Related papers: Directed transport as a mechanism for protein fold…
One of the most puzzling and unsolved challenges in molecular biology is understanding how proteins fold. Despite having advanced predictive tools that can accurately estimate the native structures of proteins, we still lack a comprehensive…
Directed-ratchet transport (DRT) in a one-dimensional lattice of spherical beads, which serves as a prototype for granular crystals, is investigated. We consider a system where the trajectory of the central bead is prescribed by a…
The transport of interacting Brownian particles in a periodic asymmetric (ratchet) substrate is studied numerically. In a zero-temperature regime, the system behaves as a reversible step motor, undergoing multiple sign reversals of the…
We show that directed ratchet transport of a driven overdamped Brownian particle subjected to a spatially periodic and symmetric potential can be reliably controlled by tailoring a biharmonic temporal force, in coherence with the…
We present and discuss a novel approach to the direct and inverse protein folding problem. The proposed strategy is based on a variational approach that allows the simultaneous extraction of amino acid interactions and the low-temperature…
Properties of transport of molecular motors are investigated. A simplified model based on the concept of Brownian ratchets is applied. We analyze a stochastic equation of motion by means of numerical methods. The transport is systematically…
An all-atom model of proteins is used to show that the same sequence of amino acids can have many alternative structures, that are very distant from, and that can be as stable as, the corresponding native structure. Such alternative…
A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical…
On the basis of the transport features and experimental phenomena observed in studies of molecular motors, we proposea double-temperature ratchet model of coupled motors to reveal the dynamical mechanism of cooperative transport of motors…
A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…
Transport of a particle in a spatially periodic harmonic potential under the influence of a slowly time-dependent unbiased periodic external force is studied. The equations of motion are the same as in the problem of a slowly forced…
We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding…
We study the Hamiltonian dynamics of a one-dimensional chain of linearly coupled particles in a spatially periodic potential which is subjected to a time-periodic mono-frequency external field. The average over time and space of the related…
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…
We study directed transport in periodically forced scattering systems in the regime of fast and strong driving where the dynamics is mixed to chaotic and adiabatic approximations do not apply. The model employed is a square potential well…
The existence and properties of an exact universal excitation waveform for optimal enhancement of directed ratchet transport are deduced from the criticality scenario giving rise to ratchet universality, and confirmed by numerical…
We give an overview over recent studies on the model of Active Brownian Motion (ABM) coupled to reservoirs providing free energy which may be converted into kinetic energy of motion. First, we present an introduction to a general concept of…
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…
We show by numerical simulations that a non rotationally symmetric body, whose orientation is fixed and whose center of mass can only slide along a rectilinear guide, under the effect of inelastic collisions with a surrounding gas of…
We model an overdamped Brownian particle that is subject to resetting facilitated by a ratchet potential on a spatially periodic domain. This asymmetric potential switches on with a constant rate, but switches off again only upon the…