Related papers: On discovering functions in actin filament automat…
Active filaments, such as microtubules with attached cargo-carrying motor proteins, are important dynamic structures for fluid transport in and around living cells. The mathematical models of active filaments appearing in the literature…
We report two-photon resonance fluorescence of an individual semiconductor artificial atom. By non-linearly driving a single quantum dot via a two-photon transition, we probe the linewidth of the two-photon processes and show that, similar…
The articulation process of dynamical networks is studied with a functional map, a minimal model for the dynamic change of relationships through iteration. The model is a dynamical system of a function $f$, not of variables, having a…
The memristor is a device whose resistance changes depending on the polarity and magnitude of a voltage applied to the device's terminals. We design a minimalistic model of a regular network of memristors using structurally-dynamic cellular…
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…
We study complex networks of stochastic two-state units. Our aim is to model discrete stochastic excitable dynamics with a rest and an excited state. Both states are assumed to possess different waiting time distributions. The rest state is…
A random boolean cellular automaton is a network of boolean gates where the inputs, the boolean function, and the initial state of each gate are chosen randomly. In this article, each gate has two inputs. Let $a$ (respectively $c$) be the…
We consider transformations between attractor basins of binary cylindrical cellular automata resulting from mutations. A t-point mutation of a state consists in toggling t sites in that state. Results of such mutations are described by a…
We study an atomic signaling game under stochastic evolutionary dynamics. There is a finite number of players who repeatedly update from a finite number of available languages/signaling strategies. Players imitate the most fit agents with…
Intermediate filaments form an essential structural network, spread throughout the cytoplasm and play a key role in cell mechanics, intracellular organization and molecular signaling. The maintenance of the network and its adaptation to the…
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…
We review the physical properties of macromolecular networks, consisting of semiflexible polymers such as actin. We start by giving a theoretical analysis of the conformational statistics and mechanical response of single filaments.…
The excitation ansatz for tensor networks is a powerful tool for simulating the low-lying quasiparticle excitations above ground states of strongly correlated quantum many-body systems. Recently, the two-dimensional tensor network class of…
We call `bits' a sequence of devices indexed by positive integers, where every device can be in two states: $0$ (idle) and $1$ (active). Start from the `ground state' of the system when all bits are in $0$-state. In our first Binary…
We simulate the nonlocal Stokesian hydrodynamics of an elastic filament which is active due a permanent distribution of stresslets along its contour. A bending instability of an initially straight filament spontaneously breaks flow symmetry…
Actin is a key component of the cytoskeleton, which plays central roles in cell motility, division, growth, and tensile strength. To enable this wide range of transient mechanical processes and properties, networks of actin filaments…
We present an extension of the Hamiltonian of the two dimensional limit of the vibron model encompassing all possible interactions up to four-body operators. We apply this Hamiltonian to the modeling of the experimental bending spectrum of…
We present a computational method for finding attractors (ergodic sets of states) of Boolean networks under asynchronous update. The approach is based on a systematic removal of state transitions to render the state transition graph…
We Propose A Novel Automaton Model which uses Arithmetic Operations as the Evolving Rules, each cell has the states of the Natural Numbers k = (N), a radius of r = 1/2 and operates on an arbitrary input size. The Automaton reads an…
Vibrational motions in electronically excited states can be observed by either time and frequency resolved infrared absorption or by off resonant stimulated Raman techniques. Multipoint correlation function expressions are derived for both…