Related papers: Exceptional error minimization in putative primord…
The rules that specify how the information contained in DNA codes amino acids, is called "the genetic code". Using a simplified version of the Penna nodel, we are using computer simulations to investigate the importance of the genetic code…
This paper characterizes the inherent power of evolutionary algorithms. This power depends on the computational properties of the genetic encoding. With some encodings, two parents recombined with a simple crossover operator can sample from…
We study superdense coding with uniformly accelerated particle in single mode approximation and beyond single mode approximation. We use four different functions, the capacity of superdense coding, negativity, discord and the probability of…
The primitive data for deducing the Miyazawa-Jernigan contact energy or BLOSUM score matrix consists of pair frequency counts. Each amino acid corresponds to a conditional probability distribution. Based on the deviation of such conditional…
In this paper, we consider a concatenated coding based class of DNA storage codes in which the selected molecules are constrained to be taken from an ``inner'' codebook associated with the sequencing channel. This codebook is used in a…
Quantum states are very delicate, so it is likely some sort of quantum error correction will be necessary to build reliable quantum computers. The theory of quantum error-correcting codes has some close ties to and some striking differences…
Many modified genetic codes are found in specific genomes in which one or more codons have been reassigned to a different amino acid from that in the canonical code. We present a model that unifies four possible mechanisms for reassignment,…
Fault-tolerant quantum computers which can solve hard problems rely on quantum error correction. One of the most promising error correction codes is the surface code, which requires universal gate fidelities exceeding the error correction…
The present work is devoted to describe a set of rules explaining the discriminating versus non-discriminating behavior of the di-basic stages and to characterize the role of each base in determining such a behavior. Bases are analyze as…
This note represents the further progress in understanding the determination of the genetic code by Golden mean (Rakocevic, 1998). Three classes of amino acids that follow from this determination (the 7 "golden" amino acids, 7 of their…
Decoders that provide an estimate of the probability of a logical failure conditioned on the error syndrome ("soft-output decoders") can reduce the overhead cost of fault-tolerant quantum memory and computation. In this work, we construct…
In special coordinates (codon position--specific nucleotide frequencies) bacterial genomes form two straight lines in 9-dimensional space: one line for eubacterial genomes, another for archaeal genomes. All the 348 distinct bacterial…
We derive a single-letter upper bound to the mismatched-decoding capacity for discrete memoryless channels. The bound is expressed as the mutual information of a transformation of the channel, such that a maximum-likelihood decoding error…
The study of the fundamental limits of information systems is a central theme in information theory. Both the traditional analytical approach and the recently proposed computational approach have significant limitations, where the former is…
Pre-transformed polar codes (PTPCs) form a class of codes that perform close to the finite-length capacity bounds. The minimum distance and the number of minimum weight codewords are two decisive properties for their performance. In this…
There is an intrinsic relationship between the molecular evolution in primordial period and the properties of genomes and proteomes of contemporary species. The genomic data may help us understand the driving force of evolution of life at…
Evolutionary theorizing resembles building an aircraft while also piloting it; new results change the scaffold for older ideas, requiring revised strategy to remain airborne. A calculated kinetic pathway exists that, under explicit…
For a simple model of mutually interacting qubits it is shown how the errors induced by mutual interactions can be eliminated using concatenated coding. The model is solved exactly for arbitrary interaction strength, for two well-known…
We derive various error exponents in the bee identification problem under two different decoding rules. Under na\"ive decoding, which decodes each bee independently of the others, we analyze a general discrete memoryless channel and a…
The prediction of the three-dimensional structures of the native state of proteins from the sequences of their amino acids is one of the most important challenges in molecular biology. An essential ingredient to solve this problem within…