Related papers: Actin automata with memory
We present a new classification of elementary cellular automata. It is based on the structure of the network of states, connected with the transitions between them; the latter are determined by the automaton rule. Recently an algorithm has…
Associative memory models retrieve stored information through content-based addressing, mimicking the neural processes of animal brains. The classical Hopfield network-based models store memories as vectors of discrete values and have good…
Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these…
Biological molecular machines are enzymes that simultaneously catalyze two processes, one donating free energy and second accepting it. Recent studies show that most native protein enzymes have a rich stochastic dynamics that often…
Understanding the role of non-equilibrium driving in self-organization is crucial for developing a predictive description of biological systems, yet it is impeded by their complexity. The actin cytoskeleton serves as a paradigm for how…
Polymerization of actin proteins into dynamic structures is essential to eukaryotic cell life. This has motivated a large body of in vitro experiments measuring polymerization kinetics of individual filaments. Here we model these kinetics,…
In this paper we present a novel approach to automatically infer parameters of spiking neural networks. Neurons are modelled as timed automata waiting for inputs on a number of different channels (synapses), for a given amount of time (the…
Myosin II is the muscle molecular motor that works in two bipolar arrays in each thick filament of the striated (skeletal and cardiac) muscle, converting the chemical energy into steady force and shortening by cyclic ATP--driven…
The actin cytoskeleton is an active semi-flexible polymer network whose non-equilibrium properties coordinate both stable and contractile behaviors to maintain or change cell shape. While myosin motors drive the actin cytoskeleton…
Motor-proteins are responsible for transport inside cells. Harnessing their activity is key towards developing new nano-technologies, or functional biomaterials. Cytoskeleton-like networks, recently tailored in vitro, result from the…
Understanding the structures of biological macromolecules is highly important as they are closely associated with cellular functionalities. Comprehending the precise organization actin filaments is crucial because they form the dynamic…
The synthetic actin network arouses great interest as bio-material due to its soft and wet nature that mimics many biological scaffolding structures. Inside the cell, the actin network is regulated by tens of actin-binding proteins (ABP's),…
The actin cytoskeleton in living cells has many types of crosslinkers. The mechanical interplay between these different crosslinker types is an open issue in cytoskeletal mechanics. We develop a framework to study the cooperativity and…
Many biological processes involve the action of molecular motors that interact with the cell cytoskeleton. Some processes, such as the transport of cargoes is achieved mainly by the action of individual motors. Other, such as cell motility…
Biology stores information and computes at the molecular scale, yet the ways in which it does so are often distinct from human-engineered computers. Mapping biological computation onto architectures familiar to computer science remains an…
We develop a theory of aggregation using statistical mechanical methods. An example of a complicated aggregation system with several levels of structures is peptide/protein self-assembly. The problem of protein aggregation is important for…
We use Langevin dynamics simulations to study dynamical behaviour of a dense planar layer of active semi-flexible filaments. Using the strength of active force and the thermal persistence length as parameters, we map a detailed phase…
Absorbing phase transitions (APTs) are widespread in non-equilibrium systems, spanning condensed matter, epidemics, earthquakes, ecology, and chemical reactions. APTs feature an absorbing state in which the system becomes entrapped, along…
In this work, we investigate the computational aspects of asynchronous cellular automata (ACAs), a modification of cellular automata in which cells update independently, following an asynchronous schedule. We introduce flip automata…
The neural networks of the human brain act as very efficient parallel processing computers co-ordinating memory related responses to a multitude of input signals from sensory organs. Information storage, update and appropriate retrieval are…