The geometry of syntax and semantics for directed file transformations

We introduce a conceptual framework that associates syntax and semantics with vertical and horizontal directions in principal bundles and related constructions. This notion of geometry corresponds to a mechanism for performing goal-directed file transformations such as "eliminate unsafe syntax" and suggests various engineering practices

Exponential Networks and Representations of Quivers

We study the geometric description of BPS states in supersymmetric theories with eight supercharges in terms of geodesic networks on suitable spectral curves. We lift and extend several constructions of Gaiotto-Moore-Neitzke from gauge theory to local Calabi-Yau threefolds and related models. The differential is multi-valued on the covering curve and features a new type of logarithmic singularity in order to account for D0-branes and non-compact D4-branes, respectively. We describe local rules for the three-way junctions of BPS trajectories relative to a particular framing of the curve. We reproduce BPS quivers of local geometries and illustrate the wall-crossing of finite-mass bound states in several new examples. We describe first steps toward understanding the spectrum of framed BPS states in terms of such "exponential networks."Comment: 82 pages, 60 figures, typos fixe

Applications of dynamic programming tp problems of routing pipework and cables

Imperial Users onl

An Introduction to Programming for Bioscientists: A Python-based Primer

Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in the biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by fundamental developments in hardware, software, and algorithms. These advances have influenced, and even engendered, a phenomenal array of bioscience fields, including molecular evolution and bioinformatics; genome-, proteome-, transcriptome- and metabolome-wide experimental studies; structural genomics; and atomistic simulations of cellular-scale molecular assemblies as large as ribosomes and intact viruses. In short, much of post-genomic biology is increasingly becoming a form of computational biology. The ability to design and write computer programs is among the most indispensable skills that a modern researcher can cultivate. Python has become a popular programming language in the biosciences, largely because (i) its straightforward semantics and clean syntax make it a readily accessible first language; (ii) it is expressive and well-suited to object-oriented programming, as well as other modern paradigms; and (iii) the many available libraries and third-party toolkits extend the functionality of the core language into virtually every biological domain (sequence and structure analyses, phylogenomics, workflow management systems, etc.). This primer offers a basic introduction to coding, via Python, and it includes concrete examples and exercises to illustrate the language's usage and capabilities; the main text culminates with a final project in structural bioinformatics. A suite of Supplemental Chapters is also provided. Starting with basic concepts, such as that of a 'variable', the Chapters methodically advance the reader to the point of writing a graphical user interface to compute the Hamming distance between two DNA sequences.Comment: 65 pages total, including 45 pages text, 3 figures, 4 tables, numerous exercises, and 19 pages of Supporting Information; currently in press at PLOS Computational Biolog

Gene Family Histories: Theory and Algorithms

Detailed gene family histories and reconciliations with species trees are a prerequisite for studying associations between genetic and phenotypic innovations. Even though the true evolutionary scenarios are usually unknown, they impose certain constraints on the mathematical structure of data obtained from simple yes/no questions in pairwise comparisons of gene sequences. Recent advances in this field have led to the development of methods for reconstructing (aspects of) the scenarios on the basis of such relation data, which can most naturally be represented by graphs on the set of considered genes. We provide here novel characterizations of best match graphs (BMGs) which capture the notion of (reciprocal) best hits based on sequence similarities. BMGs provide the basis for the detection of orthologous genes (genes that diverged after a speciation event). There are two main sources of error in pipelines for orthology inference based on BMGs. Firstly, measurement errors in the estimation of best matches from sequence similarity in general lead to violations of the characteristic properties of BMGs. The second issue concerns the reconstruction of the orthology relation from a BMG. We show how to correct estimated BMG to mathematically valid ones and how much information about orthologs is contained in BMGs. We then discuss implicit methods for horizontal gene transfer (HGT) inference that focus on pairs of genes that have diverged only after the divergence of the two species in which the genes reside. This situation defines the edge set of an undirected graph, the later-divergence-time (LDT) graph. We explore the mathematical structure of LDT graphs and show how much information about all HGT events is contained in such LDT graphs

Incremental Inductive Coverability for Alternating Finite Automata

V tejto práci navrhujeme špecializáciu algoritmu inductive incremental  coverability, ktorá rieši problém prázdnosti alternujúcich konečných automatov. Experimentujeme s rôznymi návrhovými rozhodnutiami, analyzujeme ich a dokazujeme ich korektnosť. Aj keď je známe, že problém je sám o sebe PSpace-ťažký, zameriavame sa na to, aby bolo rozhodovanie prázdnosti výpočetne prijateľné v niektorých triedach automatov s praktickým využitím. Dosiahli sme niekoľko zaujímavýcch výsledkov v porovnaní so špičkovými algoritmami, predovšetkým v porovnaní s algoritmami založenými na protireťazcoch.In this work, we propose a specialization of the inductive incremental coverability algorithm that solves alternating finite automata emptiness problem. We experiment with various design decisions, analyze them and prove their correctness. Even though the problem itself is PSpace-complete, we are focusing on making the decision of emptiness computationally feasible for some practical classes of applications. We have obtained interesting comparative results against state-of-the-art algorithms, especially in comparison with antichain-based algorithms.

Analysis of effectiveness of three forest interventionist techniques and proposal of a new and integrated model of forest restoration

We assessed the efficacy of three different forest intervention techniques, in terms of phytosociological and edaphic responses, that were implemented in 2007. In a farm where trees are planted and managed for cellulose production as well as set aside for environmental conservation, four stands were analysed: three of them were considered degraded and were managed using different intervention techniques (transposition, perch, and abandonment), and a fourth stand comprising pristine vegetation was considered a control (reference). Floristic and phytosociology data were collected in three 10 × 10 m plots established in each stand. Also, a total of 48 soil samples were collected to analyse physical and chemical attributes of the topsoil for the different stands. In terms of biodiversity, all the treatments showed significantly lower values when compared to the reference area. However, the soils in all the treatment and reference stands are similar in terms of physical and chemical attributes. Taking into account the specificities of each restoration technique, we verified that the integrated use of a set of management practices, constituted by the (1) abandonment of the area and (2) following a selective killing of the eucalyptus, is the most suitable and promising model to provide fast and effective restoration in terms of environmental indicators