Related papers: Simulating a Chemically-Fueled Molecular Motor wit…
Kinetics of dislocations is studied by means of computer simulation during intensive plastic deformation. The dynamical effect in the form of soliton-like wave of sharply disrupted interparticle bonds is observed. Along with it, micropores…
In a single molecule assay, the motion of a molecular motor is often inferred from measuring the stochastic trajectory of a large probe particle attached to it. We discuss a simple model for this generic set-up taking into account…
Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…
Classical molecular dynamics simulations of hydrogen plasmas have been performed with emphasis on the analysis of equilibration process. Theoretical basis of simulation model as well as numerically relevant aspects -- such as the proper…
Dynamic properties of molecular motors that fuel their motion by actively interacting with underlying molecular tracks are studied theoretically via discrete-state stochastic ``burnt-bridge'' models. The transport of the particles is viewed…
The average kinetic energy is widely used to characterize temperature in molecular dynamics (MD) simulation. In this letter, the applicability of three types of average kinetic energy as measures of temperature is investigated, i.e., the…
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…
The performance of a molecular motor, characterized by its power output and energy efficiency, is investigated in the motor design space spanned by the stepping rate function and the motor-track interaction potential. Analytic results and…
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…
Like their larger micron-scale counterparts, {\AA}ngstr\"om-scale chemically self-propelled motors use asymmetric catalytic activity to produce self-generated concentration gradients that lead to directed motion. Unlike their micron-scale…
The phase behaviour and dynamics of molecular ionic liquids are studied using primitive models and extensive computer simulations. The models account for size disparity between cation and anion, charge location on the cation, and…
Very recently [Phys. Rev. E 82, 021921 (2010)] a simple mechanism was presented by which a molecule subjected to forced oscillations, out of thermal equilibrium, can maintain quantum entanglement between two of its quantum degrees of…
We prove that for a combined system of classical and quantum particles, it is possible to write a dynamics for the classical particles that incorporates in a natural way the Boltzmann equilibrium population for the quantum subsystem. In…
Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, vapour-liquid interfaces, and biomolecules in contact with water-oil interfaces. Novel molecular models of alkali halide salts are presented and…
The single-particle and collective dynamics of systems comprising Janus motors, solvent and reactive solute species maintained in nonequilibrium states are investigated. Reversible catalytic reactions with the solute species take place on…
In the presence of ATP, molecular motors generate active force dipoles that drive suspensions of protein filaments far from thermodynamic equilibrium, leading to exotic dynamics and pattern formation. Microscopic modelling can help to…
We study conditions under which carbon clusters of different sizes form and stabilize. {We describe an approach to equilibrium by simulating tenuous carbon gas dynamics to long times.} First, we use reactive molecular dynamics simulations…
Molecular dynamics (MD) simulation based on Langevin equation has been widely used in the study of structural, thermal properties of matters in difference phases. Normally, the atomic dynamics are described by classical equations of motion…
Unlike macroscopic engines, the molecular machinery of living cells is strongly affected by fluctuations. Stochastic Thermodynamics uses Markovian jump processes to model the random transitions between the chemical and configurational…
We present an approach for carrying out non-adiabatic molecular dynamics simulations of systems in which non-adiabatic transitions arise from the coupling between the classical atomic motions and a quasi-continuum of electronic quantum…