Related papers: Directed transport as a mechanism for protein fold…
We show that the correlated stochastic fluctuation of the friction coefficient can give rise to long-range directional motion of a particle undergoing Brownian random walk in a constant periodic energy potential landscape. The occurrence of…
Individual movements of a rod-like self-propelled particle on a flat substrate are quantified. Biological systems that fit into this description may be the Gram-negative delta-proteobacterium Myxococcus xanthus, Gram-negative bacterium…
In many important cellular processes, including mRNA translation, gene transcription, phosphotransfer, and intracellular transport, biological "particles" move along some kind of "tracks". The motion of these particles can be modeled as a…
This review is a tutorial for scientists interested in the problem of protein structure prediction, particularly those interested in using coarse-grained molecular dynamics models that are optimized using lessons learned from the energy…
Designing protein sequences that fold into a target 3D structure, known as protein inverse folding, is a fundamental challenge in protein engineering. While recent deep learning methods have achieved impressive performance by recovering…
A geometric analysis of the global properties of the energy landscape of a minimalistic model of a polypeptide is presented, which is based on the relation between dynamical trajectories and geodesics of a suitable manifold, whose metric is…
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…
In this paper we show that a dynamical description of the protein folding process provides an effective representation of equilibrium properties and it allows for a direct investigation of the mechanisms ruling the approach towards the…
Models of protein energetics which neglect interactions between amino acids that are not adjacent in the native state, such as the Go model, encode or underlie many influential ideas on protein folding. Implicit in this simplification is a…
We propose an alternative mechanism for intracellular cargo transport which results from motor induced longitudinal fluctuations of cytoskeletal microtubules (MT). The longitudinal fluctuations combined with transient cargo binding to the…
We study experimentally, numerically and analytically, the dynamics of a chiral active particle (cm-sized robots), pulled at a constant translational velocity. We show that the system can be mapped to a Brownian particle driven across a…
Suspensions of anisotropic Brownian particles are commonly encountered in a wide array of applications such as drug delivery and manufacturing of fiber-reinforced composites. Technological applications and fundamental studies of small…
We study origin, parameter optimization, and thermodynamic efficiency of isothermal rocking ratchets based on fractional subdiffusion within a generalized non-Markovian Langevin equation approach. A corresponding multi-dimensional Markovian…
Inverse protein folding is challenging due to its inherent one-to-many mapping characteristic, where numerous possible amino acid sequences can fold into a single, identical protein backbone. This task involves not only identifying viable…
We investigate the transport of Brownian particles in a two-dimensional potential under the action of a uniform external force. The potential is periodic in one direction and confines the particle to a narrow channel of varying…
Theory of multi-dimensional representation of free energy surface of protein folding is developed by adopting structural order parameters of multiple regions in protein as multiple coordinates. Various scenarios of folding are classified in…
The guiding and transport of energy, for example of electromagnetic waves underpins many technologies that have shaped modern society, ranging from long distance optical fibre telecommunications to on-chip optical processors. Traditionally,…
A ratchet model for coupled Brownian motors, inspired by the motion of individual two-headed molecular motors on cytoskeletal filaments, is proposed. Such motors are modeled as two elastically coupled Brownian particles, each of which moves…
Transport of ions and small molecules across the cell membrane against electrochemical gradients is catalyzed by integral membrane proteins that use a source of free energy to drive the energetically uphill flux of the transported…
Many active particles, both of biological and synthetic origin, can have a light controllable propulsion speed, a property that in biology is commonly referred to as photokinesis. Here we investigate directed transport of photokinetic…