Computational Analysis of Genetic Code Variations Optimized for the Robustness against Point Mutations with Wobble-like Effects

It is believed that the codon–amino acid assignments of the standard genetic code (SGC) help to minimize the negative effects caused by point mutations. All possible point mutations of the genetic code can be represented as a weighted graph with weights that correspond to the probabilities of these mutations. The robustness of a code against point mutations can be described then by means of the so-called conductance measure. This paper quantifies the wobble effect, which was investigated previously by applying the weighted graph approach, and seeks optimal weights using an evolutionary optimization algorithm to maximize the code’s robustness. One result of our study is that the robustness of the genetic code is least influenced by mutations in the third position—like with the wobble effect. Moreover, the results clearly demonstrate that point mutations in the first, and even more importantly, in the second base of a codon have a very large influence on the robustness of the genetic code. These results were compared to single nucleotide variants (SNV) in coding sequences which support our findings. Additionally, it was analyzed which structure of a genetic code evolves from random code tables when the robustness is maximized. Our calculations show that the resulting code tables are very close to the standard genetic code. In conclusion, the results illustrate that the robustness against point mutations seems to be an important factor in the evolution of the standard genetic code.

The Security of Cryptosystems Based on Error-Correcting Codes

Quantum computers are distinguished by their enormous storage capacity and relatively high computing speed. Among the cryptosystems of the future, the best known and most studied which will resist when using this kind of computer are cryptosystems based on error-correcting codes. The use of problems inspired by the theory of error-correcting codes in the design of cryptographic systems adds an alternative to cryptosystems based on number theory, as well as solutions to their vulnerabilities. Their security is based on the problem of decoding a random code that is NP-complete. In this chapter, we will discuss the cryptographic properties of error-correcting codes, as well as the security of cryptosystems based on code theory.

Evolution of the Standard Genetic Code

A near-universal Standard Genetic Code (SGC) implies a single origin for present Earth life. To study this unique event, I compute paths to the SGC, comparing different plausible histories. Notably, SGC-like coding emerges from traditional evolutionary mechanisms, and a superior route can be identified. To objectively measure evolution, progress values from 0 (random coding) to 1 (SGC-like) are defined: these measure fractions of random-code-to-SGC distance. Progress types are spacing/distance/delta Polar Requirement, detecting space between identical assignments/mutational distance to the SGC/chemical order, respectively. The coding system is based on selected RNAs performing aminoacyl-RNA synthetase reactions. Acceptor RNAs exhibit SGC-like Crick wobble; alternatively, non-wobbling triplets uniquely encode 20 amino acids/start/stop. Triplets acquire 22 functions by stereochemistry, selection, coevolution, or at random. Assignments also propagate to an assigned triplet’s neighborhood via single mutations, but can also decay. A vast code universe makes futile evolutionary paths plentiful. Thus, SGC evolution is critically sensitive to disorder from random assignments. Evolution also inevitably slows near coding completion. The SGC likely avoided these difficulties, and two suitable paths are compared. In late wobble, a majority of non-wobble assignments are made before wobble is adopted. In continuous wobble, a uniquely advantageous early intermediate yields an ordered SGC. Revised coding evolution (limited randomness, late wobble, concentration on amino acid encoding, chemically conservative coevolution with a chemically ordered elite) produces varied full codes with excellent joint progress values. A population of only 600 independent coding tables includes SGC-like members; a Bayesian path toward more accurate SGC evolution is available.

Application of DCT to problem of collision resolution in RFID SAW systems by using correlation method

The article is devoted to SAW RFID systems. A problem of collision resolution by using a correlation method is under consideration. Collision is resolves by means of two correlation features, by the correlation function of the signal and by the correlation function of the DCT from the signal. A program, which is implements such collision resolution algorithm, was written. A collision is creating by using a simulation model of RFID tag. The model can generate a response from tag with «own» or with a random code, or can generate a collision of responses with random codes, which may contain or not contain an «own» code. The results of the algorithm’s operation are presented for the cases of reading from two to ten tags simultaneously. In addition to the main function, the algorithm implements error-correcting coding and decoding functions. It allows eliminating errors in case when there is no collision of tags, but a level of channel noise is high. The error-correcting coding is implemented by Reed-Solomon codes.

Achievable Information Rates for Probabilistic Amplitude Shaping: An Alternative Approach via Random Sign-Coding Arguments

Probabilistic amplitude shaping (PAS) is a coded modulation strategy in which constellation shaping and channel coding are combined. PAS has attracted considerable attention in both wireless and optical communications. Achievable information rates (AIRs) of PAS have been investigated in the literature using Gallager’s error exponent approach. In particular, it has been shown that PAS achieves the capacity of the additive white Gaussian noise channel (Böcherer, 2018). In this work, we revisit the capacity-achieving property of PAS and derive AIRs using weak typicality. Our objective is to provide alternative proofs based on random sign-coding arguments that are as constructive as possible. Accordingly, in our proofs, only some signs of the channel inputs are drawn from a random code, while the remaining signs and amplitudes are produced constructively. We consider both symbol-metric and bit-metric decoding.

Photon Counting LIDAR Based on True Random Coding

In this paper, a true random coding photon counting LIDAR is described, in which a Gm-APD (Geiger mode avalanche photodiode) acts as the true random sequence signal generator. The true random coding method not only improves the anti-crosstalk capability of the system, but also greatly reduces the 1-bit missed detection caused by the limited Gm-APD count rate. The experiment verifies the feasibility of the true random sequence used in a photon counting LIDAR ranging system, and a simple and intuitive evaluation model of true random sequence autocorrelation is proposed. Finally, the influence of system parameters (mean echo photon number, mean pulse count density, sequence length, mean noise count) on detection probability is explored. In general, this paper proves that the true random code photon counting LIDAR is an effective target detection method, and provides a new idea for the research of an anti-crosstalk LIDAR system.