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It has long been hypothesized that futile cycles in cellular metabolism are involved in the regulation of biochemical pathways. Following the work of Newsholme and Crabtree, we develop a quantitative theory for this idea based on…
We study a stochastic two-species chemical reaction system with two mechanisms. One mechanism consists of chemical interactions which govern the overall drift of species amounts in the system; the other mechanism consists of resampling,…
We study a Michaelis-Menten reaction for a single two-state enzyme molecule, whose transition rates between the two conformations are modulated by an harmonically oscillating external force. In particular, we obtain a range of optimal…
For cellular biochemical reaction systems where the numbers of molecules is small, significant noise is associated with chemical reaction events. This molecular noise can give rise to behavior that is very different from the predictions of…
This article develops a fundamental insight into the behavior of neuronal membranes, focusing on their responses to stimuli measured with power spectra in the frequency domain. It explores the use of linear and nonlinear (quadratic…
The type IV pilus retraction motor is found in many important bacterial pathogens. It is the strongest known linear motor protein and is required for bacterial infectivity. We characterize the dynamics of type IV pilus retraction in terms…
Cells sense their surrounding by employing intracellular signaling pathways that transmit hormonal signals from the cell membrane to the nucleus. TGF-$\beta$/SMAD signaling encodes various cell fates, controls tissue homeostasis and is…
Autocatalytic reaction system with a small number of molecules is studied numerically by stochastic particle simulations. A novel state due to fluctuation and discreteness in molecular numbers is found, characterized as extinction of…
The Notch-Delta signaling pathway mediates cell differentiation implicated in many regulatory processes including spatiotemporal patterning in tissues by promoting alternate cell fates between neighboring cells. At the multicellular level,…
Switch-like responses arising from bistability have been linked to cell signaling processes and memory. Revealing the shape and properties of the set of parameters that lead to bistability is necessary to understand the underlying…
In the cerebral cortex, neurons are subject to a continuous bombardment of synaptic inputs originating from the network's background activity. This leads to ongoing, mostly subthreshold membrane dynamics that depends on the statistics of…
In this work, the dynamics of a self-propelled stochastic particle under the influence of an axisymmetric light field was experimentally studied. The particle under consideration has the main characteristic of carrying a light sensor in an…
Genes are connected in complex networks of interactions where often the product of one gene is a transcription factor that alters the expression of another. Many of these networks are based on a few fundamental motifs leading to switches…
We present a stochastic neural automata in which activity fluctuations and synaptic intensities evolve at different temperature, the latter moving through a set of stored patterns. The network thus exhibits various retrieval phases,…
We have studied the entropy-driven mechanism leading to stationary patterns formation in stochastic systems with local dynamics and non-Fickian diffusion. We have shown that a multiplicative noise fulfilling a fluctuation-dissipation…
Existing mathematical models of the shoot apical meristem (SAM) explain nucleation and confinement of a stem cell domain by Turing's mechanism, assuming that the diffusion coefficients of the activator (WUSCHEL) and inhibitor (CLAVATA) are…
SRAM bitcells in retention mode behave as autonomous stochastic nonlinear dynamical systems. From observation of variability-aware transient noise simulations, we provide an unidimensional model, fully characterizable by conventional…
The multisite phosphorylation-dephosphorylation cycle is a motif repeatedly used in cell signaling. This motif itself can generate a variety of dynamic behaviors like bistability and ultrasensitivity without direct positive feedbacks. In…
The chemotaxis pathway in the bacterium Escherichia coli allows cells to detect changes in external ligand concentration (e.g. nutrients). The pathway regulates the flagellated rotary motors and hence the cells' swimming behaviour, steering…
Sliding-induced topological transitions in biphenylene bilayers are investigated, considering various stacking configurations which are analyzed from a symmetry perspective and described in detail,highlighting the intricate patterns of…