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Developing epithelial tissues coordinate cell proliferation and mechanical forces to achieve proper size and shape. As epithelial cells tightly adhere together to form the confluent tissue, the distribution of cell areas significantly…
Various biological cells secrete diffusing chemical compounds into their environment for communication purposes. Secretion usually takes place over the cell membrane in a spatially heterogeneous manner. Mathematical models of these…
The mechanism and driving forces of chromosome segregation in the bacterial cell cycle of E. coli is one of the least understood events in its life cycle. Using principles of entropic repulsion between polymer loops confined in a cylinder,…
A theory of fractional kinetics of glial cancer cells is presented. A role of the migration-proliferation dichotomy in the fractional cancer cell dynamics in the outer-invasive zone is discussed an explained in the framework of a continuous…
Deep generative models such as diffusion and flow matching are powerful machine learning tools capable of learning and sampling from high-dimensional distributions. They are particularly useful when the training data appears to be…
Spatial profiling technologies in biology, such as imaging mass cytometry (IMC) and spatial transcriptomics (ST), generate high-dimensional, multi-channel data with strong spatial alignment and complex inter-channel relationships.…
The Dynamic Template model of biological cell membranes and the cytoplasm as spatially organised fluid layers is extended to plant cells, and is shown to offer a feasible shear driven mechanism for the co-alignment of internal and external…
Collective cell migration contributes to embryogenesis, wound healing and tumor metastasis. Cell monolayer migration experiments help understanding what determines the movement of cells far from the leading edge. Inhibiting cell…
Optical tracking in vivo experiments reveal that diffusion of particles in biological cells is strongly enhanced in the presence of ATP and the experimental data for animal cells could previously be reproduced within a phenomenological…
We study theoretically the replication of Kinetoplast DNA consisting of several thousands separate mini-circles found in organisms of the class Kinetoplastida. When the cell is not actively dividing these are topologically connected in a…
We present here a detailed description of the model of ran-driven nuclear transduction in living cells to be published elswere. The mathematical model presented is the first to account for the active transport of molecules along the…
The regulation of cellular function is often controlled at the level of gene transcription. Such genetic regulation usually consists of interacting networks, whereby gene products from a single network can act to control their own…
This paper considers particle propagation in a cylindrical molecular communication channel, e.g. a simplified model of a blood vessel. Emitted particles are influenced by diffusion, flow, and a vertical force induced e.g. by gravity or…
The particle-in-cell numerical method of plasma physics balances a trade-off between computational cost and intrinsic noise. Inference on data produced by these simulations generally consists of binning the data to recover the particle…
Our knowledge of how individual cells self-organize to form complex multicellular systems is being revolutionized by a data outburst, coming from high-throughput experimental breakthroughs such as single-cell RNA sequencing and spatially…
An inhomogeneous profile of chemostatted species generates a rich variety of patterns in glycolytic waves depicted in a Selkov reaction-diffusion framework here. A key role played by diffusion amplitude and symmetry in the chemostatted…
Lipid rafts are heterogeneous dynamic lipid domains of the cell membranes that are involved in several biological processes, like protein and lipids specific transport and signaling. Our understanding of lipid raft formation is still…
This paper presents a real-time simulation involving ''protozoan-like'' cells that evolve by natural selection in a physical 2D ecosystem. Selection pressure is exerted via the requirements to collect mass and energy from the surroundings…
We introduce and analyze a model for the transport of particles or energy in extended lattice systems. The dynamics of the model acts on a discrete phase space at discrete times but has nonetheless some of the characteristic properties of…
Synthesis of protein molecules in a cell are carried out by ribosomes. A ribosome can be regarded as a molecular motor which utilizes the input chemical energy to move on a messenger RNA (mRNA) track that also serves as a template for the…