Towards quantum-chemical method development for arbitrary basis functions

We present the design of a flexible quantum-chemical method development framework, which supports employing any type of basis function. This design has been implemented in the light-weight program package molsturm, yielding a basis-function-independent self-consistent field scheme. Versatile interfaces, making use of open standards like python, mediate the integration of molsturm with existing third-party packages. In this way both rapid extension of the present set of methods for electronic structure calculations as well as adding new basis function types can be readily achieved. This makes molsturm well-suitable for testing novel approaches for discretising the electronic wave function and allows comparing them to existing methods using the same software stack. This is illustrated by two examples, an implementation of coupled-cluster doubles as well as a gradient-free geometry optimisation, where in both cases, an arbitrary basis functions could be used. molsturm is open-source and can be obtained from https://molsturm.org.Comment: 15 pages and 7 figure

Quantum chemistry with Coulomb Sturmians:Construction and convergence of Coulomb Sturmian basis sets at the Hartree-Fock level

The first discussion of basis sets consisting of exponentially decaying Coulomb Sturmian functions for modelling electronic structures is presented. The proposed basis set construction selects Coulomb Sturmian functions using separate upper limits to their principle, angular momentum and magnetic quantum numbers. Their common Coulomb Sturmian exponent is taken as a fourth parameter. The convergence properties of such basis sets are investigated for second and third row atoms at the Hartree-Fock level. Thereby important relations between the values of the basis set parameters and the physical properties of the electronic structure are recognised. For example, an unusually large limit for the angular momentum quantum number in unrestricted Hartree-Fock calculations can be linked to the breaking of spherical symmetry in such cases. Furthermore, a connection between the optimal, i.e. minimum-energy, Coulomb Sturmian exponent and the average Slater exponents values obtained by Clementi and Raimondi (E. Clementi and D. L. Raimondi, J. Chem. Phys. 38, 2686 (1963)) is made. These features of Coulomb Sturmian basis sets emphasise their ability to correctly reproduce the physical features of Hartree-Fock wave functions.Comment: 16 pages, 14 figures, supporting inf

Reduced basis surrogates for quantum spin systems based on tensor networks

Within the reduced basis methods approach, an effective low-dimensional subspace of a quantum many-body Hilbert space is constructed in order to investigate, e.g., the ground-state phase diagram. The basis of this subspace is built from solutions of snapshots, i.e., ground states corresponding to particular and well-chosen parameter values. Here, we show how a greedy strategy to assemble the reduced basis and thus to select the parameter points can be implemented based on matrix-product-states (MPS) calculations. Once the reduced basis has been obtained, observables required for the computation of phase diagrams can be computed with a computational complexity independent of the underlying Hilbert space for any parameter value. We illustrate the efficiency and accuracy of this approach for different one-dimensional quantum spin-1 models, including anisotropic as well as biquadratic exchange interactions, leading to rich quantum phase diagrams.Comment: 15 pages, 13 figure

Ortho-to-para ratio of NH2. Herschel-HIFI observations of ortho- and para-NH2 rotational transitions towards W31C, W49N, W51 and G34.3+0.1

We have used the Herschel-HIFI instrument to observe both nuclear spin symmetries of amidogen (NH2) towards the high-mass star-forming regions W31C (G10.6-0.4), W49N (G43.2-0.1), W51 (G49.5-0.4) and G34.3+0.1. The aim is to investigate the ratio of nuclear spin types, the ortho-to-para ratio (OPR), of NH2. The excited NH2 transitions are used to construct radiative transfer models of the hot cores and surrounding envelopes in order to investigate the excitation and possible emission of the ground state rotational transitions of ortho-NH2 N_(K_a,K_c} J=1_(1,1) 3/2 - 0_(0,0) 1/2 and para-NH2 2_(1,2) 5/2 - 1_(0,1) 3/2$ used in the OPR calculations. Our best estimate of the average OPR in the envelopes lie above the high temperature limit of three for W49N, specifically 3.5 with formal errors of \pm0.1, but for W31C, W51, and G34.3+0.1 we find lower values of 2.5\pm0.1, 2.7\pm0.1, and 2.3\pm0.1, respectively. Such low values are strictly forbidden in thermodynamical equilibrium since the OPR is expected to increase above three at low temperatures. In the translucent interstellar gas towards W31C, where the excitation effects are low, we find similar values between 2.2\pm0.2 and 2.9\pm0.2. In contrast, we find an OPR of 3.4\pm0.1 in the dense and cold filament connected to W51, and also two lower limits of >4.2 and >5.0 in two other translucent gas components towards W31C and W49N. At low temperatures (T \lesssim 50 K) the OPR of H2 is <10^-1, far lower than the terrestrial laboratory normal value of three. In such a "para-enriched H2" gas, our astrochemical models can reproduce the variations of the observed OPR, both below and above the thermodynamical equilibrium value, by considering nuclear-spin gas-phase chemistry. The models suggest that values below three arise in regions with temperatures >20-25 K, depending on time, and values above three at lower temperatures

Chassis organism from Corynebacterium glutamicum – a top-down approach to identify and delete irrelevant gene clusters

Unthan S, Baumgart M, Radek A, et al. Chassis organism from Corynebacterium glutamicum – a top-down approach to identify and delete irrelevant gene clusters. Biotechnology Journal. 2015;10(2):290-301

Mid-IR Observations of T Tauri stars: Probing the Star-Disk Connection in Rotational Evolution

We present mid-IR N-band (\lambda_{eff} = 10.2\micron) photometry of a carefully selected sample of T Tauri stars thought to be single from the Taurus-Auriga molecular cloud. Infrared excesses in these stars are generally attributed to circumstellar dust-disks. Combining observations at 2.16\micron (K$_{s}$-band) and 10.2\micron (N-band) we probe a region in the circumstellar dust-disk from a few stellar radii through the terrestrial planet zone (0.02-1.0AU). By analyzing the distribution of the $(K_{s}-N)$ color index with respect to previously measured photometric rotation periods we investigate what role circumstellar disks play in the rotational evolution of the central star. The resulting positive correlation between these two variables is consistent with the notion that a star-disk interaction facilitates the regulation of angular momentum during the T Tauri stage. We also demonstrate, how including non-single stars in such an analysis will \textit{weaken} any correlation in the relation between $(K_{s}-N)$ color and period. To further understand disk properties we also present SEDs for a few objects with new ground based M-band (\lambda_{eff} = 4.8\micron) and Q-band (\lambda_{eff} = 20\micron) data and compare them to a geometrically thin, optically-thick disk model.Comment: 9 pages, 4 figure

Characterizing benthic macroinvertebrate and algal biological condition gradient models for California wadeable Streams, USA

The Biological Condition Gradient (BCG) is a conceptual model that describes changes in aquatic communities under increasing levels of anthropogenic stress. The BCG helps decision-makers connect narrative water quality goals (e.g., maintenance of natural structure and function) to quantitative measures of ecological condition by linking index thresholds based on statistical distributions (e.g., percentiles of reference distributions) to expert descriptions of changes in biological condition along disturbance gradients. As a result, the BCG may be more meaningful to managers and the public than indices alone. To develop a BCG model, biological response to stress is divided into 6 levels of condition, represented as changes in biological structure (abundance and diversity of pollution sensitive versus tolerant taxa) and function. We developed benthic macroinvertebrate (BMI) and algal BCG models for California perennial wadeable streams to support interpretation of percentiles of reference-based thresholds for bioassessment indices (i.e., the California Stream Condition Index [CSCI] for BMI and the Algal Stream Condition Index [ASCI] for diatoms and soft-bodied algae). Two panels (one of BMI ecologists and the other of algal ecologists) each calibrated a general BCG model to California wadeable streams by first assigning taxa to specific tolerance and sensitivity attributes, and then independently assigning test samples (264 BMI and 248 algae samples) to BCG Levels 1–6. Consensus on the assignments was developed within each assemblage panel using a modified Delphi method. Panels then developed detailed narratives of changes in BMI and algal taxa that correspond to the 6 BCG levels. Consensus among experts was high, with 81% and 82% expert agreement within 0.5 units of assigned BCG level for BMIs and algae, respectively. According to both BCG models, the 10th percentiles index scores at reference sites corresponded to a BCG Level 3, suggesting that this type of threshold would protect against moderate changes in structure and function while allowing loss of some sensitive taxa. The BCG provides a framework to interpret changes in aquatic biological condition along a gradient of stress. The resulting relationship between index scores and BCG levels and narratives can help decision-makers select thresholds and communicate how these values protect aquatic life use goals

Different paths to the modern state in Europe: the interaction between domestic political economy and interstate competition

Theoretical work on state formation and capacity has focused mostly on early modern Europe and on the experience of western European states during this period. While a number of European states monopolized domestic tax collection and achieved gains in state capacity during the early modern era, for others revenues stagnated or even declined, and these variations motivated alternative hypotheses for determinants of fiscal and state capacity. In this study we test the basic hypotheses in the existing literature making use of the large date set we have compiled for all of the leading states across the continent. We find strong empirical support for two prevailing threads in the literature, arguing respectively that interstate wars and changes in economic structure towards an urbanized economy had positive fiscal impact. Regarding the main point of contention in the theoretical literature, whether it was representative or authoritarian political regimes that facilitated the gains in fiscal capacity, we do not find conclusive evidence that one performed better than the other. Instead, the empirical evidence we have gathered lends supports to the hypothesis that when under pressure of war, the fiscal performance of representative regimes was better in the more urbanized-commercial economies and the fiscal performance of authoritarian regimes was better in rural-agrarian economie

Hypothesis: primary antiangiogenic method proposed to treat early stage breast cancer

<p>Abstract</p> <p>Background</p> <p>Women with Down syndrome very rarely develop breast cancer even though they now live to an age when it normally occurs. This may be related to the fact that Down syndrome persons have an additional copy of chromosome 21 where the gene that codes for the antiangiogenic protein Endostatin is located. Can this information lead to a primary antiangiogenic therapy for early stage breast cancer that indefinitely prolongs remission? A key question that arises is when is the initial angiogenic switch thrown in micrometastases? We have conjectured that avascular micrometastases are dormant and relatively stable if undisturbed but that for some patients angiogenesis is precipitated by surgery. We also proposed that angiogenesis of micrometastases very rarely occurs before surgical removal of the primary tumor. If that is so, it seems possible that we could suggest a primary antiangiogenic therapy but the problem then arises that starting a therapy before surgery would interfere with wound healing.</p> <p>Results</p> <p>The therapy must be initiated at least one day prior to surgical removal of the primary tumor and kept at a Down syndrome level perhaps indefinitely. That means the drug must have virtually no toxicity and not interfere meaningfully with wound healing. This specifically excludes drugs that significantly inhibit the VEGF pathway since that is important for wound healing and because these agents have some toxicity. Endostatin is apparently non-toxic and does not significantly interfere with wound healing since Down syndrome patients have no abnormal wound healing problems.</p> <p>Conclusion</p> <p>We propose a therapy for early stage breast cancer consisting of Endostatin at or above Down syndrome levels starting at least one day before surgery and continuing at that level. This should prevent micrometastatic angiogenesis resulting from surgery or at any time later. Adjuvant chemotherapy or hormone therapy should not be necessary. This can be continued indefinitely since there is no acquired resistance that develops, as happens in most cancer therapies.</p

FimH Adhesin of Type 1 Fimbriae Is a Potent Inducer of Innate Antimicrobial Responses Which Requires TLR4 and Type 1 Interferon Signalling

Components of bacteria have been shown to induce innate antiviral immunity via Toll-like receptors (TLRs). We have recently shown that FimH, the adhesin portion of type 1 fimbria, can induce the innate immune system via TLR4. Here we report that FimH induces potent in vitro and in vivo innate antimicrobial responses. FimH induced an innate antiviral state in murine macrophage and primary MEFs which was correlated with IFN-β production. Moreover, FimH induced the innate antiviral responses in cells from wild type, but not from MyD88−/−, Trif−/−, IFN−α/βR−/− or IRF3−/− mice. Vaginal delivery of FimH, but not LPS, completely protected wild type, but not MyD88−/−, IFN-α/βR−/−, IRF3−/− or TLR4−/− mice from subsequent genital HSV-2 challenge. The FimH-induced innate antiviral immunity correlated with the production of IFN-β, but not IFN-α or IFN-γ. To examine whether FimH plays a role in innate immune induction in the context of a natural infection, the innate immune responses to wild type uropathogenic E. coli (UPEC) and a FimH null mutant were examined in the urinary tract of C57Bl/6 (B6) mice and TLR4-deficient mice. While UPEC expressing FimH induced a robust polymorphonuclear response in B6, but not TLR4−/− mice, mutant bacteria lacking FimH did not. In addition, the presence of TLR4 was essential for innate control of and protection against UPEC. Our results demonstrate that FimH is a potent inducer of innate antimicrobial responses and signals differently, from that of LPS, via TLR4 at mucosal surfaces. Our studies suggest that FimH can potentially be used as an innate microbicide against mucosal pathogens