Related papers: Depletion interactions modulate coupled folding an…

We study the role of active coupling on the transport properties of homogeneously charged macromolecules in an infinitely dilute solution. An enzyme becomes actively bound to a segment of the macromolecule, exerting an electrostatic force…

Effective interactions inherently encompass many-body effects that appear unified. Analyzing these in reverse, that is, separating them into contributions from pairs, triples, or larger groups, is typically intricate and seldom pursued.…

Molecular dynamics simulations of interacting soft disks confined in a heterogeneous quenched matrix of soft obstacles show dynamics which is fundamentally different from that of hard disks. The interactions between the disks can enhance…

The spatial organization of cell membrane glycoproteins and glycolipids is critical for mediating the binding of ligands, receptors, and macromolecules on the plasma membrane. However, we currently do not have the methods to quantify the…

Numerous problems in development, regeneration, and disease involve simultaneous evolution of both spatial organization and the internal state of the constituents in addition to local interactions and crowding. This motivates us to study a…

The well-posedness and regularity properties of diffusion-aggregation equations, emerging from interacting particle systems, are established on the whole space for bounded interaction force kernels by utilizing a compactness convergence…

Collective response of the plasma medium is well known and has been explored extensively in several contexts. The single particle response is typically treated as collisional interactions leading to dissipative effects. In this manuscript a…

The dynamical behavior of binary mixtures consisting of highly charged colloidal particles is studied by means of Brownian dynamics simulations. We investigate differently sized, but identically charged particles with nearly identical…

Large scale molecular dynamics and grand canonical Monte Carlo simulation techniques are used to study the behavior of the interdiffusion of a solvent into an entangled polymer matrix as the state of the polymer changes from a melt to a…

Associative polymer networks have shown a major promise in fabrication of self-healing and responsive materials. The can also serve as simple models to study more complex biological systems where transient interactions play an important…

Polymers adopt extended coil and compact globule states according to the balance between entropy and interaction energies. The transition of a polymer between an extended coil state and compact globule state can be induced by changing…

Interfacial properties of colloid--polymer mixtures are examined within an effective one--component representation, where the polymer degrees of freedom are traced out, leaving a fluid of colloidal particles interacting via polymer--induced…

In this paper, we employ Molecular Dynamics computer simulations to study and compare the statics and dynamics of linear and circular (ring) polymer chains in entangled solutions of different densities. While we confirm that linear chain…

Periodically sheared colloids at low densities demonstrate a dynamical phase transition from an inactive to active phase as the strain amplitude is increased. The inactive phase consists of no collisions/contacts between particles in the…

Intercellular exchange networks are essential for the adaptive capabilities of populations of cells. While diffusional exchanges have traditionally been difficult to map, recent advances in nanotechnology enable precise probing of exchange…

Biomolecular condensates composed of intrinsically disordered proteins (IDPs) are vital for proper cellular function, and their dysfunction is associated with diseases including neurodegeneration and cancer. Despite their biological…

We study the dynamics of polymer chains in a bath of self-propelled particles (SPP) by extensive Langevin dynamics simulations in a two dimensional system. Specifically, we analyse the polymer looping properties versus the SPP activity and…

We use Markov state models (MSMs) to analyze the dynamics of a $\beta$-hairpin-forming peptide in Monte Carlo (MC) simulations with interacting protein crowders, for two different types of crowder proteins [bovine pancreatic trypsin…

Ion clustering has been proposed as a mechanism leading to the peculiar 'anomalous underscreening' phenomenon seen for electrostatic interactions between charge surfaces immersed in concentrated electrolytes. These interactions have been…

Modeling approaches of suspended, rod-like particles and recent experimental data have shown that depletion forces display different signatures depending on the orientation of these particles. It has been shown that axial attraction of two…