A variety of computational models have been developed to describe active matter at different length and time scales. The diversity of the methods and the challenges in modeling active matterranging from molecular motors and cytoskeletal filaments over artificial and biological swimmers on microscopic to groups of animals on macroscopic scales-mainly originate from their out-ofequilibrium character, multiscale nature, nonlinearity, and multibody interactions. In the present review, various modeling approaches and numerical techniques are addressed, compared, and differentiated to illuminate the innovations and current challenges in understanding active matter. The complexity increases from minimal microscopic models of dry active matter toward microscopic models of active matter in fluids. Complementary, coarse-grained descriptions and continuum models are elucidated. Microscopic details are often relevant and strongly affect collective behaviors, which implies that the selection of a proper level of modeling is a delicate choice, with simple models emphasizing universal properties and detailed models capturing specific features. Finally, current approaches to further advance the existing models and techniques to cope with real-world applications, such as complex media and biological environments, are discussed.2
We study the effect of polydispersity on the macroscopic physical properties of granular packings in two and three dimensions. A mean-field approach is developed to approximate the macroscale quantities as functions of the microscopic ones. We show that the trace of the fabric and stress tensors are proportional to the mean packing properties (e.g., packing fraction, average coordination number, and average normal force) and dimensionless correction factors, which depend only on the moments of the particle-size distribution. Similar results are obtained for the elements of the stiffness tensor of isotropic packings in the linear affine response regime. Our theoretical predictions are in good agreement with the simulation results.
We propose a stochastic model for the intersection of two urban streets. The vehicular traffic at the intersection is controlled by a set of traffic lights which can be operated subject to fix-time as well as traffic adaptive schemes. Vehicular dynamics is simulated within the framework of the probabilistic cellular automata and the delay experienced by the traffic at each individual street is evaluated for specified time intervals. Minimising the total delay of both streets gives rise to the optimum signalisation of traffic lights. We propose some traffic responsive signalisation algorithms which are based on the concept of cut-off queue length and cut-off density.
We show that the flagellar number affects the intrinsic dynamics of swimming bacteria and governs their transport efficiency.
Transmembrane receptor clustering is a ubiquitous phenomenon in pro- and eukaryotic cells to physically sense receptor/ligand interactions and subsequently translate an exogenous signal into a cellular response. Despite that receptor cluster formation has been described for a wide variety of receptors, ranging from chemotactic receptors in bacteria to growth factor and neurotransmitter receptors in mammalian cells, a mechanistic understanding of the underlying molecular processes is still puzzling. In an attempt to fill this gap we followed a combined experimental and theoretical approach by dissecting and modulating cargo binding, internalization and cellular response mediated by KDEL receptors (KDELRs) at the mammalian cell surface after interaction with a model cargo/ligand. Using a fluorescent variant of ricin toxin A chain as KDELR-ligand (eGFP-RTAH/KDEL), we demonstrate that cargo binding induces dose-dependent receptor cluster formation at and subsequent internalization from the membrane which is associated and counteracted by anterograde and microtubule-assisted receptor transport to preferred docking sites at the plasma membrane. By means of analytical arguments and extensive numerical simulations we show that cargo-synchronized receptor transport from and to the membrane is causative for KDELR/cargo cluster formation at the mammalian cell surface.
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