相关论文: Single-ensemble nonequilibrium path-sampling estim…
We propose an efficient novel path sampling-based framework designed to accelerate the investigation of rare events in complex molecular systems. A key innovation is the shift from sampling restricted path ensemble distributions, as in…
Quantitative evaluations of the free energy of materials must take into account thermal and zero-point energy fluctuations. While these effects can easily be estimated within a harmonic approximation, corrections arising from the anharmonic…
We present a simple and robust technique to extract kinetic rate models and thermodynamic quantities from single molecule time traces. SMACKS (Single Molecule Analysis of Complex Kinetic Sequences) is a maximum likelihood approach that…
A fluctuation relation, which is an extended form of the Jarzynski equality, is introduced and discussed. We show how to apply this relation in order to evaluate the free energy landscape of simple systems. These systems are manipulated by…
Motivated by applications to 3D printing, this paper presents two algorithms for calculating an ensemble of solutions to heat conduction problems. The ensemble average is the most likely temperature distribution and its variance gives an…
We derive and solve a differential equation satisfied by the probability distribution of the work done on a single biomolecule in a mechanical unzipping experiment. The unzipping is described as a thermally activated escape process in an…
We review uses of the generalized-ensemble algorithms for free-energy calculations in protein folding. Two of the well-known methods are multicanonical algorithm and replica-exchange method; the latter is also referred to as parallel…
A free energy landscape estimation-method based on Bayesian inference is presented and used for comparing the efficiency of thermally enhanced sampling methods with respect to regular molecular dynamics, where the simulations are carried…
To quantify the progress in development of algorithms and forcefields used in molecular simulations, a method for the assessment of the sampling quality is needed. We propose a general method to assess the sampling quality through the…
Almost 25 years ago, Jarzynski published a paper in which it was asserted: the work done, W, in driving a system from state A to state B, characterized by the Helmholtz free energies FA and FB, satisfies an equality in which an average over…
We present a method for the direct evaluation of the difference between the free energies of two crystalline structures, of different symmetry. The method rests on a Monte Carlo procedure which allows one to sample along a path, through…
The theory of phenomenological Non-equilibrium Thermodynamics is extended by includimg stochastic processes in order to account for recently derived thermodynamical relations such as the Jarzynski equality. Four phenomenological axioms are…
We extend the theory of stochastic thermodynamics in three directions: (i) instead of a continuously monitored system we consider measurements only at an arbitrary set of discrete times, (ii) we allow for imperfect measurements and…
The remarkable accuracy and versatility of single-molecule techniques make possible new measurements that are not feasible in bulk assays. Among these, the precise estimation of folding free energies using fluctuation theorems in…
Recent developments in statistical mechanics have allowed the estimation of equilibrium free energies from the statistics of work measurements during processes that drive the system out of equilibrium. Here a different class of processes is…
Conventional simulations of complex systems in the canonical ensemble suffer from the quasi-ergodicity problem. A simulation in generalized ensemble overcomes this difficulty by performing a random walk in potential energy space and other…
We present a method for determining the free energy dependence on a selected number of collective variables using an adaptive bias. The formalism provides a unified description which has metadynamics and canonical sampling as limiting…
We propose a new method to compute the free energy or enthalpy of fluids or disordered solids by computer simulation . The main idea is to construct a reference system by freezing one representative configuration, and then carry out a…
We derive the differential equation describing the time evolution of the work probability distribution function of a stochastic system which is driven out of equilibrium by the manipulation of a parameter. We consider both systems described…
We introduce a new statistical quantity the energy to test whether two samples originate from the same distributions. The energy is a simple logarithmic function of the distances of the observations in the variate space. The distribution of…