Related papers: Sequence heterogeneity and the dynamics of molecul…
Many cell functions are accomplished thanks to intracellular transport mechanisms of macromolecules along filaments. Molecular motors such as dynein or kinesin are proteins playing a primary role in these processes. The behavior of such…
Molecular motors perform active movements along cytoskeletal filaments and drive the traffic of organelles and other cargo particles in cells. In contrast to the macroscopic traffic of cars, however, the traffic of molecular motors is…
Intracellular transport is an essential function in eucaryotic cells, facilitated by motor proteins - proteins converting chemical energy into kinetic energy. It is known that motor proteins work in teams enabling unidirectional and…
Dynamic properties of molecular motors whose motion is powered by interactions with specific lattice bonds are studied theoretically with the help of discrete-state stochastic "burnt-bridge" models. Molecular motors are depicted as random…
Analytical formulas for effective drift, diffusivity, run times, and run lengths are derived for an intracellular transport system consisting of a cargo attached to two cooperative but not identical molecular motors (for example, kinesin-1…
As engineering advances toward the nanoscale, understanding design principles for molecular motors becomes increasingly valuable. Many molecular motors consist of coupled components transducing one free-energy source into another. Here, we…
We here examine the nonlinear dynamics of artificial homogeneous DNA chain relying on the plain-base rotator model. It is shown that such dynamics can exhibit kink and antikink solitons of sine-Gordon type. In that respect we propose…
We study the deterministic dynamics of a periodically driven particle in the underdamped case in a spatially symmetric periodic potential. The system is subjected to a space-dependent friction coefficient, which is similarly periodic as the…
Bidirectional variants of stochastic many particle models for transport by molecular motors show a strong tendency to form macroscopic clusters on static lattices. Inspired by the fact that the microscopic tracks for molecular motors are…
Dynamic heterogeneity is expected to be a key concept for understanding the origin of slow dynamics near the glass transition. In previous studies, quantitative evaluations of dynamic heterogeneity have been attempted using two different…
Inspired by the need for effective stochastic models to describe the complex behavior of biological motor proteins that move on linear tracks exact results are derived for the velocity and dispersion of simple linear sequential models (or…
A chemical kinetic model of the elongation dynamics of RNA polymerase along a DNA sequence is introduced. The proposed model governs the discrete movement of the RNA polymerase along a DNA template, with no consideration given to elastic…
We study the mechanical and thermodynamic properties of different traffic models for kinesin which are relevant in biological and experimental contexts. We find that motor-motor interactions play a fundamental role by enhancing the…
Using the model for the processive movement of a dimeric kinesin we proposed before, we study the dynamics of a number of mutant homodimeric and heterodimeric kinesins that were constructed by Kaseda et al. (Kaseda, K., Higuchi, H. and…
Many types of molecular motors have been proposed and synthesized in recent years, displaying different kinds of motion, and fueled by different driving forces such as light, heat, or chemical reactions. We propose a new type of molecular…
We present Brownian dynamics simulations of the facilitated diffusion of a protein, modelled as a sphere with a binding site on its surface, along DNA, modelled as a semi-flexible polymer. We consider both the effect of DNA organisation in…
This thesis focuses on the mechanisms of energy transport in multidimensional heterogeneous lattice models, studying in particular the case of the Klein-Gordon model of coupled anharmonic oscillators in one and two spatial dimensions. We…
The influence of decoherence and bonding on the linear conductance of single double-stranded DNA molecules is examined by fitting a phenomenological statistical model developed recently (EPJB {\bf 68}, 237 (2009)) to experimental results.…
We consider random walks on quasi one dimensional lattices, as introduced in \cite{FS}. This mathematical setting covers a large class of discrete kinetic models for non-cooperative molecular motors on periodic tracks. We derive general…
Motivated by experiments on single-headed kinesin KIF1A, we develop a model of intra-cellular transport by interacting molecular motors. It captures explicitly not only the effects of ATP hydrolysis, but also the ratchet mechanism which…