Boolean networks with reliable dynamics

We investigated the properties of Boolean networks that follow a given reliable trajectory in state space. A reliable trajectory is defined as a sequence of states which is independent of the order in which the nodes are updated. We explored numerically the topology, the update functions, and the state space structure of these networks, which we constructed using a minimum number of links and the simplest update functions. We found that the clustering coefficient is larger than in random networks, and that the probability distribution of three-node motifs is similar to that found in gene regulation networks. Among the update functions, only a subset of all possible functions occur, and they can be classified according to their probability. More homogeneous functions occur more often, leading to a dominance of canalyzing functions. Finally, we studied the entire state space of the networks. We observed that with increasing systems size, fixed points become more dominant, moving the networks close to the frozen phase.Comment: 11 Pages, 15 figure

Duel and sweep algorithm for order-preserving pattern matching

Given a text $T$ and a pattern $P$ over alphabet $\Sigma$, the classic exact matching problem searches for all occurrences of pattern $P$ in text $T$. Unlike exact matching problem, order-preserving pattern matching (OPPM) considers the relative order of elements, rather than their real values. In this paper, we propose an efficient algorithm for OPPM problem using the "duel-and-sweep" paradigm. Our algorithm runs in $O(n + m\log m)$ time in general and $O(n + m)$ time under an assumption that the characters in a string can be sorted in linear time with respect to the string size. We also perform experiments and show that our algorithm is faster that KMP-based algorithm. Last, we introduce the two-dimensional order preserved pattern matching and give a duel and sweep algorithm that runs in $O(n^2)$ time for duel stage and $O(n^2 m)$ time for sweeping time with $O(m^3)$ preprocessing time.Comment: 13 pages, 5 figure

Security of practical private randomness generation

Measurements on entangled quantum systems necessarily yield outcomes that are intrinsically unpredictable if they violate a Bell inequality. This property can be used to generate certified randomness in a device-independent way, i.e., without making detailed assumptions about the internal working of the quantum devices used to generate the random numbers. Furthermore these numbers are also private, i.e., they appear random not only to the user, but also to any adversary that might possess a perfect description of the devices. Since this process requires a small initial random seed, one usually speaks of device-independent randomness expansion. The purpose of this paper is twofold. First, we point out that in most real, practical situations, where the concept of device-independence is used as a protection against unintentional flaws or failures of the quantum apparatuses, it is sufficient to show that the generated string is random with respect to an adversary that holds only classical-side information, i.e., proving randomness against quantum-side information is not necessary. Furthermore, the initial random seed does not need to be private with respect to the adversary, provided that it is generated in a way that is independent from the measured systems. The devices, though, will generate cryptographically-secure randomness that cannot be predicted by the adversary and thus one can, given access to free public randomness, talk about private randomness generation. The theoretical tools to quantify the generated randomness according to these criteria were already introduced in [S. Pironio et al, Nature 464, 1021 (2010)], but the final results were improperly formulated. The second aim of this paper is to correct this inaccurate formulation and therefore lay out a precise theoretical framework for practical device-independent randomness expansion.Comment: 18 pages. v3: important changes: the present version focuses on security against classical side-information and a discussion about the significance of these results has been added. v4: minor changes. v5: small typos correcte

Supergravity Higgs Inflation and Shift Symmetry in Electroweak Theory

We present a model of inflation in a supergravity framework in the Einstein frame where the Higgs field of the next to minimal supersymmetric standard model (NMSSM) plays the role of the inflaton. Previous attempts which assumed non-minimal coupling to gravity failed due to a tachyonic instability of the singlet field during inflation. A canonical K\"{a}hler potential with \textit{minimal coupling} to gravity can resolve the tachyonic instability but runs into the $\eta$-problem. We suggest a model which is free of the $\eta$-problem due to an additional coupling in the K\"{a}hler potential which is allowed by the Standard Model gauge group. This induces directions in the potential which we call K-flat. For a certain value of the new coupling in the (N)MSSM, the K\"{a}hler potential is special, because it can be associated with a certain shift symmetry for the Higgs doublets, a generalization of the shift symmetry for singlets in earlier models. We find that K-flat direction has $H_u^0=-H_d^{0*}.$ This shift symmetry is broken by interactions coming from the superpotential and gauge fields. This direction fails to produce successful inflation in the MSSM but produces a viable model in the NMSSM. The model is specifically interesting in the Peccei-Quinn (PQ) limit of the NMSSM. In this limit the model can be confirmed or ruled-out not just by cosmic microwave background observations but also by axion searches.Comment: matches the published version at JCA

Hybrid quantum computing with ancillas

In the quest to build a practical quantum computer, it is important to use efficient schemes for enacting the elementary quantum operations from which quantum computer programs are constructed. The opposing requirements of well-protected quantum data and fast quantum operations must be balanced to maintain the integrity of the quantum information throughout the computation. One important approach to quantum operations is to use an extra quantum system - an ancilla - to interact with the quantum data register. Ancillas can mediate interactions between separated quantum registers, and by using fresh ancillas for each quantum operation, data integrity can be preserved for longer. This review provides an overview of the basic concepts of the gate model quantum computer architecture, including the different possible forms of information encodings - from base two up to continuous variables - and a more detailed description of how the main types of ancilla-mediated quantum operations provide efficient quantum gates.Comment: Review paper. An introduction to quantum computation with qudits and continuous variables, and a review of ancilla-based gate method

The effect of protein mutations on drug binding suggests ensuing personalised drug selection

The advent of personalised medicine promises a deeper understanding of mechanisms and therefore therapies. However, the connection between genomic sequences and clinical treatments is often unclear. We studied 50 breast cancer patients belonging to a population-cohort in the state of Qatar. From Sanger sequencing, we identified several new deleterious mutations in the estrogen receptor 1 gene (ESR1). The effect of these mutations on drug treatment in the protein target encoded by ESR1, namely the estrogen receptor, was achieved via rapid and accurate protein-ligand binding affinity interaction studies which were performed for the selected drugs and the natural ligand estrogen. Four nonsynonymous mutations in the ligand-binding domain were subjected to molecular dynamics simulation using absolute and relative binding free energy methods, leading to the ranking of the efficacy of six selected drugs for patients with the mutations. Our study shows that a personalised clinical decision system can be created by integrating an individual patient's genomic data at the molecular level within a computational pipeline which ranks the efficacy of binding of particular drugs to variant proteins

Log-Poisson Cascade Description of Turbulent Velocity Gradient Statistics

The Log-Poisson phenomenological description of the turbulent energy cascade is evoked to discuss high-order statistics of velocity derivatives and the mapping between their probability distribution functions at different Reynolds numbers. The striking confirmation of theoretical predictions suggests that numerical solutions of the flow, obtained at low/moderate Reynolds numbers can play an important quantitative role in the analysis of experimental high Reynolds number phenomena, where small scales fluctuations are in general inaccessible from direct numerical simulations

Physical tests for Random Numbers in Simulations

We propose three physical tests to measure correlations in random numbers used in Monte Carlo simulations. The first test uses autocorrelation times of certain physical quantities when the Ising model is simulated with the Wolff algorithm. The second test is based on random walks, and the third on blocks of n successive numbers. We apply the tests to show that recent errors in high precision simulations using generalized feedback shift register algorithms are due to short range correlations in random number sequences. We also determine the length of these correlations.Comment: 16 pages, Post Script file, HU-TFT-94-

CAPAS: A context-aware system architecture for physical activities monitoring

Attribute grammars are widely used by compiler-generators since it allows complete specifications of static semantics. They can also be applied to other fields of research, for instance, to human activities recognition. This paper aims to present CAPAS, a Context-aware system Architecture to monitor Physical ActivitieS. One of the components that is present in the architecture is the attribute grammar which is filled after the prediction is made according to the data gathered from the user through the sensors. According to some predefined rules, the physical activity is validated after an analysis on the attribute grammar, if it meets those requirements. Besides that it proposes an attribute grammar itself which should be able to be incorporated in a system in order to validate the performed physical activity.This work has been supported by FCT – Fundação˜ para a Ciência e Tecnologia within the Project Scope: ˆ UID/CEC/00319/2019