Mitochondrial DNA (mtDNA) and plastid DNA (ptDNA) encode vital bioenergetic apparatus, and mutations in these organelle DNA (oDNA) molecules can be devastating. In the germline of several animals, a genetic “bottleneck” increases cell-to-cell variance in mtDNA heteroplasmy, allowing purifying selection to act to maintain low proportions of mutant mtDNA. However, most eukaryotes do not sequester a germline early in development, and even the animal bottleneck remains poorly understood. How then do eukaryotic organelles avoid Muller’s ratchet—the gradual buildup of deleterious oDNA mutations? Here, we construct a comprehensive and predictive genetic model, quantitatively describing how different mechanisms segregate and decrease oDNA damage across eukaryotes. We apply this comprehensive theory to characterise the animal bottleneck with recent single-cell observations in diverse mouse models. Further, we show that gene conversion is a particularly powerful mechanism to increase beneficial cell-to-cell variance without depleting oDNA copy number, explaining the benefit of observed oDNA recombination in diverse organisms which do not sequester animal-like germlines (for example, sponges, corals, fungi, and plants). Genomic, transcriptomic, and structural datasets across eukaryotes support this mechanism for generating beneficial variance without a germline bottleneck. This framework explains puzzling oDNA differences across taxa, suggesting how Muller’s ratchet is avoided in different eukaryotes.

No abstract

This work focuses on expressing the TSP with Time Windows (TSPTW for short) as a quadratic unconstrained binary optimization (QUBO) problem. The time windows impose time constraints that a feasible solution must satisfy. These take the form of inequality constraints, which are known to be particularly difficult to articulate within the QUBO framework. This is, we believe, the first time this major obstacle is overcome and the TSPTW is cast in the QUBO formulation. We have every reason to anticipate that this development will lead to the actual execution of small scale TSPTW instances on the D-Wave platform.

Game theory and its quantum extension apply in numerous fields that affect people's social, political, and economical life. Physical limits imposed by the current technology used in computing architectures (e.g., circuit size) give rise to the need for novel mechanisms, such as quantum inspired computation. Elements from quantum computation and mechanics combined with game-theoretic aspects of computing could open new pathways towards the future technological era. This paper associates dominant strategies of repeated quantum games with quantum automata that recognize infinite periodic inputs. As a reference, we used the PQ-PENNY quantum game where the quantum strategy outplays the choice of pure or mixed strategy with probability 1 and therefore the associated quantum automaton accepts with probability 1. We also propose a novel game played on the evolution of an automaton, where players' actions and strategies are also associated with periodic quantum automata.

Abstract:The meticulous study of finite automata has produced many important and useful results. Automata are simple yet efficient finite state machines that can be utilized in a plethora of situations. It comes, therefore, as no surprise that they have been used in classic game theory in order to model players and their actions. Game theory has recently been influenced by ideas from the field of quantum computation. As a result, quantum versions of classic games have already been introduced and studied. The PQ penny flip game is a famous quantum game introduced by Meyer in 1999. In this paper, we investigate all possible finite games that can be played between the two players Q and Picard of the original PQ game. For this purpose, we establish a rigorous connection between finite automata and the PQ game along with all its possible variations. Starting from the automaton that corresponds to the original game, we construct more elaborate automata for certain extensions of the game, before finally presenting a semiautomaton that captures the intrinsic behavior of all possible variants of the PQ game. What this means is that, from the semiautomaton in question, by setting appropriate initial and accepting states, one can construct deterministic automata able to capture every possible finite game that can be played between the two players Q and Picard. Moreover, we introduce the new concepts of a winning automaton and complete automaton for either player.

General variable neighborhood search (GVNS) is a well known and widely used metaheuristic for efficiently solving many NP-hard combinatorial optimization problems. We propose a novel extension of the conventional GVNS. Our approach incorporates ideas and techniques from the field of quantum computation during the shaking phase. The travelling salesman problem (TSP) is a well known NP-hard problem which has broadly been used for modelling many real life routing cases. As a consequence, TSP can be used as a basis for modelling and finding routes via the Global Positioning System (GPS). In this paper, we examine the potential use of this method for the GPS system of garbage trucks. Specifically, we provide a thorough presentation of our method accompanied with extensive computational results. The experimental data accumulated on a plethora of TSP instances, which are shown in a series of figures and tables, allow us to conclude that the novel GVNS algorithm can provide an efficient solution for this type of geographical problem.

Classical game theory is an important field with a long tradition of useful results. Recently, the quantum versions of classical games, such as the prisoner’s dilemma (PD), have attracted a lot of attention. This game variant can be considered as a specific type of game where the player’s actions and strategies are formed using notions from quantum computation. Similarly, state machines, and specifically finite automata, have also been under constant and thorough study for plenty of reasons. The quantum analogues of these abstract machines, like the quantum finite automata, have been studied extensively. In this work, we examine well-known conditional strategies that have been studied within the framework of the classical repeated PD game. Then, we try to associate these strategies to proper quantum finite automata that receive them as inputs and recognize them with a probability of 1, achieving some interesting results. We also study the quantum version of PD under the Eisert–Wilkens–Lewenstein scheme, proposing a novel conditional strategy for the repeated version of this game.

No abstract