An Improved Excitation Matching Method based on an Ant Colony Optimization for Suboptimal-Free Clustering in Sum-Difference Compromise Synthesis

Dealing with an excitation matching method, this paper presents a global optimization strategy for the optimal clustering in sum-difference compromise linear arrays. Starting from a combinatorial formulation of the problem at hand, the proposed technique is aimed at determining the sub-array configuration expressed as the optimal path inside a directed acyclic graph structure modelling the solution space. Towards this end, an ant colony metaheuristic is used to benefit of its hill-climbing properties in dealing with the non-convexity of the sub-arraying as well as in managing graph searches. A selected set of numerical experiments are reported to assess the efficiency and current limitations of the ant-based strategy also in comparison with previous local combinatorial search methods. (c) 2009 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other users, including reprinting/ republishing this material for advertising or promotional purposes, creating new collective works for resale or redistribution to servers or lists, or reuse of any copyrighted components of this work in other works

Radiative transfer on hierarchial grids

We present new methods for radiative transfer on hierarchial grids. We develop a new method for calculating the scattered flux that employs the grid structure to speed up the computation. We describe a novel subiteration algorithm that can be used to accelerate calculations with strong dust temperature self-coupling. We compute two test models, a molecular cloud and a circumstellar disc, and compare the accuracy and speed of the new algorithms against existing methods. An adaptive model of the molecular cloud with less than 8 % of the cells in the uniform grid produced results in good agreement with the full resolution model. The relative RMS error of the surface brightness <4 % at all wavelengths, and in regions of high column density the relative RMS error was only 10^{-4}. Computation with the adaptive model was faster by a factor of ~5. The new method for calculating the scattered flux is faster by a factor of ~4 in large models with a deep hierarchy structure, when images of the scattered light are computed towards several observing directions. The efficiency of the subiteration algorithm is highly dependent on the details of the model. In the circumstellar disc test the speed-up was a factor of two, but much larger gains are possible. The algorithm is expected to be most beneficial in models where a large number of small, dense regions are embedded in an environment with a lower mean density.Comment: Accepted to A&A; 13 pages, 8 figures; (v2: minor typos corrected

Accurate long read mapping using enhanced suffix arrays

With the rise of high throughput sequencing, new programs have been developed for dealing with the alignment of a huge amount of short read data to reference genomes. Recent developments in sequencing technology allow longer reads, but the mappers for short reads are not suited for reads of several hundreds of base pairs. We propose an algorithm for mapping longer reads, which is based on chaining maximal exact matches and uses heuristics and the Needleman-Wunsch algorithm to bridge the gaps. To compute maximal exact matches we use a specialized index structure, called enhanced suffix array. The proposed algorithm is very accurate and can handle large reads with mutations and long insertions and deletions

Parallelization of a Code for the Simulation of Self-gravitating Systems in Astrophysics. Preliminary Speed-up Results

We have preliminary results on the parallelization of a Tree-Code for evaluating gravitational forces in N-body astrophysical systems. For our Cray T3D/CRAFT implementation, we have obtained an encouraging speed-up behavior, which reaches a value of 37 with 64 processor elements (PEs). According to the Amdahl'law, this means that about 99% of the code is actually parallelized. The speed-up tests regarded the evaluation of the forces among N = 130,369 particles distributed scaling the actual distribution of a sample of galaxies seen in the Northern sky hemisphere. Parallelization of the time integration of the trajectories, which has not yet been taken into account, is both easier to implement and not as fundamental.Comment: 14 pages LaTeX + 1 EPS figure + 2 EPS colour figures, epsf.sty and aasms4.sty included; to be published in Science & Supercomputing at CINECA, Report 1997 (Bologna, Italy