Related papers: Sequence heterogeneity and the dynamics of molecul…
Motivated by experimental results on the interplay between molecular motors and tau proteins, we extend lattice-based models of intracellular transport to include a second species of particle which locally influences the motor-filament…
We model and simulate the stepping dynamics of the kinesin motor including electric and mechanical forces, environmental noise, and the complicated potentials produced by tracking and neighboring protofilaments. Our dynamical model supports…
Here we generalize our previous model of molecular motors trafficking subdiffusing cargos in viscoelastic cytosol by (i) including mechanochemical coupling between cyclic conformational fluctuations of the motor protein driven by the…
We propose a stochastic process wherein molecular transport is mediated by asymmetric nucleation of domains on a one-dimensional substrate. Track-driven mechanisms of molecular transport arise in biophysical applications such as Holliday…
RNA polymerase (RNAP) is a mobile molecular workshop that polymerizes a RNA molecule by adding monomeric subunits one by one, while moving step by step on the DNA template itself. Here we develop a theoretical model by incorporating the…
We introduce a probabilistic model for protein sliding motion along DNA during the search of a target sequence. The model accounts for possible effects due to sequence-dependent interaction between the nonspecific DNA and the protein. As an…
Motor proteins display widely different stepping patterns as they move on microtubule tracks, from the deterministic linear or helical motion performed by the protein kinesin to the uncoordinated random steps made by dynein. How these…
We use a two-state ratchet model to study the cooperative bidirectional motion of molecular motors on cytoskeletal tracks with randomly alternating polarities. Our model is based on a previously proposed model [Badoual et al., {\em Proc.…
We study the nonlinear dynamics of a completely inhomogeneous DNA chain which is governed by a perturbed sine-Gordon equation. A multiple scale perturbation analysis provides perturbed kink-antikink solitons to represent open state…
Gene transcription is a highly stochastic and dynamic process. As a result, the mRNA copy number of a given gene is heterogeneous both between cells and across time. We present a framework to model gene transcription in populations of cells…
We study the dynamics of one--dimensional discrete models of one--component active medium built up of spatially inhomogeneous chains of diffusively coupled piecewise linear maps. The nonhomogeneities (``defects'') are treated in terms of…
DNA helicases are molecular motors that use the energy from ATP hydrolysis to move along DNA, promoting the unwinding or rewinding of the double helix. Here, we use magnetic and optical tweezers to track the motion of three helicases, gp41,…
In this work we extend a recent kinetic traffic model to the case of more than one class of vehicles, each of which is characterized by few different microscopic features. We consider a Boltzmann-like framework with only binary…
The dynamics of motor protein molecules that have two subunits is investigated using simple discrete stochastic models. Exact steady-state analytical expressions are obtained for velocities and dispersions for any number of intermediate…
In recent literature there has been a lot of interest in the phenomena of noise induced transport in the absence of an average bias occurring in spatially periodic systems far from equilibrium. One of the main motivations in this area is to…
The effect of interactions on dynamics of coupled motor proteins is investigated theoretically. A simple stochastic discrete model, that allows to calculate explicitly the dynamic properties of the system, is developed. It is shown that…
Many cellular processes rely on the cell's ability to transport material to and from the nucleus. Networks consisting of many microtubules and actin filaments are key to this transport. Recently, the inhibition of intracellular transport…
We consider the dynamics of cargo driven by a collection of interacting molecular motors in the context of an asymmetric simple exclusion processes (ASEP). The model is formulated to account for i) excluded volume interactions, ii) the…
Dynamical heterogeneity (DH) in non-equilibrium systems is a topic of profound interest yet an open question. In a model system of constantly driven oppositely charged binary colloidal suspension, we explore DH in a model lane-forming…
Soliton dynamics in a large variety of longitudinally modulated lattices are studied in terms of phase space analysis for an effective particle approach and direct numerical simulations. Complex soliton dynamics are shown to depend strongly…