On an "interaction by moments" property of four center integrals

The four center integrals needed in the Hartree Fock approximation and in TDDFT linear response are known to be difficult to calculate for orbitals of the Slater type or of finite range. We show that the interaction of pairs of products that do not mutually intersect may be replaced by the interaction of their moments, of which there are O(N). Only quadruplets of orbitals 'close' to one another need an explicit calculation and the total calculational effort therefore scales as O(N). We provide a new and concise proof of this "interaction by moments" property.Comment: The context of this note is the implementation of TDDFT linear response for extended molecular system

A Parallel Iterative Method for Computing Molecular Absorption Spectra

We describe a fast parallel iterative method for computing molecular absorption spectra within TDDFT linear response and using the LCAO method. We use a local basis of "dominant products" to parametrize the space of orbital products that occur in the LCAO approach. In this basis, the dynamical polarizability is computed iteratively within an appropriate Krylov subspace. The iterative procedure uses a a matrix-free GMRES method to determine the (interacting) density response. The resulting code is about one order of magnitude faster than our previous full-matrix method. This acceleration makes the speed of our TDDFT code comparable with codes based on Casida's equation. The implementation of our method uses hybrid MPI and OpenMP parallelization in which load balancing and memory access are optimized. To validate our approach and to establish benchmarks, we compute spectra of large molecules on various types of parallel machines. The methods developed here are fairly general and we believe they will find useful applications in molecular physics/chemistry, even for problems that are beyond TDDFT, such as organic semiconductors, particularly in photovoltaics.Comment: 20 pages, 17 figures, 3 table

On the Kohn--Sham density response in a localized basis set

We construct the Kohn--Sham density response function $\chi_{0}$ in a previously described basis of the space of orbital products. The calculational complexity of our construction is $O(N^{2}N_{\omega})$ for a molecule of $N$ atoms and in a spectroscopic window of $N_{\omega}$ frequency points. As a first application, we use $\chi_{0}$ to calculate molecular spectra from the Petersilka--Gossmann--Gross equation. With $\chi_{0}$ as input, we obtain correct spectra with an extra computational effort that grows also as $O(N^2 N_{\omega})$ and, therefore, less steeply in $N$ than the $O(N^{3})$ complexity of solving Casida's equations. Our construction should be useful for the study of excitons in molecular physics and in related areas where $\chi_{0}$ is a crucial ingredient.Comment: 20 pages, 11 figure

Current state of the art in TDDFT code

International audienceWe present a TDDFT code developed in the framework of NOSSI project. The code is capable to compute absorption spectra in linear response regime. The method for calculating of the Kohn-Sham response function is outlined. Complexity of the method is discussed in detail. Testing of the shared memory parallelization and examples of spectra are given

Extension of LCAO to excited states: non interacting response and molecular spectra

International audienceWe present the algorithm for a fast calculation of the Kohn-Sham response function in a localized basis set. Examples of spectra are given and parallelization approach is outlined

SPVE : Sistema de publicação de vagas de estágio

Orientador: Irapuru Haruo FlóridoMonografia (graduação) - Universidade Federal do Paraná, Escola Técnica, Curso de Tecnologia em InformáticaInclui bibliografi

Identification of regulatory variants associated with genetic susceptibility to meningococcal disease.

Non-coding genetic variants play an important role in driving susceptibility to complex diseases but their characterization remains challenging. Here, we employed a novel approach to interrogate the genetic risk of such polymorphisms in a more systematic way by targeting specific regulatory regions relevant for the phenotype studied. We applied this method to meningococcal disease susceptibility, using the DNA binding pattern of RELA - a NF-kB subunit, master regulator of the response to infection - under bacterial stimuli in nasopharyngeal epithelial cells. We designed a custom panel to cover these RELA binding sites and used it for targeted sequencing in cases and controls. Variant calling and association analysis were performed followed by validation of candidate polymorphisms by genotyping in three independent cohorts. We identified two new polymorphisms, rs4823231 and rs11913168, showing signs of association with meningococcal disease susceptibility. In addition, using our genomic data as well as publicly available resources, we found evidences for these SNPs to have potential regulatory effects on ATXN10 and LIF genes respectively. The variants and related candidate genes are relevant for infectious diseases and may have important contribution for meningococcal disease pathology. Finally, we described a novel genetic association approach that could be applied to other phenotypes