Related papers: Peptide size dependent active transport in the pro…
In this paper we discuss the dynamics and transport properties of a massive particle, in a time dependent periodic potential of the ratchet type, with a dissipative environment. The directional currents and characteristics of the motion are…
We study the dynamics of hydration water/protein association in folded proteins, using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition…
In this paper a lattice model for the diffusional transport of particles in the interphase cell nucleus is proposed. The dynamic behaviour of single chains on the lattice is investigated and Rouse scaling is verified. Dynamical dense…
The motion of overdamped particles in a one-dimensional spatially-periodic potential is considered. The potential is also randomly-fluctuating in time, due to multiplicative colored noise terms, and has a deterministic tilt. Numerical…
Transport across heterogeneous, patchy environments is a ubiquitous phenomenon spanning fields of study including ecological movement, intracellular transport and regions of specialised function in a cell. These regions or patches may be…
The thermal ratchets model toggles a spatially periodic asymmetric potential to rectify random walks and achieve transport of diffusing particles. We numerically solve the governing equation for the full dynamics of an infinite 1D ratchet…
Molecular dynamics simulations have revealed a dramatic increase, with increasing temperature, of the amplitude of electrostatic fluctuations caused by water at the active site of metalloprotein plastocyanin. The increased breadth of…
Biomembranes wrapping cells and organelles are not only the partitions that separate the insides but also dynamic fields for biological functions accompanied by membrane shape changes. In this review, we discuss the spatiotemporal patterns…
Detailed calculations of the transport coefficients of a recently introduced particle-based model for fluid dynamics with a non-ideal equation of state are presented. Excluded volume interactions are modeled by means of biased stochastic…
Simulation results of the thermal conductivity ${\cal L}$ of Dissipative Particle Dynamics model with Energy Conservation (DPDE) are reported. We also present an analysis of the transport equations and the transport coefficients for DPDE…
We study the contribution of advection by thermal velocity fluctuations to the effective diffusion coefficient in a mixture of two indistinguishable fluids. The enhancement of the diffusive transport depends on the system size L and grows…
Various charge migration mechanisms in the DNA are studied within the framework of the Peyrard-Bishop-Holstein model which has been widely used to address charge dynamics in this macromolecule. To analyze these mechanisms we consider…
Active fluids operate by constantly dissipating energy at the particle level to perform a directed motion, yielding dynamics and phases without any equilibrium equivalent. The emerging behaviors have been studied extensively, yet…
Particles moving along curved trajectories will diffuse if the curvature fluctuates sufficiently in either magnitude or orientation. We consider particles moving at a constant speed with either a fixed or with a Gaussian distributed…
Transport phenomena are fundamental in Physics. They allow for information and energy to be exchanged between individual constituents of communication systems, networks or even biological entities. Environmental noise will generally hinder…
Intracellular transport of large cargoes, such as organelles, vesicles or large proteins, is a complex dynamical process that involves the interplay of ATP-consuming molecular motors, cytoskeleton filaments and the viscoelastic cytoplasm.…
The effect of interactions on dynamics of coupled motor proteins is investigated theoretically. A simple stochastic discrete model, that allows to calculate explicitly the dynamic properties of the system, is developed. It is shown that…
The thermodynamic properties for three different types of off-lattice four-strand beta-sheet protein models interacting via a hybrid Go-type potential have been investigated. Discontinuous molecular dynamic simulations have been performed…
Enhanced colloidal transport beyond the limit imposed by diffusion is usually achieved through external fields. Here, we demonstrate the ballistic transport of a colloidal sphere using internal sources of energy provided by an attached…
Thermal transport properties of amorphous carbon has attracted increasing attention due to its extreme thermal properties: It has been reported to have among the highest thermal conductivity for bulk amorphous solids up to $\sim$ 37…