Publications
Publications in reversed chronological order.
2020
A multilevel statistical toolkit to study animal social networks: the Animal Network Toolkit Software (ANTs) R package.
In Scientific Reports 2020.
The possible role played by individual attributes, sociodemographic characteristics and/or ecological pressures in the interaction between animals and the development of social relationships between them is of great interest in animal ecology and evolutionary biology. Social Network Analysis is an ideal tool to study these types of questions. The Animal Network Toolkit Software (ANTs) R package was specifically developed to provide all the different social network analysis techniques currently used in the study of animal social networks. This global package enables users to (1) compute global, polyadic and nodal network measures; (2) perform data randomisation: data stream and network (node and link) permutations; (3) perform statistical permutation tests for static or temporal network analyses, and (4) visualise networks. ANTs allows researchers to perform multilevel network analyses ranging from individual network measures to interaction patterns and the analysis of the overall network structure, and carry out static or temporal network analyses without switching between different R packages, thus making a substantial contribution to advances in the study of animal behaviour. ANTs outperforms existing R packages for the computation speed of network measures and permutations.A quantum approach to calculate differential and total cross sections for electron impact ionization of molecular targets.
In Journal of Physics: Conference Series 2020.
We present a theoretical approach to calculate the cross sections for the ionization of molecules by single electron impact. It is based on the First Born approximation (FBA), describing the ejected electron by a distorted wave (DW). The cross sections are calculated for an average molecular orientation with the proper average method. Single-center molecular wave functions are generated using Gaussian making this method easily applicable to any molecule. We show the calculated cross sections of some molecular targets of varying complexity.Electron impact ionization of pyrimidine: differential and total cross sections.
In Journal of Physics: Conference Series 2020.
We provide theoretical cross sections for the ionization of pyrimidine by electron impact. The theoretical framework is based on a quantum approach making use of particular tools to overcome the computing challenges. The developed methodology allows to determine not only the total but also the triple, double and simple differential cross sections. This approach was previously used to calculate the triple differential cross sections of many molecules. Here, we demonstrate that it can be used to calculate more integrated cross sections of a molecule of biological interest: pyrimidine.ComputeOps: Container for High Performance Computing.
In EPJ Web of Conferences 2020.
The High Performance Computing (HPC) domain aims to optimize code in order to use the latest multicore and parallel technologies including specific processor instructions. In this computing framework, portability and reproducibility are key concepts. A way to handle these requirements is to use Linux containers. These “light virtual machines” allow to encapsulate applications within its environment in Linux processes. Containers have been recently rediscovered due to their abilities to provide both multi-infrastructure environnement for developers and system administrators and reproducibility due to image building file. Two container solutions are emerging: Docker for microservices and Singularity for computing applications. We present here the status of the \textlessb\textgreaterComputeOps\textlessb/\textgreater project which has the goal to study the benefit of containers for HPC applications.
2019
A Roadmap for HEP Software and Computing R&D for the 2020s.
In Computing and Software for Big Science 2019.
Particle physics has an ambitious and broad experimental programme for the coming decades. This programme requires large investments in detector hardware, either to build new facilities and experiments, or to upgrade existing ones. Similarly, it requires commensurate investment in the R&D of software to acquire, manage, process, and analyse the shear amounts of data to be recorded. In planning for the HL-LHC in particular, it is critical that all of the collaborating stakeholders agree on the software goals and priorities, and that the efforts complement each other. In this spirit, this white paper describes the R&D activities required to prepare for this software upgrade.A spatial network analysis of resource partitioning between bumblebees foraging on artificial flowers in a flight cage.
In Movement Ecology 2019.
Individual bees exhibit complex movement patterns to efficiently exploit small areas within larger plant populations. How such individual spatial behaviours scale up to the collective level, when several foragers visit a common area, has remained challenging to investigate, both because of the low resolution of field movement data and the limited power of the statistical descriptors to analyse them. To tackle these issues we video recorded all flower visits (N = 6205), and every interaction on flowers (N = 628), involving foragers from a bumblebee (Bombus terrestris) colony in a large outdoor flight cage (880 m2), containing ten artificial flowers, collected on five consecutive days, and analysed bee movements using networks statistics.ComputeOps: containers for High Performance Computing.
In EPJ Web of Conferences 2019.
The High Performance Computing (HPC) domain aims to optimize code to use the latest multicore and parallel technologies including specific processor instructions. In this computing framework, portability and reproducibility are key concepts. A way to handle these requirements is to use Linux containers. These "light virtual machines" allow users to encapsulate applications within its environment in processes. Containers have been recently highlighted because they provide multi-infrastructure environnement for both developers and system administrators. Furthermore, they offer reproducibility due to image building files. Two container solutions are emerging: \textlessb\textgreaterDocker\textlessb/\textgreater for micro-services and \textlessb\textgreaterSingularity\textlessb/\textgreater for computing applications. We present here the \textlessb\textgreaterCom-puteOps\textlessb/\textgreater project which investigates the container benefits for HPC applications.
2018
Triple differential cross sections for the ionization of tetrahydrofuran by electron impact.
In Journal of Physics B: Atomic, Molecular and Optical Physics 2018.
We provide triple differential cross sections (TDCS) for the ionization of tetrahydrofuran (THF) by single electron impact in coplanar asymmetric kinematics in the intermediate energy regime. For the Cs and C2 THF isomers, the analysis is carried out using (i) the highest occupied molecular orbitals energies available from ab initio calculations, and (ii) the TDCSs computed from a Coulomb wave (CW) and a distorted wave (DW) to describe the ejected electron. The calculated TDCSs using both the CW and DW models are in better agreement with experimental data than those obtained using the molecular three-body distorted wave model. Hence, we show that the developed framework can be applied to a relatively complex molecule and that the proposed models successfully describe the ionization of both THF isomers.
2017
Triple differential cross sections for the ionization of formic acid by electron impact.
In Journal of Physics B: Atomic, Molecular and Optical Physics 2017.
Theoretical triple differential cross sections for the simple ionization of the two outermost valence orbitals of formic acid monomer are given in this work. The first Born approximation is used to describe the collision dynamics with one Coulomb wave function for the ejected electron. Single-center molecular wave functions are generated using the Gaussian 09 program. The cross sections are calculated for an average molecular orientation with the proper average method. The results show that the proposed framework provides better agreement with experimental data than the previously used orientation averaged molecular orbital approximation. Consequently, this work shows the importance of performing the orientation averaging on the cross sections and not on the molecular wave functions. It also provides a methodology that reduces the complexity of calculations while maintaining a good quality of the results.
2016
Understanding Dynamics of Information Transmission in Drosophila melanogaster Using a Statistical Modeling Framework for Longitudinal Network Data (the RSiena Package).
In Frontiers in Psychology 2016.
Social learning – the transmission of behaviors through observation or interaction with conspecifics – can be viewed as a decision-making process driven by interactions among individuals. Animal group structures change over time and interactions among individuals occur in particular orders that may be repeated following specific patterns, change in their nature, or disappear completely. Here we used a stochastic actor-oriented model built using the RSiena package in R to estimate individual behaviors and their changes through time, by analyzing the dynamic of the interaction network of the fruit fly Drosophila melanogaster during social learning experiments. In particular, we re-analyzed an experimental dataset where uninformed flies, left free to interact with informed ones, acquired and later used information about oviposition site choice obtained by social interactions. We estimated the degree to which the uninformed flies had successfully acquired the information carried by informed individuals using the proportion of eggs laid by uninformed flies on the medium their conspecifics had been trained to favor. Regardless of the degree of information acquisition measured in uninformed individuals, they always received and started interactions more frequently than informed ones did. However, information was efficiently transmitted (i.e. uninformed flies predominantly laid eggs on the same medium informed ones had learn to prefer) only when the difference in contacts sent between the two fly types was small. Interestingly, we found that the degree of reciprocation, the tendency of individuals to form mutual connections between each other, strongly affected oviposition site choice in uninformed flies. This work highlights the great potential of RSiena and its utility in the studies of interaction networks among non-human animals.
2012
A New Boson with a Mass of 125 GeV Observed with the CMS Experiment at the Large Hadron Collider.
In Science 2012.
The Higgs boson was postulated nearly five decades ago within the framework of the standard model of particle physics and has been the subject of numerous searches at accelerators around the world. Its discovery would verify the existence of a complex scalar field thought to give mass to three of the carriers of the electroweak force—the W+, W–, and Z0 bosons—as well as to the fundamental quarks and leptons. The CMS Collaboration has observed, with a statistical significance of five standard deviations, a new particle produced in proton-proton collisions at the Large Hadron Collider at CERN. The evidence is strongest in the diphoton and four-lepton (electrons and/or muons) final states, which provide the best mass resolution in the CMS detector. The probability of the observed signal being due to a random fluctuation of the background is about 1 in 3 × 106. The new particle is a boson with spin not equal to 1 and has a mass of about 125 giga–electron volts. Although its measured properties are, within the uncertainties of the present data, consistent with those expected of the Higgs boson, more data are needed to elucidate the precise nature of the new particle. The CMS detector team describes their experiment and observation of decay products from a standard model Higgs boson, allowing its mass to be determined. The CMS detector team describes their experiment and observation of decay products from a standard model Higgs boson, allowing its mass to be determined.
2011
Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on.
In Journal of Cheminformatics 2011.
The Blue Obelisk movement was established in 2005 as a response to the lack of Open Data, Open Standards and Open Source (ODOSOS) in chemistry. It aims to make it easier to carry out chemistry research by promoting interoperability between chemistry software, encouraging cooperation between Open Source developers, and developing community resources and Open Standards.
2006
Molecular tectonics: generation of 2-D molecular networks by combination of coordination and hydrogen bonds.
In New Journal of Chemistry 2006.
The combination of two organic tectons 1 and 2, based on a 1,4-phenylenediamine backbone functionalised with two pyridine units through amide junctions with HgCl2, leads to the formation of two types of 2-D networks, one of the purely metallo-organic type, based on only coordination bonds, and the other combining both coordination and hydrogen bonds.Molecular tectonics: generation of 1- and 2-D copper coordination networks by positional isomeric tectons based on a phenylenediamine backbone bearing two isonicotinoyl moieties.
In New Journal of Chemistry 2006.
The combination of three isomeric organic tectons 1–3 based on 1,2-, 1,3- and 1,4-phenylenediamine backbones bearing two isonicotinoyl groups with a Cu(OAc)2 neutral complex leads to the formation of 1-D and 2-D coordination networks. Whereas for both tectons 1 and 2 the network is generated through the interconnection of the organic moieties by copper dimers of the paddle-wheel type, in the case of 3, the 2-D network is formed by another type of connector, a binuclear copper complex for which the two metal centres adopt an octahedral coordination geometry.
2002
Design of 3-D coordination networks: topology and metrics.
In Chemical Communications 2002.
Using 4,4′,4″-tricyanotriphenylmethanol 1 as a hetero-tetradentate tecton with C3v symmetry bearing three CN and one OH group, under self-assembly conditions a 3-D coordination network was obtained in the presence of Ag+ cations acting as a tetrahedral metallic tecton; due to the metrics of 1 (three long and one short distance between the central C atom and N and O coordination sites, respectively), the 3-D network is of pseudo-diamondoid type with different cavity sizes; although a two-fold homo-interpenetration is observed for the 3-D networks, the remaining space is occupied by CHCl3, MeOH solvent molecules and SbF6− anions.
1998
Thiacalixarenes: Synthesis and structural analysis of thiacalix[4]arene and of p-tert-butylthiacalix[4]arene.
In Tetrahedron Letters 1998.
The synthesis of tetrathiacalix[4]arene was achieved by the detertiobutylation of p-tert-butyltetrathiacalix[4]arene. X-ray diffraction studies revealed that in the solid state whereas p-tert-butyltetrathiacalix[4]arene forms inclusion complexes with solvent molecules, tetrathiacalix[4]arene undergoes self-inclusion leading to trimeric units. The same behaviour in the crystalline phase was also demonstrated for calix[4]arene.