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The Biham-Middleton-Levine (BML) traffic model, a cellular automaton with east-bound and north-bound cars moving by turns on a square lattice, has been an underpinning model in the study of collective behaviour by cars, pedestrians and even…
In this letter we propose a model which explains ultrafast and efficient photoisomerization reactions as driven by transitions between quasistationary states of one dimensional (1D) double well potential of an excited electronic state. This…
With the formal construction of a thermodynamic spring, I describe the mechanics, energetics, entropy, and kinetics of a binary mechanical model system. A protein that transitions between two metastable structural states behaves as a…
The transverse motion inside a Stark decelerator plays a large role in the total efficiency of deceleration. We differentiate between two separate regimes of molecule loss during the slowing process. The first mechanism involves distributed…
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…
In single-molecule experiments, the dynamics of molecular motors are often observed indirectly by measuring the trajectory of an attached bead in a motor-bead assay. In this work, we propose a method to extract the step size and stalling…
The cytoplasm of a living cell is crowded with several macromolecules of different shapes and sizes. Molecular diffusion in such a medium becomes anomalous due to the presence of macromolecules and diffusivity is expected to decrease with…
Transitions between solid-like and fluid-like states in living tissues have been found in steps of embryonic development and in stages of disease progression. Our current understanding of these transitions has been guided by experimental…
Molecular machines transduce free energy between different forms throughout all living organisms. While truly machines in their own right, unlike their macroscopic counterparts molecular machines are characterized by stochastic…
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…
In this paper, a new method to efficiently simulate diffusion controlled second order chemical reactions is derived and applied to site-specific DNA-binding proteins. The protein enters a spherical cell and propagates via two competing…
Three problems in the statistical mechanics of models for an assembly of molecular motors interacting with cytoskeletal filaments are reviewed. First, a description of the hydrodynamical behaviour of density-density correlations in…
Catalysis, the acceleration of product formation by a substance that is left unchanged, typically results from multiple elementary processes, including diffusion of the reactants toward the catalyst, chemical steps, and release of the…
Chemical affinities are responsible for driving active matter systems out of equilibrium. At the nano-scale, molecular machines interact with the surrounding environment and are subjected to external forces. The mechano-chemical coupling…
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…
Biomolecular motors use free energy to drive a variety of cellular tasks, including the transport of cargo, such as vesicles and organelles. We find that the widely-used `constant-force' approximation for the effect of cargo on motor…
We have developed a two dimensional stochastic molecular dynamics model for the description of intra cellular collective motion of bio motors, in particular Kinesins, on a microtubular track. The model is capable or reproducing the…
Intracellular cargos which are transported by molecular motors move stochastically along cytoskeleton filaments. In particular for bidirectionally transported cargos it is an open question whether the characteristics of their motion can…
Brownian particles interacting sequentially with distinct temperatures and driving forces at each stroke have been tackled as a reliable alternative for the construction of engine setups. However they can behave very inefficiently depending…
In recent years, several artificial molecular motors driven and controlled by electric currents have been proposed. Similar to Brownian machines, these systems work by turning random inelastic tunneling events into a directional rotation of…