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It is known that the majority of the human genome consists of repeated sequences. Furthermore, it is believed that a significant part of the rest of the genome also originated from repeated sequences and has mutated to its current form. In…
Spin dependent recombination in GaAsN offers many interesting possibilities in the design of spintronic devices mostly due to its astounding capability to reach conduction band electron spin polarizations close to 100% at room temperature.…
Snapping of a slender structure is utilized in a wide range of natural and man-made systems, mostly to achieve rapid movement without relying on muscle-like elements. Although several mechanisms for elastic energy storage and rapid release…
When a ribbon or tube is twisted far enough it forms buckles and wrinkles. Its new geometry can be strikingly ordered, or hopelessly disordered. Here we study this process in a tube with hybrid boundary conditions: one end a cylinder, and…
Single-nucleotide polymorphisms (SNPs) account for most variations between human genomes. We show how, if the genomes in a database differ only by a reasonable number of SNPs and the substrings between those SNPs are unique, then we can…
While planets in the solar system only have a low inclination with respect to the ecliptic there is mounting evidence that in extrasolar systems the inclination can be very high, at least for close-in planets. One process to alter the…
Population structure has been known to substantially affect evolutionary dynamics. Networks that promote the spreading of fitter mutants are called amplifiers of natural selection, and those that suppress the spreading of fitter mutants are…
The mechanical environment of a substrate plays a key role in influencing the behavior of adherent biological cells. Traditional tunable substrates have limitations as their mechanical properties cannot be dynamically altered in-situ during…
Self-positioned nanomembranes such as rolled-up tubes and wrinkled thin films have been potential systems for a variety of applications and basic studies on elastic properties of nanometer-thick systems. Although there is a clear driving…
Signal transduction networks can form highly interconnected systems within cells due to network crosstalk, the sharing of input signals between multiple downstream responses. To better understand the evolutionary design principles…
The phenomenon of cell sorting/segregation, by which cells organise spatially into clusters of specific cell type or function, is essential for tissue morphogenesis. This self-organization process involves an interplay between mechanical,…
Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing…
Motivation: Genome rearrangement plays an important role in evolutionary biology and has profound impacts on phenotype in organisms ranging from microbes to humans. The mechanisms for genome rearrangement events remain unclear. Lots of…
A new model for evolving Evolutionary Algorithms (EAs) is proposed in this paper. The model is based on the Multi Expression Programming (MEP) technique. Each MEP chromosome encodes an evolutionary pattern that is repeatedly used for…
The evolution of various competing cell types in tissues, and the resulting persistent tissue population, is studied numerically and analytically in a particle-based model of active tissues. Mutations change the properties of cells in…
We propose a model for evolution aiming to reproduce statistical features of fossil data, in particular the distributions of extinction events, the distribution of species per genus and the distribution of lifetimes, all of which are known…
Empirical substitution matrices represent the average tendencies of substitutions over various protein families by sacrificing gene-level resolution. We develop a codon-based model, in which mutational tendencies of codon, a genetic code,…
Evolutionary optimization algorithms are often derived from loose biological analogies and struggle to leverage information obtained during the sequential course of optimization. An alternative promising approach is to leverage data and…
Loop extrusion is one of the main processes shaping chromosome organisation across the cell cycle, yet its role in regulating DNA entanglement and nucleoplasm viscoelasticity remains overlooked. We simulate entangled solutions of linear…
Protein structures are much more conserved than sequences during evolution. Based on this observation, we investigate the consequences of structural conservation on protein evolution. We study seven of the most studied protein folds,…