Quantum chemistry is a discipline which relies heavily on very expensive numerical computations. The scaling of correlated wave function methods lies, in their standard implementation, between and , where N is proportional to the system size. Therefore, performing accurate calculations on chemically meaningful systems requires (i) approximations that can lower the computational scaling and (ii) efficient implementations that take advantage of modern massively parallel architectures. Quantum Package is an open-source programming environment for quantum chemistry specially designed for wave function methods. Its main goal is the development of determinant-driven selected configuration interaction (sCI) methods and multireference second-order perturbation theory (PT2). The determinant-driven framework allows the programmer to include any arbitrary set of determinants in the reference space, hence providing greater methodological freedom. The sCI method implemented in Quantum Package is based on the CIPSI (Configuration Interaction using a Perturbative Selection made Iteratively) algorithm which complements the variational sCI energy with a PT2 correction. Additional external plugins have been recently added to perform calculations with multireference coupled cluster theory and range-separated density-functional theory. All the programs are developed with the IRPF90 code generator, which simplifies collaborative work and the development of new features. Quantum Package strives to allow easy implementation and experimentation of new methods, while making parallel computation as simple and efficient as possible on modern supercomputer architectures. Currently, the code enables, routinely, to realize runs on roughly 2 000 CPU cores, with tens of millions of determinants in the reference space. Moreover, we have been able to push up to 12 288 cores in order to test its parallel efficiency. In the present manuscript, we also introduce some key new developments: (i) a renormalized second-order perturbative correction for efficient extrapolation to the full CI limit and (ii) a stochastic version of the CIPSI selection performed simultaneously to the PT2 calculation at no extra cost.

<div> <div> <div> <p> </p><div> <div> <div> <p>Quantum Package is an open-source programming environment for quantum chemistry specially designed for wave function methods. Its main goal is the development of determinant-driven selected configuration interaction (sCI) methods and multi-reference second-order perturbation theory (PT2). The determinant-driven framework allows the programmer to include any arbitrary set of determinants in the reference space, hence providing greater method- ological freedoms. The sCI method implemented in Quantum Package is based on the CIPSI (Configuration Interaction using a Perturbative Selection made Iteratively) algorithm which complements the variational sCI energy with a PT2 correction. Additional external plugins have been recently added to perform calculations with multireference coupled cluster theory and range-separated density-functional theory. All the programs are developed with the IRPF90 code generator, which simplifies collaborative work and the development of new features. Quantum Package strives to allow easy implementation and experimentation of new methods, while making parallel computation as simple and efficient as possible on modern supercomputer architectures. Currently, the code enables, routinely, to realize runs on roughly 2 000 CPU cores, with tens of millions of determinants in the reference space. Moreover, we have been able to push up to 12 288 cores in order to test its parallel efficiency. In the present manuscript, we also introduce some key new developments: i) a renormalized second-order perturbative correction for efficient extrapolation to the full CI limit, and ii) a stochastic version of the CIPSI selection performed simultaneously to the PT2 calculation at no extra cost. </p> </div> </div> </div> </div> </div> </div>

The interactions of killer Ig–like receptor 2D (KIR2D) with HLA-C ligands contribute to functional NK cell education and regulate NK cell functions. Although simple alloreactive rules have been established for inhibitory KIR2DL, those governing activating KIR2DS function are still undefined, and those governing the formation of the KIR2D repertoire are still debated. In this study, we investigated the specificity of KIR2DL1/2/3 and KIR2DS1/2, dissected each KIR2D function, and assessed the impact of revisited specificities on the KIR2D NK cell repertoire formation from a large cohort of 159 KIR and HLA genotyped individuals. We report that KIR2DL2+ and KIR2DL3+ NK cells reacted similarly against HLA-C+ target cells, irrespective of C1 or C2 allele expression. In contrast, KIR2DL1+ NK cells specifically reacted against C2 alleles, suggesting a larger spectrum of HLA-C recognition by KIR2DL2 and KIR2DL3 than KIR2DL1. KIR2DS2+ KIR2DL2− NK cell clones were C1-reactive irrespective of their HLA-C environment. However, when KIR2DS2 and KIR2DL2 were coexpressed, NK cell inhibition via KIR2DL2 overrode NK cell activation via KIR2DS2. In contrast, KIR2DL1 and KIR2DS2 had an additive enhancing effect on NK cell responses against C1C1 target cells. KIR2DL2/3/S2 NK cells predominated within the KIR repertoire in KIR2DL2/S2+ individuals. In contrast, the KIR2DL1/S1 NK cell compartment is dominant in C2C2 KIR2DL2/S2− individuals. Moreover, our results suggest that together with KIR2DL2, activating KIR2DS1 and KIR2DS2 expression limits KIR2DL1 acquisition on NK cells. Altogether, our results suggest that the NK cell repertoire is remolded by the activating and inhibitory KIR2D and their cognate ligands.

A suite of tools for the analysis of magnetically induced currents is introduced.These are applicable to both the weak-field regime, well described by linear response perturbation theory, and to the high-field regime, which is inaccessible to such methods.A disc-based quadrature scheme is proposed for the analysis of magnetically induced current susceptibilities, providing quadratures that are consistently defined between different molecular systems and applicable to both planar 2D and general 3D molecular systems in a black-box manner. The applicability of the approach is demonstrated for a range of planar ring systems, the ground and excited states of the benzene molecule and the ring, bowl and cage isomers of the C 20 molecule in the presence of a weak magnetic field. In the presence of a strong magnetic field, the para-to dia-magnetic transition of the BH molecule is studied, demonstrating that magnetically induced currents present a visual interpretation of this phenomenon, providing insight beyond that accessible using linear-response methods.

The main-group 6p elements did not receive much attention in the development of recent density functionals. In many cases it is still difficult to choose among the modern ones a relevant functional for various applications. Here, we illustrate the case of astatine species (At, Z = 85) and we report the first, and quite complete, benchmark study on several properties concerning such species. Insights on geometries, transition energies and thermodynamic properties of a set of 19 astatine species, for which reference experimental or theoretical data has been reported, are obtained with relativistic (two-component) density functional theory calculations. An extensive set of widely used functionals is employed. The hybrid meta-generalized gradient approximation (meta-GGA) PW6B95 functional is overall the best choice. It is worth noting that the range-separated HSE06 functional as well as the old and very popular B3LYP and PBE0 hybrid-GGAs appear to perform quite well too. Moreover, we found that astatine chemistry in solution can accurately be predicted using implicit solvent models, provided that specific parameters are used to build At cavities. © 2016 Wiley Periodicals, Inc.

CMV infection represents a major complication in hematopoietic stem cell transplantation, which compromises graft outcome. Downregulation of HLA class I expression is one mechanism by which CMV evades T cell–mediated immune detection, rendering infected cells vulnerable to killer cell Ig-like receptor (KIR)+ NK cells. In this study, we observed that the amplified NKG2C+ NK cell population observed specifically in CMV seropositive individuals mainly expressed KIR2DL receptors. We have shown that HLA class I expression was downregulated on CMV-infected immature dendritic cells (iDCs), which escape to HLA-A2-pp65–specific T lymphocytes but strongly trigger the degranulation of KIR2D+ NK cells. CMV infection conferred a vulnerability of C2C2+ iDCs to educated KIR2DL1+ and KIR2DL3+ NK cell subsets. Alloreactivity of KIR2DL1+ NK cell subsets against C1C1+ iDCs was maintained independently of CMV infection. Unexpectedly, CMV-infected C1C1+ iDCs did not activate KIR2DL3+ NK cell reactivity, suggesting a potential CMV evasion to KIR2DL3 NK cell recognition. Altogether, the coexpression of KIR and NKG2C on expanded NK cell subsets could be related to a functional contribution of KIR in CMV infection and should be investigated in hematopoietic stem cell transplantation, in which the beneficial impact of CMV infection has been reported on the graft-versus-leukemia effect.

cancérologie, UMR892, UFR Médecine et Techniques médicales, Nantes, France NK-cell function is regulated by a balance between inhibitory and activating killer cell immunoglobulin-like receptors (KIR) that specifically recognize HLA class I molecules. Using KIR-specific mAb to discriminate between KIR2DS1 and KIR2DL1 receptors, we show that KIR2DS1 + NK cells are C2-alloreactive only from C2 À individuals. Moreover, using an in vitro model of NK-cell expansion, we show here that the frequency of KIR2DL1 + NK cells is significantly higher in the absence of C2 ligand on stimulator EBV-B cells than in its presence. This observation was made regardless of the presence or absence of the autologous C2 ligand, suggesting that the C2 À EBV-B stimulator cells used in this in vitro model could activate unlicensed KIR2DL1 + NK cells. In the case of KIR2DL1 + /S1 + genotyped individuals, KIR2DS1 + NK-cell frequency was increased after stimulation with C2 + compared with C2 À stimulator B cells, but only from C2 À individuals. Altogether, these data highlight the C2 alloreactivity of KIR2DS1 + NK cells that is only observed in C2 À individuals. These results provide new insights into the way in which NK KIR cell expansion might be regulated in an allogeneic environment.

Summary Natural killer (NK) cells are key components of the innate anti‐viral and anti‐tumour immune responses. NK cell function is regulated by the interaction of killer cell immunoglobulin‐like receptors (KIR) with human leucocyte antigen (HLA) class I molecules. In this study, we report on the generation of KIR‐specific antibodies allowing for discrimination between activating and inhibitory KIR. For this purpose, BALB/c mice were immunized with human KIR2DS2 recombinant protein. The precise specificity of KIR2DS2‐specific clones was determined on KIR‐transfected BW cells and KIR‐genotyped NK cells. When used in combination with EB6 (KIR2DL1/2DS1) or GL183 (KIR2DL2/2DL3/2DS2), two KIR‐specific monoclonal antibodies (mAbs), 8C11 (specific for KIR2DL1/2DL2/2DL3/2DS2) and 1F12 (specific for KIR2DL3/2DS2), discriminated activating KIR2DS1 (8C11− EB6+) from inhibitory KIR2DL1 (8C11+ GL183−) and KIR2DL2 (1F12− GL183+), while excluding the main HLA‐Cw‐specific KIR. Using these mAbs, KIR2DS1 was shown to be expressed on the surface of NK cells from all individuals genotyped as KIR2DS1+ (n = 23). Moreover, KIR2DS1 and KIR2DL1 were independently expressed on NK cells. We also determined the amino acid position recognized by the 8C11 and 1F12 mAbs, which revealed that some KIR2DL1 allele‐encoded proteins are not recognized by 8C11. Because most available anti‐KIR mAbs recognize both inhibitory and activating forms of KIR, these newly characterized antibodies should help assess the expression of activating and inhibitory KIR and their functional relevance to NK biology.