of our recent studies performed along this direction. In
particular, we discuss how the path integral formulation of the molecular
dynamics allows to overcome some of the long-standing problems and limitations
which emerge when simulating the protein folding dynamics at the atomistic
level of detail.Comment: Prepared for the proceedings of the "XII Meeting on the Problems of
Theoretical Nuclear Physics" (Cortona11
Dominant Folding Pathways of a WW Domain
We investigate the folding mechanism of the WW domain Fip35 using a realistic
atomistic force field by applying the Dominant Reaction Pathways (DRP)
approach. We find evidence for the existence of two folding pathways, which
differ by the order of formation of the two hairpins. This result is consistent
with the analysis of the experimental data on the folding kinetics of WW
domains and with the results obtained from large-scale molecular dynamics (MD)
simulations of this system. Free-energy calculations performed in two
coarse-grained models support the robustness of our results and suggest that
the qualitative structure of the dominant paths are mostly shaped by the native
interactions. Computing a folding trajectory in atomistic detail only required
about one hour on 48 CPU's. The gain in computational efficiency opens the door
to a systematic investigation of the folding pathways of a large number of
globular proteins
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