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At Alife VI, Mark Bedau proposed some evolutionary statistics as a means of classifying different evolutionary systems. Ecolab, whilst not an artificial life system, is a model of an evolving ecology that has advantages of mathematical…
We show that adiabatic, super-Hubble, and almost scale invariant density fluctuations are produced by cosmic strings in a contracting universe. An essential point is that isocurvature perturbations produced by topological defects such as…
As pathogens spread in a population of hosts, immunity is built up and the pool of susceptible individuals is depleted. This generates selective pressure, to which many human RNA viruses, such as influenza virus or SARS-CoV-2, respond with…
One striking feature of bacterial motion is their ability to swim upstream along corners and crevices, by leveraging hydrodynamic interactions. This motion through anatomic ducts or medical devices might be at the origin of serious…
Eukaryote cells have a flexible shape, which dynamically changes according to the function performed by the cell. One mechanism for deforming the cell membrane into the desired shape is through the expression of curved membrane proteins.…
Convergence extension, the simultaneous elongation of tissue along one axis while narrowing along a perpendicular axis, occurs during embryonic development. A fundamental process that contributes to shaping the organism, it happens in many…
We present a two-species population model in a well-mixed environment where the dynamics involves, in addition to birth and death, changes due to environmental factors and inter-species interactions. The novel dynamical components are…
A hypothesis of the evolution of the genetic code is proposed, the leading mechanism of which is the nucleotide spontaneous damage leading to AT-enrichment of the genome. The hypothesis accounts for stability of the genetic code towards…
We study a system of two cavities each encapsulating a qubit and an oscillator degrees of freedom. An ultrastrong interaction strength between the qubit and the oscillator is assumed, and the photons are allowed to hop between the cavities.…
Microbiota contribute to many dimensions of host phenotype, including disease. To link specific microbes to specific phenotypes, microbiome-wide association studies compare microbial abundances between two groups of samples. Abundance…
Biomolecular condensates self-assemble when proteins and nucleic acids spontaneously demix to form droplets within the crowded intracellular milieu. This simple mechanism underlies the formation of a wide variety of membraneless…
Traffic-like collective movements are observed at almost all levels of biological systems. Molecular motor proteins like, for example, kinesin and dynein, which are the vehicles of almost all intra-cellular transport in eukayotic cells,…
Immunotherapy has recently shown important clinical successes in a substantial number of oncology indications. Additionally, the tumor somatic mutation load has been shown to associate with response to these therapeutic agents, and specific…
Background: Trypanosoma brucei is the causative agent of human African sleeping sickness and Nagana in cattle. In addition to being an important pathogen T. brucei has developed into a model system in cell biology. Results: Using Stable…
We extend the notion of compressed quantum simulation to the XY-model. We derive a quantum circuit processing log(n) qubits which simulates the 1D XY-model describing n qubits. In particular, we demonstrate how the adiabatic evolution can…
Biologists have long observed periodic-like oxygen consumption oscillations in yeast populations under certain conditions and several unsatisfactory explanations for this phenomenon have been proposed. These "autonomous oscillations" have…
We study the bifurcations of a set of nine nonlinear ordinary differential equations that describe the regulation of the cyclin-dependent kinase that triggers DNA synthesis and mitosis in the budding yeast, Saccharomyces cerevisiae. We show…
More virulent strains of influenza virus subtypes H1N1 appeared in 2007 and H3N2 in 2011. The amino acid differences from prior less virulent strains appear to be small when tabulated through sequence alignments and counting site identities…
Motile organisms can form stable agglomerates such as cities or colonies. In the outbreak of a highly contagious disease, the control of large-scale epidemic spread depends on factors like the number and size of agglomerates, travel rate…
There is an intrinsic relationship between the molecular evolution in primordial period and the properties of genomes and proteomes of contemporary species. The genomic data may help us understand the driving force of evolution of life at…