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Cells often exhibit different and stable phenotypes from the same DNA sequence. Robustness and plasticity of such cellular states are controlled by diverse transcriptional and epigenetic mechanisms, among them the modification of…
RNA-Seq technology allows for studying the transcriptional state of the cell at an unprecedented level of detail. Beyond quantification of whole-gene expression, it is now possible to disentangle the abundance of individual alternatively…
DNA supercoiling plays an important role in a variety of cellular processes. The torsional stress related with supercoiling may be also involved in gene regulation through the local structure and dynamics of the double helix. To check this…
The universal genetic code presents a fundamental paradox in molecular biology. Recent advances in synthetic biology have demonstrated that the code is remarkably flexible--organisms can survive with 61 codons instead of 64, natural…
The accumulation of beneficial mutations on many competing genetic backgrounds in rapidly adapting populations has a striking impact on evolutionary dynamics. This effect, known as clonal interference, causes erratic fluctuations in the…
Many organisms exhibit branching morphologies that twist around each other and become entangled. Entanglement occurs when different objects interlock, creating complex and often irreversible configurations. This physical phenomenon is…
Many elastic structures exhibit rapid shape transitions between two possible equilibrium states: umbrellas become inverted in strong wind and hopper popper toys jump when turned inside-out. This snap-through is a general motif for the…
Sex chromosomes have evolved repeatedly across the Tree of Life, yet their evolutionary fates differ strikingly. In sharp contrast to mammals and birds with degenerated, stable Y/W chromosomes, in most amphibians, teleosts, non avian…
Certain bacteria form filamentous colonies when the cells fail to separate after dividing. In Bacillus subtilis, Bacillus thermus, and cyanobacteria, the filaments can wrap into complex supercoiled structures as the cells grow. The…
The Extended Evolutionary Synthesis (EES) is beginning to fulfill the whole promise of Darwinian insight through its extension of evolutionary understanding from the biological domain to include cultural information evolution. Several…
The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity between them are essential building blocks…
An intriguing unanswered question about the evolution of bilateral animals with internal skeletons is how an internal skeleton evolved in the first place. Computational modeling of the development of bilateral symmetric organisms suggests…
Ancestral sequence reconstruction (ASR) aims to infer extinct protein sequences at internal nodes of a phylogenetic tree. Classical ASR methods are typically based on continuous-time Markov substitution models, but they treat sites largely…
We investigate the physical mechanisms for spin-dependent recombination of a strongly bound pair of triplet excitons generated by singlet fission and forming a spin quintet (total spin of two) bi-exciton. For triplet excitons the…
Prion and prion-like molecules are a type of self replicating aggregate protein that have been implicated in a variety of neurodegenerative diseases. Over recent decades the molecular dynamics of prions have been characterized both…
This paper presents a physics-based constitutive equation to predict the thermo-chemical aging in elastomers. High-temperature oxidation in elastomers is a complex phenomenon. The macromolecular network of elastomers' microstructures…
We examine the evolution of expression patterns and the organization of genetic information in populations of self-replicating digital organisms. Seeding the experiments with a linearly expressed ancestor, we witness the development of…
Moir\'e superlattices in twisted van der Waals materials constitute a promising platform for engineering electronic and optical properties. However, a major obstacle to fully understanding these systems and harnessing their potential is the…
The evolution equations mentioned in the title of this paper read as follows: x~n = P(n)(x1; x2) , n = 1, 2 , where l is the "discrete-time" independent variable taking integer values (l =0, 1, 2, ...), xn = xn (l) are the 2 dependent…
We analyze evolutionary dynamics on graphs, where the nodes represent individuals of a population. The links of a node describe which other individuals can be displaced by the offspring of the individual on that node. Amplifiers of…