Related papers: On discovering functions in actin filament automat…
Proteins fold using a two-state or multi-state kinetic mechanisms, but up to now there isn't a first-principle model to explain this different behaviour. We exploit the network properties of protein structures by introducing novel…
We examine a two-dimensional system of sterically repulsive interacting disks where each particle runs in a random direction. This system is equivalent to a run-and-tumble dynamics system in the limit where the run time is infinite. At low…
A two-state, three-dimensional, deterministic, reversible cellular automaton is shown to be capable of approximately circular orbits, wavelike undulations, and particle-like configurations that decay in accordance with a half-life law.
The dynamics of networks of interacting dynamical systems depend on the nature of the coupling between individual units. We explore networks of oscillatory units with coupling functions that have "dead zones", that is, the coupling…
We discuss a theoretical model for the cooperative binding dynamics of tropomyosin to actin filaments. Tropomyosin binds to actin by occupying seven consecutive monomers. The model includes a strong attraction between attached tropomyosin…
We develop a formalism to describe the equilibrium distributions for segments of confined branched networks consisting of stiff filaments. This is applicable to certain situations of cytoskeleton in cells, such as for example actin…
The tuning process of a large apparatus of many components could be represented and quantified by constructing parameter-tuning networks. The experimental tuning of the ion source of the neutral beam injector of HT-7 Tokamak is presented as…
We present a continuum level analytical model of a droplet of active contractile fluid consisting of filaments and motors. We calculate the steady state flows that result from a splayed polarisation of the filaments. We account for the…
Conway's Game of Life is the best-known cellular automaton. It is a classic model of emergence and self-organization, it is Turing-complete, and it can simulate a universal constructor. The Game of Life belongs to the set of semi-totalistic…
Entangled coherent states play pivotal roles in various fields such as quantum computation, quantum communication, and quantum sensing. We experimentally demonstrate the generation of entangled coherent states with the two-dimensional…
We present a probabilistic (ideally 50%) nondestructive interaction-free atom-photon controlled-NOT gate, where nondestructive means that all four outgoing target photon modes of the gate are available and feed-forwardable. Individual atoms…
Quantum computing employs controllable interactions to perform sequences of logical gates and entire algorithms on quantum registers. This paradigm has been widely explored, e.g., for simulating dynamics of manybody systems by decomposing…
We consider the task of computing functions $f: \mathbb{N}^k\to \mathbb{N}$, where $ \mathbb{N}$ is the set of natural numbers, by finite teams of agents modelled as deterministic finite automata. The computation is carried out in a…
The ground-state energy, the addition energies and the optical absorption spectra are derived for interacting polarons in parabolic quantum dots in three and two dimensions. A path integral formalism for identical particles is used in order…
Actin is a filamentary protein which has many remarkable properties making it an ideal system for the study of the dynamics and mechanics of semi-flexible polymer solutions and gels; actin has a persistence length of over 10 microns and can…
By employing single charge injections with an atomic force microscope, we investigated redox reactions of a molecule on a multilayer insulating film. First, we charged the molecule positively by attaching a single hole. Then we neutralized…
A one dimensional non-equilibrium stochastic model is proposed where each site of the lattice is occupied by a particle, which may be of type A or B. The time evolution of the model occurs through three processes: autocatalytic generation…
We consider many-body states of bosonic spinor atoms which, at the mean-field level, can be characterized by a single-particle wave function. Such states include BEC phases and insulating Mott states with one atom per site. We describe and…
A scheme is presented for realizing a quantum phase gate with three-level atoms, solid-state qubits--often called artificial atoms, or ions that share a quantum data bus such as a single mode field in cavity QED system or a collective…
Mechanochemical simulations of actomyosin networks are traditionally based on one-dimensional models of actin filaments having zero width. Here, and in the follow up paper, approaches are presented for more efficient modelling which…