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Protein collapse can be viewed as a dynamical phase transition, during which new scales and collective variables become excited while the old ones recede and fade away. This causes formidable computational bottle-necks in approaches that…
A two-dimensional \underline{Frenkel-Kontorova model} under a steady external force is used to study the nonlinear sliding friction between flat macroscopic surfaces with a lubricant layer in between. The nonequilibrium properties of the…
A dynamical model of confinement based on a microscopic transport description of the Friedberg-Lee model is extended to explicit color degrees of freedom. The string tension is reproduced by an adiabatic string formation from the nucleon…
Fluid-resistance limited transport of vesicles through narrow constrictions is a recurring theme in many biological and engineering applications. Inspired by the motor-driven movement of soft membrane-bound vesicles into closed neuronal…
Exerting a nonequilibrium drive on an otherwise equilibrium Langevin process brings the dynamics out of equilibrium but can also speedup the approach to the Boltzmann steady-state. Transverse forces are a minimal framework to achieve…
Constraint-based stoichiometric models are ubiquitous in metabolic research, with Flux Balance Analysis (FBA) being the most widely used method to describe metabolic phenotypes of cells growing in steady-state. Of the many variants of…
Two coarse-grained models for polymer chains in dense glass-forming polymer melts are studied by computer simulation: the bond-fluctuation model on a simple cubic lattice, where a bond-length potential favors long bonds, is treated by…
We present results of Monte Carlo computer simulations of a coarse-grained hydrophobic-polar Go-like heteropolymer model and discuss thermodynamic properties and kinetics of an exemplified heteropolymer, exhibiting two-state folding…
We propose a modified suspension balance model (SBM) for the flow of red blood cells (RBCs) and other deformable particle suspensions in confined geometries. Specifically, the method includes the hydrodynamic lift force generated by…
We derive a retained-spin micropolar hydrodynamic closure from the Boltzmann--Curtiss equation using a generalized Chapman--Enskog construction in which the local mean spin is retained as a quasi-slow variable. Starting from the…
A perturbation theory scheme in terms of electron hopping, which is based on the Wick theorem for Hubbard operators, is developed. Diagrammatic series contain single-site vertices connected by hopping lines and it is shown that for each…
Dynamic properties of molecular motors that fuel their motion by actively interacting with underlying molecular tracks are studied theoretically via discrete-state stochastic ``burnt-bridge'' models. The transport of the particles is viewed…
Spin squeezing in collective atomic ensembles enables quantum-enhanced metrology by reducing noise below the standard quantum limit through nonlinear interactions. Extending the one-axis and two-axis twisting paradigms of Kitagawa and Ueda,…
Brownian Dynamics simulations are an important tool for modeling the dynamics of soft matter. However, accurate and rapid computations of the hydrodynamic interactions between suspended, microscopic components in a soft material is a…
The forces that mixtures of motorized and passive crosslinking proteins collectively generate between cytoskeletal filaments within our cells are the key drivers of active cellular mechanics. Despite their importance, a unified theory to…
With an auxiliary weak external magnetic field, we reexamine the fundamental thermodynamic function, Gibbs free energy F(T, h), to study the phase transitions in the classical spin lattice models. A cross derivative, i.e. the second-order…
We analyse the dynamical evolution of a fluid with non-linear drag, for which binary collisions are elastic, described at the kinetic level by the Enskog-Fokker-Planck equation. This model system, rooted in the theory of non-linear Brownian…
Confined granular fluids, placed in a shallow box that is vibrated vertically, can achieve homogeneous stationary states thanks to energy injection mechanisms that take place throughout the system. These states can be stable even at high…
We consider thermodynamic and dynamic phase transitions in plaquette spin models of glasses. The thermodynamic transitions involve coupled (annealed) replicas of the model. We map these coupled-replica systems to a single replica in a…
From the point of view of statistical mechanics, a full characterisation of a molecular system requires the experimental determination of its possible states, their populations and the respective interconversion rates. Well-established…