Related papers: How hydrodynamic interactions alter polymer stretc…
We recently introduced a model of an asymmetric dumbbell made of two hydrodynamically coupled subunits as a minimal model for a macromolecular complex, in order to explain the observation of enhanced diffusion of catalytically active…
We study the translocation of a semiflexible polymer through extended pores with patterned stickiness, using Langevin dynamics simulations. We find that the consequence of pore patterning on the translocation time dynamics is dramatic and…
Effects of multi-gradient fields on the transport of a polymer chain have been investigated by using generalized Langevin dynamics simulations. We observe that the natural frequency of tumbling follows $Wi^{0.66}$ scaling, where $Wi$ is the…
We investigate diffusion-limited reactions between a diffusing particle and a target site on a semiflexible polymer, a key factor determining the kinetics of DNA-protein binding and polymerization of cytoskeletal filaments. Our theory…
The mechanism of hydrodynamics-induced pairing of soft particles, namely closed bilayer membranes (vesicles, a model system for red blood cells) and drops, is studied numerically with a special attention paid to the role of the confinement…
We present Brownian dynamics simulation results of a flexible linear polymer with excluded-volume interactions under shear flow in the presence of active noise. The active noise strongly affects the polymer's conformational and dynamical…
The conformation of a long linear polymer dissolved in fluid and exposed to an extensional flow is well-known to exhibit a "coil-stretch" transition, which for sufficiently long chains can lead to bistability. The present work reports…
We study the mechanical stiffening behavior in two-dimensional (2D) cross-linked networks of semiflexible biopolymer filaments under simple shear. Filamental constituents immersed in a fluid undergo thermally excited bending motions.…
The dynamics of structural relaxation in a model polymer glass subject to spatially-homogeneous, time-periodic shear deformation is investigated using molecular dynamics simulations. We study a coarse-grained bead-spring model of short…
This article gives an overview of recent theoretical and experimental findings concerning the hydrodynamic interaction between liquid-embedded particles in various confined geometries. A simple unifying description emerges, which accounts…
We investigate previously unclarified effects of fluid elasticity on shear-thickening in dilute suspensions in an Oldroyd-B viscoelastic fluid using a novel direct numerical simulation based on the smoothed profile method. Fluid elasticity…
Crystallization is often assumed to be a quasi-static process that is unaffected by details of particle transport other than the bulk diffusion coefficient. Therefore colloidal suspensions are frequently argued to be an ideal toy model for…
We explore the effect of an attractive interaction between parallel-aligned polymers, which are perpendicularly grafted on a substrate. Such an attractive interaction could be due to, e.g., reversible cross-links. The competition between…
The equilibrium properties of polymer droplets on a soft deformable surface are investigated by molecular dynamics simulations of a bead-spring model. The surface consists of a polymer brush with irreversibly end-tethered linear homopolymer…
Peritrichous bacteria swim in viscous fluids by rotating multiple helical flagellar filaments. As the bacterium swims forward, all its flagella rotate in synchrony behind the cell in a helical bundle. When the bacterium changes its…
We have developed a simulation technique of multiscale Lagrangian fluid dynamics to tackle hierarchical problems relating to historical dependency of polymeric fluid. We investigate flow dynamics of dilute polymeric fluid by using the…
We investigate entanglement dynamics in bipartite systems governed by inhomogeneous Hamiltonians of the form $H = H_L + H_R$, where $H_{L/R}$ acts only on the left or right region and is homogeneous within each region. Focusing on the XX…
Cracking the whip accelerates the tail of a chain to hit the air loudly and clearly. We proved that the similar acceleration effect causes coil deformation of driven chain-like polymers. We first preformed Monte Carlo simulations of a…
Heteropolymers are ubiquitous in both synthetic systems, such as block copolymers, and biological macromolecules, including proteins and nucleic acids. Beyond their chemical composition, these polymers often exhibit spatial variations in…
The Hamiltonian dynamics of chains of nonlinearly coupled particles is numerically investigated in two and three dimensions. Simple, off-lattice homopolymer models are used to represent the interparticle potentials. Time averages of…