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This series presents an approach to mathematical biology which makes precise the function of biological molecules. Because biological systems compute, the theory is a general purpose computer language. I build a language for efficiently…
Memory is often defined as the mental capacity of retaining information about facts, events, procedures and more generally about any type of previous experience. Memories are remembered as long as they influence our thoughts, feelings, and…
A connection is established between discrete stochastic model describing microscopic motion of fluctuating cells, and macroscopic equations describing dynamics of cellular density. Cells move towards chemical gradient (process called…
Neuromorphic Computing (NC), which emulates neural activities of the human brain, is considered for low-power implementation of artificial intelligence. Towards realizing NC, fabrication, and investigations of hardware elements such as…
Biological nanomachines are nanometer-size macromolecular complexes that catalyze chemical reactions in the presence of substrate molecules. The catalytic functions carried out by such nanomachines in the cytoplasm, and biological membranes…
In this letter we present the results of a simple model for intercellular communication via calcium oscillations, motivated in part by a recent experimental study. The model describes two cells (a "donor" and "sensor") whose intracellular…
The role of hydrodynamic mixing in astrophysics is reviewed, emphasizing connections with laser physics experiments and inertial confinement fusion (ICF). Computer technology now allows two dimensional (2D) simulations, with complex…
Synaptic transmission between neurons is governed by a cascade of stochastic reaction-diffusion events that lead to calcium-induced vesicle release of neurotransmitter. Since experimental measurements of such systems are challenging due…
Spatial transcriptomics methods capture cellular measurements such as gene expression and cell types at specific locations in a cell, helping provide a localized picture of tissue health. Traditional visualization techniques superimpose the…
In multicellular organisms, cells coordinate their activities through cell-cell communication (CCC), which is crucial for development, tissue homeostasis, and disease progression. Recent advances in single-cell and spatial omics…
One of the major resource requirements of computers - ranging from biological cells to human brains to high-performance (engineered) computers - is the energy used to run them. Those costs of performing a computation have long been a focus…
We present a detailed physiological model of the retina that includes the biochemistry and electrophysiology of phototransduction, neuronal electrical coupling, and the spherical geometry of the eye. The model is a parabolic-elliptic system…
The increasing interest in understanding the behavior of the biological neural networks, and the increasing utilization of artificial neural networks in different fields and scales, both require a thorough understanding of how neuromorphic…
Metabolic oscillations in single cells underlie the mechanisms behind cell synchronization and cell-cell communication. For example, glycolytic oscillations mediated by biochemical communication between cells may synchronize the pulsatile…
We propose a design methodology to facilitate fault tolerance of deep learning models. First, we implement a many-core fault-tolerant neuromorphic hardware design, where neuron and synapse circuitries in each neuromorphic core are enclosed…
Mathematical and computational models can assist in gaining an understanding of cell behavior at many levels of organization. Here, we review models in the literature that focus on eukaryotic cell motility at 3 size scales: intracellular…
The increase of existing computational capabilities has made simulation emerge as a third discipline of Science, lying midway between experimental and purely theoretical branches [1, 2]. Simulation enables the evaluation of quantities which…
Essential introduction to glial cells with emphasis on astrocytes, microglia and their interplay in reactive astrogliosis.
Computational modeling helps neuroscientists to integrate and explain experimental data obtained through neurophysiological and anatomical studies, thus providing a mechanism by which we can better understand and predict the principles of…
Multicellular collective migration is a ubiquitous strategy of cells to translocate spatially in diverse tissue environments to accomplish a wide variety of biological phenomena, viz. embryonic development, wound healing, and tumor…