Beyond the Random Phase Approximation for the Electron Correlation Energy: The Importance of Single Excitations

The random phase approximation (RPA) for the electron correlation energy, combined with the exact-exchange energy, represents the state-of-the-art exchange-correlation functional within density-functional theory (DFT). However, the standard RPA practice -- evaluating both the exact-exchange and the RPA correlation energy using local or semilocal Kohn-Sham (KS) orbitals -- leads to a systematic underbinding of molecules and solids. Here we demonstrate that this behavior is largely corrected by adding a "single excitation" (SE) contribution, so far not included in the standard RPA scheme. A similar improvement can also be achieved by replacing the non-self-consistent exact-exchange total energy by the corresponding self-consistent Hartree-Fock total energy, while retaining the RPA correlation energy evaluated using Kohn-Sham orbitals. Both schemes achieve chemical accuracy for a standard benchmark set of non-covalent intermolecular interactions.Comment: 5 pages, 4 figures, and an additional supplementary materia

Advances in Hydrogeochemical Indicators for the Discovery of New Geothermal Resources in the Great Basin, USA

This report summarizes the results of Phase I work for a go/no go decision on Phase II funding. In the first objective, we assessed the extent to which fluid-mineral equilibria controlled deep water compositions in geothermal systems across the Great Basin. Six systems were evaluated: Beowawe; Desert Peak; Dixie Valley; Mammoth; Raft River; Roosevelt. These represent a geographic spread of geothermal resources, in different geological settings and with a wide range of fluid compositions. The results were used for calibration/reformulation of chemical geothermometers that reflect the reservoir temperatures in producing reservoirs. In the second objective, we developed a reactive -transport model of the Desert Peak hydrothermal system to evaluate the processes that affect reservoir fluid geochemistry and its effect on solute geothermometry. This included testing geothermometry on “reacted” thermal water originating from different lithologies and from near-surface locations where the temperature is known from the simulation. The integrated multi-component geothermometer (GeoT, relying on computed mineral saturation indices) was tested against the model results and also on the systems studied in the first objective

An HPC-Based Hydrothermal Finite Element Simulator for Modeling Underground Response to Community-Scale Geothermal Energy Production

Geothermal heat, as renewable energy, shows great advantage with respect to its environmental impact due to its significantly lower CO2 emissions than conventional fossil fuel. Open and closed-loop geothermal heat pumps, which utilize shallow geothermal systems, are an efficient technology for cooling and heating buildings, especially in urban areas. Integrated use of geothermal energy technologies for district heating, cooling, and thermal energy storage can be applied to optimize the subsurface for communities to provide them with multiple sustainable energy and community resilience benefits. The utilization of the subsurface resources may lead to a variation in the underground environment, which might further impact local environmental conditions. However, very few simulators can handle such a highly complex set of coupled computations on a regional or city scale. We have developed high-performance computing (HPC) based hydrothermal finite element (FE) simulator that can simulate the subsurface and its hydrothermal conditions at a scale of tens of km. The HPC simulator enables us to investigate the subsurface thermal and hydrologic response to the built underground environment (such as basements and subways) at the community scale. In this study, a coupled hydrothermal simulator is developed based on the open-source finite element library deal.II. The HPC simulator was validated by comparing the results of a benchmark case study against COMSOL Multiphysics, in which Aquifer Thermal Energy Storage (ATES) is modeled and a process of heat injection into ATES is simulated. The use of an energy pile system at the Treasure Island redevelopment site (San Francisco, CA, USA) was selected as a case study to demonstrate the HPC capability of the developed simulator. The simulator is capable of modeling multiple city-scale geothermal scenarios in a reasonable amount of time.Comment: 46th Workshop on Geothermal Reservoir Engineering Stanford University, Stanford, California, February 15-17, 202

Petrology and Geochemistry of Boninite Series Volcanic Rocks,Chichi-jima, Bonin Islands, Japan

An Eocene submarine boninite series volcanic center isexposed on the island of Chichi-jima, Bonin Islands, Japan. Five rocktypes, boninite, bronzite andesite, dacite, quartz dacite, and rhyolite,were distinguished within the boninite volcanic sequence on the basis ofpetrographic and geochemical observations. Boninite lavas contain highmagnesium, nickel, and chromium contentsindicative of primitive melts,but have high silica contents relative to other mantle-derived magmas.All boninite series lavas contain very low incompatible elementconcentrations, and concentrations of high-field strength elements inprimitive boninite lavas are less than half of those found in depletedmid-ocean ridge basalts. Abundances of large-ion lithophile elements arerelatively high in boninite series lavas, similar to the enrichmentsobserved in many island arc lavas. Trends for both major and traceelement data suggest that the more evolved lavas of the boninite magmaseries were derived primarily through high-level fractionalcrystallization of boninite. Textural features, such as resorption andglomeroporphyrocrysts, and reverse chemical zonations suggest that magmamixing contributed to the development of the quartz dacitelavas

Geothermal Play Fairway Analysis, Part 2: GIS Methodology

Play Fairway Analysis (PFA) in geothermal exploration originates from a systematic methodology developed within the petroleum industry and is based on a geologic, geophysical, and hydrologic framework of identified geothermal systems. We tailored this methodology to study the geothermal resource potential of the Snake River Plain and surrounding region, but it can be adapted to other geothermal resource settings. We adapted the PFA approach to geothermal resource exploration by cataloging the critical elements controlling exploitable hydrothermal systems, establishing risk matrices that evaluate these elements in terms of both probability of success and level of knowledge, and building a code-based ‘processing model’ to process results. A geographic information system was used to compile a range of different data types, which we refer to as elements (e.g., faults, vents, heat flow, etc.), with distinct characteristics and measures of confidence. Discontinuous discrete data (points, lines, or polygons) for each element were transformed into continuous interpretive 2D grid surfaces called evidence layers. Because different data types have varying uncertainties, most evidence layers have an accompanying confidence layer which reflects spatial variations in these uncertainties. Risk layers, as defined here, are the product of evidence and confidence layers, and are the building blocks used to construct Common Risk Segment (CRS) maps for heat, permeability, and seal, using a weighted sum for permeability and heat, but a different approach with seal. CRS maps quantify the variable risk associated with each of these critical components. In a final step, the three CRS maps were combined into a Composite Common Risk Segment (CCRS) map, using a modified weighted sum, for results that reveal favorable areas for geothermal exploration. Additional maps are also presented that do not mix contributions from evidence and confidence (to allow an isolated view of evidence and confidence), as well as maps that calculate favorability using the product of components instead of a weighted sum (to highlight where all components are present). Our approach helped to identify areas of high geothermal favorability in the western and central Snake River Plain during the first phase of study and helped identify more precise local drilling targets during the second phase of work. By identifying favorable areas, this methodology can help to reduce uncertainty in geothermal energy exploration and development

Comparative genomic analysis of Leishmania (Viannia) peruviana and Leishmania (Viannia) braziliensis

BACKGROUND: The Leishmania (Viannia) braziliensis complex is responsible for most cases of New World tegumentary leishmaniasis. This complex includes two closely related species but with different geographic distribution and disease phenotypes, L. (V.) peruviana and L. (V.) braziliensis. However, the genetic basis of these differences is not well understood and the status of L. (V.) peruviana as distinct species has been questioned by some. Here we sequenced the genomes of two L. (V.) peruviana isolates (LEM1537 and PAB-4377) using Illumina high throughput sequencing and performed comparative analyses against the L. (V.) braziliensis M2904 reference genome. Comparisons were focused on the detection of Single Nucleotide Polymorphisms (SNPs), insertions and deletions (INDELs), aneuploidy and gene copy number variations. RESULTS: We found 94,070 variants shared by both L. (V.) peruviana isolates (144,079 in PAB-4377 and 136,946 in LEM1537) against the L. (V.) braziliensis M2904 reference genome while only 26,853 variants separated both L. (V.) peruviana genomes. Analysis in coding sequences detected 26,750 SNPs and 1,513 indels shared by both L. (V.) peruviana isolates against L. (V.) braziliensis M2904 and revealed two L. (V.) braziliensis pseudogenes that are likely to have coding potential in L. (V.) peruviana. Chromosomal read density and allele frequency profiling showed a heterogeneous pattern of aneuploidy with an overall disomic tendency in both L. (V.) peruviana isolates, in contrast with a trisomic pattern in the L. (V.) braziliensis M2904 reference. Read depth analysis allowed us to detect more than 368 gene expansions and 14 expanded gene arrays in L. (V.) peruviana, and the likely absence of expanded amastin gene arrays. CONCLUSIONS: The greater numbers of interspecific SNP/indel differences between L. (V.) peruviana and L. (V.) braziliensis and the presence of different gene and chromosome copy number variations support the classification of both organisms as closely related but distinct species. The extensive nucleotide polymorphisms and differences in gene and chromosome copy numbers in L. (V.) peruviana suggests the possibility that these may contribute to some of the unique features of its biology, including a lower pathology and lack of mucosal development. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-1928-z) contains supplementary material, which is available to authorized users

Quantitative plane-resolved crystal growth and dissolution kinetics by coupling in situ optical microscopy and diffusion models : the case of salicylic acid in aqueous solution

The growth and dissolution kinetics of salicylic acid crystals are investigated in situ by focusing on individual microscale crystals. From a combination of optical microscopy and finite element method (FEM) modeling, it was possible to obtain a detailed quantitative picture of dissolution and growth dynamics for individual crystal faces. The approach uses real-time in situ growth and dissolution data (crystal size and shape as a function of time) to parametrize a FEM model incorporating surface kinetics and bulk to surface diffusion, from which concentration distributions and fluxes are obtained directly. It was found that the (001) face showed strong mass transport (diffusion) controlled behavior with an average surface concentration close to the solubility value during growth and dissolution over a wide range of bulk saturation levels. The (1̅10) and (110) faces exhibited mixed mass transport/surface controlled behavior, but with a strong diffusive component. As crystals became relatively large, they tended to exhibit peculiar hollow structures in the end (001) face, observed by interferometry and optical microscopy. Such features have been reported in a number of crystals, but there has not been a satisfactory explanation for their origin. The mass transport simulations indicate that there is a large difference in flux across the crystal surface, with high values at the edge of the (001) face compared to the center, and this flux has to be redistributed across the (001) surface. As the crystal grows, the redistribution process evidently can not be maintained so that the edges grow at the expense of the center, ultimately creating high index internal structures. At later times, we postulate that these high energy faces, starved of material from solution, dissolve and the extra flux of salicylic acid causes the voids to close