Related papers: Peptide size dependent active transport in the pro…
Molecular transport maintains cellular structures and functions. For example, lipid and protein diffusion sculpts the dynamic shapes and structures on the cell membrane that perform essential cellular functions, such as cell signaling.…
Transport of molecular motors along protein filaments in a half-closed geometry is a common feature of biologically relevant processes in cellular protrusions. Using a lattice gas model we study how the interplay between active and…
Intracellular transport processes are essential to the healthy development of many organisms as well as more generally to healthy cellular function. The complex dynamics and interactions between protein molecules and filaments on different…
The study of fluctuation-induced transport is concerned with the directed motion of particles on a substrate when subjected to a fluctuating external field. Work over the last two decades provides now precise clues on how the average…
Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…
We study spatial correlations in the transport of energy between two baths at different temperatures. To do this, we introduce a minimal model in which energy flows from one bath to another through two subsystems. We show that the…
We introduce a model of information packet transport on networks in which the packets are posted by a given rate and move in parallel according to a local search algorithm. By performing a number of simulations we investigate the major…
Close to equilibrium, the exchange of particles and heat between macroscopic systems at different temperatures and different chemical potentials is known to be governed by a matrix of transport coefficients which is positive and symmetric.…
We discuss the problem of proteasomal degradation of proteins. Though proteasomes are important for all aspects of the cellular metabolism, some details of the physical mechanism of the process remain unknown. We introduce a stochastic…
Understanding the role of active fluctuations in physics is a problem in statu nascendi appearing both as a hot topic and a major challenge. The reason for this is the fact that they are inherently non-equilibrium. This feature opens a…
It is shown that a small subset of modes which are likely to be involved in protein functional motions of large amplitude can be determined by retaining the most robust normal modes obtained using different protein models. This result…
Using analytical calculations and computer simulations we consider both the lateral diffusion of a membrane protein and the fluctuation spectrum of the membrane in which the protein is embedded. The membrane protein interacts with the…
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…
This article examines the spatial {dynamics of bed load particles} in water. We focus particularly on the fluctuations of particle activity, which is defined as the number of moving particles per unit bed {length}. Based on a stochastic…
Biological transport is supported by collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the…
Heat dissipation is ubiquitous in living systems, which constantly convert distinct forms of energy into each other. The transport of thermal energy in liquids and even within proteins is well understood but kinetic energy transfer across a…
The stability of a flexible fluid membrane containing a distribution of mobile, active proteins (e.g. proton pumps) is shown to depend on the structure and functional asymmetry of the proteins. A stable active membrane is in a…
Normal mode analysis is a widely used technique for reconstructing conformational changes of proteins from the knowledge of native structures. In this Letter, we investigate to what extent normal modes capture the salient features of the…
Thermodynamic transport phenomena in the system consisting of many hard-disks confined in a circular tube with a temperature difference are discussed. Here, temperatures on parts of the walls of the tube are imposed by stochastic boundary…
Transport of molecules across membrane channels is investigated theoretically using exactly solvable one-dimensional discrete-state stochastic models. An interaction between molecules and membrane pores is modeled via a set of binding sites…