Related papers: Cooperative ligation breaks sequence symmetry and …

Cooperative interactions pervade in a broad range of many-body populations, such as ecological communities, social organizations, and economic webs. We investigate the dynamics of a population of two equivalent species A and B that are…

Complex DNA topological structures, including polymer loops, are frequently observed in biological processes when protein molecules simultaneously bind to several distant sites on DNA. However, the molecular mechanisms of formation of these…

We study a simple solvable model describing the genesis of monomer sequences for hetero-polymers (such as proteins), as the result of the equilibration of a slow stochastic genetic selection process which is assumed to be driven by the…

To investigate the origin of cooperative behaviors, we developed an evolutionary model of sequential strategies and tested our model with computer simulations. The sequential strategies represented by stochastic machines were evaluated…

The genetic information that dictates the structure and function of all life forms is encoded in the DNA. In 1953, Watson and Crick first presented the double helical structure of a DNA molecule. Their findings unearthed the desire to…

Sequence comparison and alignment has had an enormous impact on our understanding of evolution, biology, and disease. Comparison and alignment of biological networks will likely have a similar impact. Existing network alignments use…

To unveil the logic of cell from a level of chemical reaction dynamics, we need to clarify how ensemble of chemicals can autonomously produce the set of chemical, without assuming a specific external control echanism. A cell consists of a…

Speciation is fundamental to the huge diversity of life on Earth. Evidence suggests reproductive isolation arises most commonly in allopatry with a higher speciation rate in small populations. Current theory does not address this dependence…

Protein sequences serve as a natural record of the evolutionary constraints that shape their functional structures. We show that it is possible to use only sequence information to go beyond predicting native structures and global stability…

The emergence of replicases that can replicate themselves is a central issue in the origin of life. Recent experiments suggest that such replicases can be realized if an RNA polymerase ribozyme is divided into fragments short enough to be…

Genomic data are rapidly resolving the tree of living species calibrated to time, the timetree of life, which will provide a framework for research in diverse fields of science. Previous analyses of taxonomically restricted timetrees have…

Life uses non-equilibrium mechanisms to create ordered structures not attainable at equilibrium; the resulting order is assumed to provide functional benefits that outweigh costs of time and energy needed by these mechanisms. Here, we show…

Biosystems contain an almost infinite amount of vital important details, which together ensure their life. There are, however, some common structures and reactions in the systems: the homochirality of carbohydrates and proteins, the…

Understanding the emergence and sustainability of cooperation is a fundamental problem in evolutionary biology and is frequently studied by the framework of evolutionary game theory. A very powerful mechanism to promote cooperation is…

In recent experiments with ion traps, long-range interactions were associated with the exceptionally fast propagation of perturbation, while in some theoretical works they have also been related with the suppression of propagation. Here, we…

Initiating replication synchronously at multiple origins of replication allows the bacterium Escherichia coli to divide even faster than the time it takes to replicate the entire chromosome in nutrient-rich environments. What mechanisms…

Recent 3D organ reconstitution studies show that a group of stem cells can establish a body axis and acquire different fates in a spatially organized manner. How such symmetry breaking happens in the absence of external spatial cues, and…

We explore the emergence of cooperation in the framework of evolutionary game theory. First we introduce the cooperation problem in a novel way that we believe it have important consequences in how problem is addressed. Then we present a…

We study two mechanisms for the formation of protein patterns near membranes of living cells by mathematical modelling. Self-assembly of protein domains by electrostatic lipid-protein interactions is contrasted with self-organization due to…

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…