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Understanding how transient dynamics unfold in response to localized inputs is central to predicting and controlling signal propagation in network systems, including neural processing, epidemic intervention, and power-grid resilience.…
We study the statistical physics of a surprising phenomenon arising in large networks of excitable elements in response to noise: while at low noise, solutions remain in the vicinity of the resting state and large-noise solutions show…
Chemical reactions in multidimensional systems are often described by a rank-1 saddle, whose stable and unstable manifolds intersect in the normally hyperbolic invariant manifold (NHIM). Trajectories started on the NHIM in principle never…
Under normal operations, memristive devices undergo variability in time and space and have internal dynamics. Interplay of memory and stochastic signal processing in memristive devices makes them candidates for performing bio-inspired tasks…
Noise-assisted transport phenomena highlight the nontrivial interplay between environmental effects and quantum coherence in achieving maximal efficiency. Due to the complexity of biochemical systems and their environments, effective open…
Using a stochastic generalization of the Hodgkin–Huxley model, we consider the influence of intrinsic channel noise on the synchronization between the spiking activity of the excitable membrane and an externally applied periodic…
A molecular motor is made of either a single macromolecule or a macromolecular complex. Just like their macroscopic counterparts, molecular motors "transduce" input energy into mechanical work. All the nano-motors considered here operate…
A system with multiple transient memories can remember a set of inputs but subsequently forgets almost all of them, even as they are continually applied. If noise is added, the system can store all memories indefinitely. The phenomenon has…
We report a realization of an associative memory signal/information processing system based on simple enzyme-catalyzed biochemical reactions. Optically detected chemical output is always obtained in response to the triggering input, but the…
Biological systems encode function not primarily in steady states, but in the structure of transient responses elicited by time-varying stimuli. Overshoots, biphasic dynamics, adaptation kinetics, fold-change detection, entrainment, and…
Unlike macroscopic engines, the molecular machinery of living cells is strongly affected by fluctuations. Stochastic Thermodynamics uses Markovian jump processes to model the random transitions between the chemical and configurational…
In stochastic modeling, the excess entropy -- the mutual information shared between a process's past and future -- represents the fundamental lower bound of the memory needed to simulate its dynamics. However, this bound cannot be saturated…
The dissipative curve-crossing problem provides a paradigm for electron-transfer (ET) processes in condensed media. It establishes the simplest conceptual test bed to study the influence of the medium's dynamics on ET kinetics both on the…
We consider a stochastic process with long-range dependence perturbed by multiplicative noise. The marginal distributions of both the original process and the noise have regularly-varying tails, with tail indices $\alpha,\alpha'>0$,…
Signaling in enzymatic networks is typically triggered by environmental fluctuations, resulting in a series of stochastic chemical reactions, leading to corruption of the signal by noise. For example, information flow is initiated by…
Recent experiments indicate that electromagnetic hysteresis behavior can be exhibited at the molecular level.A MD simulation using 2-body potentials and switches to form and break bonds is implemented to determine whether chemical reaction…
The interplay between structure and function is crucial in determining some emerging properties of many natural systems. Here we use an adaptive neural network model inspired in observations of synaptic pruning that couples activity and…
Networks of biochemical reactions, like cellular metabolic networks, are kept in non-equilibrium steady states by the exchange fluxes connecting them to the environment. In most cases, feasible flux configurations can be derived from…
Simplified stochastic models are widely used in the study of frequency-resolved noise propagation in biochemical reaction networks, a common measure being the coherence between random fluctuations in molecule number trajectories. Such…
Synthesis of protein molecules in a cell are carried out by ribosomes. A ribosome can be regarded as a molecular motor which utilizes the input chemical energy to move on a messenger RNA (mRNA) track that also serves as a template for the…