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A generalized multibaker map with periodic boundary conditions is shown to model boundary-driven transport, when the driving is applied by a ``perturbation'' of the dynamics localised in a macroscopically small region. In this case there…
Transport of molecular motors, stimulated by interactions with specific links between consecutive binding sites (called ``bridges''), is investigated theoretically by analyzing discrete-state stochastic ``burnt-bridge'' models. When an…
Using numerical simulations, we study the dynamical evolution of particles interacting via competing long-range repulsion and short-range attraction in two dimensions. The particles are compressed using a time-dependent quasi-one…
In the presence of ATP, molecular motors generate active force dipoles that drive suspensions of protein filaments far from thermodynamic equilibrium, leading to exotic dynamics and pattern formation. Microscopic modelling can help to…
We study numerically a lattice model of semiflexible homopolymers with nearest neighbor attraction and energetic preference for straight joints between bonded monomers. For this we use a new algorithm, the "Pruned-Enriched Rosenbluth…
A general theoretical framework is derived for the recently developed multi-state trajectory (MST) approach from the time dependent Schr\"odinger equation, resulting in equations of motion for coupled nuclear-electronic dynamics equivalent…
We provide extended evidence that mode-coupling theory (MCT) of supercooled liquids for the ${\mathsf F}_{12}$ schematic model admits a microscopic realization based on facilitated spin models with tunable facilitation. Depending on the…
Cytoskeletal gels are engineered prototypes that mimic the contractile behavior of a cell in-vitro. They are composed of an active polymer matrix and a liquid solvent. Their contraction kinetics is governed by two dynamic phenomena:…
Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…
The stress-gradient theory has a third order tensor as kinematic degree of freedom, which is work-conjugate to the stress gradient. This tensor was called micro-displacements just for dimensional reasons. Consequently, this theory requires…
A modeling framework for the internal conformational dynamics and external mechanical movement of single biological macromolecules in aqueous solution at constant temperature is developed. Both the internal dynamics and external movement…
The effect of a thermal environment on electron (or hole) transfer through molecular bridges and on the electron conduction properties of such bridges is studied. Our steady state formalism based on an extension of the Redfield theory (D.…
Living things benefit from exquisite molecular sensitivity in many of their key processes, including DNA replication, transcription and translation, chemical sensing, and morphogenesis. At thermodynamic equilibrium, the basic biophysical…
In many organisms, cell division is driven by the constriction of a cytokinetic ring, which consists of actin filaments and crosslinking proteins. While it has long been believed that the constriction is driven by motor proteins, it has…
In this work we propose an extension to the analytical one-dimensional model proposed by E. Gnecco (Phys. Rev. Lett. 84:1172) to describe friction. Our model includes normal forces and the dependence with the angular direction of movement…
In this study we evaluate, at full atomic detail, the folding processes of two small helical proteins, the B domain of protein A and the Villin headpiece. Folding kinetics are studied by performing a large number of ab initio Monte Carlo…
Capturing the dynamics of active particles, i.e., small self-propelled agents that both deform and are deformed by a fluid in which they move is a formidable problem as it requires coupling fine scale hydrodynamics with large scale…
Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
The Metropolis Monte Carlo (MC) method is used to extract reaction kinetics from a given equilibrium distribution of states of a complex system. The approach is illustrated by the folding/unfolding reaction for two proteins - a model…
We present a method to investigate the kinetics of protein folding on a long time-scale and the dynamics underlying the formation of secondary and tertiary structures during the entire reaction. The approach is based on the formal analogy…