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The Hodgkin-Huxley (HH) model is a powerful model to explain different aspects of spike generation in excitable cells. However, the HH model was proposed in 1952 when the real structure of the ion channel was unknown. It is now common…
Histological examination is crucial for cancer diagnosis, including hematoxylin and eosin (H&E) staining for mapping morphology and immunohistochemistry (IHC) staining for revealing chemical information. Recently developed two-color…
We study pattern formation in a 2-D reaction-diffusion (RD) sub-cellular model characterizing the effect of a spatial gradient of a plant hormone distribution on a family of G-proteins associated with root-hair (RH) initiation in the plant…
A feed-forward loop (FFL) is a common gene-regulatory motif in which usually the upstream regulator is a protein, a transcription factor, that regulates the expression of the target protein in two parallel pathways. Here, we study a…
The rapid growth of large-scale AI models has intensified energy consumption and data-movement challenges in modern datacenters. Photonic accelerators offer a promising path by executing the linear matrix multiplications of transformer…
The concept of hyperbolic flux tubes (HFTs) is a generalization of the concept of separator field lines for coronal magnetic fields with a trivial magnetic topology. An effective mechanism of a current layer formation in HFTs is proposed.…
Vagus nerve stimulation (VNS) has emerged as a promising therapeutic intervention across various neurological and psychiatric conditions, including epilepsy, depression, and stroke rehabilitation; however, its mechanisms of action on neural…
We propose a new mechanism for the achievment of homochirality in life without any autocatalytic production process. Our model consists of a spontaneous production together with a recycling cross inhibition in a closed system. It is shown…
Brain function emerges from coordinated activity across anatomically connected regions, where structural connectivity (SC) -- the network of white matter pathways - provides the physical substrate for functional connectivity (FC) -- the…
Considering that life on earth evolved about 3.7 billion years ago, vertebrates are young, appearing in the fossil record during the Cambrian explosion about 542 to 515 million years ago. Results from sequence analyses of genomes from…
We investigate two well-known approaches for extending the fewest switches surface hopping (FSSH) algorithm to periodic time-dependent couplings. The first formalism acts as if the instantaneous adiabatic electronic states were standard…
An apporach for the sensing of small amounts of chemical and biochemical material is presented. A frequency selective surface (FSS) made from asymmetric split ring resonators (aDSR) is excited with free space radiation. Due to interference…
A new class of phenomena discussed in this review is based on interaction between spatially separated, but closely located ferromagnets and superconductors. They are called Ferromagnet-Superconductor Hybrids (FSH). These systems include…
The genetic regulatory network (GRN) plays a key role in controlling the response of the cell to changes in the environment. Although the structure of GRNs has been the subject of many studies, their large scale structure in the light of…
Glycosylation is a highly complex process to produce a diverse repertoire of cellular glycans that are attached to proteins and lipids. Glycans are involved in fundamental biological processes, including protein folding and clearance, cell…
Shear-thickening fluids (STFs) become more viscous under shear stress, which makes them useful for many engineering and scientific applications. However, their behavior under normal forces, especially when these forces are applied…
We present diffSPH, a novel open-source differentiable Smoothed Particle Hydrodynamics (SPH) framework developed entirely in PyTorch with GPU acceleration. diffSPH is designed centrally around differentiation to facilitate optimization and…
In many sensory systems, transmembrane receptors are spatially organized in large clusters. Such arrangement may facilitate signal amplification and the integration of multiple stimuli. However, this organization likely also affects the…
Epithelial to mesenchymal transition (EMT) plays important roles in embryonic development, tissue regeneration and cancer metastasis. While several feedback loops have been shown to regulate EMT, it remains elusive how they coordinately…
Goal-driven selective attention (GDSA) is a remarkable function that allows the complex dynamical networks of the brain to support coherent perception and cognition. Part I of this two-part paper proposes a new control-theoretic framework,…