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Acceleration of Le Bail fitting method on parallel platforms

Mařík, Ondřej, Šimeček, Ivan (2015)

Programs and Algorithms of Numerical Mathematics

Le Bail fitting method is procedure used in the applied crystallography mainly during the crystal structure determination. As in many other applications, there is a need for a great performance and short execution time. In this paper, we describe utilization of parallel computing for mathematical operations used in Le Bail fitting. We present an algorithm implementing this method with highlighted possible approaches to its aforementioned parallelization. Then, we propose a sample parallel version...

Fast and accurate methods of independent component analysis: A survey

Petr Tichavský, Zbyněk Koldovský (2011)


This paper presents a survey of recent successful algorithms for blind separation of determined instantaneous linear mixtures of independent sources such as natural speech or biomedical signals. These algorithms rely either on non-Gaussianity, nonstationarity, spectral diversity, or on a combination of them. Performance of the algorithms will be demonstrated on separation of a linear instantaneous mixture of audio signals (music, speech) and on artifact removal in electroencephalogram (EEG).

Genetic and Tabu search algorithms for peptide assembly problem

Jacek Błażewicz, Marcin Borowski, Piotr Formanowicz, Tomasz Głowacki (2010)

RAIRO - Operations Research

Determining amino acid sequences of protein molecules is one of the most important issues in molecular biology. These sequences determine protein structure and functionality. Unfortunately, direct biochemical methods for reading amino acid sequences can be used for reading short sequences only. This is the reason, which makes peptide assembly algorithms an important complement of these methods. In this paper, a genetic algorithm solving the problem of short amino acid sequence assembly is presented....

Modelling Evolution of Regulatory Networks in Artificial Bacteria

Y. Sanchez-Dehesa, D. Parsons, J. M. Peña, G. Beslon (2008)

Mathematical Modelling of Natural Phenomena

Studying the evolutive and adaptative machanisms of prokayotes is a complicated task. As these machanisms cannot be easily studied "in vivo", it is necessary to consider other methods. We have therefore developed the RAevol model, a model designed to study the evolution of bacteria and their adaptationto the environment. Our model simulates the evolution of a population of artificial bacteria in a changing environment, providing us with an insight into the strategies that digital organisms develop...

Typical Atherosclerotic Plaque Morphology

R. N. Poston, D. R.M. Poston (2010)

Mathematical Modelling of Natural Phenomena

Atherosclerosis always develops in plaques, and the reasons are not clear. We test the hypothesis that plaque morphology results from a self-perpetuating propagating process driven by macrophages (Mphs). A computer model of atherogenesis was written in which the computer screen represents a surface view of a flattened area of an arterial wall on which greatly accelerated atherogenesis is depicted. Rate of Mph recruitment from blood monocytes is set as a steeply rising function of the number of...

Using R to Build and Assess Network Models in Biology

G. Hartvigsen (2011)

Mathematical Modelling of Natural Phenomena

In this paper we build and analyze networks using the statistical and programming environment R and the igraph package. We investigate random, small-world, and scale-free networks and test a standard problem of connectivity on a random graph. We then develop a method to study how vaccination can alter the structure of a disease transmission network. We also discuss a variety of other uses for networks in biology.

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