Creating Responsive Information Systems with the Help of SSADM

In this paper, a program for a research is outlined. Firstly, the concept of responsive information systems is defined and then the notion of the capacity planning and software performance engineering is clarified. Secondly, the purpose of the proposed methodology of capacity planning, the interface to information systems analysis and development methodologies (SSADM), the advantage of knowledge-based approach is discussed. The interfaces to CASE tools more precisely to data dictionaries or repositories (IRDS) are examined in the context of a certain systems analysis and design methodology (e.g. SSADM)

Quantum natural gradient generalised to non-unitary circuits

Variational quantum circuits are promising tools whose efficacy depends on their optimisation method. For noise-free unitary circuits, the quantum generalisation of natural gradient descent was recently introduced. The method can be shown to be equivalent to imaginary time evolution, and is highly effective due to a metric tensor reconciling the classical parameter space to the device's Hilbert space. Here we generalise quantum natural gradient to consider arbitrary quantum states (both mixed and pure) via completely positive maps; thus our circuits can incorporate both imperfect unitary gates and fundamentally non-unitary operations such as measurements. Whereas the unitary variant relates to classical Fisher information, here we find that quantum Fisher information defines the core metric in the space of density operators. Numerical simulations indicate that our approach can outperform other variational techniques when circuit noise is present. We finally assess the practical feasibility of our implementation and argue that its scalability is only limited by the number and quality of imperfect gates and not by the number of qubits.Comment: 20 pages, 6 figure

Quantum Analytic Descent

Variational algorithms have particular relevance for near-term quantum computers but require non-trivial parameter optimisations. Here we propose Analytic Descent: Given that the energy landscape must have a certain simple form in the local region around any reference point, it can be efficiently approximated in its entirety by a classical model -- we support these observations with rigorous, complexity-theoretic arguments. One can classically analyse this approximate function in order to directly `jump' to the (estimated) minimum, before determining a more refined function if necessary. We verify our technique using numerical simulations: each analytic jump can be equivalent to many thousands of steps of canonical gradient descent.Comment: 14 pages, 4 figure

Probabilistic Interpolation of Quantum Rotation Angles

Quantum computing requires a universal set of gate operations; regarding gates as rotations, any rotation angle must be possible. However a real device may only be capable of $B$ bits of resolution, i.e. it might support only $2^B$ possible variants of a given physical gate. Naive discretization of an algorithm's gates to the nearest available options causes coherent errors, while decomposing an impermissible gate into several allowed operations increases circuit depth. Conversely, demanding higher $B$ can greatly complexify hardware. Here we explore an alternative: Probabilistic Angle Interpolation (PAI). This effectively implements any desired, continuously parametrised rotation by randomly choosing one of three discretised gate settings and postprocessing individual circuit outputs. The approach is particularly relevant for near-term applications where one would in any case average over many runs of circuit executions to estimate expected values. While PAI increases that sampling cost, we prove that a) the approach is optimal in the sense that PAI achieves the least possible overhead and c) the overhead is remarkably modest even with thousands of parametrised gates and only $7$ bits of resolution available. This is a profound relaxation of engineering requirements for first generation quantum computers where even $5-6$ bits of resolution may suffice and, as we demonstrate, the approach is many orders of magnitude more efficient than prior techniques. Moreover we conclude that, even for more mature late-NISQ hardware, no more than $9$ bits will be necessary.Comment: 15 pages, 5 figures -- includes proof of optimality of protocol, generalisation to non-uniform settings et

Synthesis of Indole-Coupled KYNA Derivatives via C–N Bond Cleavage of Mannich Bases

KYNAs, a compound with endogenous neuroprotective functions and an indole that is a building block of many biologically active compounds, such as a variety of neurotransmitters, are reacted in a transformation building upon Mannich bases. The reaction yields triarylmethane derivatives containing two biologically potent skeletons, and it may contribute to the synthesis of new, specialised neuroprotective compounds. The synthesis has been investigated via two procedures and the results were compared to those of previous studies. A possible alternative reaction route through acid catalysis has been established

Alkoxyalkylation of Electron-Rich Aromatic Compounds

Alkoxyalkylation and hydroxyalkylation methods utilizing oxo-compound derivatives such as aldehydes, acetals or acetylenes and various alcohols or water are widely used tools in preparative organic chemistry to synthesize bioactive compounds, biosensors, supramolecular compounds and petrochemicals. The syntheses of such molecules of broad relevance are facilitated by acid, base or heterogenous catalysis. However, degradation of the N-analogous Mannich bases are reported to yield alkoxyalkyl derivatives via the retro-Mannich reaction. The mutual derivative of all mentioned species are quinone methides, which are reported to form under both alkoxy- and aminoalkylative conditions and via the degradation of the Mannich-products. The aim of this review is to summarize the alkoxyalkylation (most commonly alkoxymethylation) of electron-rich arenes sorted by the methods of alkoxyalkylation (direct or via retro-Mannich reaction) and the substrate arenes, such as phenolic and derived carbocycles, heterocycles and the widely examined indole derivatives

Distributed Simulation of Statevectors and Density Matrices

Classical simulation of quantum computers is an irreplaceable step in the design of quantum algorithms. Exponential simulation costs demand the use of high-performance computing techniques, and in particular distribution, whereby the quantum state description is partitioned between a network of cooperating computers - necessary for the exact simulation of more than approximately 30 qubits. Distributed computing is notoriously difficult, requiring bespoke algorithms dissimilar to their serial counterparts with different resource considerations, and which appear to restrict the utilities of a quantum simulator. This manuscript presents a plethora of novel algorithms for distributed full-state simulation of gates, operators, noise channels and other calculations in digital quantum computers. We show how a simple, common but seemingly restrictive distribution model actually permits a rich set of advanced facilities including Pauli gadgets, many-controlled many-target general unitaries, density matrices, general decoherence channels, and partial traces. These algorithms include asymptotically, polynomially improved simulations of exotic gates, and thorough motivations for high-performance computing techniques which will be useful for even non-distributed simulators. Our results are derived in language familiar to a quantum information theory audience, and our algorithms formalised for the scientific simulation community. We have implemented all algorithms herein presented into an isolated, minimalist C++ project, hosted open-source on Github with a permissive MIT license, and extensive testing. This manuscript aims both to significantly improve the high-performance quantum simulation tools available, and offer a thorough introduction to, and derivation of, full-state simulation techniques.Comment: 56 pages, 18 figures, 28 algorithms, 1 tabl

A word of caution about biological inference - Revisiting cysteine covalent state predictions

The success of methods for predicting the redox state of cysteine residues from the sequence environment seemed to validate the basic assumption that this state is mainly determined locally. However, the accuracy of predictions on randomized sequences or of non-cysteine residues remained high, suggesting that these predictions rather capture global features of proteins such as subcellular localization, which depends on composition. This illustrates that even high prediction accuracy is insufficient to validate implicit assumptions about a biological phenomenon. Correctly identifying the relevant underlying biochemical reasons for the success of a method is essential to gain proper biological insights and develop more accurate and novel bioinformatics tools. 2014 The Authors. Published by Elsevier B.V. on behalf of the Federation of European Biochemical Societies. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/)

Systematic analysis of somatic mutations driving cancer: Uncovering functional protein regions in disease development

Background: Recent advances in sequencing technologies enable the large-scale identification of genes that are affected by various genetic alterations in cancer. However, understanding tumor development requires insights into how these changes cause altered protein function and impaired network regulation in general and/or in specific cancer types. Results: In this work we present a novel method called iSiMPRe that identifies regions that are significantly enriched in somatic mutations and short in-frame insertions or deletions (indels). Applying this unbiased method to the complete human proteome, by using data enriched through various cancer genome projects, we identified around 500 protein regions which could be linked to one or more of 27 distinct cancer types. These regions covered the majority of known cancer genes, surprisingly even tumor suppressors. Additionally, iSiMPRe also identified novel genes and regions that have not yet been associated with cancer. Conclusions: While local somatic mutations correspond to only a subset of genetic variations that can lead to cancer, our systematic analyses revealed that they represent an accompanying feature of most cancer driver genes regardless of the primary mechanism by which they are perturbed during tumorigenesis. These results indicate that the accumulation of local somatic mutations can be used to pinpoint genes responsible for cancer formation and can also help to understand the effect of cancer mutations at the level of functional modules in a broad range of cancer driver genes. Reviewers: This article was reviewed by Sándor Pongor, Michael Gromiha and Zoltán Gáspári. © 2016 Mészáros et al