Subtle Structural Features Research Articles

Seismic attribute-based characterization of coalbed methane reservoirs: An example from the Fruitland Formation, San Juan basin, New Mexico

The Fruitland Formation of the San Juan basin is the largest producer of coalbed methane in the world. Production patterns vary from one well to another throughout the basin, reflecting factors such as coal thickness and fracture and cleat density. In this study, we integrated conventional P-wave three-dimensional (3-D) seismic and well data to investigate geological controls on production from a thick, continuous coal seam in the lower part of the Fruitland Formation. Our objective was to show the potential of using 3-D seismic data to predict coal thickness, as well as the distribution and orientation of subtle structures that may be associated with enhanced permeability zones. To do this, we first derived a seismic attribute-based model that predicts coal thickness. We then used curvature attributes derived from seismic horizons to detect subtle structural features that might be associated with zones of enhanced permeability. Production data show that the best producing wells are associated with seismically definable structural features and thick coal. Although other factors (e.g., completion practices and coal type) affect coalbed methane production, our results suggest that conventional 3-D seismic data, integrated with wire-line logs and production data, are useful for characterizing coalbed methane reservoirs.

High resolution 3D seismic reflection acquisition applied to coal mining

In recent years significant improvements in survey design, acquisition and processing technologies have advanced high resolution 3D seismic reflection imaging. However, shallow coal applications require high-resolution imagery that is more costly than conventional petroleum-scale reflection. The 3D seismic grid design fundamentally controls the effective spatial sampling and signal-to-noise ratio of the final seismic volume. Whilst orthogonal, brick and slant-line shot-receiver geometries have all been employed, the latter has been found to produce fewer imaging artefacts, at a lower shot density and line-kilometre preparation cost. For targets at depths typical of underground coal-mining operations (70 to 700 m), a CMP bin size of approximately 50 square meters provides an optimal trade-off between spatial resolution and acquisition cost. If the bin size is increased beyond this point, the definition of subtle structural features in the target coal seam is compromised. In typical coal imaging situations, dynamite charge sizes are in the range of 150g-400g which are small enough to provide necessary bandwidth, whilst still generating acceptable signal levels. Practical experience has determined that optimum source coupling is achieved by locating the charge at least 2m below base of weathering, and at least 12m below surface. To minimise the reduction in high-frequency fidelity, geophones with a natural frequency of at least 30 Hz are best.

ダリール油田における地震探査の適用

The Daleel oil field is located at the western corner of the Wadi Aswad contractarea of Japex Oman Ltd. Basic seismic exploration of 2, 883km in line length in this area wascarried out during 1981-1983. Several additional seismic surveys including two 3D surveys wereperformed later in the Daleel oil field and adjacent area for the purpose of reservoir delineation. Specifications of the former field data acquisition were basically 120 channel and 60 fold. Westarted first with end-on spread at 30m receiver and source intervals, and a few months laterchanged it to split spread at 50m receiver and source intervals. The latter specifications weresimilar to so-called ‘(ideal) stack array’ which was discussed later a lot on The Leading Edge ofGeophysics in 1986. This change seems to have contributed to speeding up work progress and toacquiring data in requisition of broad band, no much skew, and wide dynamic range, with leastnoise for tracing subtle and cache information. The stack array was generally good as spacedomain filter design and needed no much additional, irrationally large labor efforts.Uphole shooting from the depth of 40m on average at 465 points was useful not only forcalibrating weathering correction data, but also studying shallow layer situations, which did notalways fit typical two layer model.Interpretation pitfalls were checked occasionally on cross points of lines when trackingstratigraphical or lithological features in 2D seismic sections.After checking surface seismic velocity data with those of nearby wells we found veryreasonable harmony between them and successfully estimated a standard velocity function.Our main concern was to delineate reservoir features of the Daleel area. The effort delineatingthem also resulted in better definition of fault systems and subtle structural features. Everyinformation used here contributed to integrating complete interpretation.

Sequence analysis of an artificial family of RNA-binding peptides.

Diverse peptide sequences recognizing the lambda boxB RNA hairpin were previously isolated from a library encoding the 22-residue lambda N peptide with random amino acids at positions 13-22 using mRNA display. We have statistically analyzed amino acid distributions in 65 unique sequences from rounds 11 and 12 of this selection and evaluated the resulting structural and functional predictions by alanine-scanning mutagenesis and circular dichroism spectrometry. This artificial sequence family has a consensus structure that continues the bent alpha helix of lambda N up to position 17 when bound to lambda boxB. A charge pair (E(14)R(15)) and hydrophobic patch (A(21)L(22) or V(21)L(22)) have important functional roles in this context. Notably, amino acid covariance reveals six specific pairs of random region positions with >95% significant linkage and strong overall helical (i+1, i+3, and i+4) couplings. The covariance analysis suggests that (1) the sequence context of every residue in each insert has been optimized, (2) selected sequences are local optima on a rugged fitness landscape, and (3) it is possible to detect more subtle structural features with artificial protein sequence families than natural homologs. Our results provide a framework for investigating the structures of in vitro selected proteins by functional minimization, reselection, and covariance analysis.

Crystal structure of tropomyosin at 7 �ngstroms resolution

Tropomyosin is a 400A-long coiled coil that polymerizes to form a continuous filament that associates with actin in muscle and numerous non-muscle cells. Tropomyosin and troponin together form a calcium-sensitive switch that is responsible for thin-filament regulation of striated muscle. Subtle structural features of the molecule, including non-canonical aspects of its coiled-coil motif, undoubtedly influence its association with f-actin and its role in thin filament regulation. Previously, careful inspection of native diffraction intensities was sufficient to construct a model of tropomyosin at 9A resolution in a spermine-induced crystal form that diffracts anisotropically to 4A resolution. Single isomorphous replacement (SIR) phasing has now provided an empirical determination of the structure at 7A resolution. A novel method of heavy-atom analysis was used to overcome difficulties in interpretation of extremely anisotropic diffraction. The packing arrangement of the molecules in the crystal, and important aspects of the tropomyosin geometry such as non-uniformities of the pitch and variable bending and radius of the coiled coil are evident.

Effect of Hydrotropes on the Volume Phase Transition in Poly(N-isopropylacrylamide) Hydrogel

With a view to understand the complex molecular forces involved in the volume phase transition (VPT) exhibited by poly(N-isopropylacrylamide) hydrogels the effect of hydrotropes on VPT was monitored. Hydroxybenzenes, hydroxybenzoates, and benzenesulfonates, which constitute the class of hydrotropes, are capable of solubilizing a variety of nonpolar organic molecules in water. Hydrotropes permit an assessment of subtle molecular and structural features on the VPT because ortho, meta, and para isomers differ in their hydrotropy. Among the compounds studied, in a selected concentration range we observed that dihydroxybenzoic acid is the most efficient in lowering the transition temperature and salicylate anion raises the transition temperature while m-hydroxybenzoate offers minimum perturbation. The results are indicative of entropic cooperativity of many interactions stabilizing a conformation as the driving force for the volume phase transition.

Abstract: Subsurface Structure and Sequence Stratigraphy of the Western Margin of the Hugoton Embayment, Morton County, Kansas 

In low-relief basins mapping the subtle structural and stratigraphic features required for effective exploration and production of hydrocarbons can be difficult. The Hugoton Embayment, containing the giant Hugoton and Panoma gas fields, is an example of such a basin. We have used digital wireline logs and a new approach, termed pseudoseismic, to map subtle structural and stratigraphic features on the western edge of the Hugoton Embayment in Morton County, Kansas. Mapped were four previously poorly constrained faults and low-relief structural noses plunging into basin. Eight Wolfcampian sequences also were defined and mapped. The extreme landward position of these sequences has influenced their geometries and results in a modified sequence-stratigraphic model for the Wolfcampian rocks of southwestern Kansas. The sequence model places nonmarine-dominated strata in the latehighstand systems tract. Pinchouts of marine-dominated reservoir-prone lithologies within the Wolfcampian sequences, coupled with structural features, seem to be controlling factors on production from the Hugoton and Panoma gas fields. These stratigraphic and structure problems are not unique to the Hugoton Embayment. The approaches and results could have widespread application in other basins and mature exploration provinces.

An EXAFS study of rare-earth phosphate glasses in the vicinity of the metaphosphate composition

A study of rare-earth phosphate glasses, in the vicinity of the metaphosphate composition, has been undertaken at different temperatures using the extended X-ray absorption fine structure (EXAFS) facility at the Synchrotron Radiation Source, Daresbury Laboratory, UK. The metaphosphate-like glasses examined contained the rare-earth elements La, Sm, Eu and Gd as R 3+ ions. The experiments were carried out at room temperature, 145 and 79 K. The data show that the first shell surrounding rare-earth ions contains only oxygen atoms at a mean distance of ∼2.2–2.4 Å. The `lanthanide contraction' is clearly observed, i.e., the R–O distance decreases with increasing atomic number. The observed R(−O) coordination numbers are in the range 5–7. A second correlation shell was found, associated with phosphorus atoms around the central rare-earth atom (∼3.5 Å), and another rare-earth:oxygen correlation was also identified (∼4 Å). Static disorder dominates the Debye–Waller term, but thermal disorder is not negligible. Within the accuracy of the EXAFS data, no significant structural variations were observed over the temperature range studied. We conclude that the anomalous bulk properties are associated with either subtle structural features or primarily due to rare-earth ion interactions.

Specificity in structure‐based drug design: Identification of a novel, selective inhibitor of Pneumocystis carinii dihydrofolate reductase

Specificity is an important aspect of structure-based drug design. Distinguishing between related targets in different organisms is often the key to therapeutic success. Pneumocystis carinii is a fungal opportunist which causes a crippling pneumonia in immunocompromised individuals. We report the identification of novel inhibitors of P. cariniidihydrofolate reductase (DHFR) that are selective versus inhibition of human DHFR using computational molecular docking techniques. The Fine Chemicals Directory, a database of commercially available compounds, was screened with the DOCK program suite to produce a list of potential P. carinii DHFR inhibitors. We then used a postdocking refinement directed at discerning subtle structural and chemical features that might reflect species specificity. Of 40 compounds predicted to exhibit anti-PneumocystisDHFR activity, each of novel chemical framework, 13 (33%) show IC50 values better than 150 μM in an enzyme assay. These inhibitors were further assayed against human DHFR: 10 of the 13 (77%) bind preferentially to the fungal enzyme. The most potent compound identified is a 7 μM inhibitor of P. carinii DHFR with 25-fold selectivity. The ability of molecular docking methods to locate selective inhibitors reinforces our view of structure-based drug discovery as a valuable strategy, not only for identifying lead compounds, but also for addressing receptor specificity. Proteins 29:59–67, 1997. © 1997 Wiley-Liss, Inc.

Specificity in structure-based drug design: Identification of a novel, selective inhibitor ofPneumocystis carinii dihydrofolate reductase

Specificity is an important aspect of structure-based drug design. Distinguishing between related targets in different organisms is often the key to therapeutic success. Pneumocystis carinii is a fungal opportunist which causes a crippling pneumonia in immunocompromised individuals. We report the identification of novel inhibitors of P. carinii dihydrofolate reductase (DHFR) that are selective versus inhibition of human DHFR using computational molecular docking techniques. The Fine Chemicals Directory, a database of commercially available compounds, was screened with the DOCK program suite to produce a list of potential P. carinii DHFR inhibitors. We then used a postdocking refinement directed at discerning subtle structural and chemical features that might reflect species specificity. Of 40 compounds predicted to exhibit anti-Pneumocystis DHFR activity, each of novel chemical framework, 13 (33%) show IC50 values better than 150 microM in an enzyme assay. These inhibitors were further assayed against human DHFR: 10 of the 13 (77%) bind preferentially to the fungal enzyme. The most potent compound identified is a 7 microM inhibitor of P. carinii DHFR with 25-fold selectivity. The ability of molecular docking methods to locate selective inhibitors reinforces our view of structure-based drug discovery as a valuable strategy, not only for identifying lead compounds, but also for addressing receptor specificity.

Cytochrome c activation of CPP32-like proteolysis plays a critical role in a Xenopus cell-free apoptosis system.

In a cell-free system based on Xenopus egg extracts, Bcl-2 blocks apoptotic activity by preventing cytochrome c release from mitochondria. We now describe in detail the crucial role of cytochrome c in this system. The mitochondrial fraction, when incubated with cytosol, releases cytochrome c. Cytochrome c in turn induces the activation of protease(s) resembling caspase-3 (CPP32), leading to downstream apoptotic events, including the cleavage of fodrin and lamin B1. CPP32-like protease activity plays an essential role in this system, as the caspase inhibitor, Ac-DEVD-CHO, strongly inhibited fodrin and lamin B1 cleavage, as well as nuclear morphology changes. Cytochrome c preparations from various vertebrate species, but not from Saccharomyces cerevisiae, were able to initiate all signs of apoptosis. Cytochrome c by itself was unable to process the precursor form of CPP32; the presence of cytosol was required. The electron transport activity of cytochrome c is not required for its pro-apoptotic function, as Cu- and Zn-substituted cytochrome c had strong pro-apoptotic activity, despite being redox-inactive. However, certain structural features of the molecule were required for this activity. Thus, in the Xenopus cell-free system, cytosol-dependent mitochondrial release of cytochrome c induces apoptosis by activating CPP32-like caspases, via unknown cytosolic factors.

Ferromagnetism in a New Structural, Phase of [Fe(C5Me5)2] [TCNQ

Abstract The five integrated-stack charge-transfer salts [M(C5Me5)2][TCNQ] (M═Mn,Cr) and [M(C5Me5)2][TCNE] (M═Fe, Mn, Cr) are bulk ferromagnets, whereas [Fe(C5Me5)2][TCNQ] was reported to exist as two different phases, a metamagnet and a paramagnet. We now report that with careful control of the crystallization conditions, it is possible to isolate a new structural phase of [Fe(C5Me5)2][TCNQ] which is a bulk 3-D ferromagnet with Tc = 3.1 K. Thus [Fe(C5Me5)2][TCNQ] is the first example of a single compound giving rise to three distinctly different magnetic phenomena, a finding that will permit an assessment of the subtle structural features that control magnetic ordering in this class of materials.

DNA Alkylation Properties of CC-1065 and Duocarmycin Analogs Incorporating the 2,3,10,10a-Tetrahydrocyclopropa[d]benzo[f]quinol-5-one Alkylation Subunit: Identification of Subtle Structural Features That Contribute to the Regioselectivity of the Adenine N3 Alkylation Reaction

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDNA Alkylation Properties of CC-1065 and Duocarmycin Analogs Incorporating the 2,3,10,10a-Tetrahydrocyclopropa[d]benzo[f]quinol-5-one Alkylation Subunit: Identification of Subtle Structural Features That Contribute to the Regioselectivity of the Adenine N3 Alkylation ReactionDale L. Boger and Philippe MesiniCite this: J. Am. Chem. Soc. 1995, 117, 47, 11647–11655Publication Date (Print):November 1, 1995Publication History Published online1 May 2002Published inissue 1 November 1995https://doi.org/10.1021/ja00152a004RIGHTS & PERMISSIONSArticle Views169Altmetric-Citations25LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (3 MB) Get e-AlertsSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts

Acoustic wave‐equation traveltime and waveform inversion of crosshole seismic data

A hybrid wave‐equation traveltime and waveform inversion method is presented that reconstructs the interwell velocity distribution from crosshole seismic data. This inversion method, designated as WTW, retains the advantages of both full wave inversion and traveltime inversion; i.e., it is characterized by reasonably fast convergence which is somewhat independent of the initial model, and it can resolve detailed features of the velocity model. In principle, no traveltime picking is required and the computational cost of the WTW method is about the same as that for full wave inversion. We apply the WTW method to synthetic data and field crosshole data collected by Exxon at their Friendswood, Texas, test site. Results show that the WTW tomograms are much richer in structural information relative to the traveltime tomograms. Subtle structural features in the WTW Friendswood tomogram are resolved to a spatial resolution of about 1.5 m, yet are smeared or completely absent in the traveltime tomogram. This suggests that it might be better to obtain high quality (distinct reflections) crosshole data at intermediate frequencies, compared to intermediate quality data (good quality first arrivals, but the reflections are buried in noise) at high frequencies. Comparison of the reconstructed velocity profile with a log in the source well shows very good agreement within the 0–200 m interval. The 200–300 m interval shows acceptable agreement in the velocity fluctuations, but the tomogram’s velocity profile differs from the sonic log velocities by a DC shift. This highlights both the promise and the difficulty with the WTW method; it can reconstruct both the and high wavenumber parts of the model, but it can have difficulty recovering the very low wavenumber parts of the model.

OVERVIEWS: Airborne geophysics in Western Australia

Aeromagnetics became recognised as a valuable aid to exploration in Western Australia during the nickel boom of the 1960s. The now commonplace term aeromagnetics evolved during the 1980s, mainly to meet demands of a resurgent gold exploration industry which required a greater understanding of geological structure and rock type than was possible with conventional field mapping. High-resolution aeromagnetic surveys are typically flown at a line spacing of 200 m, a terrain clearance of 60 m and with a magnetometer sampling interval of 7 m. Imaging of the data provides a greater range of options for highlighting subtle structural features than conventional contours. Image maps may be interpreted using skills of photogeology and satellite-image interpretation and have been a major factor in bridging the communication gap between geophysicists and geologists. The effectiveness of radiometric data in Western Australia, collected simultaneously on virtually all high-resolution aeromagnetic surveys, has been constrained by lack of outcrop and transported soils. In appropriate areas the method is successful at mapping different types of felsic igneous, sedimentary and metasedimentary rocks, and also in identifying hydrothermal alteration zones displaying potassic enrichment. Problems of high surface conductivity have, in the past, limited the application of airborne time-domain electromagnetic surveys. The new generation of digital systems (e.g., QUESTEM) has improved depths of penetration through the real-time removal of unwanted noise. Airborne time-domain electromagnetics is no longer only an anomaly detector, but a three-dimensional regional conductivity mapping tool which, when integrated with magnetic data, enables the targeting of bedrock conductors to be controlled by interpreted geology.

Airborne Geophysics in Western Australia

Aeromagnetics became recognised as a valuable aid to exploration in Western Australia during the 'nickel boom' of the 1960s. The now commonplace term 'high-resolution aeromagnetics evolved during the 1980s, mainly to meet demands of a resurgent gold exploration industry which required a greater understanding of geological structure and rock type than was possible with conventional field mapping. High-resolution aeromagnetic surveys are typically flown at a line spacing of 200 m, a terrain clearance of 60 m and with a magnetometer sampling interval of 7 m. Imaging of the data provides a greater range of options for highlighting subtle structural features than conventional contours. Image maps may be interpreted using skills of photogeology and satellite-image interpretation and have been a major factor in bridging the communication gap between geophysicists and geologists. The effectiveness of radiometric data in Western Australia, collected simultaneously on virtually all high-resolution aeromagnetic surveys, has been constrained by lack of outcrop and transported soils. In appropriate areas the method is successful at mapping different types of felsic igneous, sedimentary and metasedimentary rocks, and also in identifying hydrothermal alteration zones displaying potassic enrichment. Problems of high surface conductivity have, in the past, limited the application of airborne time-domain electromagnetic surveys. The new generation of digital systems (e.g., QUESTEM) has improved depths of penetration through the real-time removal of unwanted noise. Airborne time-domain electromagnetics is no longer only an anomaly detector, but a three-dimensional regional conductivity mapping tool which, when integrated with magnetic data, enables the targeting of bedrock conductors to be controlled by interpreted geology.

Molecular dynamics studies on mutants of Cu, Zn superoxide dismutase: The functional role of charged residues in the electrostatic loop VII

Molecular dynamics (MD) calculations have been performed on mutants of superoxide dismutase (SOD) on some residues present in the electrostatic loop. These calculations have provided the solution structures for the mutants Thr-137-->Ile and Arg; Lys-136-->Ala; Glu-132-->Gln; Glu-133-->Gln; Glu-132, Glu-133-->Gln-132, Gln-133 and-->Gln-132, Lys-133. The structural and dynamic properties of these mutants have been correlated with the catalytic properties and available spectroscopic data. The water molecule present in the active site close to the copper ion in wild type (WT) SOD is missing in the MD average structure of the Thr-137-->Ile mutant, while this molecule is present in the MD average structures of all the other mutants and of WT SOD. This agrees with the experimental data. This is an important result that shows the validity of our calculations and their ability to reproduce even subtle structural features. Addition of one or more positive charges on the 132 and/or 133 positions does not sizably perturb the structure of the active site channel, while the introduction of a positively charged residue (Arg) on position 137 has a large effect on the structure of the electrostatic loop. Analysis of the MD average structures of these mutants has pointed out that the simple electrostatic effects of charged residues in the channel are not the only factor relevant for enzymatic behavior but that the structure of the electrostatic loop and the location of the charged residues also contribute to the catalytic properties of SOD.

Occurrence of a quasicrystalline phase in the Ti-Fe(Ni)-Si system

Extensive studies have been carried out regarding the possible occurrence of the icosahedral phase in the rapidly solidified Ti-Fe(Ni)-Si alloy system in a wide range of compositions. Transmission electron microscopy and x-ray-diffraction data reveal the formation of the icosahedral phase in ${\mathrm{Ti}}_{68}$${\mathrm{Fe}}_{26\mathrm{\ensuremath{-}}\mathit{x}}$${\mathrm{Ni}}_{\mathit{x}}$${\mathrm{Si}}_{6}$ where x\ensuremath{\le}9. In addition to the sharp diffraction spots conforming to the icosahedral point group, subtle structural features manifested by spot shifts, asymmetry in the spot shape, and diffuse intensity have been observed in electron-diffraction patterns. A particular composition has been found, ${\mathrm{Ti}}_{56}$${\mathrm{Fe}}_{5}$${\mathrm{Ni}}_{23}$${\mathrm{Si}}_{16}$, that exhibits a metastable fcc phase with lattice parameter close to 1.79 nm. We also report on structural transformations of the icosahedral and metastable crystalline phases originating as a result of annealing (icosahedral and metastable crystalline phases change to the equilibrium crystalline phase at 900 \ifmmode^\circ\else\textdegree\fi{}C).

Infrared and Raman Group Frequencies of Cyclic Imides

Infrared and Raman spectra of several examples of each of three classes of cyclic imides have been examined. Spectra-structure correlations have been sought for each of the classes, with particular emphasis being placed on the 1600–1800 cm−1 region. The spectra in this region are often complex, reflecting subtle structural features in the condensed phases. Group frequencies for substituted succinimides, phthalimides, and maleimides are proposed.

Attribute Extraction: An Important Application in Any Detailed 3-D Interpretation Study: ABSTRACT

Today, three-dimensional (3-D) seismic is playing an increasingly important role in appraisal and development planning. At first, 3-D datasets were aimed at analyzing the structural style and the mapping of complex fields; more recently, 3-D seismic has proved its value in defining details at reservoir level. Several examples of 3-D interpretations will demonstrate that pore content, reservoir facies, and very small faults can often be mapped confidently on 3-D seismic. The importance of the use of horizon attribute displays such as amplitude, dip, and azimuth in the detection of subtle structural and stratigraphic features will be illustrated.