Related papers: Solvent-quality dependent contact formation dynami…
It is argued that some phase--transitions observed in models of non-equilibrium wetting phenomena are related to contact processes with long-range interactions. This is investigated by introducing a model where the activation rate of a site…
We cast the problem of protein transfer free energy within the formalism of density functional theory (DFT), treating the protein as a source of external potential that acts upon the solvent. Solvent excluded volume, solvent-accessible…
Diffusion in a multidimensional energy surface with minima and barriers is a problem of importance in statistical mechanics and also has wide applications, such as protein folding. To understand it in such a system, we carry out theory and…
Fluid three-phase equilibria, with phases $\alpha, \beta, \gamma$, are studied close to a tricritical point, analytically and numerically, in a mean-field density-functional theory with two densities. Employing Griffiths' scaling for the…
Using three-dimensional Go lattice models with side chains for proteins, we investigate the dependence of folding times on protein length. In agreement with previous theoretical predictions, we find that the folding time grows as a power…
A fundamental paradigm in polymer physics is that macromolecular conformations in equilibrium can be described by universal scaling laws, being key for structure, dynamics, and function of soft (biological) matter and in the materials…
In extending the conventional dynamic models, we consider a simple model to account for the environment fluctuations of particle atoms in a protein system and derive the elastic incoherent structure factor (EISF) and the incoherent…
We present an approximate method for calculating the electrostatic free energy of concentrated protein solutions. Our method uses a cell model and accounts for both the coulomb energy and the entropic cost of Donnan salt partitioning. The…
In a one-dimensional elastic medium with finite correlation length and purely relaxational dynamics, we calculate the time dependence of the elastic force F(t) exchanged between two active inclusions that trigger an elastic deformation at…
We determine the phase diagrams of conservative diffusive contact processes by means of numerical simulations. These models are versions of the ordinary diffusive single-creation, pair-creation and triplet-creation contact processes in…
Diffusion-limited association reactions are ubiquitous in nature. They are particularly important for biological reactions, where the reaction rates are often determined by the diffusive transport of the molecules on two-dimensional…
We study the quench dynamics of the three-dimensional Kitaev (spin) model under a linear drive using both exact numerical calculations and analytical "independent crossing approximation". Unlike the two-dimensional Kitaev model, the…
We have studied the critical properties of the contact process on a square lattice with quenched site dilution by Monte Carlo simulations. This was achieved by generating in advance the percolating cluster, through the use of an appropriate…
Many processes in cell biology involve diffusion in a domain $\Omega$ that contains a target $\calU$ whose boundary $\partial \calU$ is a chemically reactive surface. Such a target could represent a single reactive molecule, an…
Viscoelasticity and rate-dependent adhesion of soft matter lead to difficulties in modeling the 'relatively simple' problem of a rigid sphere in contact with a viscoelastic half-space. For this reason, approximations in describing surface…
Thermal contact is the archetype of non-equilibrium processes driven by constant non-equilibrium constraints enforced by reservoirs exchanging conserved microscopic quantities. In models with a finite number of possible configurations, if…
It is experimentally well-established that non-equilibrium long-range correlations of concentration fluctuations appear in free diffusion of a solute in a solvent, but it remains unknown how such correlations are established dynamically. We…
The fluctuation-dissipation mechanism underlying non-equilibrium transport in low-energy heavy-ion reactions remains unclear. Although the time-dependent Hartree-Fock (TDHF) method provides a reasonable description of average reaction…
The physics of active systems of self-propelled particles, in the regime of a dense liquid state, is an open puzzle of great current interest, both for statistical physics and because such systems appear in many biological contexts. We…
Reaction-diffusion systems have been proposed as a model for pattern formation and morphogenesis. The Fickian diffusion typically employed in these constructions model the Brownian motion of particles. The biological and chemical elements…