Large scale parallelization in stochastic coupled cluster.

Coupled cluster theory is a vital cornerstone of electronic structure theory and is being applied to ever-larger systems. Stochastic approaches to quantum chemistry have grown in importance and offer compelling advantages over traditional deterministic algorithms in terms of computational demands, theoretical flexibility, or lower scaling with system size. We present a highly parallelizable algorithm of the coupled cluster Monte Carlo method involving sampling of clusters of excitors over multiple time steps. The behavior of the algorithm is investigated on the uniform electron gas and the water dimer at coupled-cluster levels including up to quadruple excitations. We also describe two improvements to the original sampling algorithm, full non-composite, and multi-spawn sampling. A stochastic approach to coupled cluster results in an efficient and scalable implementation at arbitrary truncation levels in the coupled cluster expansion.

Accurate Exchange-Correlation Energies for the Warm Dense Electron Gas.

The density matrix quantum Monte Carlo (DMQMC) method is used to sample exact-on-average N-body density matrices for uniform electron gas systems of up to 10^{124} matrix elements via a stochastic solution of the Bloch equation. The results of these calculations resolve a current debate over the accuracy of the data used to parametrize finite-temperature density functionals. Exchange-correlation energies calculated using the real-space restricted path-integral formalism and the k-space configuration path-integral formalism disagree by up to ∼10% at certain reduced temperatures T/T_{F}≤0.5 and densities r_{s}≤1. Our calculations confirm the accuracy of the configuration path-integral Monte Carlo results available at high density and bridge the gap to lower densities, providing trustworthy data in the regime typical of planetary interiors and solids subject to laser irradiation. We demonstrate that the DMQMC method can calculate free energies directly and present exact free energies for T/T_{F}≥1 and r_{s}≤2.

Linked coupled cluster Monte Carlo.

We consider a new formulation of the stochastic coupled cluster method in terms of the similarity transformed Hamiltonian. We show that improvement in the granularity with which the wavefunction is represented results in a reduction in the critical population required to correctly sample the wavefunction for a range of systems and excitation levels and hence leads to a substantial reduction in the computational cost. This development has the potential to substantially extend the range of the method, enabling it to be used to treat larger systems with excitation levels not easily accessible with conventional deterministic methods.

Understanding and improving the efficiency of full configuration interaction quantum Monte Carlo.

Within full configuration interaction quantum Monte Carlo, we investigate how the statistical error behaves as a function of the parameters which control the stochastic sampling. We define the inefficiency as a measure of the statistical error per particle sampling the space and per time step and show there is a sizeable parameter regime where this is minimised. We find that this inefficiency increases sublinearly with Hilbert space size and can be reduced by localising the canonical Hartree-Fock molecular orbitals, suggesting that the choice of basis impacts the method beyond that of the sign problem.

Minimising biases in full configuration interaction quantum Monte Carlo.

We show that Full Configuration Interaction Quantum Monte Carlo (FCIQMC) is a Markov chain in its present form. We construct the Markov matrix of FCIQMC for a two determinant system and hence compute the stationary distribution. These solutions are used to quantify the dependence of the population dynamics on the parameters defining the Markov chain. Despite the simplicity of a system with only two determinants, it still reveals a population control bias inherent to the FCIQMC algorithm. We investigate the effect of simulation parameters on the population control bias for the neon atom and suggest simulation setups to, in general, minimise the bias. We show a reweight ing scheme to remove the bias caused by population control commonly used in diffusion Monte Carlo [Umrigar et al., J. Chem. Phys. 99, 2865 (1993)] is effective and recommend its use as a post processing step.

Semi-stochastic full configuration interaction quantum Monte Carlo: Developments and application.

We expand upon the recent semi-stochastic adaptation to full configuration interaction quantum Monte Carlo (FCIQMC). We present an alternate method for generating the deterministic space without a priori knowledge of the wave function and present stochastic efficiencies for a variety of both molecular and lattice systems. The algorithmic details of an efficient semi-stochastic implementation are presented, with particular consideration given to the effect that the adaptation has on parallel performance in FCIQMC. We further demonstrate the benefit for calculation of reduced density matrices in FCIQMC through replica sampling, where the semi-stochastic adaptation seems to have even larger efficiency gains. We then combine these ideas to produce explicitly correlated corrected FCIQMC energies for the beryllium dimer, for which stochastic errors on the order of wavenumber accuracy are achievable.

Interaction picture density matrix quantum Monte Carlo.

The recently developed density matrix quantum Monte Carlo (DMQMC) algorithm stochastically samples the N-body thermal density matrix and hence provides access to exact properties of many-particle quantum systems at arbitrary temperatures. We demonstrate that moving to the interaction picture provides substantial benefits when applying DMQMC to interacting fermions. In this first study, we focus on a system of much recent interest: the uniform electron gas in the warm dense regime. The basis set incompleteness error at finite temperature is investigated and extrapolated via a simple Monte Carlo sampling procedure. Finally, we provide benchmark calculations for a four-electron system, comparing our results to previous work where possible.

The effect of quantization on the full configuration interaction quantum Monte Carlo sign problem.

The sign problem in full configuration interaction quantum Monte Carlo (FCIQMC) without annihilation can be understood as an instability of the psi-particle population to the ground state of the matrix obtained by making all off-diagonal elements of the Hamiltonian negative. Such a matrix, and hence the sign problem, is basis dependent. In this paper, we discuss the properties of a physically important basis choice: first versus second quantization. For a given choice of single-particle orbitals, we identify the conditions under which the fermion sign problem in the second quantized basis of antisymmetric Slater determinants is identical to the sign problem in the first quantized basis of unsymmetrized Hartree products. We also show that, when the two differ, the fermion sign problem is always less severe in the second quantized basis. This supports the idea that FCIQMC, even in the absence of annihilation, improves the sign problem relative to first quantized methods. Finally, we point out some theoretically interesting classes of Hamiltonians where first and second quantized sign problems differ, and others where they do not.

Linear-scaling time-dependent density-functional theory in the linear response formalism.

We present an implementation of time-dependent density-functional theory (TDDFT) in the linear response formalism enabling the calculation of low energy optical absorption spectra for large molecules and nanostructures. The method avoids any explicit reference to canonical representations of either occupied or virtual Kohn-Sham states and thus achieves linear-scaling computational effort with system size. In contrast to conventional localised orbital formulations, where a single set of localised functions is used to span the occupied and unoccupied state manifold, we make use of two sets of in situ optimised localised orbitals, one for the occupied and one for the unoccupied space. This double representation approach avoids known problems of spanning the space of unoccupied Kohn-Sham states with a minimal set of localised orbitals optimised for the occupied space, while the in situ optimisation procedure allows for efficient calculations with a minimal number of functions. The method is applied to a number of medium sized organic molecules and a good agreement with traditional TDDFT methods is observed. Furthermore, linear scaling of computational cost with system size is demonstrated on (10,0) carbon nanotubes of different lengths.

The sign problem and population dynamics in the full configuration interaction quantum Monte Carlo method.

The recently proposed full configuration interaction quantum Monte Carlo method allows access to essentially exact ground-state energies of systems of interacting fermions substantially larger than previously tractable without knowledge of the nodal structure of the ground-state wave function. We investigate the nature of the sign problem in this method and how its severity depends on the system studied. We explain how cancellation of the positive and negative particles sampling the wave function ensures convergence to a stochastic representation of the many-fermion ground state and accounts for the characteristic population dynamics observed in simulations.

Mixed isotype class II antigen expression. A novel class II molecule is expressed on a murine B cell lymphoma.

The structures of Ia molecules expressed by two BALB/c B cell lymphoma lines, A20-1.11 (A20) and 2PK3, were analyzed in an effort to explain the differences in antigen-presenting capacity displayed by these cells. Alloreactive T cell hybridomas specific for I-Ad and antigen-specific, I-Ad-restricted T cells responded well to A20 as the APC. The same alloreactive T cell hybridomas responded weakly or not at all to 2PK3 and the responses of the antigen-specific, I-Ad-restricted T cells were consistently lower to antigen presented by 2PK3 as compared with A20. T cells restricted to I-Ed responded equally well to either A20 or 2PK3 as APC. Additionally 2PK3, but not A20, stimulated a strong syngeneic mixed lymphocyte response. Structural analyses of the Ia antigens revealed that I-A and I-E molecules were expressed by A20, whereas an I-E and a novel I-A-like molecule were expressed by 2PK3. The novel class II molecule was affinity purified from 2PK3 cells using an mAb specific for Ad beta (MK-D6), and this molecule was subsequently shown by an RIA to react with an E alpha-specific mAb (14-4-4S) as well. Chain-specific polyclonal antisera raised against I-A and I-E alpha and beta chains indicated that the 2PK3 "I-A" alpha chain reacted in immunoblot with E alpha-specific and not A alpha-specific antisera, whereas the beta chain reacted with A beta- and not E beta-specific antisera. Peptide map and partial amino acid sequence analyses indicated that the "I-A" molecule expressed by 2PK3 represented a mixed isotype structure resulting from the pairing of Ed alpha with Ad beta. By immunofluorescence staining analysis, 2PK3 did not react with an mAb specific for Ad alpha. 2PK3 was capable of limited antigen presentation through the mixed isotype molecule to I-Ad-restricted OVA-specific T cell hybridomas, although the responses induced were low compared with presentation through I-A on A20. Previous descriptions of the expression of mixed isotype class II molecules in the mouse have resulted primarily from DNA-mediated gene transfer experiments. The results presented indicate that a mixed isotype class II molecule can be expressed naturally.

Expression and characterization of recombinant interferon gamma (IFN-gamma) from the nine-banded armadillo (Dasypus novemcinctus) and its effect on Mycobacterium leprae-infected macrophages.

Armadillos (Dasypus novemcinctus) manifest the full histopathological spectrum of leprosy, and are hosts of choice for in vivo propagation of Mycobacterium leprae. Though potentially useful as a model of leprosy pathogenesis, few armadillo-specific reagents exist. We have identified a region of high homology to the interferon gamma (IFN-gamma) of other mammals within the recently published armadillo whole genomic sequence. cDNA was made from ConA-stimulated armadillo peripheral blood mononuclear cells (PBMC), amplified, and cloned into a pET expression vector for transformation and over-expression in Escherichia coli. The recombinant protein (rDnIFN-gamma) was characterized by western blot and its biological function confirmed with bioassays including intracellular killing of Toxoplasma gondii and induction of indoleamine 2, 3-dioxygenase activity. In using rIFN-gamma to activate macrophages from mice, humans or armadillos, similar to humans, rIFN-gamma-activated armadillo MPhi did not produce nitrite and or inhibit the viability of M. leprae in vitro. Conversely, murine rIFN-gamma-activated mouse MPhi produced high levels of nitrite and killed intracellular M. leprae in vitro. These data indicate that the response of armadillo MPhi to rDnIFN-gamma is similar to that which occurs in humans, and demonstrates a potentially important value of the armadillo as a model in leprosy research.

Further biochemical characterization of Mycobacterium leprae laminin-binding proteins.

It has been demonstrated that the alpha2 chain of laminin-2 present on the surface of Schwann cells is involved in the process of attachment of Mycobacterium leprae to these cells. Searching for M. leprae laminin-binding molecules, in a previous study we isolated and characterized the cationic proteins histone-like protein (Hlp) and ribosomal proteins S4 and S5 as potential adhesins involved in M. leprae-Schwann cell interaction. Hlp was shown to bind alpha2-laminins and to greatly enhance the attachment of mycobacteria to ST88-14 Schwann cells. In the present study, we investigated the laminin-binding capacity of the ribosomal proteins S4 and S5. The genes coding for these proteins were PCR amplified and their recombinant products were shown to bind alpha2-laminins in overlay assays. However, when tested in ELISA-based assays and in adhesion assays with ST88-14 cells, in contrast to Hlp, S4 and S5 failed to bind laminin and act as adhesins. The laminin-binding property and adhesin capacity of two basic host-derived proteins were also tested, and only histones, but not cytochrome c, were able to increase bacterial attachment to ST88-14 cells. Our data suggest that the alanine/lysine-rich sequences shared by Hlp and eukaryotic H1 histones might be involved in the binding of these cationic proteins to laminin.

Characterization of human T cell clones specific for coronavirus 229E.

Coronaviruses (CV) are pleomorphic enveloped RNA viruses that are ubiquitous in nature, causing a variety of diseases in both man and domestic animals. In man, CV are generally associated with upper respiratory tract infections. The two prototype strains that are the best studied human CV isolates and which are thought to be responsible for most of the respiratory infections caused by CV are called 229E and OC43. Humoral responses consisting of neutralizing antibodies to CV are present in most individuals by six years of age. Although the cellular immune response to CV in man has not been characterized at all, it is known that the spike (S) and nucleocapsid (N) proteins elicit the major cell mediated immune responses in the mouse. This report describes the production and characterization of eleven independently isolated T cell clones that are specific for the human CV(HCV) 229E. The T cell clones are CD4+ and presumably recognize a processed viral peptide presented by class II molecules on the surface of antigen presenting cells. Of six 229E-specific T cell clones tested against purified viral proteins, three recognize the 180 kD spike glycoprotein while the other three recognize the 55 kD nucleocapsid phosphoprotein. Analysis of the human T cell mediated response to HCV will provide information regarding which viral proteins elicit the immunodominant response, what the fine specificity of these T cell clones are (immuno-dominant peptides), and what the T cell receptor (TCR) and cytokine usage is of these virus specific clones.

A successful and necessary evolution to shared leadership: a hospital's story.

The success and adaptability of healthcare organizations will depend more and more on their ability to draw on the capabilities of their people. Tillsonburg District Memorial Hospital, a rural Ontario hospital, has evolved an organization and culture based on shared leadership and decision-making responsibility. Today this extends to front-line teams. This did not come about, however, without continuous effort. Successful transition takes preparation, guidance, much thought, commitment and patience.

Expression and function of mixed isotype MHC class II molecules in normal mice.

Mixed isotype MHC class II molecules (E alpha dA beta d) occur at extremely low levels on the surface of normal mouse B cells and macrophages, as determined by surface staining with an E alpha dA beta d-specific hamster mAb, H71-258.41. The surface levels of mixed isotype on the B cell lymphoma line A20 are approximately 1 to 2% that of surface I-A, whereas the levels of these molecules on normal mouse B cells were estimated to be at least two to four times less than those on A20. Nevertheless, other investigators have recently reported that immunization of normal H-2d mice with the sperm whale myoglobin peptide 110-121 (SWM(110-121)) elicits T cells, predominantly, V beta 8.2+, that recognize the peptide only in context of E alpha A beta. We have characterized a large number of SWM(110-121)-specific T cell hybridomas from several strains of H-2d haplotype mice. All of the V beta 8.2+ 110-121-specific hybridomas were found to be restricted by E alpha dA beta d, whereas, of the V beta 8.2- 110-121-specific group, approximately half recognized the peptide through E alpha dA beta d whereas the remainder were restricted by either I-Ad or I-Ed. mAb inhibition experiments revealed that 14-4-4S (E alpha-specific) could block presentation by mixed isotype completely, while MK-D6 (A beta d-specific) and H71-258.41 (E alpha dA beta d-specific) only inhibited presentation when the concentration of peptide was limiting. Although A20 expresses very low levels of mixed isotype, 10 to 100 nmol of the peptide produced a detectable response, illustrating the remarkable efficiency in presenting this peptide through E alpha dA beta d. The ability of normal mouse APC to use this restriction element despite its extremely low expression has important implications for the activation of T cells by low levels of peptide-MHC complexes.

Characterization of defective I-A surface expression in a mixed isotype expressing murine B cell lymphoma: continued expression of E alpha d A beta d despite competition from restored A alpha d A beta d pairs.

The BALB/c-derived mouse B cell lymphoma line, 2PK3, expresses mixed isotype E alpha dA beta d and classical I-E class II molecules on its surface, but normal surface I-A expression is not detectable. Northern blot analysis showed comparable amounts of A alpha mRNA in 2PK3 as compared to another Iad expressing B cell lymphoma, A20, which predominantly expresses I-A and I-E. Sequence analysis of 2PK3 A alpha cDNA revealed a single nucleotide difference in the signal sequence that would result in a proline for leucine substitution at position - 12. In vitro translation of 2PK3 A alpha mRNA gave results suggesting that the signal peptide mutation prevented translocation of the A alpha protein across the rough endoplasmic reticulum which would provide an explanation for the lack of I-A expression in 2PK3. I-A expression was restored by transfecting a functional A alpha d gene into 2PK3. Although I-A was expressed at high levels in some transfectants, in all cases significant levels of mixed isotype were still detected. Functional studies performed using antigen-specific I-A(d)-restricted and E alpha d-A beta d-specific T cell hybridomas confirmed the levels of expression of I-A(d) and E alpha dA beta d respectively on the transfectants and showed that these molecules were functional. An interesting observation from this study is the continued expression of significant levels of E alpha dA beta d in spite of competition from restored expression of I-A(d).

The application of proteomics in defining the T cell antigens of Mycobacterium tuberculosis.

The complete sequencing of the Mycobacterium tuberculosis genome offers a unique opportunity to fully elucidate the biology of this human pathogen. One aspect of significant importance is the definition of T cell antigens. This report describes the development and implementation of a proteomic approach to defining such antigens. Large quantities of subcellular protein fractions of M. tuberculosis were resolved by two-dimensional liquid phase electrophoresis (2-D LPE), resulting in 355 and 299 fractions of culture filtrate and cytosolic proteins, respectively. Analysis of these fractions against splenocytes of C57Bl/6 mice infected with M. tuberculosis resulted in the identification of 37 fractions that stimulated a dominant T cell response, as measured by the production of interferon-gamma. Additionally, when the 2-D LPE fractions were assayed against splenocytes harvested at 10 and 40 days post infection significant changes in the T cell response were observed. Molecular characterization of the proteins contained in each of the 38 immunodominant fractions by liquid chromatography-mass spectrometry and liquid chromatography-tandem mass spectrometry resulted in the identification of 30 individual proteins. Many of these represented previously defined antigens. However 17 of these proteins were novel T cell antigens. The data presented demonstrate that proteomics offers a rapid and facile approach for elucidation of immunodominant T cell antigens of pathogenic bacteria.

Monoclonal antibodies specific for antigens expressed by rat type II alveolar epithelial and nonciliated bronchiolar cells.

Markers specific for various lung cells are useful for studies of cellular differentiation and function. We have produced monoclonal antibodies that bind to isolated rat type II alveolar epithelial cells in an ELISA. Two such antibodies, 2C1 and 3F9, specifically labeled type II cells and nonciliated bronchiolar cells by indirect immunofluorescence of rat lung. A third antibody, 2A3, recognized isolated type II cells by ELISA and immunofluorescence, but did not bind to sections of whole lung. Further immunofluorescence studies on adult rat tissue showed that neither 2C1 nor 3F9 labeled other lung cells or cells in kidney, small intestine, brain, or trachea. The antigen or antigens recognized by 2C1 and 3F9 was not detectable at day 15 of fetal lung gestation but was detectable by day 21. Immunofluorescence studies carried out on 0.5-microns frozen sections of lung tissue demonstrated that both 2C1 and 3F9 bound to cell surface antigens, which are expressed in a highly polarized fashion on the luminal surface of the alveolus and bronchiole. The rat cell line, L2, which displays some similarities to type II cells, did not display positive immunofluorescence to 2A3, 2C1, or 3F9. The antibodies 2C1 and 3F9 are distinct from and apparently more specific than previously described monoclonal antibodies raised to rat type II cells. Alveolar type II and nonciliated bronchiolar cells share several common features. Both cell types contain the surfactant apoprotein SP-A, proliferate in response to lung injury, develop in the late stages of gestation, take up and catabolize platelet-activating factor, contain high levels of cytochrome P-450, and can be induced to form tumors in response to chemical carcinogens. The recognition of highly specific surface antigen(s) on both nonciliated bronchiolar cells and type II cells demonstrates yet another characteristic shared by the two cell types.