Abstract This article considers the application of Langevin dynamics to sampling and investigates how choose damping parameter in for purpose maximizing thoroughness sampling. Also, it computation measures thoroughness. Graphic abstract

Fluctuation theorems based on time-reversal have provided remarkable insight into the non-equilibrium statistics of thermodynamic quantities like heat, work, and entropy production. These types laws impose constraints distributions certain trajectory functionals that reflect underlying dynamical symmetries. In this we introduce a detailed fluctuation theorem for Langevin dynamics follows from G...

We present a derivation of a coarse-grained description, in the form of a generalized Langevin equation, from the Langevin dynamics model that describes the dynamics of bio-molecules. The focus is placed on the form of the memory kernel function, the colored noise, and the second fluctuation-dissipation theorem that connects them. Also presented is a hierarchy of approximations for the memory a...

We directly extend Kurchans’ work on the fluctuation theorem to general finite state space Markov jump processes and general Langevin dynamics. All systems are treated in a unified manner and we show that this directly reproduces (and corrects) the results of Lebowitz and Spohn in the Langevin case. For the jump process the quantity, for which the fluctuation theorem holds, is different from th...

In this paper, we propose a novel technique to implement stochastic gradient methods, which are beneficial for learning from large datasets, through accelerated stochastic dynamics. A stochastic gradient method is based on mini-batch learning for reducing the computational cost when the amount of data is large. The stochasticity of the gradient can be mitigated by the injection of Gaussian nois...

BACKGROUND Brownian Dynamics (BD) is a coarse-grained implicit-solvent simulation method that is routinely used to investigate binary protein association dynamics, but due to its efficiency in handling large simulation volumes and particle numbers it is well suited to also describe many-protein scenarios as they often occur in biological cells. RESULTS Here we introduce our "brownmove" simula...

We analyse the Langevin dynamics of the random walk, the scalar field, the X-Y model and the spinoidal decomposition. We study the deviations from the equilibrium dynamics theorems (FDT and homogeneity), the asymptotic behaviour of the systems and the