Related papers: Relationship between promoter sequence and its str…
Eco-evolutionary frameworks can explain certain features of communities in which ecological and evolutionary processes occur over comparable timescales. Here, we investigate whether an evolutionary dynamics may interact with the spatial…
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…
We investigate the distribution of oscillator strengths for the recombination of excitons in a two dimensional sample, trapped in local minima of the confinement potential: the results are derived from a statistical topographic model of the…
Transcription factors (TF) play an essential role in the cell as locus- and condition-specific recruiters of transcriptional machinery or chromatin-modifying complexes. However, predicting the in vivo profile of TF occupancy along the…
Current practices of quantifying performance by productivity leads serious concerns for psychological well-being of doctoral students and influence of research environment is often neglected in research evaluations. Acknowledgements in…
Understanding of the evolutionary origins of protein structures represents a key component of the understanding of molecular evolution as a whole. Here we seek to elucidate how the features of an underlying protein structural "space" might…
The role of mentorship on protege performance is a matter of importance to academic, business, and governmental organizations. While the benefits of mentorship for proteges, mentors and their organizations are apparent, the extent to which…
Social hierarchy is important that can not be ignored in human socioeconomic activities and in the animal world. Here we incorporate this factor into the evolutionary game to see what impact it could have on the cooperation outcome. The…
The possible role of quantum effects in transfer of genetic information is studied. It's argued that the nucleotides selection during DNA replication is performed by means of proton tunneling between nucleotide and DNA-polimerase bound by…
A chain of connected genes with activation-repression links is analysed. It is shown that for various promoter activity functions (parametrised by Hill coefficient) the equations describing the concentrations of transcription factors, are…
The phase-separation occurring in a system of mutually interacting proteins that can bind on specific sites of a chromatin fiber is here investigated. This is achieved by means of extensive Molecular Dynamics simulations of a simple polymer…
Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…
Preprints have been considered primarily as a supplement to journal-based systems for the rapid dissemination of relevant scientific knowledge and have historically been supported by studies indicating that preprints and published reports…
Drug gradients are believed to play an important role in the evolution of bacteria resistant to antibiotics and tumors resistant to anti-cancer drugs. We use a statistical physics model to study the evolution of a population of malignant…
We study an evolutionary spatial prisoner's dilemma game where the fitness of the players is determined by both the payoffs from the current interaction and their history. We consider the situation where the selection timescale is slower…
Much information is stored in amino acid composition of protein and base composition of DNA. We simulated the evolution of amino acid frequencies and genomic GC content by a linguistic model. It is showed that the evolution of genetic code…
Consider a large Boolean network with a feed forward structure. Given a probability distribution on the inputs, can one find, possibly small, collections of input nodes that determine the states of most other nodes in the network? To answer…
The genetic material of a eukaryotic cell comprises both nuclear DNA (ncDNA) and mitochondrial DNA (mtDNA). These differ markedly in several aspects but nevertheless must encode proteins that are compatible with one another. Here we…
Mitochondrial function relies on the coordinated expression of mitochondrial and nuclear genes, exhibiting remarkable resilience regardless the susceptibility of mitochondrial DNA (mtDNA) to accumulate harmful mutations. A suggested…
BACKGROUND: An important question is whether evolution favors properties such as mutational robustness or evolvability that do not directly benefit any individual, but can influence the course of future evolution. Functionally similar…