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The problem of evolutionary complexification of life is considered one of the fundamental aspects in contemporary evolutionary theory. Parasitism is ubiquitous, inevitable, and arises as soon as the first replicators appear, even during the…
Pattern formation in drying protein droplets continues to attract considerable research attention because it can be linked to specific protein-protein interactions. An extensive study of the drying evolution and the final crack patterns are…
Chlamydiae are bacteria with an interesting unusual developmental cycle. A single bacterium in its infectious form (elementary body, EB) enters the host cell, where it converts into its dividing form (reticulate body, RB), and divides by…
Metabolic scaling is one of the most important patterns in biology. Theory explaining the 3/4-power size-scaling of biological metabolic rate does not predict the non-linear scaling observed for smaller life forms. Here we present a new…
The evolution of multicellular organisms from monocellular ancestors represents one of the greatest advances of the history of life. The assembly of such multicellular organisms requires signalling and response between cells: over millions…
Eukarya and Bacteria are the most evolutionarily distant domains of life, which is reflected by differences in their cellular structure and physiology. For example, Eukarya feature membrane-bound organelles such as nuclei and mitochondria,…
We study a $U(N)\times U(N)$ symmetric scalar field model in four and three dimensions. First, using our data in four dimensions in the weak coupling region, we demonstrate explicitly that the observed first order phase transition is…
Here we review the development of protein scaling theory, starting from backgrounds in mathematics and statistical mechanics, and leading to biomedical applications. Evolution has organized each protein family in different ways, but scaling…
In this work, the dynamics of fluctuations in gene expression time series is investigated. By using collected data of gene expression from yeast and human organisms, we found that the fluctuations of gene expression level and its average…
In biology, the evolution of increasingly cooperative groups has shaped the history of life. Genes collaborate in the control of cells; cells efficiently divide tasks to produce cohesive multicellular individuals; individual members of…
This paper presents EINCASM, a prototype system employing a novel framework for studying emergent intelligence in organisms resembling slime molds. EINCASM evolves neural cellular automata with NEAT to maximize cell growth constrained by…
Most conspicuous organisms are multicellular and most multicellular organisms develop somatic cells to perform specific, non-reproductive tasks. The ubiquity of this division of labor suggests that it is highly advantageous. In this paper,…
Physarum Polycephalum is a unicellular slime mold that has been intensely studied due to its ability to solve mazes, find shortest paths, generate Steiner trees, share knowledge, remember past events, and its applications to unconventional…
Thermodynamic scaling theory, previously applied mainly to small proteins, here analyzes quantitative evolution of the titled functional network giant hub enzymes. The broad domain structure identified homologically is confirmed…
In multi-cellular organisms, cells differentiate into multiple types as they divide. States of these cell types, as well as their numbers, are known to be robust to external perturbations; as conceptualized by Waddington's epigenetic…
Evolution of genetic code is studied as the change in the choice of enzymes that are used to synthesize amino acids from the genetic information of nucleic acids. We propose the following theory: the differentiation of physiological states…
What is life. Schrodingers question is discussed here for a specific protein, villin, which builds cells in tissues that detect taste and sound. Villin is represented by a sequence of 827 amino acids bound to a peptide backbone chain. We…
We introduce a simple model of yeast-like growth of fungi colonies, which exhibits a continuous roughening transition far from equilibrium from a smooth ($\alpha = 0$) to rough phase ($\alpha = 1/2$) in 1+1 dimensions. At the transition…
Mechanisms of immunity, and of the host-pathogen interactions in general are among the most fundamental problems of medicine, ecology, and evolution studies. Here, we present a microscopic, protein-level, sequence-based model of immune…
Biology offers many examples of large-scale, complex, concurrent systems: many processes take place in parallel, compete on resources and influence each other's behavior. The scalable modeling of biological systems continues to be a very…