Related papers: Towards the cellular-scale simulation of motor-dri…
Active matter consists of self-propelled elements exhibits fascinating collective motions ranging from biological to artificial systems. Among wide varieties of active matter systems, reconstituted bio-filaments moving on molecular motor…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
Living systems are made of active materials with microscopic components that work together to perform macroscopic biological tasks. The breakdown of these collective functionalities leads to diseases, which, conversely, could be treated by…
Processive molecular motors which drive the traffic of organelles in cells move in a directed way along cytoskeletal filaments. On large time scales, they perform motor walks, i.e., peculiar random walks which arise from the repeated…
Inspired by the complex influence of the globular crosslinking proteins on the formation of biofilament bundles in living organisms, we study and analyze a theoretical model for the structure and thermodynamics of bundles of helical…
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 matter---ranging from molecular motors and cytoskeletal…
In cells and in vitro assays the number of motor proteins involved in biological transport processes is far from being unlimited. The cytoskeletal binding sites are in contact with the same finite reservoir of motors (either the cytosol or…
This paper presents a software platform, named BiNS2, able to simulate diffusion-based molecular communications with drift inside blood vessels. The contribution of the paper is twofold. First a detailed description of the simulator is…
Active matter systems may be characterised by the conversion of energy into active motion, e.g. the self-propulsion of microorganisms. Artificial active colloids form models which exhibit essential properties of more complex biological…
It is known from the wave-like motion of microtubules in motility assays that the piconewton forces that motors produce can be sufficient to bend the filaments. In cellular phenomena such as cytosplasmic streaming, molecular motors…
We propose a novel mechanism of cell motility, which relies on the coupling of actin polymerization at the cell membrane to geometric confinement. We consider a polymerizing viscoelastic cytoskeletal gel confined in a narrow channel, and…
One common feature of a vehicle, an ant and a kinesin motor is that they all convert chemical energy, derived from fuel or food, into mechanical energy required for their forward movement; such objects have been modelled in recent years as…
Active matter agents consume internal energy or extract energy from the environment for locomotion and force generation. Already rather generic models, such as ensembles of active Brownian particles, exhibit phenomena, which are absent at…
Building mathematical models of brains is difficult because of the sheer complexity of the problem. One potential starting point is through basal cognition, which gives abstract representation of a range of organisms without central nervous…
Intracellular transport along microtubules or actin filaments, powered by molecular motors such as kinesins, dyneins or myosins, has been recently modeled using one-dimensional driven lattice gases. We discuss some generalizations of these…
In this paper, we develop and analyze a minimal model for a 2D network of cross-linked actin filaments and myosin motors, representing the cortical cytoskeleton of eukaryotic cells. We implement coarse-grained representations of force…
Epithelial cell monolayers show remarkable displacement and velocity correlations over distances of ten or more cell sizes that are reminiscent of supercooled liquids and active nematics. We show that many observed features can be described…
Eukaryotic cells are mechanically supported by a polymer network called the cytoskeleton, which consumes chemical energy to dynamically remodel its structure. Recent experiments in vivo have revealed that this remodeling occasionally…
We propose a mechanism of cell motility which is based on contraction and does not require protrusion. The contraction driven translocation of a cell is due to internal flow of the cytoskeleton generated by molecular motors. Each motor…
The functioning of machines typically requires a concerted action of their parts. This requirement also holds for molecular motors that drive vital cellular processes and imposes constraints on their conformational changes as well as the…