Related papers: Thermodynamic fluctuations in freely jointed chain…
In the standard framework of thermodynamics the work produced or consumed in a process is a random variable whose average value is bounded by the change in the free energy of the system. This work is calculated without regard for the size…
We make use of the previously developed formalism for a monomer ensemble and include angular dependence of the segments of the polymer chains thus described. In particular we show how to deal with stiffness when the polymer chain is…
Molecular dynamics simulation methods are used to study the folding of polymer chains into packed cubic states. The polymer model, based on a chain of linked sites moving in the continuum, includes both excluded volume and torsional…
We study self avoiding random walks in an environment where sites are excluded randomly, in two and three dimensions. For a single polymer chain, we study the statistics of the time averaged monomer density and show that these are well…
Molecular dynamics simulations are used to investigate the conformations of a single polymer chain, represented by the Kremer-Grest bead-spring model, in a solution with a Lennard-Jones liquid as the solvent when the interaction strength…
The process of fluctuations of trajectory observables of stochastic systems is related to processes with independent increments from the risk theory. The first-passage times of variables of the thermodynamics of trajectories, in particular,…
Protein folding is a universal process, very fast and accurate, which works consistently (as it should be) in a wide range of physiological conditions. The present work is based on three premises, namely: ($i$) folding reaction is a process…
Fluctuating hydrodynamics provides a model for fluids at mesoscopic scales where thermal fluctuations can have a significant impact on the behavior of the system. Here we investigate a model for fluctuating hydrodynamics of a single…
Constitutive equations are derived for the time-dependent behavior of particle-reinforced elastomers at isothermal loading with finite strains. A rubbery polymer is modelled as a network of macromolecules bridged by junctions which can slip…
We solve a two dimensional model for polymer chain folding in the presence of mechanical pulling force ($f$) exactly using equilibrium statistical mechanics. Using analytically derived expression for the partition function we determine the…
Dynamical frictional phenomena are studied theoretically in a two-chain model with incommensurate structure. A perturbation theory with respect to the interchain interaction reveals the contributions from phonons excited in each chain to…
The general fluctuation theory is reviewed with special attention to the role played by different ensembles, and is extended to incorporate stationary metastable states obtained in the long time limit. The fluctuation in a quantity depends…
Wetting and drying phenomena are studied for flexible and semiflexible polymer solutions via coarse-grained molecular dynamics simulations and density functional theory calculations. The study is based on the use of Young's equation for the…
We develop a methodology for the calculation of surface free energies based on the probability distribution of a wandering interface. Using a simple extension of the NpT sampling, we allow the interface area to randomly probe the available…
Many glass-forming fluids exhibit a remarkable thermodynamic scaling in which dynamic properties, such as the viscosity, the relaxation time, and the diffusion constant, can be described under different thermodynamic conditions in terms of…
We study jamming in model freely rotating polymers as a function of chain length $N$ and bond angle $\theta_0$. The volume fraction at jamming, $\phi_J(\theta_0)$, is minimal for rigid-rod-like chains ($\theta_0 = 0$), and increases…
One of the major challenges in stochastic thermodynamics is to compute the distributions of stochastic observables for small-scale systems for which fluctuations play a significant role. Hitherto much theoretical and experimental research…
The response of thermodynamic systems perturbed out of an equilibrium steady-state is described by the reciprocal and the fluctuation-dissipation relations. The so-called fluctuation theorems extended the study of fluctuations far beyond…
The statistics of the heat exchanged between two quantum XX spin chains prepared at different temperatures is studied within the assumption of weak coupling. This provides simple formulas for the average heat and its corresponding…
We investigate the probability distribution of the quantum fluctuations of thermodynamic functions of finite, ballistic, phase-coherent Fermi gases. Depending on the chaotic or integrable nature of the underlying classical dynamics, on the…