Related papers: Modeling non-genetic information dynamics in cells…
Genetic regulatory networks enable cells to respond to the changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits…
Data-driven dynamic models of cell biology can be used to predict cell response to unseen perturbations. Recent work (CellBox) had demonstrated the derivation of interpretable models with explicit interaction terms, in which the parameters…
We consider an anisotropically two-dimensional diffusion of a charged molecule (particle) through a large biological channel under an external voltage. The channel is modeled as a cylinder of three structure parameters: radius, length, and…
Novel ion traps that provide either a static or a dynamic magnetic gradient field allow for the use of radio frequency (rf) radiation for coupling internal and motional states of ions, which is essential for conditional quantum logic. We…
Ion transport in biological tissues is crucial in the study of many biological and pathological problems. Some multi-cellular structures, like smooth muscles on the vessel walls, could be treated as periodic bi-domain structures, which…
Various biological cells secrete diffusing chemical compounds into their environment for communication purposes. Secretion usually takes place over the cell membrane in a spatially heterogeneous manner. Mathematical models of these…
Based on bottom-up assembly of highly variable neural cells units, the nervous system can reach unequalled level of performances with respect to standard materials and devices used in microelectronic. Reproducing these basic concepts in…
The statistical field theory of information dynamics on complex networks concerns the dynamical evolution of large classes of models of complex systems. Previous work has focused on networks where nodes carry an information field, which…
A comprehensive description of molecular electron transfer reactions is essential for our understanding of fundamental phenomena in bio-energetics and molecular electronics. Experimental studies of molecular systems in condensed-phase…
A thermodynamically motivated neural network model is described that self-organizes to transport charge associated with internal and external potentials while in contact with a thermal reservoir. The model integrates techniques for rapid,…
Computational neuroscience relies on large-scale dynamical-systems models of neurons, with a vast amount of offline, pre-simulation, tuned parameters, with models often tied to their brain simulators. These fixed parameters lead to stiff…
Information is instrumental in our understanding of thermodynamics. Their interplay has been studied through completely degenerate Hamiltonians whereby the informational contributions to thermodynamic transformations can be isolated. In…
A local turbulence model is developed to study energy cascades in the heliosheath and outer heliosphere (OH) based on self-consistent two-dimensional fluid simulations. The model describes a partially ionized magnetofluid OH that couples a…
We introduce a novel framework of reservoir computing. Cellular automaton is used as the reservoir of dynamical systems. Input is randomly projected onto the initial conditions of automaton cells and nonlinear computation is performed on…
The effect of a magnetic field on the characteristics of capacitively coupled radio frequency discharges is investigated and found to be substantial. A one-dimensional particle-in-cell simulation shows that geometrically symmetric…
The prediction of complex dynamics remains an open problem across many domains of physics, where nonlinearities and multiscale interactions severely limit the reliability of conventional forecasting methods. Quantum reservoir computing…
Adaptive physical and biological systems continually process fluctuating information from their environments. When the environment is nonstationary, inference itself becomes a nonequilibrium process with thermodynamic cost. We analyse a…
As demand for computational resources reaches unprecedented levels, research is expanding into the use of complex material substrates for computing. In this study, we interface with a model of a hydrodynamic system, under development by a…
Cellular regulatory dynamics is driven by large and intricate networks of interactions at the molecular scale, whose sheer size obfuscates understanding. In light of limited experimental data, many parameters of such dynamics are unknown,…
Directional ion transport across membranes maintains living systems in nonequilibrium, which underlies chemiosmotic energy conversion. However, the physical origin of collectively organized ion transport in primitive cellular systems…