Related papers: Evolutionary timeline of a modeled cell
A variational lattice model is proposed to define an evolution of sets from a single point (nucleation) following a criterion of "maximization" of the perimeter. At a discrete level, the evolution has a "checkerboard" structure and its…
Multicellular self-organization drives development in biological organisms, yet a comprehensive theory is lacking as basic properties of cells can complicate common approaches. Framing such properties by dynamic graphs led to new…
The evolutionary origin of universal statistics in biochemical reaction network is studied, to explain the power-law distribution of reaction links and the power-law distributions of chemical abundances. Using cell models with catalytic…
Stem cells are characterized by their ability to self-renew, as well as to differentiate and give rise to new populations of cells. Stem cell divisions are crucial for generative processes that occur during early development, and later in…
Accurately determining and classifying the structure of complex networks is the focus of much current research. One class of network of particular interest are metabolic pathways, which have previously been studied from a graph theoretical…
Ecological systems show a variety of characteristic patterns of biodiversity in space and time. It is a challenge for theory to find models that can reproduce and explain the observed patterns. Since the advent of island biogeography these…
The molecular machinery of life is largely created via self-organisation of individual molecules into functional assemblies. Minimal coarse-grained models, where a whole macromolecule is represented by a small number of particles, can be of…
With a view to connecting random mutation on the molecular level to punctuated equilibrium behavior on the phenotype level, we propose a new model for biological evolution, which incorporates random mutation and natural selection. In this…
The organization of cells within tissues plays a vital role in various biological processes, including development and morphogenesis. As a result, understanding how cells self-organize in tissues has been an active area of research. In our…
An analytical model for the evolution of the boundary of the new phase in transformations ruled by nucleation and growth is presented. Both homogeneous and heterogeneous nucleation have been considered: The former includes transformations…
Cell growth in size is a complex process coordinated by intrinsic and environmental signals. In a recent work [Tzur et al., Science, 2009, 325:167-171], size distributions in an exponentially growing population of mammalian cells were used…
The evolution of complexity has been a central theme for Biology [2] and Artificial Life research [1]. It is generally agreed that complexity has increased in our universe, giving way to life, multi-cellularity, societies, and systems of…
We study analytically and numerically a model metabolic cycle composed of an arbitrary number of species of catalytically active particles. Each species converts a substrate into a product, the latter being used as the substrate by the next…
A key process in the life of any multicellular organism is its development from a single egg into a full grown adult. The first step in this process often consists of forming a tissue layer out of randomly placed cells on the surface of the…
Very recently we have developed a dynamic network model for eco-systems that achieved ``unification'' of ``micro'' and ``macro''-evolution. We now propose an extension of our model so as to stabilize the eco-system and describe {\it…
Based on symmetry consideration of migration and shape deformations, we formulate phenomenologically the dynamics of cell crawling in two dimensions. Forces are introduced to change the cell shape. The shape deformations induce migration of…
We aim to understand the evolution of the genetic composition of cancer cell populations. To achieve this, we consider an individual-based model representing a cell population where cells divide, die and mutate along the edges of a finite…
Multicellular organisms comprise a diverse collection of stable tissues built from different cell types. It remains unclear how large numbers of interacting cells can precisely coordinate their gene expression during tissue…
Cellular biology exists embedded in a world dominated by random dynamics and chance. Many vital molecules and pieces of cellular machinery diffuse within cells, moving along random trajectories as they collide with the other biomolecular…
Regulatory networks consist of interacting molecules with a high degree of mutual chemical specificity. How can these molecules evolve when their function depends on maintenance of interactions with cognate partners and simultaneous…