Using Automated Reasoning Systems on Molecular Computing

This paper is focused on the interplay between automated reasoning systems (as theoretical and formal devices to study the correctness of a program) and DNA computing (as practical devices to handle DNA strands to solve classical hard problems with laboratory techniques). To illustrate this work we have proven in the PVS proof checker, the correctness of a program, in a sticker based model for DNA computation, solving the pairwise disjoint families problem. Also we introduce the formalization of the Floyd–Hoare logic for imperative programs

Self-replication and evolution of DNA crystals

Is it possible to create a simple physical system that is capable of replicating itself? Can such a system evolve interesting behaviors, thus allowing it to adapt to a wide range of environments? This paper presents a design for such a replicator constructed exclusively from synthetic DNA. The basis for the replicator is crystal growth: information is stored in the spatial arrangement of monomers and copied from layer to layer by templating. Replication is achieved by fragmentation of crystals, which produces new crystals that carry the same information. Crystal replication avoids intrinsic problems associated with template-directed mechanisms for replication of one-dimensional polymers. A key innovation of our work is that by using programmable DNA tiles as the crystal monomers, we can design crystal growth processes that apply interesting selective pressures to the evolving sequences. While evolution requires that copying occur with high accuracy, we show how to adapt error-correction techniques from algorithmic self-assembly to lower the replication error rate as much as is required

An Algorithmic Argument for Nonadaptive Query Complexity Lower Bounds on Advised Quantum Computation

This paper employs a powerful argument, called an algorithmic argument, to prove lower bounds of the quantum query complexity of a multiple-block ordered search problem in which, given a block number i, we are to find a location of a target keyword in an ordered list of the i-th block. Apart from much studied polynomial and adversary methods for quantum query complexity lower bounds, our argument shows that the multiple-block ordered search needs a large number of nonadaptive oracle queries on a black-box model of quantum computation that is also supplemented with advice. Our argument is also applied to the notions of computational complexity theory: quantum truth-table reducibility and quantum truth-table autoreducibility.Comment: 16 pages. An extended abstract will appear in the Proceedings of the 29th International Symposium on Mathematical Foundations of Computer Science, Lecture Notes in Computer Science, Springer-Verlag, Prague, August 22-27, 200

Quantum Weakly Nondeterministic Communication Complexity

We study the weakest model of quantum nondeterminism in which a classical proof has to be checked with probability one by a quantum protocol. We show the first separation between classical nondeterministic communication complexity and this model of quantum nondeterministic communication complexity for a total function. This separation is quadratic.Comment: 12 pages. v3: minor correction

Discrete Logarithm in GF(2809) with FFS

International audienceThe year 2013 has seen several major complexity advances for the discrete logarithm problem in multiplicative groups of small- characteristic finite fields. These outmatch, asymptotically, the Function Field Sieve (FFS) approach, which was so far the most efficient algorithm known for this task. Yet, on the practical side, it is not clear whether the new algorithms are uniformly better than FFS. This article presents the state of the art with regard to the FFS algorithm, and reports data from a record-sized discrete logarithm computation in a prime-degree extension field

Resolution of Linear Algebra for the Discrete Logarithm Problem Using GPU and Multi-core Architectures

In cryptanalysis, solving the discrete logarithm problem (DLP) is key to assessing the security of many public-key cryptosystems. The index-calculus methods, that attack the DLP in multiplicative subgroups of finite fields, require solving large sparse systems of linear equations modulo large primes. This article deals with how we can run this computation on GPU- and multi-core-based clusters, featuring InfiniBand networking. More specifically, we present the sparse linear algebra algorithms that are proposed in the literature, in particular the block Wiedemann algorithm. We discuss the parallelization of the central matrix--vector product operation from both algorithmic and practical points of view, and illustrate how our approach has contributed to the recent record-sized DLP computation in GF($2^{809}$).Comment: Euro-Par 2014 Parallel Processing, Aug 2014, Porto, Portugal. \<http://europar2014.dcc.fc.up.pt/\&gt

A faster pseudo-primality test

We propose a pseudo-primality test using cyclic extensions of $\mathbb Z/n \mathbb Z$. For every positive integer $k \leq \log n$, this test achieves the security of $k$ Miller-Rabin tests at the cost of $k^{1/2+o(1)}$ Miller-Rabin tests.Comment: Published in Rendiconti del Circolo Matematico di Palermo Journal, Springe

A BQP-complete problem related to the Ising model partition function via a new connection between quantum circuits and graphs

We present a simple construction that maps quantum circuits to graphs and vice-versa. Inspired by the results of D.A. Lidar linking the Ising partition function with quadratically signed weight enumerators (QWGTs), we also present a BQP-complete problem for the additive approximation of a function over hypergraphs related to the generating function of Eulerian subgraphs for ordinary graphs. We discuss connections with the Ising partition function.Comment: 12 pages, 2 figure

Class Field Theory and the First Case of Fermat’s Last Theorem

Wetensch. publicatieFaculteit der Wiskunde en Natuurwetenschappe

A common algebraic description for probabilistic and quantum computations

AbstractThrough the study of gate arrays we develop a unified framework to deal with probabilistic and quantum computations, where the former is shown to be a natural special case of the latter. On this basis we show how to encode a probabilistic or quantum gate array into a sum-free tensor formula which satisfies the conditions of the partial trace problem, and vice-versa; that is, given a tensor formula F of order n×1 over a semiring S plus a positive integer k, deciding whether the kth partial trace of the matrix valSn,n(F·FT) fulfills a certain property. We use this to show that a certain promise version of the sum-free partial trace problem is complete for the class pr- BPP (promise BPP) for formulas over the semiring (Q+,+,·) of the positive rational numbers, for pr-BQP (promise BQP) in the case of formulas defined over the field (Q+,+,·), and if the promise is given up, then completeness for PP is shown, regardless whether tensor formulas over positive rationals or rationals in general are used. This suggests that the difference between probabilistic and quantum polytime computers may ultimately lie in the possibility, in the latter case, of having destructive interference between computations occurring in parallel. Moreover, by considering variants of this problem, classes like ⊕P, NP, C=P, its complement co-C=P, the promise version of Valiant's class UP, its generalization promise SPP, and unique polytime US can be characterized by carrying the problem properties and the underlying semiring