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Memories are stored, retained, and recollected through complex, coupled processes operating on multiple timescales. To understand the computational principles behind these intricate networks of interactions we construct a broad class of…
The TGF-beta pathway plays a central role in tissue homeostasis and morphogenesis. It transduces a variety of extracellular signals into intracellular transcriptional responses that control a plethora of cellular processes, including cell…
Living organisms continuously harness energy to perform complex functions for their adaptation and survival while part of that energy is dissipated in the form of heat or chemical waste. Determining the energetic cost and the efficiency of…
We take up the challenge of designing realistic computational models of large interacting cell populations. The goal is essentially to bring Gillespie's celebrated stochastic methodology to the level of an interacting population of cells.…
Many cellular processes involve information processing and decision making. We can probe these processes at increasing molecular detail. The analysis of heterogeneous data remains a challenge that requires new ways of thinking about cells…
We propose a biologically plausible computational model of working memory (WM) implemented by the spiking neuron network (SNN) interacting with a network of astrocytes. SNN is modelled by the synaptically coupled Izhikevich neurons with a…
Persistent activity is postulated to drive neural network plasticity and learning. To investigate its underlying cellular mechanisms, we developed a biophysically tractable model that explains the emergence, sustenance, and eventual…
Biological functionality of cellular aggregates is largely influenced by the activity and displacements of individual constituent cells. From a theoretical perspective this activity can be characterized by hydrodynamic transport…
In preimplantation mammalian embryos, the second cell fate decision introduces spatial patterns of embryonic and extra-embryonic precursor cells. The transcription factors NANOG and GATA6 are the earliest markers for the two cell types and…
This contribution belongs to a combinatorial approach to hyperbolic geometry and it is aimed at possible applications to computer simulations. It is based on the splitting method which was introduced by the author and which is reminded in…
Recent experimental studies strongly suggest the influence of glial purinergic transmission in the modulation of synaptic dynamics. By releasing adenosine triphosphate (ATP), which accumulates as adenosine, astrocytes tonically suppressed…
Recent advancements in the ability to construct three-dimensional (3D) tissues and organoids from stem cells and biomaterials have not only opened abundant new research avenues in disease modeling and regenerative medicine but also have…
Various neurophysiological and cognitive functions are based on transferring information between spiking neurons via a complex system of synaptic connections. In particular, the capacity of presynaptic inputs to influence the postsynaptic…
Stochastic dynamics govern many important processes in cellular biology, and an underlying theoretical approach describing these dynamics is desirable to address a wealth of questions in biology and medicine. Mathematical tools exist for…
In this article, we propose a general framework to study the dynamics and topology of cellular networks that capture the geometry of cell packings in two-dimensional tissues. Such epithelia undergo large-scale deformation during…
The importance of molecular-scale forces in sculpting biological form and function has been acknowledged for more than a century. Accounting for forces in biology is a problem that lies at the intersection of soft condensed matter physics,…
This chapter sheds light on the synaptic organization of the brain from the perspective of computational neuroscience. It provides an introductory overview on how to account for empirical data in mathematical models, implement such models…
The degrees of freedom of multi-compartment mathematical models for energy metabolism of a neuron-astrocyte complex may offer a key to understand the different ways in which the energetic needs of the brain are met. In this paper we address…
Mathematical model of spiking neuron network (SNN) supplied by astrocytes is investigated. The astrocytes are specific type of brain cells which are not electrically excitable but inducing chemical modulations of neuronal firing. We…
The problem of the transformation of microscopic information to the macroscopic level is an intriguing challenge in computational neuroscience, but also of general mathematical importance. Here, a phenomenological mathematical model is…