Related papers: Directed transport as a mechanism for protein fold…
Inertia is intrinsic to many living and synthetic active systems, from animals and robotic agents to colloidal swimmers, and it strongly shapes transport. Many such systems employ intermittent restart protocols to regulate exploration.…
The mathematical formulation of the model for molecular movement of single motor proteins driven by cyclic biochemical reactions in an aqueous environment leads to a drifted Brownian motion characterized by coupled diffusion equations. In…
Effective locomotion in nature happens by transitioning across multiple modes (e.g., walk, run, climb). Despite this, far more mechanistic understanding of terrestrial locomotion has been on how to generate and stabilize around…
Protein folding processes are generally described statistically with the help of multidimensional free energy landscape, typically reduced to a 1-D free energy profile along good reaction co-ordinate. There are many physical parameters…
We present a simple model of protein folding dynamics that captures key qualitative elements recently seen in all-atom simulations. The goals of this theory are to serve as a simple formalism for gaining deeper insight into the physical…
A Brownian particle's random motions can be rectified by a periodic potential energy landscape that alternates between two states, even if both states are spatially symmetric. If the two states differ only by a discrete translation, the…
We reveal the mechanism of subdiffusion which emerges in a straightforward, one dimensional classical nonequilibrium dynamics of a Brownian ratchet driven by both a time-periodic force and Gaussian white noise. In a tailored parameter set…
Proteins are large and complex molecular machines. In order to perform their function, most of them need energy, e.g. either in the form of a photon, like in the case of the visual pigment rhodopsin, or through the breaking of a chemical…
Proteins must fold quickly to acquire their biologically functional three-dimensional native structures. Hence, these are mainly stabilized by local contacts, while intricate topologies such as knots are rare. Here, we reveal the existence…
We present a very simple model for realizing directed transport with cold atoms in a pair of periodically flashed optical lattices. The origin of this ratchet effect is explained and its robustness demonstrated under imperfections typical…
Diffusive transport of particles or, more generally, small objects is a ubiquitous feature of physical and chemical reaction systems. In configurations containing confining walls or constrictions transport is controlled both by the…
We theoretically investigate the flow of the atomic excitations in a driven chiral-coupled atomic chain with nonreciprocal decay channels. This one-dimensional system allows infinite-range dipole-dipole interaction, and enables directional…
Biological transport networks are highly optimized structures that ensure power-efficient distribution of fluids across various domains, including animal vasculature and plant venation. Theoretically, these networks can be described as…
Applications such as digital microfluidics and bio-diagnostics rely on droplet locomotion. A prominent example of such motion is durotaxis, a phenomenon that requires a stiffness gradient along a surface for the transport of liquids, cells,…
We present a comprehensive account of directed transport in one-dimensional Hamiltonian systems with spatial and temporal periodicity. They can be considered as Hamiltonian ratchets in the sense that ensembles of particles can show directed…
With a view to numerical applications we address the following question: given an ergodic Brownian diffusion with a unique invariant distribution, what are the invariant distributions of the duplicated system consisting of two trajectories?…
We propose a dynamical model for non-specific DNA-protein interaction, which is based on the 'bead-spring' model previously developed by other groups, and investigate its properties using Brownian Dynamics simulations. We show that the…
We develop a theory of optimal transport for stationary random measures with a focus on stationary point processes and construct a family of distances on the set of stationary random measures. These induce a natural notion of interpolation…
Transport of colloid particles through narrow channels is ubiquitous in cell biology as well as becoming increasingly important for microfluidic applications or targeted drug delivery. Membrane channels in cells are useful models for…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…