Related papers: Modulating internal transition kinetics in respons…
We consider two particles performing continuous-time nearest neighbor random walk on $\mathbb Z$ and interacting with each other when they are at neighboring positions. Typical examples are two particles in the partial exclusion process or…
We review theoretical models of individual motility as well as collective dynamics and pattern formation of active particles. We focus on simple models of active dynamics with a particular emphasis on nonlinear and stochastic dynamics of…
We study self-organisation of collective motion as a thermodynamic phenomenon, in the context of the first law of thermodynamics. It is expected that the coherent ordered motion typically self-organises in the presence of changes in the…
We study the effect of the crowded nature of the cellular cytoplasm on the translocation of a polymer through a pore in a membrane. By systematically treating the entropic penalty due to crowding, we show that the translocation dynamics are…
We study the collective dynamics of repulsive self-propelled particles. The particles are governed by coupled equations of motion that include polar self-propulsion, damping of velocity and of polarity, repulsive particle-particle…
Unlike their model membrane counterparts, biological membranes are richly decorated with a heterogeneous assembly of membrane proteins. These proteins are so tightly packed that their excluded area interactions can alter the free energy…
We analyze the dynamics of Brownian ratchets in a confined environment. The motion of the particles is described by a Fick-Jakobs kinetic equation in which the presence of boundaries is modeled by means of an entropic potential. The cases…
We study a system of self-propelled disks that perform run-and-tumble motion, where particles can adopt more than one internal state. One of those internal states can be transmitted to another particle if the particle carrying this state…
Active particle systems are a class of non-equilibrium systems composed of self-propelled Brownian particles; through interactions between particles within the system, a variety of intriguing collective behaviors can emerge. Based on…
Brownian Dynamics algorithms are widely used for simulating soft-matter and biochemical systems. In recent times, their application has been extended to the simulation of coarse-grained models of cellular networks in simple organisms. In…
We study the one-dimensional motion of a Brownian particle inside a confinement described by two reactive boundaries which can partially reflect or absorb the particle. Understanding the effects of such boundaries is important in physics,…
We study the dynamics of quantum excitations inside macromolecules which can undergo conformational transitions. In the first part of the paper, we use the path integral formalism to rigorously derive a set of coupled equations of motion…
Collective and directed motility or swarming is an emergent phenomenon displayed by many self-organized assemblies of active biological matter such as clusters of embryonic cells during tissue development, cancerous cells during tumor…
A simple phenomenological model for describing the conformational dynamics of biological macromolecules via the nonlinearity-induced instabilities is proposed. It is shown that the interaction between charges and bending degrees of freedom…
We show that the force generated by active enzyme molecules are strong enough to influence the dynamics of their surroundings under artificial crowded environments. We measured the behavior of polymer microparticles in a…
Dynamical polydispersity in single-particle properties, for example a fluctuating particle size, shape, charge density, etc., is intrinsic to responsive colloids (RCs), such as biomacromolecules or microgels, but is typically not resolved…
We present Langevin dynamics simulations that study the collective behavior of driven particles embedded in a densely packed background consisting of passive particles. Depending on the driving force, the densities of driven and passive…
The emergence of collective motion, also known as flocking or swarming, in groups of moving individuals who orient themselves using only information from their neighbors is a very general phenomenon that is manifested at multiple spatial…
We study the collective behaviour of an ensemble of coupled motile elements whose interactions depend on time and are alternatively attractive or repulsive. The evolution of interactions is driven by individual internal variables with…
Classical swarm models, exemplified by the Cucker--Smale framework, provide foundational insights into collective alignment but exhibit fundamental limitations in capturing the adaptive, heterogeneous behaviours intrinsic to living systems.…