Related papers: Mathematical modeling of variability in intracellu…
To advance understanding of cellular metabolism and reduce batch-to-batch variability in cell culture processes, this study introduces a multi-scale hybrid modeling framework designed to simulate and predict the dynamic behavior of CHO cell…
Self-generated gradients have atttracted a lot of attention in the recent biological literature. It is considered as a robust strategy for a group of cells to find its way during a long journey. This note is intended to discuss various…
Ageing of lithium-ion batteries results in irreversible reduction in performance. Intrinsic variability between cells, caused by manufacturing differences, occurs throughout life and increases with age. Researchers need to know the minimum…
Single-cell reference atlases are large-scale, cell-level maps that capture cellular heterogeneity within an organ using single cell genomics. Given their size and cellular diversity, these atlases serve as high-quality training data for…
We have developed a coarse-grained formulation for modeling the dynamic behavior of cells quantitatively, based on stochasticity and heterogeneity, rather than on biochemical reactions. We treat each reaction as a continuous-time stochastic…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
How cells reliably infer information about their environment is a fundamentally important question. While sensing and signaling generally start with cell-surface receptors, the degree of accuracy with which a cell can measure external…
Amoeboid motion is a dynamic mode of cell motility essential for processes such as the immune response and wound healing. This review examines recent developments in the mathematical and computational modeling of amoeboid crawling, focusing…
Hybrid modeling provides an effective solution to cope with multiple time scales dynamics in systems biology. Among the applications of this method, one of the most important is the cell cycle regulation. The machinery of the cell cycle,…
Spatial heterogeneity is a hallmark of living systems, even at the molecular scale in individual cells. A key example is the partitioning of membrane-bound proteins via lipid domain formation or cytoskeleton-induced corralling. Yet the…
Mechanics and biochemical signaling are both often deregulated in cancer, leading to cancer cell phenotypes that exhibit increased invasiveness, proliferation, and survival. The dynamics and interactions of cytoskeletal components control…
We discuss several aspects of creation of adequate mathematical models in other sciences. In particular, many difficulties stem from great complexity of the source systems and the presence of a variety of uncertain factors. We illustrate…
Cells regulate themselves via dizzyingly complex biochemical processes called signaling pathways. These are usually depicted as a network, where nodes represent proteins and edges indicate their influence on each other. In order to…
The recent development of single-cell transcriptomics has enabled gene expression to be measured in individual cells instead of being population-averaged. Despite this considerable precision improvement, inferring regulatory networks…
Ordinary differential equation models are nowadays widely used for the mechanistic description of biological processes and their temporal evolution. These models typically have many unknown and non-measurable parameters, which have to be…
The goal of this paper is to show why the framework of communication complexity seems suitable for the study of cellular automata. Researchers have tackled different algorithmic problems ranging from the complexity of predicting to the…
The abrupt outbreak and transmission of biological diseases has always been a long-time concern of humankind. For long, mathematical modeling has served as a simple and yet efficient tool to investigate, predict, and control spread of…
Dynamics maintaining diversity of cell types in a multi-cellular system are studied in relationship with the plasticity of cellular states. First, we introduce a new theoretical framework, reaction-diffusion system on `chemical species…
Molecular Communication (MC) is a communication strategy that uses molecules as carriers of information, and is widely used by biological cells. As an interdisciplinary topic, it has been studied by biologists, communication theorists and a…
Signals recorded from neurons with extracellular planar sensors have a wide range of waveforms and amplitudes. This variety is a result of different physical conditions affecting the ion currents through a cellular membrane. The…