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Enzymes are on the front lines of evolution. All living organisms rely on highly efficient, specific enzymes for growth, sustenance, and reproduction; and many diseases are a consequence of a mutation on an enzyme that affects its catalytic…
The emergence of spatial patterns and organized growth is a hallmark of developing tissues. While symmetry-breaking and scaling laws govern these processes, how cells coordinate spatial patterning with size regulation remains unclear. Here,…
We study a stochastic model proposed recently in the genetic literature to explain the heterogeneity of cell populations or of gene products. Cells are located in two colonies, whose sizes fluctuate as birth and migration processes in…
In physics, I noticed subjects not explained by formulas were often not studied, like how uncontrolled growth systems changed form. Weather, businesses, societies, environments, communities, cultures, groups, relationships, lives, and…
We use the oscillating Min proteins of Escherichia coli as a prototype system to illustrate the current state and potential of modeling protein dynamics in space and time. We demonstrate how a theoretical approach has led to striking new…
This paper deals with a model of cellular growth called "Epigenetic Tracking", whose key features are: i) distinction bewteen "normal" and "driver" cells; ii) presence in driver cells of an epigenetic memory, that holds the position of the…
We explain how hierarchical organization of biological systems emerges naturally during evolution, through a transition in the units of individuality. We will show how these transitions are the result of competing selective forces operating…
The evolution of structure in biology is driven by accretion and change. Accretion brings together disparate parts to form bigger wholes. Change provides opportunities for growth and innovation. Here we review patterns and processes that…
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…
We present a general computational theory of stem cell networks and their developmental dynamics. Stem cell networks are special cases of developmental control networks. Our theory generates a natural classification of all possible stem…
Motivated by the wide range of known self-replicating systems, some far from genetics, we study a system composed by individuals having an internal dynamics with many possible states that are partially stable, with varying mutation rates.…
Humans and animals excel in combining information from multiple sensory modalities, controlling their complex bodies, adapting to growth, failures, or using tools. These capabilities are also highly desirable in robots. They are displayed…
One of the main properties of biological systems is modularity, which manifests itself at all levels of their organization, starting with the level of molecular genetics, ending with the level of whole organisms and their communities. In a…
A punctuated equilibrium model of biological evolution with relative fitness between different species being the fundamental driving force of evolution is introduced. Mutation is modeled as a fitness updating cellular automaton process…
We study the mathematical properties of a general model of cell division structured with several internal variables. We begin with a simpler and specific model with two variables, we solve the eigenvalue problem with strong or weak…
Global models of planet formation tend to begin with an initial set of planetary embryos for the sake simplicity. While this approach gives valuable insights on the evolution of the initial embryos, the initial distribution itself is a bold…
Biological evolution continuously refines the design of species, resulting in highly optimised organisms over hundreds of millennia. Intuitively, we expect that random changes-evolution's primary mechanism-are more likely to be harmful than…
The mechanism of bacterial cell size control has been a mystery for decades, which involves the well-coordinated growth and division in the cell cycle. The revolutionary modern techniques of microfluidics and the advanced live imaging…
During embryonic development, regeneration and homeostasis, cells have to physically integrate into their target tissues, where they ultimately execute their function. Despite a significant body of research on how mechanical forces instruct…
We model evolution of plants in a world, made up of different locations, with multiple environments (mutually exclusive and collectively exhaustive subsets of locations). Each environment (landmass) has temperature, rainfall, and other…