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Sensing and reciprocating cellular systems (SARs) are important for the operation of many biological systems. Production in interferon (IFN) SARs is achieved through activation of the Jak-Stat pathway, and downstream upregulation of IFN…
The FitzHugh-Nagumo (FHN) model, from computational neuroscience, has attracted attention in nonlinear dynamics studies as it describes the behavior of excitable systems and exhibits interesting bifurcation properties. The accurate…
The activation/repression of a given gene is typically regulated by multiple transcription factors (TFs) that bind at the gene regulatory region and recruit RNA polymerase (RNAP). The interactions between the promoter region and TFs and…
Inverse stochastic resonance (ISR) is a phenomenon where noise reduces rather than increases the firing rate of a neuron, sometimes leading to complete quiescence. ISR was first experimentally verified with cerebellar Purkinje neurons.…
We formulate the Fast-Weights Homeostatic Reentry Network (FHRN) as a continuous-time neural-ODE system, revealing its role as a norm-regulated reentrant dynamical process. Starting from the discrete reentry rule $x_t = x_t^{(\mathrm{ex})}…
Second-harmonic generation (SHG) is a fundamental nonlinear optical process widely used in photonics; however, it is strictly forbidden in the bulk of centrosymmetric materials due to their inversion symmetry. Nevertheless, applying an…
This article is devoted to the theoretical and numerical analysis of a network of excitatory and inhibitory neurons of Hodgkin-Huxley (HH) type, for which the topology is inspired by that of a single local layer of visual cortex V1. Our…
Transcription factors (TFs), the key players in transcriptional regulation, have attracted great experimental attention, yet the functions of most human TFs remain poorly understood. Recent capabilities in genome-wide protein binding…
Cellular transformations which involve a significant phenotypical change of the cell's state use bistable biochemical switches as underlying decision systems. In this work, we aim at linking cellular decisions taking place on a time scale…
Hill function is one of the widely used gene transcription regulation models. Its attribute of fitting may result in a lack of an underlying physical picture, yet the fitting parameters can provide information about biochemical reactions,…
Gonadotrophin-releasing hormone receptor (GnRH1R) is a promising therapeutic target for the treatment of uterine diseases. To date, several GnRH1R antagonists are available in clinical investigation without satisfying multiple property…
Gene regulatory networks (GRNs) are essential for understanding cell fate decisions and disease mechanisms, yet cross-species GRN inference from single-cell RNA-seq data remains challenging due to noise, sparsity, and cross-species…
Time-resolved femtosecond stimulated Raman spectroscopy (FSRS) is a powerful tool for investigating ultrafast structural and vibrational dynamics in light absorbing systems. However, the technique generally requires exposing a sample to…
Rhizomes play fundamental roles in plant evolution, persistence, and environmental adaptation by enabling clonal propagation, resource storage, and stress resilience. Despite their ecological and agronomic importance across diverse plant…
This paper proposes a neuronal circuitry layout and synaptic plasticity principles that allow the (pyramidal) neuron to act as a "combinatorial switch". Namely, the neuron learns to be more prone to generate spikes given those combinations…
Functional electrical stimulation (FES) is a prevalent technique commonly used to activate muscles in individuals with neurological disorders. Traditional FES strategies predominantly utilize low-frequency (LF) stimulation, which evokes…
Galaxy formation and evolution involves a variety of effectively stochastic processes that operate over different timescales. The Extended Regulator model provides an analytic framework for the resulting variability (or `burstiness') in…
Regulatory networks consist of interacting molecules with a high degree of mutual chemical specificity. How can these molecules evolve when their function depends on maintenance of interactions with cognate partners and simultaneous…
Functional connectivity (FC) between brain regions tracks symptom severity in many neuropsychiatric disorders. Transcranial magnetic stimulation (TMS) directly alters regional activity and indirectly alters FC. Predicting how FC will change…
Plasmodium falciparum 70 kDa heat shock proteins (PfHsp70s) are expressed at all stages of the pathogenic erythrocytic phase of the malaria parasite lifecycle. There are six PfHsp70s, all of which have orthologues in other plasmodial…