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Register a new userMost probable transition path in an overdamped system for a finite transition time
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Added by
Stanislav Soskin M.
Publication date
2006
fields
Physics
and research's language is
English
Authors
S.M. Soskin
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The most probable transition path in a one-dimensional overdamped system is rigorously proved to possess less than two turning points. The proof is valid for any potentials, transition times, initial and final transition points.
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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.
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.
We study the finite-temperature behavior of the Lipkin-Meshkov-Glick model, with a focus on correlation properties as measured by the mutual information. The latter, which quantifies the amount of both classical and quantum correlations, is computed exactly in the two limiting cases of vanishing magnetic field and vanishing temperature. For all other situations, numerical results provide evidence of a finite mutual information at all temperatures except at criticality. There, it diverges as the logarithm of the system size, with a prefactor that can take only two values, depending on whether the critical temperature vanishes or not. Our work provides a simple example in which the mutual information appears as a powerful tool to detect finite-temperature phase transitions, contrary to entanglement measures such as the concurrence.
We present the first detailed numerical study in three dimensions of a first-order phase transition that remains first-order in the presence of quenched disorder (specifically, the ferromagnetic/paramagnetic transition of the site-diluted four states Potts model). A tricritical point, which lies surprisingly near to the pure-system limit and is studied by means of Finite-Size Scaling, separates the first-order and second-order parts of the critical line. This investigation has been made possible by a new definition of the disorder average that avoids the diverging-variance probability distributions that plague the standard approach. Entropy, rather than free energy, is the basic object in this approach that exploits a recently introduced microcanonical Monte Carlo method.
We study a stochastic lattice gas of particles in one dimension with strictly finite-range interactions that respect the fracton-like conservation laws of total charge and dipole moment. As the charge density is varied, the connectivity of the systems charge configurations under the dynamics changes qualitatively. We find two distinct phases: Near half filling the system thermalizes subdiffusively, with almost all configurations belonging to a single dynamically connected sector. As the charge density is tuned away from half filling there is a phase transition to a frozen phase where locally active finite bubbles cannot exchange particles and the system fails to thermalize. The two phases exemplify what has recently been referred to as weak and strong Hilbert space fragmentation, respectively. We study the static and dynamic scaling properties of this weak-to-strong fragmentation phase transition in a kinetically constrained classical Markov circuit model, obtaining some conjectured exact critical exponents.
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