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We propose a model for the dynamics of a probe embedded in a living cell, where both thermal fluctuations and nonequilibrium activity coexist. The model is based on a confining harmonic potential describing the elastic cytoskeletal matrix,…
A lecture notes style review of the equilibrium statistical mechanics of recurrent neural networks with discrete and continuous neurons (e.g. Ising, coupled-oscillators). To be published in the Handbook of Biological Physics…
Cortical neurons emit seemingly erratic trains of action potentials or "spikes," and neural network dynamics emerge from the coordinated spiking activity within neural circuits. These rich dynamics manifest themselves in a variety of…
In this paper, we synthesize two aperiodic-sampled deep neural network (DNN) control schemes, based on the closed-loop tracking stability guarantees. By means of the integral quadratic constraint coping with the input-output behaviour of…
Coherent coupling between a large number of qubits is the goal for scalable approaches to solid state quantum information processing. Prototype systems can be characterized by spectroscopic techniques. Here, we use pulsed-continuous wave…
The intracellular transport process plays an important role in delivering essential materials throughout branched geometries of neurons for their survival and function. Many neurodegenerative diseases have been associated with the…
We provide a detailed multiscale analysis of a system of particles interacting through a dynamical network of links. Starting from a microscopic model, via the mean field limit, we formally derive coupled kinetic equations for the particle…
We consider a three-node fully connected network (Delta network) showing that a coherent population trapping phenomenon occurs, generalizing results for the Lambda network known to support a dark state. Transport in such structures provides…
We model a particulate flow of constant velocity through confined geometries, ranging from a single channel to a bundle of $N_c$ identical coupled channels, under conditions of reversible blockage. Quantities of interest include the exiting…
Models of complex networks often incorporate node-intrinsic properties abstracted as hidden variables. The probability of connections in the network is then a function of these variables. Real-world networks evolve over time, and many…
We study the model of a molecular switch comprised of a molecule with a soft vibrational degree of freedom coupled to metallic leads. In the presence of strong electron-ion interaction, different charge states of the molecule correspond to…
We use an adiabatic approximation in terms of instantaneous resonances to study the steady-state and time-dependent transport properties of interacting electrons in biased resonant tunneling heterostructures. This approach leads, in a…
In neural circuits, synaptic strengths influence neuronal activity by shaping network dynamics, and neuronal activity influences synaptic strengths through activity-dependent plasticity. Motivated by this fact, we study a recurrent-network…
Classical molecular dynamics and electro-diffusion theories have achieved profound success in elucidating ion selectivity and gating mechanisms. However, reconciling strict selectivity with high flux permeation in Angstrom-scaled biological…
In this work, we study the dynamical robustness in a system consisting of both active and inactive oscillators. We analytically show that the dynamical robustness of such system is determined by the cross link density between active and…
The flow of ions through permeable channels causes voltage drop in physiological nanodomains such as synapses, dendrites and dendritic spines, and other protrusions. How the voltage changes around channels in these nanodomains has remained…
In this paper we present a network model to study the impact of spatial distribution of constituents, coupling between them and diffusive processes in the context of biological situations. The model is in terms of network of mobile elements…
We consider the coherent exciton transport, modeled by continuous-time quantum walks, on Erd\"{o}s-R\'{e}ny graphs in the presence of a random distribution of traps. The role of trap concentration and of the substrate dilution is deepened…
We study dense mixtures of passive and active self-aligning disks with isotropic or anisotropic mobility. We find that the passive fraction controls an order-disorder transition that is continuous in the isotropic case and discontinuous in…
We derive a monotonicity property for general, transient flows of a commodity transferred throughout a network, where the flow is characterized by density and mass flux dynamics on the edges with density continuity and mass balance…