Related papers: Evolution of the genetic code. Emergence of stop c…
Generative models for source code are an interesting structured prediction problem, requiring to reason about both hard syntactic and semantic constraints as well as about natural, likely programs. We present a novel model for this problem…
We carefully analyze how the abundance of Nitrogen over Oxygen evolves when dependent on metallicity stellar yields with a primary component of N proceeding from AGBs stars are used. We show the results obtained with a chemical evolution…
Using the MOCCA code, we study the evolution of globular clusters (GCs) with multiple stellar populations. For this purpose, the MOCCA code has been significantly extended to take into account the formation of an enriched population of…
A model is presented relating the evolution of genomic GC content over time to AT$\rightarrow$GC and GC$\rightarrow$AT mutation rates. By employing It\^o calculus it is shown that if mutation rates in asexually reproducing organisms are…
In the first paper of this series, we included the effects of population genetics in the agent-based Monte Carlo code HERITAGE under the hypothesis of neutral phenotypic effects. It implied that mutations (genetic changes) had only neutral…
The premise of genetic analysis is that a causal link exists between phenotypic and allelic variation. Yet it has long been documented that mutant phenotypes are not a simple result of a single DNA lesion, but rather are due to interactions…
The function of the organism hinges on the performance of its information-processing networks, which convey information via molecular recognition. Many paths within these networks utilize molecular codebooks, such as the genetic code, to…
A new class of error-correcting quantum codes is introduced capable of stabilizing qubits against spontaneous decay arising from couplings to statistically independent reservoirs. These quantum codes are based on the idea of using an…
In view of the critical behavior exhibited by a statistical model describing a one dimensional crystal containing isotopic impurities and the fact that for impurity mass parameter 3 times the host mass the critical temperature can attain…
Models of codon evolution are commonly used to identify positive selection. Positive selection is typically a heterogeneous process, i.e., it acts on some branches of the evolutionary tree and not others. Previous work on DNA models showed…
Cotranslational folding depends on the folding speed and stability of the nascent protein. It remains difficult, however, to predict which proteins cotranslationally fold. Here, we simulate evolution of model proteins to investigate how…
The evolution of cooperation often depends upon population structure, yet nearly all models of cooperation implicitly assume that this structure remains static. This is a simplifying assumption, because most organisms possess genetic traits…
Cryptic genetic sequences have attenuated effects on phenotypes. In the classic view, relaxed selection allows cryptic genetic diversity to build up across individuals in a population, providing alleles that may later contribute to…
We numerically study the effects of two forms of quenched disorder on the anyons of the toric code. Firstly, a new class of codes based on random lattices of stabilizer operators is presented, and shown to be superior to the standard square…
In this paper, we construct new sequences of asymptotically good convolutional codes. These sequences are obtained from sequences of transitive, self-orthogonal and self-dual block codes that attain the Tsfasman-Vladut-Zink bound.…
A fundamental aspect of the quantum-to-classical limit is the transition from a non-commutative algebra of observables to commutative one. However, this transition is not possible if we only consider unitary evolutions. One way to describe…
Recent discoveries of gravitational wave sources have advanced our knowledge about the formation of compact object binaries. At present, many questions about the stellar origins of binary neutron stars remain open. We explore the evolution…
We raise the hypothesis that the density fluctuations field which originates the growth of large scale structures is a combination of two or more distributions. By applying the statistical analysis of finite mixture distributions to a…
We explicitly construct an infinite family of asymptotically good concatenated quantum stabilizer codes where the outer code uses CSS-type quantum Reed-Solomon code and the inner code uses a set of special quantum codes. In the field of…
Control over spin dynamics has been obtained in NMR via coherent averaging, which is implemented through a sequence of RF pulses, and via quantum codes which can protect against incoherent evolution. Here, we discuss the design and…