Search results for " algorithm"
showing 10 items of 2538 documents
Genomic determinants of protein folding thermodynamics in prokaryotic organisms.
2004
Here we investigate how thermodynamic properties of orthologous proteins are influenced by the genomic environment in which they evolve. We performed a comparative computational study of 21 protein families in 73 prokaryotic species and obtained the following main results. (i) Protein stability with respect to the unfolded state and with respect to misfolding are anticorrelated. There appears to be a trade-off between these two properties, which cannot be optimized simultaneously. (ii) Folding thermodynamic parameters are strongly correlated with two genomic features, genome size and G+C composition. In particular, the normalized energy gap, an indicator of folding efficiency in statistical…
Discrimination and selection of new potential antibacterial compounds using simple topological descriptors.
2003
Abstract The aim of the work was to discriminate between antibacterial and non-antibacterial drugs by topological methods and to select new potential antibacterial agents from among new structures. The method used for antibacterial activity selection was a linear discriminant analysis (LDA). It is possible to obtain a QSAR interpretation of the information contained in the discriminant function. We make use of the pharmacological distribution diagrams (PDDs) as a visualizing technique for the identification and selection of new antibacterial agents.
A supramolecular system that strictly follows the binding mechanism of conformational selection
2020
Induced fit and conformational selection are two dominant binding mechanisms in biology. Although induced fit has been widely accepted by supramolecular chemists, conformational selection is rarely studied with synthetic systems. In the present research, we report a macrocyclic host whose binding mechanism is unambiguously assigned to conformational selection. The kinetic and thermodynamic aspects of this system are studied in great detail. It reveals that the kinetic equation commonly used for conformational selection is strictly followed here. In addition, two mathematical models are developed to determine the association constants of the same guest to the two host conformations. A “confo…
A Probabilistic Analysis About the Concepts of Difficulty and Usefulness of a Molecular Ranking Classification
2013
Discerning between the concepts of difficulty and usefulness of a molecular ranking classification is of significant importance in virtual design chemistry. Here, both concepts are viewed from the statistical and practical point of view according to the standard definitions of enrichment and statistical significance p-values. These parameters are useful not only to compare distinct rankings obtained for the same molecular database, but also in order to compare the ones established in distinct molecular sets from an objective point of view.
Self-organized modularization in evolutionary algorithms.
2005
The principle of modularization has proven to be extremely successful in the field of technical applications and particularly for Software Engineering purposes. The question to be answered within the present article is whether mechanisms can also be identified within the framework of Evolutionary Computation that cause a modularization of solutions. We will concentrate on processes, where modularization results only from the typical evolutionary operators, i.e. selection and variation by recombination and mutation (and not, e.g., from special modularization operators). This is what we call Self-Organized Modularization. Based on a combination of two formalizations by Radcliffe and Altenber…
Risk forecasting models and optimal portfolio selection
2005
This study analyses, from an investor's perspective, the performance of several risk forecasting models in obtaining optimal portfolios. The plausibility of the homoscedastic hypothesis implied in the classical Markowitz model is dicussed and more general models which take into account assymetry and time varying risk are analysed. Specifically, it studies whether ARCH-type based models obtain portfolios whose risk-adjusted returns exceed those of the classical Markowitz model. The same analysis is performed with models based on the Lower Partial Moment (LPM) which take into account the assymetry in the distribution of returns. The results suggest that none of the models achieve a clearly su…
The Many Faces of a Translation
2000
First-order translations have recently been characterized as the maps computed by aperiodic single-valued nondeterministic finite transducers (NFTs). It is shown here that this characterization lifts to "V-translations" and "V-single-valued-NFTs", where V is an arbitrary monoid pseudovariety. More strikingly, 2-way V-machines are introduced, and the following three models are shown exactly equivalent to Eilenberg's classical notion of a bimachine when V is a group variety or when V is the variety of aperiodic monoids: V-translations, V-single-valued-NFTs and 2-way V-transducers.
Efficient smart-camera accelerator: A configurable motion estimator dedicated to video codec
2013
Smart cameras are used in a large range of applications. Usually the smart cameras transmit the video or/and extracted information from the video scene, frequently on compressed format to fit with the application requirements. An efficient hardware accelerator that can be adapted and provide the required coding performances according to the events detected in the video, the available network bandwidth or user requirements, is therefore a key element for smart camera solutions. We propose in this paper to focus on a key part of the compression system: motion estimation. We have developed a flexible hardware implementation of the motion estimator based on FPGA component, fully compatible with…
A genetic algorithm for scratch removal in static images
2002
This paper investigates the removal of line scratches from old moving pictures and gives a twofold contribution. First, it presents a simple technique for detecting the scratches, based on an analysis of the statistics of the grey levels. Second, the scratch removal is approached as an optimisation problem, which is solved by using a genetic algorithm. The method can be classified as a static approach, as it works independently on each single frame of the sequence. It does not require any a-priori knowledge of the absolute position of the scratch, nor an external starting population of chromosomes for the genetic algorithm. The central column of the line scratch once detected is changed wit…
Experimental Study of Six Different Implementations of Parallel Matrix Multiplication on Heterogeneous Computational Clusters of Multicore Processors
2010
Two strategies of distribution of computations can be used to implement parallel solvers for dense linear algebra problems for Heterogeneous Computational Clusters of Multicore Processors (HCoMs). These strategies are called Heterogeneous Process Distribution Strategy (HPS) and Heterogeneous Data Distribution Strategy (HDS). They are not novel and have been researched thoroughly. However, the advent of multicores necessitates enhancements to them. In this paper, we present these enhancements. Our study is based on experiments using six applications to perform Parallel Matrix-matrix Multiplication (PMM) on an HCoM employing the two distribution strategies.