Towards Understanding the Origin of Genetic Languages

Molecular biology is a nanotechnology that works--it has worked for billions of years and in an amazing variety of circumstances. At its core is a system for acquiring, processing and communicating information that is universal, from viruses and bacteria to human beings. Advances in genetics and experience in designing computers have taken us to a stage where we can understand the optimisation principles at the root of this system, from the availability of basic building blocks to the execution of tasks. The languages of DNA and proteins are argued to be the optimal solutions to the information processing tasks they carry out. The analysis also suggests simpler predecessors to these languages, and provides fascinating clues about their origin. Obviously, a comprehensive unraveling of the puzzle of life would have a lot to say about what we may design or convert ourselves into.Comment: (v1) 33 pages, contributed chapter to "Quantum Aspects of Life", edited by D. Abbott, P. Davies and A. Pati, (v2) published version with some editin

Dynamic Influence Networks for Rule-based Models

We introduce the Dynamic Influence Network (DIN), a novel visual analytics technique for representing and analyzing rule-based models of protein-protein interaction networks. Rule-based modeling has proved instrumental in developing biological models that are concise, comprehensible, easily extensible, and that mitigate the combinatorial complexity of multi-state and multi-component biological molecules. Our technique visualizes the dynamics of these rules as they evolve over time. Using the data produced by KaSim, an open source stochastic simulator of rule-based models written in the Kappa language, DINs provide a node-link diagram that represents the influence that each rule has on the other rules. That is, rather than representing individual biological components or types, we instead represent the rules about them (as nodes) and the current influence of these rules (as links). Using our interactive DIN-Viz software tool, researchers are able to query this dynamic network to find meaningful patterns about biological processes, and to identify salient aspects of complex rule-based models. To evaluate the effectiveness of our approach, we investigate a simulation of a circadian clock model that illustrates the oscillatory behavior of the KaiC protein phosphorylation cycle.Comment: Accepted to TVCG, in pres

Synchronous Subsequentiality and Approximations to Undecidable Problems

We introduce the class of synchronous subsequential relations, a subclass of the synchronous relations which embodies some properties of subsequential relations. If we take relations of this class as forming the possible transitions of an infinite automaton, then most decision problems (apart from membership) still remain undecidable (as they are for synchronous and subsequential rational relations), but on the positive side, they can be approximated in a meaningful way we make precise in this paper. This might make the class useful for some applications, and might serve to establish an intermediate position in the trade-off between issues of expressivity and (un)decidability.Comment: In Proceedings GandALF 2015, arXiv:1509.0685

Applying Grover's algorithm to AES: quantum resource estimates

We present quantum circuits to implement an exhaustive key search for the Advanced Encryption Standard (AES) and analyze the quantum resources required to carry out such an attack. We consider the overall circuit size, the number of qubits, and the circuit depth as measures for the cost of the presented quantum algorithms. Throughout, we focus on Clifford$+T$ gates as the underlying fault-tolerant logical quantum gate set. In particular, for all three variants of AES (key size 128, 192, and 256 bit) that are standardized in FIPS-PUB 197, we establish precise bounds for the number of qubits and the number of elementary logical quantum gates that are needed to implement Grover's quantum algorithm to extract the key from a small number of AES plaintext-ciphertext pairs.Comment: 13 pages, 3 figures, 5 tables; to appear in: Proceedings of the 7th International Conference on Post-Quantum Cryptography (PQCrypto 2016

Toda joia, toda beleza! Finding what is left in the margins or regime collisions: A pluralist take on managerialism

This paper has two authors, two titles and is written in the form of a dialogue,rather than conveying a unitary voice, as one would instead expect of a coauthored paper. The reason for this is that the articulation of the authors' disagreement, despite the identification of each of them with “the left”, is precisely the object of inquiry. After briefly introducing the problem on which the authors’ discussion takes place, namely regime collisions, and the clash of approaches that are available to (decide whether to) deal with them, a dialogue follows, in which the authors’ voices are clearly separated as they discuss the specific issue of the measurement of quality as a (managerialist) proposal to “solve” regime collisions, and contrast that to more openly politicised views of approaching regime collisions. In the end, the main features of such discussion are examined in such a way as to bring forth the peculiar self-consciousness that pluralist spaces give rise to, weakening and downsizing every point of view that appoints itself as the “higher” vantage point from which to describe the world and enumerate problems, and stimulating a constant oscillation between perspectives. This commitment to a pluralistic confrontation and the ensuing hybridization of perspectives is, we argue, at the heart of the idea of “the left” which we both identify with

One-Counter Automata with Counter Observability

In a one-counter automaton (OCA), one can produce a letter from some finite alphabet, increment and decrement the counter by one, or compare it with constants up to some threshold. It is well-known that universality and language inclusion for OCAs are undecidable. In this paper, we consider OCAs with counter observability: Whenever the automaton produces a letter, it outputs the current counter value along with it. Hence, its language is now a set of words over an infinite alphabet. We show that universality and inclusion for that model are PSPACE-complete, thus no harder than the corresponding problems for finite automata. In fact, by establishing a link with visibly one-counter automata, we show that OCAs with counter observability are effectively determinizable and closed under all boolean operations. Moreover, it turns out that they are expressively equivalent to strong automata, in which transitions are guarded by MSO formulas over the natural numbers with successor