Computability and analysis: the legacy of Alan Turing

We discuss the legacy of Alan Turing and his impact on computability and analysis.Comment: 49 page

Multiple sequence alignment based on set covers

We introduce a new heuristic for the multiple alignment of a set of sequences. The heuristic is based on a set cover of the residue alphabet of the sequences, and also on the determination of a significant set of blocks comprising subsequences of the sequences to be aligned. These blocks are obtained with the aid of a new data structure, called a suffix-set tree, which is constructed from the input sequences with the guidance of the residue-alphabet set cover and generalizes the well-known suffix tree of the sequence set. We provide performance results on selected BAliBASE amino-acid sequences and compare them with those yielded by some prominent approaches

Modernizing PHCpack through phcpy

PHCpack is a large software package for solving systems of polynomial equations. The executable phc is menu driven and file oriented. This paper describes the development of phcpy, a Python interface to PHCpack. Instead of navigating through menus, users of phcpy solve systems in the Python shell or via scripts. Persistent objects replace intermediate files.Comment: Part of the Proceedings of the 6th European Conference on Python in Science (EuroSciPy 2013), Pierre de Buyl and Nelle Varoquaux editors, (2014

Numerical study of the 2D lid-driven triangular cavities based on the Lattice Boltzmann method

Numerical study of two dimensional lid driven triangular cavity flow is performed via using lattice Boltzmann method on low Reynolds numbers. The equilateral triangular cavity is the first geometry to be studied, the simulation is performed at Reynolds number 500 and the numerical prediction is compared with previous work done by other scholars. Several isosceles triangular cavities are studied at different initial conditions, Reynolds numbers ranging from 100 to 3000, regardless of the geometry studied, the top lid is always moving from left to right and the driven velocity remains constant. Results are also compared with previous work performed by other scholars, the agreement is very good. According to the authors’ knowledge, this is the first time that MRT-LBM model is used to simulate the flow inside the triangular cavities. One of the advantages of this method is that it is capable of producing at low and high Reynolds numbers.Peer ReviewedPostprint (published version

A numerical method for junctions in networks of shallow-water channels

There is growing interest in developing mathematical models and appropriate numerical methods for problems involving networks formed by, essentially, one-dimensional (1D) domains joined by junctions. Examples include hyperbolic equations in networks of gas tubes, water channels and vessel networks for blood and lymph in the human circulatory system. A key point in designing numerical methods for such applications is the treatment of junctions, i.e. points at which two or more 1D domains converge and where the flow exhibits multidimensional behaviour. This paper focuses on the design of methods for networks of water channels. Our methods adopt the finite volume approach to make full use of the two-dimensional shallow water equations on the true physical domain, locally at junctions, while solving the usual one-dimensional shallow water equations away from the junctions. In addition to mass conservation, our methods enforce conservation of momentum at junctions; the latter seems to be the missing element in methods currently available. Apart from simplicity and robustness, the salient feature of the proposed methods is their ability to successfully deal with transcritical and supercritical flows at junctions, a property not enjoyed by existing published methodologies. Systematic assessment of the proposed methods for a variety of flow configurations is carried out. The methods are directly applicable to other systems, provided the multidimensional versions of the 1D equations are available