Search results for "computational"

Extracting string motif bases for quorum higher than two

2012

Bases of generators of motifs consisting of strings in which some positions can be occupied by a don’t care provide a useful conceptual tool for their description and a way to reduce the time and space involved in the discovery process. In the last few years, a few algorithms have been proposed for the extraction of a basis, building in large part on combinatorial properties of strings and their autocorrelations. Currently, the most efficient techniques for binary alphabets and quorum q = 2 require time quadratic in the length of the host string. The present paper explores properties of motif bases for quorum q ≥ 2, both with binary and general alphabets, by also showing that important resu…

Code Interoperability and Standard Data Formats in Quantum Chemistry and Quantum Dynamics: The Q5/Q5cost Data Model

2014

Code interoperability and the search for domain-specific standard data formats represent critical issues in many areas of computational science. The advent of novel computing infrastructures such as computational grids and clouds make these issues even more urgent. The design and implementation of a common data format for quantum chemistry (QC) and quantum dynamics (QD) computer programs is discussed with reference to the research performed in the course of two Collaboration in Science and Technology Actions. The specific data models adopted, Q5Cost and D5Cost, are shown to work for a number of interoperating codes, regardless of the type and amount of information (small or large datasets) …

Correlation Analysis of Node and Edge Centrality Measures in Artificial Complex Networks

2021

The role of an actor in a social network is identified through a set of measures called centrality. Degree centrality, betweenness centrality, closeness centrality, and clustering coefficient are the most frequently used metrics to compute the node centrality. Their computational complexity in some cases makes unfeasible, when not practically impossible, their computations. For this reason, we focused on two alternative measures, WERW-Kpath and Game of Thieves, which are at the same time highly descriptive and computationally affordable. Our experiments show that a strong correlation exists between WERW-Kpath and Game of Thieves and the classical centrality measures. This may suggest the po…

Game of Thieves and WERW-Kpath: Two Novel Measures of Node and Edge Centrality for Mafia Networks

2021

Real-world complex systems can be modeled as homogeneous or heterogeneous graphs composed by nodes connected by edges. The importance of nodes and edges is formally described by a set of measures called centralities which are typically studied for graphs of small size. The proliferation of digital collection of data has led to huge graphs with billions of nodes and edges. For this reason, we focus on two new algorithms, Game of Thieves and WERW-Kpath which are computationally-light alternatives to the canonical centrality measures such as degree, node and edge betweenness, closeness and clustering. We explore the correlation among these measures using the Spearman’s correlation coefficient …

Artificial Intelligence + Distributed Systems = Agents

2009

The connection with Wirth’s book goes beyond the title, albeit confining the area to modern Artificial Intelligence (AI). Whereas thirty years ago, to devise effective programs, it became necessary to enhance the classical algorithmic framework with approaches applied to limited and focused subdomains, in the context of broad-band technology and semantic web, applications - running in open, heterogeneous, dynamic and uncertain environments-current paradigms are not enough, because of the shift from programs to processes. Beside the structure as position paper, to give more weight to some basic assertions, results of recent research are abridged and commented upon in line with new paradigms.…

Mesh connectivity compression using convection reconstruction

2007

International audience; During a highly productive period running from 1995 to about 2002, the research in lossless compression of 3D meshes mainly consisted in a hard battle for the best bitrates. But for a few years, compression rates seem stabilized around 1.5 bit per vertex for the connectivity coding of usual meshes, and more and more work is dedicated to remeshing, lossy compression, or gigantic mesh compression, where memory and CPU optimizations are the new priority. However, the size of 3D models keeps growing, and many application fields keep requiring lossless compression. In this paper, we present a new contribution for single-rate lossless connectivity compression, which first …

A basic analysis toolkit for biological sequences

2007

This paper presents a software library, nicknamed BATS, for some basic sequence analysis tasks. Namely, local alignments, via approximate string matching, and global alignments, via longest common subsequence and alignments with affine and concave gap cost functions. Moreover, it also supports filtering operations to select strings from a set and establish their statistical significance, via z-score computation. None of the algorithms is new, but although they are generally regarded as fundamental for sequence analysis, they have not been implemented in a single and consistent software package, as we do here. Therefore, our main contribution is to fill this gap between algorithmic theory an…

Relativistic Electronic Structure Theory. Part 1. Fundamentals. By Peter Schwerdtfeger.

2004

1H and 13C shielding measurements in comparison with DFT calculations performed for two 2-(acetyloamino)-N,N-dimethyl-3-phenylacrylamide isomers

2015

Abstract We present measurements of 1H and 13C shielding for (2E)- and (2Z)-2-(acetyloamino)-N,N-dimethyl-3-phenylacrylamide isomers in solutions. Practically the same values of the shielding were obtained using internal and external referencing. For the interpretation, we explore DFT calculations of shieldings performed at the rovibrationally averaged geometries. The comparison of the experimental and theoretical results is verified both for the shielding and chemical shift. It appears that some inaccuracies in the calculations of the chemical shift can be reduced due to the error compensation while subtracting the reference shielding. As shown the measurement of magnetic shielding can be …

New QM/MM implementation of the DFTB3 method in the gromacs package.

2015

The approximate density-functional tight-binding theory method DFTB3 has been implemented in the quantum mechanics/molecular mechanics (QM/MM) framework of the Gromacs molecular simulation package. We show that the efficient smooth particle–mesh Ewald implementation of Gromacs extends to the calculation of QM/MM electrostatic interactions. Further, we make use of the various free-energy functionalities provided by Gromacs and the PLUMED plugin. We exploit the versatility and performance of the current framework in three typical applications of QM/MM methods to solve biophysical problems: (i) ultrafast proton transfer in malonaldehyde, (ii) conformation of the alanine dipeptide, and (iii) el…