BOOL-AN: A method for comparative sequence analysis and phylogenetic reconstruction

A novel discrete mathematical approach is proposed as an additional tool for molecular systematics which does not require prior statistical assumptions concerning the evolutionary process. The method is based on algorithms generating mathematical representations directly from DNA/RNA or protein sequences, followed by the output of numerical (scalar or vector) and visual characteristics (graphs). The binary encoded sequence information is transformed into a compact analytical form, called the Iterative Canonical Form (or ICF) of Boolean functions, which can then be used as a generalized molecular descriptor. The method provides raw vector data for calculating different distance matrices, which in turn can be analyzed by neighbor-joining or UPGMA to derive a phylogenetic tree, or by principal coordinates analysis to get an ordination scattergram. The new method and the associated software for inferring phylogenetic trees are called the Boolean analysis or BOOL-AN

Evolving a software development methodology for commercial ICTD projects

This article discusses the evolution of a “DistRibuted Agile Methodology Addressing Technical Ictd in Commercial Settings” (DRAMATICS) that was developed in a global software corporation to support ICTD projects from initial team setup through ICT system design, development, and prototyping, to scaling up and transitioning, to sustainable commercial models. We developed the methodology using an iterative Action Research approach in a series of commercial ICTD projects over a period of more than six years. Our learning is reflected in distinctive methodology features that support the development of contextually adapted ICT systems, collaboration with local partners, involvement of end users in design, and the transition from research prototypes to scalable, long-term solutions. We offer DRAMATICS as an approach that others can appropriate and adapt to their particular project contexts. We report on the methodology evolution and provide evidence of its effectiveness in the projects where it has been used

Parallel accelerated cyclic reduction preconditioner for three-dimensional elliptic PDEs with variable coefficients

We present a robust and scalable preconditioner for the solution of large-scale linear systems that arise from the discretization of elliptic PDEs amenable to rank compression. The preconditioner is based on hierarchical low-rank approximations and the cyclic reduction method. The setup and application phases of the preconditioner achieve log-linear complexity in memory footprint and number of operations, and numerical experiments exhibit good weak and strong scalability at large processor counts in a distributed memory environment. Numerical experiments with linear systems that feature symmetry and nonsymmetry, definiteness and indefiniteness, constant and variable coefficients demonstrate the preconditioner applicability and robustness. Furthermore, it is possible to control the number of iterations via the accuracy threshold of the hierarchical matrix approximations and their arithmetic operations, and the tuning of the admissibility condition parameter. Together, these parameters allow for optimization of the memory requirements and performance of the preconditioner.Comment: 24 pages, Elsevier Journal of Computational and Applied Mathematics, Dec 201

Advances on creep–fatigue damage assessment in notched components

In this paper, the extended Direct Steady Cyclic Analysis method (eDSCA) within the Linear Matching Method Framework (LMMF) is combined with the Stress Modified Ductility Exhaustion method and the modified Cavity Growth Factor (CGF) for the first time. This new procedure is used to systematically investigate the effect of several load parameters including load level, load type and creep dwell duration on the creep–fatigue crack initiation process in a notched specimen. The results obtained are verified through a direct comparison with experimental results available in the literature demonstrating great accuracy in predicting the crack initiation life and the driving mechanisms. Furthermore, this extensive numerical study highlighted the possible detrimental effect of the creep–ratchetting mechanism on the crack growth process. This work has a significant impact on structural integrity assessments of complex industrial components and for the better understanding of creep–fatigue lab scale tests

Rapid steady-state analysis of CLL resonant power converters

Cyclic averaging techniques are applied to the CLL resonant power converter to provide steady-state converter characteristics for rapid stress analysis. This is shown to facilitate the determination of mode duties and initial conditions through knowledge of the operational modes of the rectifier at various operating frequencies. Comparisons are made with FMA-based cyclic analyses, and Spice simulations, that show, respectively, improved accuracy and vastly improved execution speeds

Sensitivity-analysis method for inverse simulation application

An important criticism of traditional methods of inverse simulation that are based on the Newton–Raphson algorithm is that they suffer from numerical problems. In this paper these problems are discussed and a new method based on sensitivity-analysis theory is developed and evaluated. The Jacobian matrix may be calculated by solving a sensitivity equation and this has advantages over the approximation methods that are usually applied when the derivatives of output variables with respect to inputs cannot be found analytically. The methodology also overcomes problems of input-output redundancy that arise in the traditional approaches to inverse simulation. The sensitivity- analysis approach makes full use of information within the time interval over which key quantities are compared, such as the difference between calculated values and the given ideal maneuver after each integration step. Applications to nonlinear HS125 aircraft and Lynx helicopter models show that, for this sensitivity-analysis method, more stable and accurate results are obtained than from use of the traditional Newton–Raphson approach