Related papers: Directed transport as a mechanism for protein fold…
The energy landscapes of proteins have evolved to be different from most random heteropolymers. Many studies have concluded that evolutionary selection for rapid and reliable folding to a given structure that is stable at biological…
We study impact of inertia on directed transport of a Brownian particle under non-equilibrium conditions: the particle moves in a one-dimensional periodic and symmetric potential, is driven by both an unbiased time-periodic force and a…
We demonstrate the directed transport of underdamped particles in two dimensional lattices of arbitrary geometry driven by an unbiased ac-driving force. The direction of transport can be controlled via the lattice geometry as well as the…
We study analytically and numerically the overdamped, deterministic dynamics of a chain of {\it charged}, interacting particles driven by a longitudinal alternating electric field and additionally interacting with a smooth ratchet…
We analyze the diffusive transport of Brownian particles in narrow channels with periodically varying cross-section. The geometrical confinements lead to entropic barriers, the particle has to overcome in order to proceed in transport…
The directed transport of an overdamped Brownian motor moving in a spatially periodic potential that lacks reflection symmetry (i.e. a ratchet potential) is studied when driven by thermal and dichotomic nonequilibrium noise in the presence…
We suggest that Davidov's solitons, propagating through the backbone of a protein, can mediate conformational transition and folding of a protein to its native state. A simple toy model is presented in which a Non Linear Schrodinger (NLS)…
Following the ideas of Davydov's soliton theory, we study the bio-energy transport in protein molecules. By using a quantum Brownian motion model for a phonon dressed vibrational exciton, we calculate the time-dependence on the mean square…
Protein translocation in cells has been modelled by \emph{Brownian ratchets}. In such models, the protein diffuses through a nanopore. On one side of the pore, ratcheting molecules bind to the protein and hinder it to diffuse out of the…
The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases. Despite recent advances in protein structure prediction,…
In recent years, the study of biological transportation networks has attracted significant interest, focusing on their self-regulating, demand-driven nature. This paper examines a mathematical model for these networks, featuring nonlinear…
We analyze the dynamics of a classical particle in a spatially periodic potential under the influence of a periodic in time uniform force. It was shown in [S.Flach, O.Yevtushenko, Y. Zolotaryuk, Phys. Rev. Lett. 84, 2358 (2000)] that…
Brownian computers utilize thermal fluctuations as a resource for computation and hold promise for achieving ultra-low-energy computations. However, the lack of a statistical direction in Brownian motion necessitates the incorporation of…
Rectified transport of active ellipsoidal particles is numerically investigated in a two-dimensional asymmetric potential. The out-of-equilibrium condition for the active particle is an intrinsic property, which can break thermodynamical…
We construct and exactly solve a model of an extended Brownian ratchet. The model comprises an arbitrary number of heterogeneous, growing and shrinking filaments which together move a rigid membrane by a ratchet mechanism. The model draws…
We demonstrate a size sensitive experimental scheme which enables bidirectional transport and fractionation of paramagnetic colloids in a fluid medium. It is shown that two types of magnetic colloidal particles with different sizes can be…
The atomistic characterization of the transition state is a fundamental step to improve the understanding of the folding mechanism and the function of proteins. From a computational point of view, the identification of the conformations…
We study the Asymmetric Brownian Energy, a model of heat conduction defined on the one-dimensional finite lattice with open boundaries. The system is shown to be dual to the Symmetric inclusion process with absorbing boundaries. The proof…
The operation of Brownian motors is usually described in terms of out-of-equilibrium and symmetry-breaking settings, with the relevant spatiotemporal symmetries identified from the analysis of the equations of motion for the system at hand.…
We develop and analyze a model for ratchet-driven macroscopic transport of a continuous phase. The transport relies on a field-induced dewetting-spreading cycle of a liquid film with a free surface based on a switchable, spatially…