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Biomolecular conformational transitions are usually modeled as barrier crossings in a free energy landscape. The transition paths connect two local free energy minima and transition path times (TPT) are the actual durations of the crossing events. The simplest model employed to analyze TPT and to fit empirical data is that of a stochastic particle crossing a parabolic barrier. Motivated by some disagreement between the value of the barrier height obtained from the TPT distributions as compared to the value obtained from kinetic and thermodynamic analyses, we investigate here TPT for barriers which deviate from the symmetric parabolic shape. We introduce a continuous set of potentials, that starting from a parabolic shape, can be made increasingly asymmetric by tuning a single parameter. The TPT distributions obtained in the asymmetric case are very well-fitted by distributions generated by parabolic barriers. The fits, however, provide values for the barrier heights and diffusion coefficients which deviate from the original input values. We show how these findings can be understood from the analysis of the eigenvalues spectrum of the Fokker-Planck equation and highlight connections with experimental results.
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An analytical expression is derived for the transition path time distribution for a one-dimensional particle crossing of a parabolic barrier. Two cases are analyzed: (i) A non-Markovian process described by a generalized Langevin equation with a power-law memory kernel and (ii) a Markovian process with a noise violating the fluctuation-dissipation theorem, modeling the stochastic dynamics generated by active forces. In the case (i) we show that the anomalous dynamics strongly affecting the short time behavior of the distributions, but this happens only for very rare events not influencing the overall statistics. At long times the decay is always exponential, in disagreement with a recent study suggesting a stretched exponential decay. In the case (ii) the active forces do not substantially modify the short time behavior of the distribution, but lead to an overall decrease of the average transition path time. These findings offer some novel insights, useful for the analysis of experiments of transition path times in (bio)molecular systems.
The paper by Malek Mansour and Garcia [Phys. Rev. E 101, 052135 (2020)] is shown to be based on misconceptions in the stochastic formulation of chemical thermodynamics in reactive systems. Their erroneous claims, asserting that entropy production cannot be correctly evaluated using path probabilities whenever the reactive system involves more than one elementary reaction leading to the same composition changes, are refuted.
The quantum many-body problem in condensed phases is often simplified using a quasiparticle description, such as effective mass theory for electron motion in a periodic solid. These approaches are often the basis for understanding many fundamental condensed phase processes, including the molecular mechanisms underlying solar energy harvesting and photocatalysis. Despite the importance of these effective particles, there is still a need for computational methods that can explore their behavior on chemically relevant length and time scales. This is especially true when the interactions between the particles and their environment are important. We introduce an approach for studying quasiparticles in condensed phases by combining effective mass theory with the path integral treatment of quantum particles. This framework incorporates the generally anisotropic electronic band structure of materials into path integral simulation schemes to enable modeling of quasiparticles in quantum confinement, for example. We demonstrate the utility of effective mass path integral simulations by modeling an exciton in solid potassium chloride and electron trapping by a sulfur vacancy in monolayer molybdenum disulfide.
Biomolecular folding, at least in simple systems, can be described as a two state transition in a free energy landscape with two deep wells separated by a high barrier. Transition paths are the short part of the trajectories that cross the barrier. Average transition path times and, recently, their full probability distribution have been measured for several biomolecular systems, e.g. in the folding of nucleic acids or proteins. Motivated by these experiments, we have calculated the full transition path time distribution for a single stochastic particle crossing a parabolic barrier, focusing on the underdamped regime. Our analysis thus includes inertial terms, which were neglected in previous studies. These terms influence the short time scale dynamics of a stochastic system, and can be of experimental relevance in view of the short duration of transition paths. We derive the full transition path time distribution in the underdamped case and discuss the similarities and differences with the high friction (overdamped) limit.
A model computational quantum thermodynamic network is constructed with two variable temperature baths coupled by a linker system, with an asymmetry in the coupling of the linker to the two baths. It is found in computational simulations that the baths come to thermal equilibrium at different bath energies and temperatures. In a sense, heat is observed to flow from cold to hot. A description is given in which a recently defined quantum entropy $S^Q_{univ}$ for a pure state universe continues to increase after passing through the classical equilibrium point of equal temperatures, reaching a maximum at the asymmetric equilibrium. Thus, a second law account $Delta S^Q_{univ} ge 0$ holds for the asymmetric quantum process. In contrast, a von Neumann entropy description fails to uphold the entropy law, with a maximum near when the two temperatures are equal, then a decrease $Delta S^{vN} < 0$ on the way to the asymmetric equilibrium.
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