Using computed infrared intensities for the reduction of vibrational configuration interaction bases

International audienceThe Adaptive Vibrational Configuration Interaction (A-VCI) algorithm is an iterative process that computes the anharmonic spectrum of a molecule using nested bases to discretize the Hamiltonian operator. For large molecular systems, the size of the discretization space and the computation time quickly become prohibitive. It is therefore necessary to develop new methods to further limit the number of basis functions. Most of the time, the interpretation of an experimental infrared spectrum does not require the calculation of all eigenvalues but only those corresponding to vibrational states with significant intensity. In this paper, a technique that uses infrared intensities is introduced to select a subset of eigenvalues to be precisely calculated. Thus, we build smaller nested bases and reduce both the memory footprint and the computational time. We validate the advantages of this new approach on a well-studied 7-atom molecular system (C2H4O), and we apply it on a larger 10-atom molecule (C4H4N2)

Using computed infrared intensities for fast computation of vibrational spectra

The Adaptive Vibrational Configuration Interaction (A-VCI) algorithm is an iterative pro-cess able to compute the spectrum of an Hamiltonian operator, using a discretization basisas small as possible. In this work, we show how this algorithm can handle more sophis-ticated operators, which ro-vibrational Coriolis coupling terms. In order to overcome theincrease of computing and storage resources needed due to this enrichment, the InfraRed(IR) intensities are computed and used as a criterion to select only the eigenstates corre-sponding to IR active vibrational states. The benefits of this new approach are presentedfor a few well studied molecular systems (H2O, H2CO, CH2NH, CH3CN, C2H4O), and itis ultimately applied to a 10-atom molecule (C4H4N2

A-VCI: une méthode flexible pour calculer rapidement des spectres vibrationnels

The Adaptive Vibrational Configuration Interaction (A-VCI) algorithm has been introduced as a new method to efficiently reduce the dimension of the set of basis functions used in a Vibrational Configuration Interaction (VCI) process. It is based on the construction of nested basis for the discretization of the Hamiltonian operator according to a theoretical criterion that ensures the convergence of the method. The purpose of this paper is to study the properties and outline the performance details of the main steps of the algorithm. New parameters have been incorporated to increase flexibility, and their influence have been thoroughly investigated. The robustness and reliability of the method are demonstrated for the computation of the vibrational spectrum up to $3000$ cm$^{-1}$ of a widely studied $6$-atom molecule (acetonitrile). Our results are compared to the most accurate up to date computation, and we also give a new reference calculation for future work on this system. The algorithm has also been applied to a more challenging $7$-atom molecule (ethylene oxide). The computed spectrum up to $3200$ cm$^{-1}$ is the most accurate computation that exists today on such a system.L'algorithme adaptatif d'interaction de configuration vibrationnelle (A-VCI) a été introduit comme une nouvelle méthode pour réduire efficacement la dimension de l'ensemble des fonctions de base utilisées dans un processus d'interaction de configuration vibrationnelle (VCI). Il est basé sur la construction de bases emboîtées pour la discrétisation de l'opérateur Hamiltonien selon un critère théorique qui assure la convergence de la méthode. Cet article présente les propriétés de la méthode et décrit les détails des principales étapes de l'algorithme. De nouveaux paramètres sont introduits pour accroître les potentialités de la méthode et leurs influences sont étudiées. La robustesse et la fiabilité de la méthode sont démontrées pour le calcul du spectre vibrationnel jusqu'à $3000$ cm $^ {- 1}$ d'une molécule à 6 atomes (acétonitrile). Nos résultats sont comparés au calcul le plus précis à jour, et nous donnons également un nouveau calcul de référence pour les travaux futurs sur ce système. L'algorithme a également été appliqué à un système plus difficile l'oxyde d'éthylène qui comporte 7 atomes. Le spectre calculé jusqu'à $3200$ cm $^{- 1}$ est le calcul le plus précis qui existe aujourd'hui sur un tel système

Efficient basis selection for the computation of vibrational spectrum

International audienceWe propose here an efficient method to define an approximation subspace to compute the first vibrational frequencies of the molecular Hamiltonian which are those of interest in the experimental results

Optimisation of the variational method for vibrational Hamiltonian eigenvalues computation

International audienceWe propose here an efficient method to define a representative approximation subspace to compute the first eigenvalues of the vibrational Hamiltonian which are those of interest in the experimental results

Adaptive vibrational configuration interaction (A-VCI): a posteriori error estimation to efficiently compute anharmonic IR spectra

International audienceA new variational algorithm called adaptive vibrational configuration interaction (A-VCI) intended for the resolution of the vibrational Schrödinger equation was developed. The main advantage of this approach is to efficiently reduce the dimension of the active space generated into the configuration interaction (CI) process. Here, we assume that the Hamiltonian writes as a sum of products of operators. This adaptive algorithm was developed with the use of three correlated conditions i.e. a suitable starting space ; a criterion for convergence, and a procedure to expand the approximate space. The velocity of the algorithm was increased with the use of a posteriori error estimator (residue) to select the most relevant direction to increase the space. Two examples have been selected for benchmark. In the case of H 2 CO, we mainly study the performance of A-VCI algorithm: comparison with the variation-perturbation method, choice of the initial space, residual contributions. For CH 3 CN, we compare the A-VCI results with a computed reference spectrum using the same potential energy surface and for an active space reduced by about 90 %

Mineralization of Alvinella polychaete tubes at hydrothermal vents

© 2014 The Authors. Geobiology Published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License [4.0], which permits use, distribution and reproduction in any medium, provided the original work is properly cited. The attached file is the published version of the article

Species composition and habitat preferences of the nearshore fish fauna of Bonne Bay, Newfoundland

Determining biodiversity baseline is the first step toward establishing species monitoring and conservation programs. In this study we report on a 10-year survey of the fish fauna of Bonne Bay, a fjord surrounded by the Gros Morne National Park on the west coast of Newfoundland, Canada. The objectives of our study were: 1) to determine the fish fauna of Bonne Bay using standardized sampling methods; 2) to gather information on the habitats of fishes of conservation concern; and 3) to provide baseline information on Bonne Bay as a potential candidate for a National Marine Conservation Area (NMCA). Methods A survey of the fish fauna of the inner Bonne Bay was conducted each summer from 2002 to 2011 at multiple sites representing a range of fish habitats within the fjord. Sampling gears included two types of beach seine, gillnets with various mesh sizes and a bottom trawl. Species composition was statistically compared across sites within the fjord. Results We collected and identified 29 fish species from 17 families. Fish assemblages comprised anadromous, estuarine, and marine fish species, including a late-maturing type of winter skate (Leucoraja ocellata) that is rarely found in the adjacent waters of the northern Gulf of St. Lawrence. Similarity in species composition across sites reflected salinity, substrate composition, and presence of eelgrass (Zostera marina), but not the geographic distance between sites. Conclusions Bonne Bay’s adjacency to a United Nations Educational, Scientific, and Cultural Organization (UNESCO) World Heritage Site, its diverse fish fauna that includes several species of conservation concern, its potential for education and enjoyment, and its stewardship by local people are suggestive of the future candidacy as a NMCA. The data presented here will help managers assess the potential of Bonne Bay as a National Marine Conservation Area

Exome sequencing identifies germline variants in DIS3 in familial multiple myeloma

[Excerpt] Multiple myeloma (MM) is the third most common hematological malignancy, after Non-Hodgkin Lymphoma and Leukemia. MM is generally preceded by Monoclonal Gammopathy of Undetermined Significance (MGUS) [1], and epidemiological studies have identified older age, male gender, family history, and MGUS as risk factors for developing MM [2]. The somatic mutational landscape of sporadic MM has been increasingly investigated, aiming to identify recurrent genetic events involved in myelomagenesis. Whole exome and whole genome sequencing studies have shown that MM is a genetically heterogeneous disease that evolves through accumulation of both clonal and subclonal driver mutations [3] and identified recurrently somatically mutated genes, including KRAS, NRAS, FAM46C, TP53, DIS3, BRAF, TRAF3, CYLD, RB1 and PRDM1 [3,4,5]. Despite the fact that family-based studies have provided data consistent with an inherited genetic susceptibility to MM compatible with Mendelian transmission [6], the molecular basis of inherited MM predisposition is only partly understood. Genome-Wide Association (GWAS) studies have identified and validated 23 loci significantly associated with an increased risk of developing MM that explain ~16% of heritability [7] and only a subset of familial cases are thought to have a polygenic background [8]. Recent studies have identified rare germline variants predisposing to MM in KDM1A [9], ARID1A and USP45 [10], and the implementation of next-generation sequencing technology will allow the characterization of more such rare variants. [...]French National Cancer Institute (INCA) and the Fondation Française pour la Recherche contre le Myélome et les Gammapathies (FFMRG), the Intergroupe Francophone du Myélome (IFM), NCI R01 NCI CA167824 and a generous donation from Matthew Bell. This work was supported in part through the computational resources and staff expertise provided by Scientific Computing at the Icahn School of Medicine at Mount Sinai. Research reported in this paper was supported by the Office of Research Infrastructure of the National Institutes of Health under award number S10OD018522. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. The authors thank the Association des Malades du Myélome Multiple (AF3M) for their continued support and participation. Where authors are identified as personnel of the International Agency for Research on Cancer / World Health Organization, the authors alone are responsible for the views expressed in this article and they do not necessarily represent the decisions, policy or views of the International Agency for Research on Cancer / World Health Organizatio

Vaccine breakthrough hypoxemic COVID-19 pneumonia in patients with auto-Abs neutralizing type I IFNs

Life-threatening `breakthrough' cases of critical COVID-19 are attributed to poor or waning antibody response to the SARS- CoV-2 vaccine in individuals already at risk. Pre-existing autoantibodies (auto-Abs) neutralizing type I IFNs underlie at least 15% of critical COVID-19 pneumonia cases in unvaccinated individuals; however, their contribution to hypoxemic breakthrough cases in vaccinated people remains unknown. Here, we studied a cohort of 48 individuals ( age 20-86 years) who received 2 doses of an mRNA vaccine and developed a breakthrough infection with hypoxemic COVID-19 pneumonia 2 weeks to 4 months later. Antibody levels to the vaccine, neutralization of the virus, and auto- Abs to type I IFNs were measured in the plasma. Forty-two individuals had no known deficiency of B cell immunity and a normal antibody response to the vaccine. Among them, ten (24%) had auto-Abs neutralizing type I IFNs (aged 43-86 years). Eight of these ten patients had auto-Abs neutralizing both IFN-a2 and IFN-., while two neutralized IFN-omega only. No patient neutralized IFN-ss. Seven neutralized 10 ng/mL of type I IFNs, and three 100 pg/mL only. Seven patients neutralized SARS-CoV-2 D614G and the Delta variant (B.1.617.2) efficiently, while one patient neutralized Delta slightly less efficiently. Two of the three patients neutralizing only 100 pg/mL of type I IFNs neutralized both D61G and Delta less efficiently. Despite two mRNA vaccine inoculations and the presence of circulating antibodies capable of neutralizing SARS-CoV-2, auto-Abs neutralizing type I IFNs may underlie a significant proportion of hypoxemic COVID-19 pneumonia cases, highlighting the importance of this particularly vulnerable population