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Stochastic differential equations have proved to be a valuable governing framework for many real-world systems which exhibit ``noise'' or randomness in their evolution. One quality of interest in such systems is the shape of their…
A recent experiment driving colloids electromagnetically, by B\'erut et al. [2014 Europhys. Lett. 107, 60004], is an ideal paradigm for illustrating a linear response theory for nonequilibrium overdamped systems including hydrodynamic…
All ensembles of statistical mechanics are equivalent in the sense that they give the equivalent thermodynamic functions in the thermodynamic limit. However, when investigating microscopic structures in the first-order phase transition…
In modern statistics, interests shift from pursuing the uniformly minimum variance unbiased estimator to reducing mean squared error (MSE) or residual squared error. Shrinkage based estimation and regression methods offer better prediction…
Complex biological processes are usually experimented along time among a collection of individuals. Longitudinal data are then available and the statistical challenge is to better understand the underlying biological mechanisms. The…
An expression is derived for the classical free energy difference between two configurations of a system, in terms of an ensemble of finite-time measurements of the work performed in parametrically switching from one configuration to the…
We investigate the performance of entropy estimation methods, based either on block entropies or compression approaches, in the case of bidimensional sequences. We introduce a validation dataset made of images produced by a large number of…
To describe the nonequilibrium states of a system we introduce a new thermodynamic parameter - the lifetime of a system. The statistical distributions which can be obtained out of the mesoscopic description characterizing the behaviour of a…
There has been recent progress on the problem of inferring the structure of interactions in complex networks when they are in stationary states satisfying detailed balance, but little has been done for non-equilibrium systems. Here we…
Systems with both quantitative and qualitative responses are widely encountered in many applications. Design of experiment methods are needed when experiments are conducted to study such systems. Classic experimental design methods are…
In this paper we develop a general formalism of a path approach for non-equilibrium statistical mechanics. Firstly, we consider the classical Gibbs approach for states and find that this formalism is ineffective for non-equilibrium…
The appealing theoretical measure of irreversibility in a stochastic process, as the ratio of the probabilities of a trajectory and its time reversal, cannot be accessed directly in experiment since the probability of a single trajectory is…
We consider an exclusion process on a periodic one-dimensional lattice where all particles perform simple symmetric exclusion at rate $1$ except for a single tracer particle, which performs partially simple asymmetric exclusion with rate…
We study the steady-state behavior of a driven non-equilibrium lattice gas of hard-core particles with next-nearest-neighbor interaction. We calculate the exact stationary distribution of the periodic system and for a particular line in the…
Most of the existing research in assembly pathway prediction/analysis of virus cap- sids makes the simplifying assumption that the configuration of the intermediate states can be extracted directly from the final configuration of the entire…
Neural network potentials (NNPs) combine the computational efficiency of classical interatomic potentials with the high accuracy and flexibility of the ab initio methods used to create the training set, but can also result in unphysical…
A parameter method is introduced in order to estimate the relationship among the various variables of a system in equilibrium, where the potential energy functions are incompletely known or the quantum mechanical calculations very…
We develop a theory for inferring equilibrium transition rates from trajectories driven by a time dependent force using results from stochastic thermodynamics. Applying the Kawasaki relation to approximate the nonequilibrium distribution…
We propose a matching method that recovers direct treatment effects from randomized experiments where units are connected in an observed network, and units that share edges can potentially influence each others' outcomes. Traditional…
We discuss two independent methods of solution of a master equation whose biased jump transition rates account for long jumps of L\'{e}vy-stable type and nonetheless admit a Boltzmannian (thermal) equilibrium to arise in the large time…