Related papers: Mechanics, Energetics, Entropy and Kinetics of a B…

Proteins are the "work horses" in biological systems. In almost all functions specific proteins are involved. They control molecular transport processes, stabilize the cell structure, enzymatically catalyze chemical reactions; others act as…

Spinodal decomposition in a near-critical binary fluid is examined for experimental scenarios in which the liquid is quenched abruptly by changing the pressure and the subsequent phase separation occurs with no heat flow from the outside,…

Molecular machines transduce free energy between different forms throughout all living organisms. While truly machines in their own right, unlike their macroscopic counterparts molecular machines are characterized by stochastic…

The model analyzes the muscle fiber as a deformable system for which experimental data are determinated with the help of the laws of Newtonian mechanic. The model predicts the four transient phases for the shortening of a muscle fiber…

A simple lattice model, recently introduced as a generalization of the Wako--Sait\^o model of protein folding, is used to investigate the properties of widely studied molecules under external forces. The equilibrium properties of the model…

A general framework to describe a vast majority of biology-inspired systems is to model them as stochastic processes in which multiple couplings are in play at the same time. Molecular motors, chemical reaction networks, catalytic enzymes,…

Engineering molecular systems that exhibit complex behavior requires the design of kinetic barriers. For example, an effective catalytic pathway must have a large barrier when the catalyst is absent. While programming such energy barriers…

Motor proteins are active enzymatic molecules that drive a variety of biological processes, including transfer of genetic information, cellular transport, cell motility and muscles contraction. It is known that these biological molecular…

Binary random variables are the building blocks used to describe a large variety of systems, from magnetic spins to financial time series and neuron activity. In Statistical Physics the Kinetic Ising Model has been introduced to describe…

We distinguish a mechanical representation of the world in terms of point masses with positions and momenta and the chemical representation of the world in terms of populations of different individuals, each with intrinsic stochasticity,…

Binary mixtures are known to phase separate via both nucleation and spinodal decomposition, depending on the initial composition and extent of the quench. Here we develop an energy landscape view of phase separation and non-ideality in…

Protein machines often exhibit long range interplay between different sites in order to achieve their biological tasks. We investigate and characterize the non--linear energy localization and the basic mechanisms of energy transfer in…

Biological molecular machines are bifunctional enzymes that catalyze two processes: one donating free energy and the other accepting it. Recent studies show that most protein enzymes have rich stochastic dynamics of transitions between the…

Numerical computations have become a pillar of all modern quantitative sciences. Any computation involves modeling--even if often this step is not made explicit--and any model has to neglect details while still being physically accurate.…

The local balance equations for the density, momentum, and energy of a dilute gas of elastic or inelastic hard spheres, strongly confined between two parallel hard plates are obtained. The starting point is a Boltzmann-like kinetic…

In the present contribution, we derive from kinetic theory a unified fluid model for multicomponent plasmas by accounting for the electromagnetic field influence. We deal with a possible thermal nonequilibrium of the translational energy of…

Athermal (i.e. zero-temperature) under-constrained systems are typically floppy, but they can be rigidified by the application of external strain, which is theoretically well understood. Here and in the companion paper, we extend this…

Molecular machines consist of either a single protein or a macromolecular complex composed of protein and RNA molecules. Just like their macroscopic counterparts, each of these nano-machines has an engine that "transduces" input energy into…

We consider conformation dynamics of a chain-like three-body bead-spring model, in which three point masses are connected in series by two springs and the conformation is defined by the bending angle between the two springs. Previous…

We show that transport in the presence of entropic barriers exhibits peculiar characteristics which makes it distinctly different from that occurring through energy barriers. The constrained dynamics yields a scaling regime for the particle…