Related papers: Collective diffusion coefficient of proteins with …
A general model covering a large variety of the so-called adhesive or cohesive, possibly also frictional, contact interfaces between visco-elastic bodies with inertia considered in a thermodynamical context is presented. A semi-implicit…
Stochastic models of diffusion with excluded-volume effects are used to model many biological and physical systems at a discrete level. The average properties of the population may be described by a continuum model based on partial…
This paper is concerned with the effective transport properties of heterogeneous media in which there is a high contrast between the phase diffusivities. In this case the transient response of the slow phase induces a memory effect at the…
The effect of conformational fluctuations of modular macromolecules, such as enzymes, on their diffusion properties is addressed using a simple generic model of an asymmetric dumbbell made of two hydrodynamically coupled subunits. It is…
Let U be a given function defined on R^d and \pi(x) be a density function proportional to \exp -U(x). The following diffusion X(t) is often used to sample from \pi(x), dX(t)=-\nabla U(X(t)) dt+\sqrt2 dW(t),\qquad X(0)=x_0. To accelerate the…
The variance of the local density of the pair contact process with diffusion (PCPD) is investigated in a bosonic description. At the critical point of the absorbing phase transition (where the average particle number remains constant) it is…
We characterize steady-state static and dynamic properties in a broad class of mass transport processes on a periodic hypercubic lattice of volume $L^d$, where both mass and {\it center-of-mass} (CoM) remain conserved and detailed balance…
The analysis of the dynamics of tracer particles in a complex bath can provide valuable information about the microscopic behaviour of the bath. In this work, we study the dynamics of a forced tracer in a colloidal bath by means of Langevin…
We consider Lagrangian coherent structures (LCSs) as the boundaries of material subsets whose advective evolution is metastable under weak diffusion. For their detection, we first transform the Eulerian advection-diffusion equation to…
The collective diffusion coefficient $D_\mathrm{coll}$ is a key quantity for describing the macroscopic transport properties of soft matter systems. However, measuring $D_\mathrm{coll}$ is a fundamental experimental and numerical challenge,…
Despite being a fundamental tool in soft matter research, quartz crystal microbalance (QCM) analyses of discrete macromolecules in liquid so far lack a firm theoretical basis. Currently, acoustic signals are qualitatively interpreted using…
The hydrodynamic interactions among bacterial cell bodies, flagella, and surrounding boundaries are essential for understanding bacterial motility in complex environments. In this study, we demonstrate that each slender flagellum can be…
The free energies of the FCC, BCC, HCP and Simple Cubic phases for hard spheres are calculated as a function of density using the Fundamental Measure Theory models of Rosenfeld et al (PRE 55, 4245 (1997)), Tarazona (PRL 84, 694 (2001)) and…
A quasi-two-dimensional system of hard spheres strongly confined between two parallel plates is considered. The attention is focussed on the macroscopic self-diffusion process observed when the system is looked from above or from below. The…
This work develops a quantitative homogenization theory for random suspensions of rigid particles in a steady Stokes flow, and completes recent qualitative results. More precisely, we establish a large-scale regularity theory for this…
A novel formulation of second-order relativistic viscous fluid dynamics based on the effective Boltzmann equation for quasi-particles with medium-dependent masses is briefly reviewed.~The evolution equations for the shear and bulk…
This article analyzes the formulation of space-time continuous hyperbolic hydrodynamic models for systems of interacting particles moving on a lattice, by connecting their local stochastic lattice dynamics to the formulation of an…
A stochastic model for the dynamics of enzymatic catalysis in explicit, effective solvents under physiological conditions is presented. Analytically-computed first passage time densities of a diffusing particle in a spherical shell with…
We present an extension of the Poisson-Boltzmann model in which the solute of interest is immersed in an assembly of self-orienting Langevin water dipoles, anions, cations, and hydrophobic molecules, all of variable densities. Interactions…
Proteins tend to bury hydrophobic residues inside their core during the folding process to provide stability to the protein structure and to prevent aggregation. Nevertheless, proteins do expose some 'sticky' hydrophobic residues to the…