Related papers: Conformational transformations induced by the char…
Active processes in living systems generate nonequilibrium forces that deform embedded passive macromolecules. To understand how such dynamics influence polymer conformation, we study a flexible passive chain in an active nematic fluid.…
Similarly-charged polymers in solution, known as polyelectrolytes, are known to form aggregated structures in the presence of oppositely charged counterions. Understanding the dependence of the equilibrium phases and the dynamics of the…
Cellular aggregates play a significant role in the evolution of biological systems such as tumor growth, tissue spreading, wound healing, and biofilm formation. Analysis of such biological systems, in principle, includes examining the…
In the Kirchhoff model of a biopolymer, conformation dynamics can be described in terms of solitary waves, for certain special cross-section asymmetries. Applying this to the problem of electron transport, we show that the quantum effective…
Experimental evidence shows that there is a feedback between cell shape and cell motion. How this feedback impacts the collective behavior of dense cell monolayers remains an open question. We investigate the effect of a feedback that tends…
Aggregation of like-charged polymers is widely observed in biological and soft matter systems. In many systems, bundles are formed when a short-range attraction of diverse physical origin like charge-bridging, hydrogen-bonding or…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…
We present molecular dynamics simulations of aggregation kinetics in a colloidal suspension modeled as a highly asymmetric binary mixture. Starting from a configuration with largely uncorrelated colloidal particles the system relaxes by…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…
We investigate a set of design principles that link specific features of interparticle interactions to predictable structural and dynamic outcomes in two-dimensional self-assembly, a framework relevant to soft matter and biological…
We consider model of a complex particle that consists of a rigid shell and a nucleus with spatial asymmetric interaction. The particle's dynamics with the nucleus driven by a periodic excitation is considered. It is shown that…
The macroscopic behaviour of active matter arises from nonequilibrium microscopic processes. In soft materials, active stresses typically drive macroscopic shape changes, which in turn alter the geometry constraining the microscopic…
Inspired by recent experiments on chromosomal dynamics, we introduce an exactly solvable model for the interaction between a flexible polymer and a set of motor-like enzymes. The enzymes can bind and unbind to specific sites of the polymer…
Molecular dynamics simulation methods are used to study the folding of polymer chains into packed cubic states. The polymer model, based on a chain of linked sites moving in the continuum, includes both excluded volume and torsional…
Bacteria possess diverse mechanisms to regulate their motility in response to environmental and physiological signals, enabling them to navigate complex habitats and adapt their behavior. Among these mechanisms, interspecies recognition…
A simple model of an active colloid consisting of dumbbell-shaped particles that cyclically change their length without propelling themselves is proposed and analyzed. At nanoscales, it represents an idealization for bacterial cytoplasm or…
Based on Brownian Dynamics computer simulations in two dimensions we investigate aggregation scenarios of colloidal particles with directional interactions induced by multiple external fields. To this end we propose a model which allows…
Chemical affinities are responsible for driving active matter systems out of equilibrium. At the nano-scale, molecular machines interact with the surrounding environment and are subjected to external forces. The mechano-chemical coupling…
Heterogeneous distribution of passive and active domains in the chromosome plays a crucial role for its dynamic organization within the cell nucleus. Motivated by that here we investigate the steady-state conformation and dynamics of a…