Intelligent reservoir modeling of Lower Huron Shale

The work presented in this thesis is an intelligent reservoir modeling and analysis of Lower Huron Shale in eastern Kentucky. Methodology used for this analysis is a recently developed Top Down Intelligent Reservoir Modeling, that couples artificial intelligence and data mining techniques with conventional reservoir engineering methods. A total of 77 wells completed in Lower Huron Shale in eastern Kentucky were used in this study. Well production data was obtained from the company operating the wells, while completion reports and well logs were downloaded from publicly available database at Kentucky Geological Surveys website. The downloaded well logs were digitized, and detailed geological interpretation of the studied area was performed. More information about the reservoir was acquired through decline and type curve analyses and single well history matching. Single well history matching was performed with publicly available shale and tight gas reservoir simulator. All of the acquired data was used in the development of spatiotemporal dataset that was further analyzed with state of the art in artificial intelligence and data mining (fuzzy pattern recognition, artificial neural networks). Finally, reservoir was divided into zones of different relative reservoir quality and full field artificial intelligence empowered predictive model of the reservoir was developed and verified

Universal kriging of functional data: trace-variography vs cross-variography? Application to forecasting in unconventional shales

In this paper we investigate the practical and methodological use of Universal Kriging of functional data to predict unconventional shale gas production in undrilled locations from known production data. In Universal Kriging of functional data, two approaches are considered: (1) estimation by means of Cokriging of functional components (Universal Cokriging, UCok), requiring cross-variography and (2) estimation by means of trace-variography (Universal Trace-Kriging, UTrK), which avoids cross-variogram modeling. While theoretically, under known variogram structures, such approaches may be quite equivalent, their practical application implies different estimation procedures and modeling efforts. We investigate these differences from the methodological viewpoint and by means of a real field application in the Barnett shale play. An extensive Monte Carlo study inspired from such real field application is employed to support our conclusions

Cokriging for multivariate Hilbert space valued random fields: application to multi-fidelity computer code emulation

In this paper we propose Universal trace co-kriging, a novel methodology for interpolation of multivariate Hilbert space valued functional data. Such data commonly arises in multi-fidelity numerical modeling of the subsurface and it is a part of many modern uncertainty quantification studies. Besides theoretical developments we also present methodological evaluation and comparisons with the recently published projection based approach by Bohorquez et al. (Stoch Environ Res Risk Assess 31(1):53–70, 2016. https://doi.org/10.1007/s00477-016-1266-y). Our evaluations and analyses were performed on synthetic (oil reservoir) and real field (uranium contamination) subsurface uncertainty quantification case studies. Monte Carlo analyses were conducted to draw important conclusions and to provide practical guidelines for all future practitioners

Structure of the micronemal protein 2 A/I domain from Toxoplasma gondii

Toxoplasma gondii is a widespread zoonotic pathogen capable of causing serious disease in humans and animals. As an obligate intracellular parasite, T. gondii relies on the orchestrated secretion of proteins from its apical complex organelles including the multimodular, transmembrane micronemal protein 2 (MIC2) that couples recognition of the host cell with cytoskeletal reorganization of the parasite to drive invasion. To probe the basis by which the von Willebrand Factor A (vWA)-Integrin like module of TgMIC2 engages the host cell, we solved the crystal structure of a truncated form of TgMIC2A/I (TgMIC2A/Ic) phased by iodide SIRAS and refined to a resolution of 2.05 angstrom. The TgMIC2A/Ic core is organized into a central twisted beta sheet flanked by a-helices consistent with a canonical vWA fold. A restricted basic patch serves as the putative heparin binding site, but no heparin binding was detected in native gel shift assays. Furthermore, no metal was observed in the metal ion dependent adhesion site (MIDAS). Structural overlays with homologous A/I domains reveal a divergent organization of the MIDAS beta 4-alpha 4 loop in TgMIC2A/Ic, which is stabilized through the burial of Phe195 into a deep pocket formed by Gly185. Intriguingly, Gly185 appears to be unique among A/I domains to TgMIC2A/I suggesting that the divergent loop conformation may also be unique to TgMIC2A/I. Although lacking the C-terminal extension, the TgMIC2A/Ic structure reported here is the first of an A/I domain from an apicomplexan parasite and provides valuable insight into defining the molecular recognition of host cells by these widespread pathogens

Structural and Functional Characterization of SporoSAG: A SAG2-RELATED SURFACE ANTIGEN FROM TOXOPLASMA GONDII*

Toxoplasma gondii, the etiological agent of toxoplasmosis, utilizes stage-specific expression of antigenically distinct glycosylphosphatidylinositol-tethered surface coat proteins to promote and establish chronic infection. Of the three infective stages of T. gondii, sporozoites are encapsulated in highly infectious oocysts that have been linked to large scale outbreaks of toxoplasmosis. SporoSAG (surface antigen glycoprotein) is the dominant surface coat protein expressed on the surface of sporozoites. Using a bioinformatic approach, we show that SporoSAG clusters with the SAG2 subfamily of the SAG1-related superfamily (SRS) and is non-polymorphic among the 11 haplogroups of T. gondii strains. In contrast to the immunodominant SAG1 protein expressed on tachyzoites, SporoSAG is non-immunogenic during natural infection. We report the 1.60 Å resolution crystal structure of SporoSAG solved using cadmium single anomalous dispersion. SporoSAG crystallized as a monomer and displays unique features of the SRS β-sandwich fold relative to SAG1 and BSR4. Intriguingly, the structural diversity is localized to the upper sheets of the β-sandwich fold and may have important implications for multimerization and host cell ligand recognition. The structure of SporoSAG also reveals an unexpectedly acidic surface that contrasts with the previously determined SAG1 and BSR4 structures where a basic surface is predicted to play a role in binding negatively charged glycosaminoglycans. Our structural and functional characterization of SporoSAG provides a rationale for the evolutionary divergence of this key SRS family member

Structural Characterization of Apical Membrane Antigen 1 (AMA1) from Toxoplasma gondii*

Apical membrane antigen 1 (AMA1) is an essential component of the moving junction complex used by Apicomplexan parasites to invade host cells. We report the 2.0 Å resolution x-ray crystal structure of the full ectodomain (domains I, II, and III) of AMA1 from the pervasive protozoan parasite Toxoplasma gondii. The structure of T. gondii AMA1 (TgAMA1) is the most complete of any AMA1 structure to date, with more than 97.5% of the ectodomain unambiguously modeled. Comparative sequence analysis reveals discrete segments of divergence in TgAMA1 that map to areas of established functional importance in AMA1 from Plasmodium vivax (PvAMA1) and Plasmodium falciparum (PfAMA1). Inspection of the TgAMA1 structure reveals a network of apical surface loops, reorganized in both size and chemistry relative to PvAMA1/PfAMA1, that appear to serve as structural filters restricting access to a central hydrophobic groove. The terminal portion of this groove is formed by an extended loop from DII that is 14 residues shorter in TgAMA1. A pair of tryptophan residues (Trp353 and Trp354) anchor the DII loop in the hydrophobic groove and frame a conserved tyrosine (Tyr230), forming a contiguous surface that may be critical for moving junction assembly. The minimalist DIII structure folds into a cystine knot that probably stabilizes and orients the bulk of the ectodmain without providing excess surface area to which invasion-inhibitory antibodies can be generated. The detailed structural characterization of TgAMA1 provides valuable insight into the mechanism of host cell invasion by T. gondii