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Over the last decade, next-generation neural mass models have become increasingly prominent in mathematical neuroscience. These models link microscopic dynamics with low-dimensional systems of so-called firing rate equations that exactly…
The diffusion of molecules (penetrants) of variable size, shape, and chemistry through dense crosslinked polymer networks is a fundamental scientific problem that is broadly relevant in materials, polymer, physical and biological chemistry.…
Abridged abstract: Inert interactions between randomly moving entities and spatial disorder play a crucial role in quantifying the diffusive properties of a system. These interactions affect only the movement of the entities, and examples…
As first explained by the classic Asakura-Oosawa (AO) model, effective attractive forces between colloidal particles induced by depletion of nonadsorbing polymers can drive demixing of colloid-polymer mixtures into colloid-rich and…
There are many proteins or protein complexes which have multiple DNA binding domains. This allows them to bind to multiple points on a DNA molecule (or chromatin fibre) at the same time. There are also many proteins which have been found to…
Intracellular processes often rely on the timely encounter of mobile reaction partners, including intermittently motor-driven organelles. The underlying cytoskeletal network presents a complex landscape that both directs particle movement…
We use computer simulations to study the onset of collective motion in systems of interacting active particles. Our model is a swarm of active Brownian particles with internal energy depot and interactions inspired by the dissipative…
We study the dynamics of proliferating cell collectives whose microscopic constituents' growth is inhibited by macroscopic growth-induced stress. Discrete particle simulations of a growing collective show the emergence of concentric-ring…
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…
Motivated by recent nanofluidics experiments, we use Brownian dynamics and Monte Carlo simulations to study the conformation, organization and dynamics of two polymer chains confined to a single box-like cavity. The polymers are modeled as…
Single molecule and NMR measurements of protein dynamics increasingly uncover the complexity of binding scenarios. Here we describe an extended conformational selection model which embraces a repertoire of selection and adjustment…
Semi-flexible polymers in crowded environments exhibit complex dynamics that play a crucial role in various biological and material design processes. Based on the classic reptation theory, it is generally believed that semiflexible polymers…
30% of the DNA in E. coli bacteria is covered by proteins. Such high degree of crowding affect the dynamics of generic biological processes (e.g. gene regulation, DNA repair, protein diffusion etc.) in ways that are not yet fully…
Macromolecular diffusion in strongly confined geometries and crowded environments is still to a large extent an open subject in soft matter physics and biology. In this paper, we employ large-scale Langevin dynamics simulations to…
We use molecular dynamics simulations to study a semidilute, unentangled polymer solution containing well dispersed, weakly attractive nanoparticles (NP) of size ($\sigma_N$) smaller than the polymer radius of gyration $R_g$. We find that…
Designing microscopic and nanoscopic self-propelled particles and characterising their motion has become a major scientific challenge over the past decades. To this purpose, phoretic effects, namely propulsion mechanisms relying on local…
Recent studies in the collective behavior of active colloids have shown that a global polar order may emerge due to long-ranged chemo-repulsive interactions between them. Here, we report the role of pinning disorder in the flocking…
We introduce a representative minimal model for phoretically interacting active colloids. Combining kinetic theory, linear stability analyses, and a general relation between self-propulsion and phoretic interactions in auto-diffusiophoretic…
Many-body interactions in systems of active matter can cause particles to move collectively and self-organize into dynamic structures with long-range order. In cells, the self-assembly of cytoskeletal filaments is critical for cellular…
The dynamical properties and diffusive behavior of a collection of mutually interacting particles are numerically investigated for two types of long-range interparticle interactions: Coulomb-electrostatic and dipole-electrodynamic. It is…