Related papers: Directed transport as a mechanism for protein fold…
We study directed transport of overdamped particles in a periodically rocked random sawtooth potential. Two transport regimes can be identified which are characterized by a nonzero value of the average velocity of particles and a zero…
On the basis of a model we capture the role of strong attractive interaction in suppressing the rotational degrees of freedom of the system and volume exclusion in keeping microscopic symmetry-breaking intact to result in super-diffusive…
A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approach outlined previously [J. J. Portman, S. Takada, P. G.…
We introduce a class of one-dimensional lattice models in which a quantity, that may be thought of as an energy, is either transported from one site to a neighbouring one, or locally dissipated. Transport is controlled by a continuous bias…
The noise-flatness-induced hypersensitive transport of overdamped Brownian particles in a tilted ratchet system driven by multiplicative nonequilibrium three-level Markovian noise and additive white noise is considered. At low temperatures…
Using the Helmholtz decomposition of the vector field of folding fluxes in a two-dimensional space of collective variables, a potential of the driving force for protein folding is introduced. The potential has two components. One component…
The transport of Brownian particles in a slit geometry in the presence of an arbitrary two-dimensional periodic energy landscape and driven by an external force or convected by a flow field is investigated by means of macrotransport theory.…
The ratchet phenomenon is a means to get directed transport without net forces. Originally conceived to rectify stochastic motion and describe operational principles of biological motors, the ratchet effect can be used to achieve…
Water molecules, confined in a carbon nanotube, were monitored using molecular dynamics simulation. Spontaneous directional transportation during a long timescale was observed in the symmetrical nanochannel by a ratchet-like mechanism. This…
Dynamics simulations of constrained particles can greatly aid in understanding the temporal and spatial evolution of biological processes such as lateral transport along membranes and self-assembly of viruses. Most theoretical efforts in…
We demonstrate the operation of a quantum ratchet in the absence of dissipative processes within the observation time (Hamiltonian regime). An atomic rubidium Bose-Einstein condensate is exposed to a sawtooth-like optical lattice potential,…
Transport of a Brownian particle moving in a periodic potential is investigated in the presence of symmetric unbiased external force. The viscous medium is alternately in contact with the two heat reservoirs. We present the analytical…
Theoretical analysis and fully atomistic molecular dynamics simulations reveal a Brownian ratchet mechanism by which thermal fluctuations drive the net displacement of immiscible liquids confined in channels or pores with micro- or…
Cells control the size and organization of biomolecular condensates formed by liquid-liquid phase separation (LLPS), but multiple mechanisms likely contribute to this control and remain to be fully elucidated. Here we propose a…
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…
We have previously shown an analysis of our dimer model in the over-damped regime to show directed transport in equilibrium. Here we analyze the full model with inertial terms present to establish the same result. First we derive the…
We study subdiffusive overdamped Brownian ratchets periodically rocked by an external zero-mean force in viscoelastic media within the framework of non-Markovian Generalized Langevin equation (GLE) approach and associated multi-dimensional…
We study the conservative and deterministic dynamics of two nonlinearly interacting particles evolving in a one-dimensional spatially periodic washboard potential. A weak tilt of the washboard potential is applied biasing one direction for…
We present the first numerical simulation of actin-driven propulsion by elastic filaments. Specifically, we use a Brownian dynamics formulation of the dendritic nucleation model of actin-driven propulsion. We show that the model leads to a…
We consider an inertial active Ornstein-Uhlenbeck particle self-propelling in a saw-tooth ratchet potential. Using the Langevin simulation and matrix continued fraction method, the particle transport, steady state diffusion, and coherence…