Related papers: Dynamics and energetics of a molecular zipper unde…
Dynamic properties of molecular motors whose motion is powered by interactions with specific lattice bonds are studied theoretically with the help of discrete-state stochastic "burnt-bridge" models. Molecular motors are depicted as random…
The static and dynamic structure of liquid Al is studied using the orbital free ab-initio molecular dynamics method. Two thermodynamic states along the coexistence line are considered, namely T = 943 K and 1323 K for which X-ray and neutron…
The structural and dynamic properties of silica melts under high pressure are studied using molecular dynamics (MD) computer simulation. The interactions between the ions are modeled by a pairwise-additive potential, the so-called CHIK…
We demonstrate that a gas of classical particles trapped in an external asymmetric potential undergoes a quasiperiodic motion, if the temperature of its initial velocity distribution $T_{ne}$ differs from the equilibrium temperature,…
We present a consistent theory of energy balance and conversion in a single-molecule junction with strong interactions between electrons on the molecular linker (dot) and phonons in the nuclear environment where the Marcus-type electron…
An isolated mixture of smooth, inelastic hard spheres supports a homogeneous cooling state with different kinetic temperatures for each species. This phenomenon is explored here by molecular dynamics simulation of a two component fluid,…
We study dynamics of a classical particle in a one-dimensional potential, which is composed of two periodic components, that are time-independent, have equal amplitudes and periodicities. One of them is externally driven by a random force…
The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon…
Nonequilibrium steady states in an open system connecting two reservoirs of platelike colloidal particles are investigated by means of a recently proposed phenomenological dynamic density functional theory [M. Bier and R. van Roij, Phys.…
We investigate irreversibility and dissipation in single molecules that cooperatively fold/unfold in a two state manner under the action of mechanical force. We apply path thermodynamics to derive analytical expressions for the average…
We study folding in 16-monomer heteropolymers on the square lattice. For a given sequence, thermodynamic properties and stability of the native state are unique. However, the kinetics of folding depends on the model of dynamics adopted for…
Using both analytical and simulational methods, we study low-temperature nucleation rates in kinetic Ising lattice-gas models that evolve under two different Arrhenius dynamics that interpose between the Ising states a transition state…
We consider a two-dimensional lattice gas model with repulsive nearest- and next-nearest-neighbor interactions that evolves in time according to anisotropic Kawasaki dynamics. The hopping of particles along the principal directions is…
We present a self-contained engine, which is made of one or more two-level systems, each of which is coupled to a single bath, as well as to a common load composed of a particle on a tilted lattice. We show that the energy and the entropy…
We develop a theoretical description of the critical zipping dynamics of a self-folding polymer. We use tension propagation theory and the formalism of the generalized Langevin equation applied to a polymer that contains two complementary…
In this paper we consider the coalescence dynamics of a tagged particle moving in a random distribution of particles with volumes independently distributed according to a probability distribution (CTP model). We provide a rigorous…
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…
We study a stationary state of a single self-propelled, athermal particle in linear and quadratic external potentials. The self-propulsion is modeled as a fluctuating force evolving according to the Ornstein-Uhlenbeck process, independently…
A generic model of a random polypeptide chain, with discrete torsional degrees of freedom and Hookean springs connecting pairs of hydrophobic residues, reproduces the energy probability distribution of real proteins over a very large range…
For a single enzyme or molecular motor operating in an aqueous solution of non-equilibrated solute concentrations, a thermodynamic description is developed on the level of an individual trajectory of transitions between states. The concept…