Related papers: Modulating internal transition kinetics in respons…
Navigation of microorganisms is controlled by internal processes ultimately sensitive to mechanical or chemical signaling encountered along the path. In many natural environments, such as porous soils or physiological ducts, motile species…
Current mathematical frameworks for predicting the flux state and macromolecular composition of the cell do not rely on thermodynamic constraints to determine the spontaneous direction of reactions. These predictions may be biologically…
Self-propelled particles undergoing persistent motion can accumulate either through excluded-volume interactions or through quorum sensing, where self-propulsion decreases at high local density. Using kinetic balance theory and simulations,…
In active matter systems, self-propelled particles can self-organize to undergo collective motion, leading to persistent dynamical behavior out of equilibrium. In cells, cytoskeletal filaments and motor proteins self-organize into complex…
The well-known Cucker-Smale model is a macroscopic system reflecting flocking, i.e. the alignment of velocities in a group of autonomous agents having mutual interactions. In the present paper, we consider the mean-field limit of that…
Positive feedback regulation is ubiquitous in cell signaling networks, often leading to binary outcomes in response to graded stimuli. However, the role of such feedbacks in clustering, and in spatial spreading of activated molecules, has…
We have developed an experimental setup of very simple self-propelled robots to observe collective motion emerging as a result of inelastic collisions only. A circular pool and commercial RC boats were the basis of our first setup, where we…
While the impact of crowding on the diffusive transport of molecules within a cell is widely studied in biology, it has thus far been neglected in traffic systems where bulk behavior is the main concern. Here, we study the effects of…
We introduce a simple model of active transport for an ensemble of particles driven by an external shear flow. Active refers to the fact that the flow of the particles is modified by the distribution of particles itself. The model consists…
We review the effects of macromolecular crowding on the folding of RNA by considering the simplest scenario when excluded volume interactions between crowding particles and RNA dominate. Using human telomerase enzyme as an example, we…
Collective dynamics of many interacting particles have been widely studied because of a wealth of their behavioral patterns quite different from the individual traits. A selective way of birds that reacts to their neighbors is one of the…
Motor enzymes are remarkable molecular machines that use the energy derived from the hydrolysis of a nucleoside triphosphate to generate mechanical movement, achieved through different steps that constitute their kinetic cycle. These…
We present a geometric design rule for size-controlled clustering of self-propelled particles. We show that active particles that tend to rotate under an external force have an intrinsic, signed parameter with units of curvature which we…
We study the evolution of a collection of individuals subject to Brownian diffusion, reproduction and disappearance. In particular, we focus on the case where the individuals are initially prepared at equilibrium within a confined geometry.…
During the life cycle of bacterial cells the non-mixing of the two ring-shaped daughter genomes is an important prerequisite for the cell division process. Mimicking the environments inside highly crowded biological cells, we study the…
Microscopic mechanisms of natural processes are frequently understood in terms of random walk models by analyzing local particle transitions. This is because these models properly account for dynamic processes at the molecular level and…
Natural selection has shaped the evolution of cells and multi-cellular organisms such that social cooperation can often be preferred over an individualistic approach to metabolic regulation. This paper extends a framework for dynamic…
The migration of cells is relevant for processes such as morphogenesis, wound healing, and invasion of cancer cells. In order to move, single cells deform cyclically. However, it is not understood how these shape oscillations influence…
The colonisation of a soft passive material by motile cells such as bacteria is common in biology. The resulting colonies of the invading cells are often observed to exhibit intricate patterns whose morphology and dynamics can depend on a…
The ability of biological and artificial collectives to outperform solitary individuals in a wide variety of tasks depends crucially on the efficient processing of social and environmental information at the level of the collective. Here,…