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Conceptualization, theory, method developments and implementations are always of great importance and an interesting task to explore a new dimension in science and technology, which is highly solicited for various functional-driven…
Tethered particle motion experiments are versatile single-molecule techniques enabling one to address in vitro the molecular properties of DNA and its interactions with various partners involved in genetic regulations. These techniques…
In this work we study, at the single molecular level, the thermodynamic and dynamic characteristics of an enzymatic reaction comprising a rate limiting step. We investigate how the stability of the enzyme-state stationary probability…
One-dimensional hopping model is useful to describe the motion of microscopic particle in thermal noise environment, such as motor proteins. Recent experiments about the new generation of light-driven rotary molecular motors found that, the…
The recently introduced nested sampling algorithm allows the direct and efficient calculation of the partition function of atomistic systems. We demonstrate its applicability to condensed phase systems with periodic boundary conditions by…
Thermodynamic quantities, like heat, entropy, or work, are random variables, in stochastic systems. Here, we investigate the statistics of the heat exchanged by a Brownian particle subjected to a logarithm-harmonic potential. We derive…
A new variational method for studying the equilibrium states of an interacting particles system has been proposed. The statistical description of the system is realized by means of a density matrix. This method is used for description of…
The new mathematical framework based on the free energy of pure classical fluids presented in [R. D. Rohrmann, Physica A 347, 221 (2005)] is extended to multi-component systems to determine thermodynamic and structural properties of…
Thermodynamic properties of matter are conveniently expressed as functional relations between variables known as equations of state. Here we experimentally determine the compressibility, density and pressure equations of state for an…
The folding of a peptide chain into a three dimensional structure is a thermodynamically driven process such that the chain naturally evolves to form domains of similar amino acids. The formation of this domain occurs by curling the one…
The basic problem in equilibrium statistical mechanics is to compute phase space average, in which Monte Carlo method plays a very important role. We begin with a review of nonlocal algorithms for Markov chain Monte Carlo simulation in…
In a tight binding framework, we analyze the characteristics of electronic states in strongly disordered materials (hopping sites are placed randomly with no local order) with tunneling matrix elements decaying exponentially in the atomic…
Motion of particles (bodies) in presence of random effects can be considered stochastic process. However, application of widely known stochastic processes used for description of particle motion is reduced to relatively small class of…
Stochastic mass transport models are usually described by specifying hopping rates of particles between sites of a given lattice, and the goal is to predict the existence and properties of the steady state. Here we ask the reverse question:…
We present a theoretical investigation of thermal fluctuation statistics in a molecular motor. Energy transfer in the motor is described using a multidimensional discrete master equation with nearest-neighbor hopping. In this theory, energy…
We present a systematic study of the nested sampling algorithm based on the example of the Potts model. This model, which exhibits a first order phase transition for $q>4$, exemplifies a generic numerical challenge in statistical physics:…
A simple Kronig-Penney model for one-dimensional (1D) mesoscopic systems with $\delta $ peak potentials is used to study numerically the influence of a spatial disorder on the conductance fluctuations and distribution at different regimes.…
The relationship between anomalous superdiffusive behavior and particle trapping probability is analyzed on a rocking ratchet potential with spatially correlated weak disorder. The trapping probability density is shown, analytically and…
The HP model of protein folding, where the chain exists in a free medium, is investigated using a parallel Monte Carlo scheme based upon Wang-Landau sampling. Expanding on the work of Wust and Landau by introducing a lesser known replica…
Dynamic space packing (DSP) is a random process with sequential addition and removal of identical objects into space. In the lattice version, objects are particles occupying single lattice sites, and adding a particle to a lattice site…