Related papers: Modulating internal transition kinetics in respons…
Intrinsically disordered proteins (IDPs) abound in cellular regulation. Their interactions are often transitory and highly sensitive to salt concentration and posttranslational modifications. However, little is known about the effect of…
We study the influence of intrinsic noise on the structure and dynamics of responsive colloids (RCs) which actively change their size and mutual interactions. The colloidal size is explicitly resolved in our RC model as an internal degree…
Active matter physics and swarm robotics have provided powerful tools for the study and control of ensembles driven by internal sources. At the macroscale, controlling swarms typically utilizes significant memory, processing power, and…
We investigate the effect of macromolecular crowding on protein folding, using purely repulsive crowding particles and a self-organizing polymer model of protein folding. We find that the thermodynamics of folding for typical alpha-, beta-…
This paper introduces a crowd modeling and motion control approach that employs diffusion adaptation within an adaptive network. In the network, nodes collaboratively address specific estimation problems while simultaneously moving as…
Intracellular transport of vesicular cargos, organelles, and other macromolecules is an essential process to move large items through a crowded, and inhomogeneous cellular environment. In an effort to dissect the fundamental effects of…
After summarizing basic features of self-organization such as entropy export, feedbacks and nonlinear dynamics, we discuss several examples in biology. The main part of the paper is devoted to a model of active Brownian motion that allows a…
The reaction-diffusion master equation (RDME) is a standard modelling approach for understanding stochastic and spatial chemical kinetics. An inherent assumption is that molecules are point-like. Here we introduce the crowded…
We study a model of interacting random walkers that proposes a simple mechanism for the emergence of cooperation in group of individuals. Each individual, represented by a Brownian particle, experiences an interaction produced by the local…
We describe simulations of active Brownian particles carried out to explore how dynamics and clustering are influenced by particle shape. Our particles are composed of four disks, held together by springs, whose relative size can be varied.…
Protein dynamics in cells may be different from that in dilute solutions in vitro since the environment in cells is highly concentrated with other macromolecules. This volume exclusion due to macromolecular crowding is predicted to affect…
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…
The cytoplasm of a living cell is crowded with several macromolecules of different shapes and sizes. Molecular diffusion in such a medium becomes anomalous due to the presence of macromolecules and diffusivity is expected to decrease with…
In crowded systems, particle currents can be mediated by propagating collective excitations which are generated as rare events, are localized and have a finite lifetime. The theoretical description of such excitations is hampered by the…
We study a strongly interacting crowded system of self-propelled stiff filaments by event-driven Brownian dynamics simulations and an analytical theory to elucidate the intricate interplay of crowding and self-propulsion. We find a…
The spatiotemporal coordination and regulation of cell proliferation is fundamental in many aspects of development and tissue maintenance. Cells have the ability to adapt their division rates in response to mechanical constraints, yet we do…
We present an experimental study on the collective behavior of macroscopic self-propelled particles that are externally excited by light. This property allows testing the system response to the excitation intensity in a very versatile…
We investigate the motility of a growing population of cells in a idealized setting: we consider a system of hard disks in which new particles are added according to prescribed growth kinetics, thereby dynamically changing the number…
Biochemical reactions inside living cells often occur in the presence of crowders -- molecules that do not participate in the reactions but influence the reaction rates through excluded volume effects. However the standard approach to…
In this work, we study a system of passive Brownian (non-self-propelled) particles in two dimensions, interacting only through a social-like force (velocity alignment in this case) that resembles Kuramoto's coupling among phase oscillators.…