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The evolution equations of the Yukawa couplings and quark mixings are performed for the one-loop renormalisation group equations in six-dimensional models compactified in different possible ways to yield standard four space-time dimensions.…
Compartments are ubiquitous throughout biology, yet their importance stretches back to the origin of cells. In the context of origin of life, we assume that a protocell, a compartment enclosing functional components, requires $N$ components…
The budding yeast {\it Saccharomyces cerevisiae} is the first eukaryote whose genome has been completely sequenced. It is also the first eukaryotic cell whose proteome (the set of all proteins) and interactome (the network of all mutual…
The interconnected processes of protein folding, mutations, epistasis, and evolution have all been the subject of extensive analysis throughout the years due to their significance for structural and evolutionary biology. The origin…
The interaction lifetimes between condensate-forming biomolecules can dictate both the specificity of the condensate-forming species as well as the fluidity and exchange dynamics of these condensates. Using a heuristic modeling approach, we…
The evolution equations of the Yukawa couplings and quark mixings are derived for the one-loop renormalization group equations in the two Universal Extra Dimension Models (UED), that is six-dimensional models, compactified in different…
Mutations sometimes increase contagiousness for evolving pathogens. During an epidemic, scientists use viral genome data to infer a shared evolutionary history and connect this history to geographic spread. We propose a model that directly…
We study the probabilities of evolution based on random mutations and natural selection. We conclude that evolution to multicellular eukaryots, or even prokaryots, is unlikely to be the result of only random mutations. Complex organisms…
The escape process from the native valley for proteins subjected to a constant stretching force is examined using a model for a Beta-barrel. For a wide range of forces, the unfolding dynamics can be treated as one-dimensional diffusion,…
The genetic blueprint for the essential functions of life is encoded in DNA, which is translated into proteins -- the engines driving most of our metabolic processes. Recent advancements in genome sequencing have unveiled a vast diversity…
A two-step contagion model with a single seed serves as a cornerstone for understanding the critical behaviors and underlying mechanism of discontinuous percolation transitions induced by cascade dynamics. When the contagion spreads from a…
Unidirectionally coupled systems which exhibit phase transitions into an absorbing state are investigated at the multicritical point. We find that for initial conditions with isolated particles, each hierarchy level exhibits an…
Eukaryotic cells intrinsically change their shape, by changing the composition of their membrane and by restructuring their underlying cytoskeleton. We present here further studies and extensions of a minimal physical model, describing a…
Eukaryote genomes contain excessively introns, inter-genic and other non-genic sequences that appear to have no vital functional role or phenotype manifestation. Their existence, a long-standing puzzle, is viewed from the principle of…
Collective cell migration is essential for a wide range of biological processes such as: morphogenesis, wound healing, and cancer spreading. However, it is well known that migrating epithelial collectives frequently undergo jamming, stay…
Eukaryotic cells and intracellular pathogens such as bacteria or viruses utilize the actin polymerization machinery to propel themselves forward. Thereby, the onset of motion and choice of direction may be the result of a spontaneous…
We propose a discrete model to determine the metabolic scaling exponent based on Fibonacci growth patterns and discrete biological development phases. In contrast to continuous fractal models such as the West-Brown-Enquist (WBE) theory, the…
The effect of conformational fluctuations of modular macromolecules, such as enzymes, on their diffusion properties is addressed using a simple generic model of an asymmetric dumbbell made of two hydrodynamically coupled subunits. It is…
Excitability is an attribute of life, and is a driving force in the descent of complexity. Cellular electrical activity as realized by membrane proteins that act as either channels or transporters is the basis of excitability. Electrical…
It is shown that the rates of the decays Upsilon(1^3D_1) -> eta Upsilon(1S) and Upsilon(1^3D_2) -> eta Upsilon(1S) should be comparable to and likely exceed that of the recently discussed in the literature two-pion transition Upsilon(1D) ->…