Related papers: Multisite Population Epigenetic Model of Passive D…
We study a continuous time Mutually Catalytic Branching model on the $\mathbb{Z}^{d}$. The model describes the behavior of two different populations of particles, performing random walk on the lattice in the presence of branching, that is,…
Systemic properties of living cells are the result of molecular dynamics governed by so-called genetic regulatory networks (GRN). These networks capture all possible features of cells and are responsible for the immense levels of adaptation…
Movement behavior of biological entities plays a crucial role in their destiny through regulating their intraspecific and interspecific interactions as well as their interaction with surrounding environment. In spite of various models for…
Gene expression and DNA methylation are two interconnected biological processes and understanding their relationship is important in advancing understanding in diverse areas, including disease pathogenesis, environmental adaptation,…
Control of cell proliferation is a fundamental aspect of tissue physiology central to morphogenesis, wound healing and cancer. Although many of the molecular genetic factors are now known, the system level regulation of growth is still…
This paper develops a point-mutation model describing the evolutionary dynamics of a population of adult stem cells. Such a model may prove useful for quantitative studies of tissue aging and the emergence of cancer. We consider two modes…
The presence of one or more species at some spatial locations but not others is a central matter in ecology. This phenomenon is related to ecological pattern formation. Nonlocal interactions can be considered as one of the mechanisms…
When DNA molecules are heated they denature. This occurs locally so that loops of molten single DNA strands form, connected by intact double-stranded DNA pieces. The properties of this "melting" transition have been intensively…
We study the statistical properties of a simple genetic regulatory network that provides heterogeneity within a population of cells. This network consists of a binary genetic switch in which stochastic flipping between the two switch states…
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…
Multicellular systems play a key role in bioprocess and biomedical engineering. Cell ensembles encountered in these setups show phenotypic variability like size and biochemical composition. As this variability may result in undesired…
The spatial dispersal of individuals is known to play an important role in the dynamics of populations, and is central to metapopulation theory. At the same time, local adaptation to environmental conditions creates a geographic mosaic of…
I study a population model in which the reproduction rate lambda is inherited with mutation, favoring fast reproducers in the short term, but conflicting with a process that eliminates agglomerations of individuals. The model is a variant…
DNA methylation is a well-studied genetic modification crucial to regulate the functioning of the genome. Its alterations play an important role in tumorigenesis and tumor-suppression. Thus, studying DNA methylation data may help biomarker…
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…
The origin of heredity is studied as a recursive state in a replicating proto-cell consisting of many molecule species in mutually catalyzing reaction networks. Protocells divide when the number of molecules, increasing due to replication,…
We study a stochastic linear discrete metapolulation model to understand the effect of risk spreading by dispersion. We calculate analytically the stable distribution of populations that live in different habitats. The result shows that the…
We explore a model of metapopulation genetics which is based on a more ecologically motivated approach than is frequently used in population genetics. The size of the population is regulated by competition between individuals, rather than…
DNA methylation is a significant driver of cell-type heterogeneity and has been implicated in various regulatory processes ranging from cell differentiation to imprinting. As the methyl group is embedded in the DNA molecule, assessing DNA…
This paper develops a quasispecies model where cells can adopt a two-cell survival strategy. Within this strategy, pairs of cells join together, at which point one of the cells sacrifices its own replicative ability for the sake of the…