Related papers: Active Brownian agents with concentration-dependen…
We develop an agent-based model of the motion and pattern formation of vesicles. These intracellular particles can be found in four different modes of (undirected and directed) motion and can fuse with other vesicles. While the size of…
Organic synthesis stands as a cornerstone of the chemical industry. The development of robust machine learning models to support tasks associated with organic reactions is of significant interest. However, current methods rely on…
The phoretic Brownian dynamics method is shown here to be an effective approach to simulate the properties of colloidal chemophoretic based systems. The method is then optimized to allow for the comparison with results from multiparticle…
We consider various modeling levels for spatially homogeneous chemical reaction systems, namely the chemical master equation, the chemical Langevin dynamics, and the reaction-rate equation. Throughout we restrict our study to the case where…
We consider a general discrete model for heterogeneous semiflexible polymer chains. Both the thermal noise and the inhomogeneous character of the chain (the disorder) are modeled in terms of random rotations. We focus on the quenched…
Many active particles are embedded in environments that exhibit viscoelastic properties. An important class of such media lacks a single characteristic relaxation timescale when subjected to a time-dependent stress. Rather, the stress…
Biological sensory systems generally operate out of equilibrium, which often leads to their improved performance. Here, we study the sensitivity of ligand concentration for a general receptor model, which is generally in the non-equilibrium…
Realistic examples of reaction-diffusion phenomena governing spatial and spatiotemporal pattern formation are rarely isolated systems, either chemically or thermodynamically. However, even formulations of `open' reaction-diffusion systems…
Within a Lagrangian formalism we derive the time-dependent Gutzwiller approximation for general multi-band Hubbard models. Our approach explicitly incorporates the coupling between time-dependent variational parameters and a time-dependent…
In this paper we examine boundary effects in a fractional chemotactic equation derived from a kinetic transport model describing cell movement in response to chemical gradients (chemotaxis). Specifically, we analyze reflecting boundary…
The equilibrium properties of a system of passive diffusing particles in an external magnetic field are unaffected by the Lorentz force. In contrast, active Brownian particles exhibit steady-state phenomena that depend on both the strength…
The interplay between structure and dynamics in non-equilibrium steady-state is far from understood. We address this interplay by tracking Brownian Dynamics trajectories of particles in a binary colloid of opposite charges in an external…
We present a so-called adaptive Ising model (AIM) to provide a unifying explanation for sensitivity and perfect adaptation in bacterial chemotactic signalling, based on coupling among receptor dimers. In an AIM, an external field,…
We present a systematic mathematical analysis of the qualitative steady-state response to rate perturbations in large classes of reaction networks. This includes multimolecular reactions and allows for catalysis, enzymatic reactions,…
In modeling the inflammatory response to a lesion in an artery wall, there are a number of chemotactic mechanisms going on within the wall layer that lead to an arterial plaque. We introduce a rather reduced model of these dynamic…
Most biochemical reactions in living cells rely on diffusive search for target molecules or regions in a heterogeneous overcrowded cytoplasmic medium. Rapid re-arrangements of the medium constantly change the effective diffusivity felt…
We show the linear response theory of spatial-scale-dependent relaxation moduli for overdamped Brownian particle systems. We employ the Irving-Kirkwood stress tensor field as the microscopic stress tensor field. We show that the…
Atoms subject to weak coherent incident light can be treated as coupled classical linear oscillators, supporting subradiant and superradiant collective excitation eigenmodes. We identify the limits of validity of this \emph{linear classical…
Chemical reaction networks (CRN) comprise an important class of models to understand biological functions such as cellular information processing, the robustness and control of metabolic pathways, circadian rhythms, and many more. However,…
Brownian motion in a granular gas in a homogeneous cooling state is studied theoretically and by means of molecular dynamics. We use the simplest first-principle model for the impact-velocity dependent restitution coefficient, as it follows…