Related papers: Actin automata with memory
The phase behavior of charged rods in the presence of inter-rod linkers is studied theoretically as a model for the equilibrium behavior underlying the organization of actin filaments by linker proteins in the cytoskeleton. The presence of…
Reconstituted filamentous actin networks with myosin motor proteins form active gels, in which motor proteins generate forces that drive the network far from equilibrium. This motor activity can also strongly affect the network elasticity;…
Agent-based models typically treat systems in isolation, discarding environmental coupling as either computationally prohibitive or dynamically irrelevant. We demonstrate that this neglect misses essential physics: environmental degrees of…
Mounting experimental evidence suggests that brain-state-specific neural mechanisms, supported by connectomic architectures, play a crucial role in integrating past and contextual knowledge with the current, incoming flow of evidence (e.g.,…
Ordered, collective motions commonly arise spontaneously in systems of many interacting, active units, ranging from cellular tissues and bacterial colonies to self-propelled colloids and animal flocks. Active phases are especially rich when…
Cytoskeletal motors known as motor proteins are molecules that drive cellular transport along several parallel cytoskeletal filaments and support many biological processes. Experimental evidences suggest that they interact with the nearest…
We have used numerical simulations to investigate how the properties of motor proteins control the dynamical behavior of a driven flexible filament. The filament is pinned at one end and positioned on top of a patch of anchored motor…
Molecular motors are involved in key transport processes inside actin-based cellular protrusions. The motors carry cargo proteins to the protrusion tip which participate in regulating the actin polymerization, and play a key role in…
We explore the concept of memory in scalar active matter, focusing on the collective dynamics of particles whose interactions depend on their evolutionary history rather than solely on their current configuration. We introduce the idea of…
Number-conserving cellular automata are discrete dynamical systems that simulate interacting particles like e.g. grains of sand. In an earlier paper, I had already derived a uniform construction for all transition rules of one-dimensional…
We study two-dimensional cellular automata, each cell takes three states: resting, excited and refractory. A resting cell excites if number of excited neighbours lies in a certain interval (excitation interval). An excited cell become…
We model analytically the dynamics of a cytoskeletal filament in a motility assay. The filament is described as rigid rod free to slide in two dimensions. The motor proteins consist of polymeric tails tethered to the plane and modeled as…
Active automata learning (AAL) is a method to infer state machines by interacting with black-box systems. Adaptive AAL aims to reduce the sample complexity of AAL by incorporating domain specific knowledge in the form of (similar) reference…
Neural Cellular Automata (NCA) are a powerful combination of machine learning and mechanistic modelling. We train NCA to learn complex dynamics from time series of images and PDE trajectories. Our method is designed to identify underlying…
This article presents an artificial intelligence (AI) architecture intended to simulate the iterative updating of the human working memory system. It features several interconnected neural networks designed to emulate the specialized…
The dynamics group of an asynchronous cellular automaton (ACA) relates properties of its long term dynamics to the structure of Coxeter groups. The key mathematical feature connecting these diverse fields is involutions. Group-theoretic…
Collective cell migration in 3D extracellular matrix (ECM) is crucial to many physiological and pathological processes. Migrating cells can generate active pulling forces via actin filament contraction, which are transmitted to the ECM…
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…
We report the results of a numerical study of nonequilibrium steady states for a class of Hamiltonian models. In these models of coupled matter-energy transport, particles exchange energy through collisions with pinned-down rotating disks.…
Biological functions rely on ordered structures and intricately controlled collective dynamics. In contrast to systems in thermodynamic equilibrium, order is typically established and sustained in stationary states by continuous dissipation…