ALBERT

Description: An extensive seismic database covering an area of 100,000 km 2 (38,610 mi 2 ) and 16 wells are integrated to define a sequence-stratigraphic framework for the Lower Cretaceous succession in the southwestern Barents Sea. Seven sequences (S0–S6) are defined, and the geometry, trajectory, and lateral variability of decompacted seismic clinoforms are described to elucidate the depositional history of the basin and to better understand coarse-grained sediment transport from the shelf to basin. Three different clinoform scales are recognized: (1) clinoform sets with 35–60 m (115–197 ft) height, interpreted as deltaic or shoreline clinoforms; (2) clinoform sets with 60–110 m (197–361 ft) height, interpreted as sediments prograding on a continental shelf; and (3) clinoforms with greater than 150 m (〉492 ft) height, which represent shelf-margin clinoforms. Furthermore, clinoforms are grouped into two main progradation directions: (1) clinoforms prograded to the southeast in sequences 2–3, in the Fingerdjupet Subbasin and the western Bjarmeland platform, indicating a source of sediments located in the west-northwestern Barents Sea, and (2) clinoforms prograded to the southwest in sequences 1–6, in the eastern part of the Bjarmeland platform, Nordkapp Basin, and Finnmark platform, indicating a second source of sediments located in the east-northeast. Additionally, in the Hammerfest Basin, clinoforms prograded to the southeast off the Loppa high in sequences 5–6. Low-relief (35–60 m [115–197 ft]), high-gradient, and oblique clinoforms are observed within sequence 2 in the western Bjarmeland platform. The high-gradient foresets are interpreted as potential coarse-grained deposits or as a result of clinoforms prograding to progressive deeper waters, resulting in steeper foresets. Clinoforms located in the eastern part of the study area are interpreted as sourced by a mud-rich system, reflecting a long transportation distance. However, thin, heterolithic patterns in the gamma-ray log possibly reflect thin, sheetlike sands. The height of the clinoforms seems to be a factor controlling the sediment bypass to deep water in the study area. When the height is more than 200 m (656 ft), bottomset deposits are common. This study contributes to a better understanding of the paleogeography and the evolution of the frontier southwestern Barents Sea during the Early Cretaceous and to comprehending the variables increasing the bypass of coarse-grained sediments to deep-water settings.

Description: Variations in environmental and biological origins contributing to the heterogeneity of lacustrine source rocks can be illustrated in their diverse genetic facies. The Zhu 1 depression, eastern Pearl River Mouth Basin, South China Sea, is characterized by two thick, Paleogene, organic-rich synrift units, the Wenchang and Enping Formations. The integration of bulk geochemical and biomarker data with tectonic and sedimentary information provides the basis for a comprehensive assessment of the environmental and ecological changes through geologic time and their impact on the heterogeneity of these lacustrine source rocks. Both the Wenchang and Enping Formations display wide variations in total organic carbon content and hydrogen index values as well as biomarker composition, suggesting lateral and chronological changes in organic facies. Using gas chromatography–mass spectrometry and hierarchical cluster analysis, five genetic facies were identified within these two source horizons. These facies represent different organic-matter inputs and sedimentary and early diagenetic environments based on their distinctly different assemblages of 11 source-dependent biomarker ratios. Four facies were distinguished in the Wenchang Formation, and two facies were distinguished in the Enping Formation, with one being common to both formations. During the middle Eocene, the Wenchang Formation was deposited in a series of small, deep lakes of laterally variable salinity, acidity, and biofacies. During the deposition of the Enping Formation in the late Eocene and early Oligocene, the previous lakes merged into fewer lakes with shallower depth and larger areal coverage, with the biota becoming more uniform across the whole depression. The coevolution of these lacustrine settings and their biota is closely associated with the development of the Zhu 1 depression, within which multiple separate sags produced by rapid mid-Eocene subsidence finally merged into a single depositional unit during slow subsidence in the late Eocene and early Oligocene. Accordingly, an integrated model was established to provide an overview of the contrasting origins of lacustrine source rocks during the two Paleogene epochs. This model may have important implications for source-rock prediction in the undrilled parts of the basins or for reference to source-rock heterogeneity in other rift basins.

Description: Three-dimensional (3-D) printing provides an opportunity to build lab-testable models of reservoir rocks from tomographic data. This study combines tomography and 3-D printing to reproduce a sample of the Fontainebleau sandstone at different magnifications to test how this workflow can help characterization of transport properties at multiple scales. For this sandstone, literature analysis has given a porosity of 11%, permeability of 455 md, mean pore throat radius of 15 μm, and a mean grain size of 250 μm. Digital rock analysis of tomographic data from the same sample yielded a porosity of 13%, a permeability of 251 md, and a mean pore throat radius of 15.2 μm. The 3-D printer available for this study was not able to reproduce the sample’s pore system at its original scale. Instead, models were 3-D printed at 5-fold, 10-fold, and 15-fold magnifications. Mercury porosimetry performed on these 3-D models revealed differences in porosity (28%–37%) compared to the literature (11%) and to digital calculations (12.7%). Mercury may have intruded the smallest matrix pores of the printing powder and led to a greater than 50% increase in measured porosity. However, the 3-D printed models’ pore throat size distribution (15 μm) and permeability (350–443 md) match both literature data and digital rock analysis. The powder-based 3-D printing method was only able to replicate parts of the pore system (permeability and pore throats) but not the pore bodies. Other 3-D printing methods, such as resin-based stereolithography and photopolymerization, may have the potential to reproduce reservoir rock porosity more accurately.

Description: The Upper Ordovician Red River Formation has been a prolific producer of oil and gas in the Williston Basin, where it has cumulatively produced more than 750 million bbl of oil equivalent over the past half century. Previous studies have recognized petroleum source beds, referred to as kukersites, in the Red River Formation but have not determined their complete extent or hydrocarbon generation significance. Examination and analysis of 28 cores and greater than 300 wireline logs have revealed 10 distinct kukersites in the Red River D zone that can be correlated individually for tens to hundreds of miles (tens to hundreds of kilometers) across the western quarter of North Dakota. Although each Red River kukersite is typically thin (1–2 ft [0.3–0.7 m] thick), they combine to reach net thicknesses of greater than 12 ft (3.7 m) with average present day total organic carbon (TOC) values of typically 3–6 wt. %. Hydrogen index (HI) values from kukersite samples range from primarily greater than 800 mg hydrocarbons (HC)/g TOC within the northern flank of the basin to systematically decreasing to less than 100 mg HC/g TOC within the basin center. This systematic decrease in HI is interpreted to be a function of increased thermal maturity, where hydrocarbon generation has depleted kukersite organic richness. Preliminary calculations of hydrocarbon volumes generated from Red River kukersites, based on a previously developed method that calculates the volumetric decrease in original to present-day kerogen content, total approximately 66 billion bbl (1.05 x 10 10 m 3 ) of oil equivalent. This approximate generation total is more than enough to account for cumulative Red River production and supports the idea that the Red River is a self-sourced petroleum system with potentially significant remaining exploration potential.

Description: Event-based risk management (EBRM) is an improved way of describing subsurface uncertainties and their possible business impacts in a manner that facilitates specific actions to improve business performance. In EBRM, uncertainties are viewed as potential causes of risk events that could in turn lead to consequences that affect the attainment of objectives. This "causes–event–consequences" syntax aids the design of prevention measures to inhibit the causes turning into the event and mitigation measures to reduce the potential consequences should the risk event occur, and it also facilitates construction of a risk taxonomy scheme based on risk consequences, events, and causes. Using a data set of 1456 subsurface risks, each risk was described in this manner and placed in the taxonomy, and the proportion of risks in each taxonomic group was analyzed. This revealed clear trends in the relative frequency of risk groups with type of field: for example, risks related to hydrocarbon-in-place volumes are more frequently identified in deep-water oil fields and gas fields feeding liquefied natural gas plants, situations in which resource volumes are critical to support the large project capital costs. Trends were also evident with field maturity: for example, risks related to hydrocarbon-in-place volumes are more frequently identified before the field sanction decision than afterward. Several benefits have yielded from EBRM: the risk description syntax encourages the creation of meaningful risk-management actions, the taxonomy and associated risk identification frequencies assist the identification of relevant risks so that key risk areas are not overlooked and also help to anticipate future risks, and the focus on risks (rather than uncertainties) helps to focus resources (data acquisition, technical studies) onto those aspects of the subsurface that are likely to impact business outcomes.

Description: A comprehensive study of seep carbonates at the top of the organic-rich Maastrichtian to Danian Moreno Formation in the Panoche Hills (California) reveals the mechanisms of generation, expulsion, and migration of biogenic methane that fed the seeps. Two selected outcrops show that seep carbonates developed at the tip of sand dykes intrude up into the Moreno Formation from deeper sandbodies. Precipitation of methane-derived cements occurred in a succession of up to 10 repeated elementary sequences, each starting with a corrosion surface followed by dendritic carbonates, botryoidal aragonite, aragonite fans, and finally laminated micrite. Each element of the sequence reflects three stages. First, a sudden methane pulse extended up into the oxic zone of the sediments, leading to aerobic oxidation of methane and carbonate dissolution. Second, after consumption of the oxygen, anaerobic oxidation of methane coupled with sulfate reduction triggered carbonate precipitation. Third, progressive diminishment of the methane seepage led to the deepening of the reaction front in the sediment and the lowering of precipitation rates. Carbonate isotopes, with 13 C as low as –51 Peedee belemnite, indicate a biogenic origin for the methane, whereas a one-dimensional basin model suggests that the Moreno Formation was in optimal thermal conditions for bacterial methane generation at the time of seep carbonate precipitation. Methane pulses are interpreted to reflect drainage by successive episodes of sand injection into the gas-generating shale of the Moreno Formation. The seep carbonates of the Panoche Hills can thus be viewed as a record of methane production from a biogenic source rock by multiphase hydraulic fracturing.

Description: Production decline prediction is important to understand the performance and life span of oil and gas wells. The most common prediction method is decline curve fitting based on available production rate data. Such data are fit with different equations that extrapolate to future time. However, the parameters are commonly poorly constrained, especially when the production rate data are limited. In this study, we establish a novel gas isotope interpretation tool to better predict the resource quantity and life span of producing gas wells. This tool is based on the evolution of methane carbon isotope ratios ( 13 C1) caused by different gas-releasing processes during production. It requires (1) real-time methane carbon isotope ratio data, (2) continuous gas production rate data for a certain period of time, and (3) basic geological and engineering conditions. We successfully applied the production decline prediction tool to a producing shale gas well in the Barnett Shale. We obtained real-time 13 C1 data for approximately 1 yr using our proprietary, field-deployable gas chromatography–infrared isotope ratio analyzer. The prediction in this well from the isotope method showed a total reserve of up to 7.34–7.75 BCF (2.07–2.19 x 10 8 m 3 ), which was used to constrain the production decline trend of the study well. The measured production rate data were first fit using the Arps equation, which then joined to an exponential decline curve smoothly at approximately 10 yr, such that the cumulative production calculation from integration of the product rate curve equaled to the total reserve predicted by the isotope method. The novel production decline prediction method thus provided important constraint on the future well production and expected ultimate recoverable reserves.

Description: Glycine is the simplest and most polymorphic amino acid, with five phases having been structurally characterized at atmospheric or high pressure. A sixth form, the elusive ζ phase, was discovered over a decade ago as a short-lived intermediate which formed as the high-pressure ∊ phase transformed to the γ form on decompression. However, its structure has remained unsolved. We now report the structure of the ζ phase, which was trapped at 100 K enabling neutron powder diffraction data to be obtained. The structure was solved using the results of a crystal structure prediction procedure based on fully ab initio energy calculations combined with a genetic algorithm for searching phase space. We show that the fate of ζ-glycine depends on its thermal history: although at room temperature it transforms back to the γ phase, warming the sample from 100 K to room temperature yielded β-glycine, the least stable of the known ambient-pressure polymorphs.

Description: Single-particle cryogenic electron microscopy (cryo-EM) can now yield near-atomic resolution structures of biological complexes. However, the reference-based alignment algorithms commonly used in cryo-EM suffer from reference bias, limiting their applicability (also known as the `Einstein from random noise' problem). Low-dose cryo-EM therefore requires robust and objective approaches to reveal the structural information contained in the extremely noisy data, especially when dealing with small structures. A reference-free pipeline is presented for obtaining near-atomic resolution three-dimensional reconstructions from heterogeneous (`four-dimensional') cryo-EM data sets. The methodologies integrated in this pipeline include a posteriori camera correction, movie-based full-data-set contrast transfer function determination, movie-alignment algorithms, (Fourier-space) multivariate statistical data compression and unsupervised classification, `random-startup' three-dimensional reconstructions, four-dimensional structural refinements and Fourier shell correlation criteria for evaluating anisotropic resolution. The procedures exclusively use information emerging from the data set itself, without external `starting models'. Euler-angle assignments are performed by angular reconstitution rather than by the inherently slower projection-matching approaches. The comprehensive `ABC-4D' pipeline is based on the two-dimensional reference-free `alignment by classification' (ABC) approach, where similar images in similar orientations are grouped by unsupervised classification. Some fundamental differences between X-ray crystallography versus single-particle cryo-EM data collection and data processing are discussed. The structure of the giant haemoglobin from Lumbricus terrestris at a global resolution of ∼3.8 Å is presented as an example of the use of the ABC-4D procedure.

Description: The mechanical and magnetic properties of Ni–Mn–Sb intermetallic compounds are closely related to the martensitic transformation and martensite variant organization. However, studies of these issues are very limited. Thus, a thorough crystallographic investigation of the martensitic transformation orientation relationship (OR), the transformation deformation and their impact on the variant organization of an Ni50Mn38Sb12 alloy using scanning electron microscopy/electron backscatter diffraction (SEM/EBSD) was conducted in this work. It is shown that the martensite variants are hierarchically organized into plates, each possessing four distinct twin-related variants, and the plates into plate colonies, each containing four distinct plates delimited by compatible and incompatible plate interfaces. Such a characteristic organization is produced by the martensitic transformation. It is revealed that the transformation obeys the Pitsch relation ({0{\overline 1}{\overline 1}}A // {2{\overline 2}{\overline 1}}M and 〈0{\overline 1}1〉A // 〈{\overline 1}{\overline 2}2〉M; the subscripts A and M refer to austenite and martensite, respectively). The type I twinning plane K1 of the intra-plate variants and the compatible plate interface plane correspond to the respective orientation relationship planes {0{\overline 1}{\overline 1}}A and {0{\overline 1}{\overline 1}}A of austenite. The three {0{\overline 1}{\overline 1}}A planes possessed by each pair of compatible plates, one corresponding to the compatible plate interface and the other two to the variants in the two plates, are interrelated by 60° and belong to a single 〈11{\overline 1}〉A axis zone. The {0{\overline 1}{\overline 1}}A planes representing the two pairs of compatible plates in each plate colony belong to two 〈11{\overline 1}〉A axis zones having one {0{\overline 1}{\overline 1}}A plane in common. This common plane defines the compatible plate interfaces of the two pairs of plates. The transformation strains to form the variants in the compatible plates are compatible and demonstrate an edge-to-edge character. Thus, such plates should nucleate and grow simultaneously. On the other hand, the strains to form the variants in the incompatible plates are incompatible, so they nucleate and grow separately until they meet during the transformation. The results of the present work provide comprehensive information on the martensitic transformation of Ni–Mn–Sb intermetallic compounds and its impact on martensite variant organization.

Description: Based on first-principles calculations, the relationship between molecular packing and charge-transport parameters has been investigated and analysed in detail. It is found that the crystal packing forces in the flexible organic molecule 4-(1,2,2-triphenylvinyl)aniline salicylaldehyde hydrazone (A) can apparently overcome the dynamic intramolecular rotations and the intramolecular steric repulsion, effectively enhancing the molecular rigidity and decreasing the internal reorganization energy. The conducting properties of A have also been simulated within the framework of hopping models, and the calculation results show that the intrinsic electron mobility in A is much higher than the corresponding intrinsic hole mobility. These theoretical investigations provide guidance for the efficient and targeted control of the molecular packing and charge-transport properties of organic small-molecule semiconductors and conjugated polymeric materials.

Description: Opening-mode veins in cores drilled from the mudrocks overlying and underlying the major Silurian salt décollement in the Appalachian plateau (Tioga and Lawrence Counties, Pennsylvania) have mineralogic and isotopic compositions generally matching those of their host mudrocks, suggesting opening and filling amid little cross-stratal fluid motion. Calcite and most trace minerals probably entered the veins via dissolution–reprecipitation from nearby host rock. Consistent with this interpretation are the observations that (1) trace minerals within the veins, including quartz, pyrite, and dolomite, are invariably also present within the layers hosting the veins, with vein cement minerals generally reflecting the abundance and solubility of minerals in the host rock, and (2) carbon and oxygen isotopic compositions of vein-filling calcite are similar to those of calcite within the host rock, with vein-filling 18 O slightly depleted and 13 C slightly enriched. Modeling the fluid isotopic evolution, assuming vein opening and filling amid immobile connate formation water, accounts for these minor but systematic differences, which are attributable to increasing temperature and hydrocarbon maturation. An exception to the above trend is barite, which, despite its low solubility, is systematically enriched in veins with respect to the host rock. It is unclear whether barite precipitation resulted from the influx of external fluids—perhaps deriving from Silurian salt—or from barium mobilized at depth from local clays or organic material.

Description: Water salinity in the San Joaquin Valley is a function of depth, location, and stratigraphy. This paper presents a reconnaissance study of water salinity within Kern County, California, using chemical analyses from oil field produced water and water wells as well as geophysical logs. Log analysis indicates that the base of underground sources of drinking water (USDWs) (〈10,000 mg/L) slopes from northwest to southeast. Lab analyses show that USDWs extend to depths as great as 1900 m (6233.5 ft) southeast of Bakersfield. This area receives the greatest amount of fresh water recharge from streams flowing westward from the Sierras. The marine Olcese Sand is more saline than the overlying and underlying aquifers and separates the aquifers into an upper and lower USDW. Log analysis also indicates a zone of higher salinity separating zones of lower salinity in this area. Salinities in the west are higher, and depths to base USDW are variable. Although waters in many sands in the western valley are more saline than 3000 ppm total dissolved solids (TDS), numerous wells contain waters between 3000 and 10,000 ppm at depths of less than 600 m (1968.5 ft), particularly in the nonmarine Tulare Formation. At North Belridge field, a salinity reversal is apparent below 2100 m (6890 ft). Waters above this depth are approximately 40,000 mg/L TDS, whereas water salinities below 2200 m (7218 ft) range from 10,000 to 32,000 mg/L. Extremely high salinities are found in several wells less than 30 m (98 ft) deep, primarily in the northwestern area. These may be perched aquifers or lie adjacent to unmapped agricultural drainage sumps and do not reflect salinities in the regional aquifer.

Description: To assess prospective modeling trends for oolitic tidal sand shoals and explore potential patterns of reservoir heterogeneity, this study examines, quantifies, and models the cycle-scale architecture of the Holocene mobile oolitic tidal sand shoal complex at Schooner Cays, Bahamas. Process-based stratigraphic trends are captured in quantitative, geocellular models of the shoal from analyses of satellite imagery; two-dimensional, high-frequency seismic (chirp) data; and sediment cores. Data show that longitudinal tidal sand ridges extend up to 8 km (5 mi) along depositional dip, gradually transforming bankward into channel-bound, compound barforms consisting of linear, parabolic, and shoulder bars. These bars terminate into a laterally extensive (10 km [6 mi]), strike-elongate sand sheet. Each bar type includes distinct internal architecture, grain size, and sorting related to feedbacks among hydrodynamics, geomorphology, and sedimentology. Building on these data and concepts from the Holocene accumulations, this study demonstrates a methodology for quantifying and validating probabilistic stratigraphic trends prior to their inclusion in stochastic-based facies modeling algorithms. Inclusion of statistically robust facies probability volumes during truncated Gaussian simulation generated ordered and geologically accurate facies distributions relative to bar-crest centerlines, water depth, and geomorphic position. Petrophysical models that incorporate facies-specific porosity, permeability, and water saturation functions display pronounced cycle-scale heterogeneity that could provide insights into variable production rates and poor sweep efficiency commonly encountered during development of analogous oolitic reservoirs.

Description: Organic-rich and carbonate-rich Eagle Ford Shale is a self-sourced oil and gas reservoir with little alteration of gas chemistry as might be affected by petroleum expulsion and migration. As such it provides an ideal natural laboratory to quantify the compositional variation of gases generated from oil-prone type II kerogen during thermal maturation. The chemical composition of the gas released from rock crushing was conducted and integrated with Rock-Eval pyrolysis to define the empirical relationship between gas compositional parameters and thermal maturity in this study. From 10 wells in the Eagle Ford Shale in south Texas, we collected 74 core samples having a range of thermal maturity (the measured maximum temperature [ T max ] values of hydrocarbons generated in Rock-Eval pyrolysis range from 427°C to 494°C [800°F to 921°F], and the calculated equivalent vitrinite reflectance ( R oe ) values range from 0.51% to 1.73% based on T max values). Total organic carbon content ranges from 0.3% to 8.53%, with an average of 3.12% (standard deviation of 1.77%). Burial depth is from 2989.6 to 13,827.3 ft (911.2 to 4214.6 m). Our results showed that gas composition in the Eagle Ford Shale is mainly controlled by thermal maturity, and three stages of gas generation are identified based on the C 1 and C 2 concentrations of the gases released by rock crushing from Eagle Ford Shale core samples. The three stages of gas generation correspond to the following processes of organic matter conversion: (1) kerogen and bitumen thermal cracking to crude oil, (2) bitumen and heavy crude oil thermal cracking to light oil, and (3) light oil cracking to gas. Methane-rich gas and an abundance of branched butane and pentane are generated in light oil cracking to gas, resulting in high C 1 /C 2 , C 1 /(C 2 + C 3 ), i-C 4 /n-C 4 , and i-C 5 /n-C 5 ratios. Increased cracking of normal alkanes such as n-butane and n-pentane occurs in the light oil cracking to gas. Empirical equations between gas compositional parameters and thermal maturity ( T max or R oe ) are obtained for oil-prone type II. The C 1 , C 2 , C 1 /C 2 , C 1 /C 2 + C 3 , and i - C 4 /n - C 4 ratios are the five best parameters for determining thermal maturity with an exponentially derived R 2 value of 0.74. The composition of gas produced from the Eagle Ford Shale following hydraulic fracturing is used to validate the empirical equations. Calculated thermal regime for the oil production based on the produced gas is located at the peak of oil generation and the beginning of light oil cracking to gas, corresponding to T max from 454°C to 464°C (849°F to 867°F) or at an R oe ranging from 1.01% to 1.19%. Empirical equations provide a basis for interpretation of mud gas logging data and produced gas composition.

Description: Energy materials form the central part of energy devices. An essential part of their function is the ability to reversibly host charge or energy carriers, and analysis of their phase composition and structure in real time under non-equilibrium conditions is mandatory for a full understanding of their atomic-scale functional mechanism. Real-time powder diffraction is increasingly being applied for this purpose, forming a critical step in the strategic chemical engineering of materials with improved behaviour. This topical review gives examples of real-time analysis using powder diffraction of rechargeable battery electrodes and porous sorbent materials used for the separation and storage of energy-relevant gases to demonstrate advances in the insights which can be gained into their atomic-scale function.

Description: Single-particle imaging with X-ray free-electron lasers (XFELs) has the potential to provide structural information at atomic resolution for non-crystalline biomolecules. This potential exists because ultra-short intense pulses can produce interpretable diffraction data notwithstanding radiation damage. This paper explores the impact of pulse duration on the interpretability of diffraction data using comprehensive and realistic simulations of an imaging experiment at the European X-ray Free-Electron Laser. It is found that the optimal pulse duration for molecules with a few thousand atoms at 5 keV lies between 3 and 9 fs.

Description: In this paper, a new approach to calculating and restoring the effects of physical compaction in subsalt units is presented. The loading of subsalt units and associated physical compaction is controlled by a combination of suprasalt sedimentation and salt movements. Here it is proposed that the change in load affecting the subsalt units is equivalent to the thickness between paleosurfaces of the basin (regional levels) reconstructed for successive stratigraphic horizons. This is in contrast to suprasalt units, where the changes in load are equivalent to the thickness of the stratigraphic unit. The new approach is integrated into a complete workflow for sequential restoration in a salt basin, which involves (1) removing the effects of physical compaction in suprasalt units, (2) reconstructing the paleosurfaces of the basin (regional level), (3) restoring faults, (4) unfolding to the reconstructed regional level to restore the effects of salt movement in the suprasalt units, (5) reconstructing the change in load affecting subsalt units and restoring the associated physical compaction, and (6) restoring any isostasy and postrift thermal subsidence. Results obtained using this workflow are compared with other methodologies to assess the differences in subsalt sediment thickness and structural configurations. These results suggest that the workflow proposed in this paper will improve the accuracy of sequential restoration of subsalt hydrocarbon plays, allowing their structural configurations through time to be more accurately quantified, and will ultimately reduce the risks in developing subsalt resources.

Description: The Upper Jurassic Norphlet Formation is an eolian sandstone and important hydrocarbon reservoir that overlies the Louann Salt in the Gulf of Mexico (GOM). Because the sand was concentrated into dunes formed by Late Jurassic winds, determining the source areas and paleotransport direction of the sand can improve predictions of the distribution of the dune facies around the GOM. Paleo–wind-blown sediment transport into the proto-GOM was controlled by wind direction and magnitude and the extant topography of the basin and adjacent uplands. Analysis of the Norphlet Formation in the eastern GOM shows that wadis and alluvial fans controlled by the location of highs were the primary route for introducing sediment of varied provenance into the eolian erg. Eolian transport directions interpreted from dip-log analyses are south directed in southern Alabama and west to northwest directed in western Florida. Interpretations of regional, two-dimensional, prestack-depth-migrated seismic data show that erosional incision of the Middle Ground arch occurred prior to and during the time of Norphlet deposition; this as well as preexisting lows in the basement topography may have facilitated basinward sand transport of sediment that fed the Norphlet Formation erg preserved in the deep-water subsurface eastern GOM.

Description: A total of 225 rock samples and 37 oil samples from the Beibuwan Basin, South China Sea, were analyzed with geochemical and organic petrological techniques to evaluate the Eocene lacustrine source rocks and investigate controls on their properties and the distribution of different oil families in the basin. Two types of organic facies are recognized in the Liushagang Formation (LS). The first organic facies is algal-dominated and mainly occurs in the organic-rich, laminated mudstones of the middle member of the LS (LS-2) that were deposited in an anoxic, stratified, medium–deep lake environment. It is geochemically identified by its high abundance of C 30 4-methylsteranes and heavy 13 C values in the range of –22.4 to –27.5. The organic matter in this organic facies comprises type I and II 1 kerogens, with its macerals dominated by fluorescent amorphous organic matter (AOM) and exinites, indicating a highly oil-prone character. The second organic facies is of terrestrial algal origin and is mainly identified in the nonlaminated mudstones of the upper (LS-1) and lower (LS-3) members of the LS that were deposited in shallow, dysoxic, weakly stratified, freshwater environments. Source rocks of the second organic facies mainly contain type II 1 –II 2 kerogens with mixed macerals of AOM, internites, and vitrinites. It is geochemically differentiated from the algal-dominated organic facies by its relatively low abundance of C 30 4-methylsteranes and lighter 13 C values in the range of –27.20 to –28.67. Three oil groups are identified by their biomarkers and stable carbon isotopes. The first two groups (A and B) are probably end-members of two major oil families (A and B) that correspond to the algal-dominated organic facies and algal–terrestrial organic facies, respectively. Most of the discovered oils belong to group A oils that are characterized by a high abundance of C 30 4-methylsteranes and heavy 13 C values and show a good correlation with the algal-dominated organic facies in LS-2. Group B oils are found only within the LS-1 and LS-3 reservoirs, and they are recognized by their relatively low content of C 30 4-methylsteranes and lighter 13 C values, showing a close relation to the algal–terrestrial source facies within the LS-1 and LS-3 members, respectively. Group C oils display intermediate biomarker features and stable carbon isotope values and are interpreted to be a mixture of group A and B oils. The oil–source correlation reveals a strong control of organic facies on the geographic distribution of oil groups or oil fields in the basin.

Description: Due to their high technological and geological relevance, silicates are one of the most studied classes of inorganic compounds. Under ambient conditions, the silicon in silicates is almost exclusively coordinated by four oxygen atoms, while high-pressure treatment normally results in an increase in the coordination from four- to sixfold. Reported here is a high-pressure single-crystal X-ray diffraction study of danburite, CaB2Si2O8, the first compound showing a step-wise transition of Si coordination from tetrahedral to octahedral through a trigonal bipyramid. Along the compression, the Si2O7 groups of danburite first transform into chains of vertice-sharing SiO5 trigonal bipyramids (danburite-II) and later into chains of edge-sharing SiO6 octahedra (danburite-III). It is suggested that the unusual formation of an SiO5 configuration is a consequence of filling up the pentacoordinated voids in the distorted hexagonal close packing of danburite-II.

Description: Two-dimensional seismic refraction tomography was used to map the bedrock topography beneath Hallsands beach in southwest Devon, United Kingdom. Seismic refraction data were acquired from 11 spreads, 4 parallel to the beach and 7 normal to the beach, with either 12 or 24 geophones at 5-m (16-ft) spacing. Eight sediment cores were used to calibrate the velocity model. The bedrock consists of metasedimentary rocks that have a seismic velocity of 2100–2500 m/s (6900–8200 ft/s) and is overlain by variable amounts of gravel, peat, and muddy peat. Wood peat and peaty mud are differentiated within the peat as 700-m/s (2300-ft/s) velocity for wood peat and 1200-m/s (4000-ft/s) velocity for peaty mud. These refraction data were collected and processed in two dimensions, then imported into Petrel, a three-dimensional (3-D) geological modeling software package. The 3-D geologic model was built using the velocity attribute of the seismic refraction data. These selected data points were used to create 3-D horizons, surfaces, and contacts constraining the target bedrock surface from the overlying unconsolidated deposits. The bedrock surface beneath Hallsands beach is marked by two paleochannels. One paleochannel occurs in the north end of the beach beneath the axis of the modern valley. A second paleochannel occurs in the southern section of Hallsands beach centered along the axis of a tributary valley. Bedrock occurs at a depth of approximately –10 m (–33 ft) in the southern and northern sections of the main valley. Bedrock occurs at a depth of approximately –2 m (–6 ft) along the valley wall at the southern end of the beach east of the parking lot. Shore-perpendicular refraction lines differentiate layers within the peat, whereas shore-parallel lines delineate wood-peat, peaty-mud, and bedrock topography.

Description: Drilling for oil/gas and trawling on a continental shelf can cause damage to hard-bottom communities. Moving these activities offshore poses a threat to offshore communities. Habitat complexity is correlated with species diversity. The relationship of bottom relief to benthic species richness is not well understood in deeper communities. Relief may act as a proxy for species richness and disturbance risk. Geographic patterns in relief and richness are also not well understood. We gathered information on bottom relief and species richness of the sessile epibenthic community using a remotely operated vehicle. We surveyed hard bottom on the flanks of 13 banks in the north–central Gulf of Mexico, greater than 27-m (89-ft) depth, on the shelf and at the shelf edge. We found a positive asymptotic relationship between mean relief and species richness at the transect level. Secondary analyses at the drop site level revealed a similar relationship; variance was higher. The relationship was positively linear at the bank level. Analyses using standard deviation of relief yielded even stronger positive results. There was no significant relationship between species richness and latitude or longitude over the study area (215 km [133 mi]). When species richness was plotted in three dimensions, however, peaks in richness emerged in the southeastern study area and the western region, with a trough between them, coinciding with bottom relief. Species richness is positively correlated with bottom relief on banks in the northern Gulf of Mexico. Relief and species richness may be predicted at many spatial scales, up to hundreds of kilometers.

Description: Peptidoglycan is a giant molecule that forms the cell wall that surrounds bacterial cells. It is composed of alternating N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) residues connected by β-(1,4)-glycosidic bonds and cross-linked with short polypeptide chains. Owing to the increasing antibiotic resistance against drugs targeting peptidoglycan synthesis, studies of enzymes involved in the degradation of peptidoglycan, such as N-acetylglucosaminidases, may expose new, valuable drug targets. The scientific challenge addressed here is how lysozymes, muramidases which are likely to be the most studied enzymes ever, and bacterial N-acetylglucosaminidases discriminate between two glycosidic bonds that are different in sequence yet chemically equivalent in the same NAG-NAM polymers. In spite of more than fifty years of structural studies of lysozyme, it is still not known how the enzyme selects the bond to be cleaved. Using macromolecular crystallography, chemical synthesis and molecular modelling, this study explains how these two groups of enzymes based on an equivalent structural core exhibit a difference in selectivity. The crystal structures of Staphylococcus aureus N-acetylglucosaminidase autolysin E (AtlE) alone and in complex with fragments of peptidoglycan revealed that N-acetylglucosaminidases and muramidases approach the substrate at alternate glycosidic bond positions from opposite sides. The recognition pocket for NAM residues in the active site of N-acetylglucosaminidases may make them a suitable drug target.

Description: The crystal structure uniquely imparts the specific properties of a material, and thus provides the starting point for any quantitative understanding of thermoelectric properties. Cu2−xSe is an intensely studied high performing, non-toxic and cheap thermoelectric material, and here for the first time, the average structure of β-Cu2−xSe is reported based on analysis of multi-temperature single-crystal X-ray diffraction data. It consists of Se–Cu layers with additional copper between every alternate layer. The structural changes during the peculiar zT enhancing phase transition mainly consist of changes in the inter-layer distance coupled with subtle Cu migration. Just prior to the transition the structure exhibits strong negative thermal expansion due to the reordering of Cu atoms, when approached from low temperatures. The phase transition is fully reversible and group–subgroup symmetry relations are derived that relate the low-temperature β-phase to the high-temperature α-phase. Weak superstructure reflections are observed and a possible Cu ordering is proposed. The structural rearrangement may have a significant impact on the band structure and the Cu rearrangement may also be linked to an entropy increase. Both factors potentially contribute to the extraordinary zT enhancement across the phase transition.

Description: There has been significant recent interest in differentiating multicomponent solid forms, such as salts and cocrystals, and, where appropriate, in determining the position of the proton in the X—H...A—Y X−...H—A+—Y continuum in these systems, owing to the direct relationship of this property to the clinical, regulatory and legal requirements for an active pharmaceutical ingredient (API). In the present study, solid forms of simple cocrystals/salts were investigated by high-field (700 MHz) solid-state NMR (ssNMR) using samples with naturally abundant 15N nuclei. Four model compounds in a series of prototypical salt/cocrystal/continuum systems exhibiting {PyN...H—O—}/{PyN+—H...O−} hydrogen bonds (Py is pyridine) were selected and prepared. The crystal structures were determined at both low and room temperature using X-ray diffraction. The H-atom positions were determined by measuring the 15N—1H distances through 15N-1H dipolar interactions using two-dimensional inversely proton-detected cross polarization with variable contact-time (invCP-VC) 1H→15N→1H experiments at ultrafast (νR ≥ 60–70 kHz) magic angle spinning (MAS) frequency. It is observed that this method is sensitive enough to determine the proton position even in a continuum where an ambiguity of terminology for the solid form often arises. This work, while carried out on simple systems, has implications in the pharmaceutical industry where the salt/cocrystal/continuum condition of APIs is considered seriously.

Description: The conceptual relationship between crystal reactivity, stability and metastability, solubility and morphology on the one hand and shape, charge distribution, chirality and distribution of functional groups over the molecular surfaces on the other hand is discussed, via a number of examples coming from three decades of research in the field of crystal engineering at the University of Bologna. The bottom-up preparation of mixed crystals, co-crystals and photoreactive materials starting from molecular building blocks across the borders of organic, organometallic and metalorganic chemistry is recounted.

Description: A deep machine-learning technique based on a convolutional neural network (CNN) is introduced. It has been used for the classification of powder X-ray diffraction (XRD) patterns in terms of crystal system, extinction group and space group. About 150 000 powder XRD patterns were collected and used as input for the CNN with no handcrafted engineering involved, and thereby an appropriate CNN architecture was obtained that allowed determination of the crystal system, extinction group and space group. In sharp contrast with the traditional use of powder XRD pattern analysis, the CNN never treats powder XRD patterns as a deconvoluted and discrete peak position or as intensity data, but instead the XRD patterns are regarded as nothing but a pattern similar to a picture. The CNN interprets features that humans cannot recognize in a powder XRD pattern. As a result, accuracy levels of 81.14, 83.83 and 94.99% were achieved for the space-group, extinction-group and crystal-system classifications, respectively. The well trained CNN was then used for symmetry identification of unknown novel inorganic compounds.

Description: Petroleum is retained in shales either in a sorbed state or in a free form within pores and fractures. In shales with oil resource potential, organic matter properties (i.e., richness, quality, and thermal maturity) control oil retention in general. In gas shales, organic pores govern gas occurrence. Although some pores may originate via secondary cracking reactions, it is still largely unclear as to how these pores originate. Here we present case histories mainly for two classic shales, the Mississippian Barnett Shale (Texas) and the Toarcian Posidonia Shale (Lower Saxony, Germany). In both cases, shale intervals enriched in free oil or bitumen are not necessarily associated with the layers richest in organic matter but are instead associated with porous biogenic matrices. However, for the vast bulk of the shale, hydrocarbon retention and porosity evolution are strongly related to changes in kerogen density brought about by swelling and shrinkage as a function of thermal maturation. Secondary organic pores can form only after the maximum kerogen retention (swelling) ability is exceeded at T max (the temperature at maximum rate of petroleum generation by Rock-Eval pyrolysis) around 445°C (833°F), approximately 0.8% vitrinite reflectance. Shrinkage of kerogen itself leads to the formation of organic nanopores, and associated porosity increase, in the gas window.

Description: The deep high-temperature, high-pressure Lower Cretaceous Bashijiqike sandstone (buried to depths as great as 6.5–7.1 km [21,325–23,293 ft]) is an important natural gas reservoir in Keshen gas field, Kuqa depression of the Tarim basin. Reservoir quality is a critical risk factor in the development of these ultradeep reservoirs. Integrated approaches incorporating routine core analyses and mineralogical, petrographic, and geochemical analyses have been used to investigate the diagenetic history of these rocks and their effect on reservoir quality with the aim to unravel the mechanisms for maintaining anomalously high porosities in sandstones that are buried to such a great depth. These sandstones are dominantly fine- to medium-grained, moderately to well-sorted lithic arkoses and feldspathic litharenite. Most primary pores have been lost by mechanical compaction or carbonate cementation, and the reduction of porosity by mechanical compaction was more significant than that by cementation. Dissolution of framework grains contributed to the enhancement of reservoir quality. Eogenetic diagenetic alterations mainly include mechanical compaction, precipitation of calcite cements, and grain-coating clays, and mesogenetic diagenesis is characterized by dissolution of framework grain by organic acids and subsequent precipitation of clay minerals and quartz. Infiltration of meteoric water related to teleodiagenesis would result in dissolution of the framework grains. The meteoric leaching events during teleodiagenesis are of great importance for the Bashijiqike sandstones. Grain-coating clay minerals (mixed-layer illite/smectite clays) help to preserve porosity at depth by retarding quartz cementation and pressure solution. The unique burial regime as early-stage shallow burial with late-stage rapid deep burial contributes to porosity preservation in eodiagenesis. Fluid overpressure caused by intense structural compression in the middle Himalayan movement retarded compaction and helped preserve porosity in the late rapid deep burial stage. Anomalously high porosities are mainly found in medium-grained, well-sorted sandstones with grain-coating clays but with low clay and carbonate cement content, of which the porosity is preserved primarily and enhanced secondarily. The lowest porosities are associated with sandstones that are tightly compacted or cemented with carbonates or rich in detrital matrix. Porosity–depth trends may vary significantly with lithofacies because of their differences in textural and compositional attributes. Five lithofacies are defined in terms of detrital composition and texture and type and degree of diagenesis. The reservoir quality prediction models of various litho-facies are constructed, and the results of this study provide insights into mechanisms for maintaining anomalously high porosity and permeability in high-temperature, high-pressure sandstone reservoirs and may help explain hydrocarbon distribution.

Description: The lower section of the lower Silurian Qusaiba Member, Qalibah Formation, is characterized by regionally developed organic-rich shales that have sourced many of the large Paleozoic petroleum systems of Saudi Arabia. In northern Saudi Arabia, these high–total organic carbon (TOC) horizons are being assessed for their unconventional shale-gas potential. The initial phase of exploration drilling, which resulted in a quadrupling of the number of penetrations in northern Saudi Arabia, had the dual purpose of (1) assessing the high-TOC horizons as an unconventional resource play and (2) acquiring the fundamental data required to understand the geologic development of the zones of interest within the lower Qusaiba. The availability of numerous new cores from across northern Saudi Arabia enabled an extensive refinement of the existing biostratigraphy and enhanced integration between graptolite and palynomorph biozonation systems. In cores from the study area, four distinct sedimentary facies are recognized, (1) pyritic siltstone, (2) black mudstone, (3) black chert, and (4) gray shale, representing distinct paleoenvironmental conditions related to the stepped latest Ordovician and early Silurian Gondwanan deglaciation. The failure of the Gondwanan ice sheet was not a simple, short-lived, consistent melting and associated flooding of a flat continental shelf. This study highlights the complex interplay of sea-floor topography, ocean currents, sediment supply, and variations in the rate of melting of the ice sheet. With the associated rising ambient temperatures there are (1) increasing clay concentrations associated with intensifying chemical weathering of the exposed land mass and (2) progressive lowering of the carbonate compensation depth as water temperatures rise, enabling the preservation of carbonate shell material.

Description: We use finite element modeling to show that upbuilding can be a significant component of salt diapir growth in tectonically stable systems when basin sediments are elastoplastic mudrocks. The ability of such sediments to deform plastically and the dependence of their strength on confining pressure enable structural thinning, which allows salt to pierce through a relatively thick roof. Once pierced, the originally continuous roof uplifts to form a megaflap. We show that the evolution to an upturned megaflap adjacent to a salt stock causes shortening of the bedding layers in the radial and vertical directions and extension in the hoop (circumferential) direction. These deformations lead to significant shear strains within the sediments; as a result, in some areas within the upturned megaflap, mudrocks have reached their maximum level of shear resistance and are failing. Thinning and shear failure of sediments are also significant near salt walls, despite the absence of out-of-plane deformation. We illustrate that cross-sectional area and bedding line lengths are not necessarily preserved. Based on our results, we re-evaluate traditional assumptions of kinematic restoration and show that established workflows may not properly restore salt systems that interact with shallow plastic sediments. Finally, we show that when wall rocks are deformable, salt diapir shapes are not necessarily a simple function of sedimentation and salt flux rates ( q fx / Å ) and that the diapir hourglass shape might result from lateral deformation of the megaflap.

Description: Provenance of Pleistocene–Holocene deepwater sediments in the Gulf of Papua (National Science Foundation Source to Sink Focus Area) has been studied to understand sediment sources and glacioeustatic influences on sedimentary routing and to better understand processes controlling sediment sources and delivery. We show how diverse processes operate in a complex deep-sea environment over time to control sediment routing and accumulation. Quantitative detrital analyses were conducted on 53 turbidite sand and 3 terrestrial samples with scanning electron microscopy and mineral liberation analysis, which yielded a broader and more insightful classification than manual point counts. We determined that (1) multiple terrestrial sediment sources along an approximately 500-km (300-mi) basin margin converged to form one continuous deep-sea system in two major basins (〉30 cal [calibrated] ka); (2) subsequent sea level fall near the last glacial maximum (LGM) (18–22 cal ka) drove repartitioning of sediment sources to create multiple distinct depocenters, presumably caused by migration and incision of individual rivers across the newly exposed coastal plain; and (3) multiple separate deep-sea channels then regained compositional similarity near the end of the LGM. In the subsequent Holocene, deepwater sand transport shut down, except for one locality where delivery continues because of a combination of narrow shelf–slope setting, oceanographic processes, and additional volcanic supply. These findings highlight the diverse processes that must be considered for the development of deepwater petroleum systems, in terms of sediment delivery, deposition, and provenance that may affect the reservoir geometry and quality.

Description: Secondary processes within reservoir sandstones during and after hydrocarbon production are poorly understood. This study looks at the effect of secondary water fill on a sandstone reservoir within a time span of 8 yr. The reservoir rocks consist of medium-grained litharenites with large clasts of shales and carbonates. They originate from a depleted gas reservoir that has been converted into an underground storage field for natural gas. Gas production resulted in a rise of the gas–water contact of approximately 30 m (98 ft). Based on their initial and final gas and water saturations, four zones can be identified. Observed diagenetic changes in all four zones include carbonate cementation, K-feldspar overgrowths, authigenic quartz overgrowths, pyrite formation, and poorly crystallized authigenic clay minerals. However, the authigenic clay mineral fraction differs significantly within the zones. Total clay mineral content and crystallinities of smectite, chlorite, kaolinite, and illite increase from the gas-bearing to the initial water zone. Additionally, expandable clay minerals and kaolinite were not identified in the gas-bearing zone. This is different in the secondary watered zones, where smectites and kaolinites are developing. The study shows that within a maximum of 8 yr from the start of water influx into the gas zone, new clay minerals are forming. The porosity and permeability reduction caused by this artificially induced process might continue and could also be of relevance within producing reservoirs, where water saturation increases during production.

Description: Microbial nitrite reductases are denitrifying enzymes that are a major component of the global nitrogen cycle. Multiple structures measured from one crystal (MSOX data) of copper nitrite reductase at 240 K, together with molecular-dynamics simulations, have revealed protein dynamics at the type 2 copper site that are significant for its catalytic properties and for the entry and exit of solvent or ligands to and from the active site. Molecular-dynamics simulations were performed using different protonation states of the key catalytic residues (AspCAT and HisCAT) involved in the nitrite-reduction mechanism of this enzyme. Taken together, the crystal structures and simulations show that the AspCAT protonation state strongly influences the active-site solvent accessibility, while the dynamics of the active-site `capping residue' (IleCAT), a determinant of ligand binding, are influenced both by temperature and by the protonation state of AspCAT. A previously unobserved conformation of IleCAT is seen in the elevated temperature series compared with 100 K structures. DFT calculations also show that the loss of a bound water ligand at the active site during the MSOX series is consistent with reduction of the type 2 Cu atom.

Description: Traditional synthesis of metal–organic frameworks (MOFs) involves the reaction of a metal-containing precursor with an organic linker in an organic solvent at an elevated temperature, in what is termed a `solvothermal' reaction. More recently, many examples have been reported of MOF synthesis in ionic liquids (ILs), rather than an organic solvent, in `ionothermal' reactions. The high concentration of both cations and anions in an ionic liquid allows for the formation of new MOF structures in which the IL cation or anion or both are incorporated into the MOF. Most commonly, the IL cation is included in the open cavities of the MOF, countering the anionic charge of the MOF framework itself and acting as a template around which the MOF structure forms. Ionic liquids can also serve other structure-directing roles, for example, when an IL containing a single enantiomer of a chiral anion leads to a homochiral MOF, even though the IL anion is not itself incorporated into the MOF. A comprehensive review of ionothermal syntheses of MOFs, and the structure-directing effects of the ILs, is given.

Description: For martensitic transformations the macroscopic crystal strain is directly related to the corresponding structural rearrangement at the microscopic level. In situ optical microscopy observations of the interface migration and the change in crystal shape during a displacive single crystal to single crystal transformation can contribute significantly to understanding the mechanism of the process at the atomic scale. This is illustrated for the dehydration of samarium oxalate decahydrate in a study combining optical microscopy and single-crystal X-ray diffraction.

Description: The application domain of accurate and efficient CE-B3LYP and CE-HF model energies for intermolecular interactions in molecular crystals is extended by calibration against density functional results for 1794 molecule/ion pairs extracted from 171 crystal structures. The mean absolute deviation of CE-B3LYP model energies from DFT values is a modest 2.4 kJ mol−1 for pairwise energies that span a range of 3.75 MJ mol−1. The new sets of scale factors determined by fitting to counterpoise-corrected DFT calculations result in minimal changes from previous energy values. Coupled with the use of separate polarizabilities for interactions involving monatomic ions, these model energies can now be applied with confidence to a vast number of molecular crystals. Energy frameworks have been enhanced to represent the destabilizing interactions that are important for molecules with large dipole moments and organic salts. Applications to a variety of molecular crystals are presented in detail to highlight the utility and promise of these tools.

Description: The northern deep-water Gulf of Mexico is one of the most active deep-water petroleum provinces in the world. This paper introduces the regional geologic setting for the northern deep-water Gulf of Mexico and briefly discusses the importance of technology in developing the area’s resources. Exploration has focused on four major geologic provinces: Basins, Subsalt, Fold Belt, and Abyssal Plain. These provinces formed from the complex interactions between Mesozoic–Cenozoic sedimentation and tectonics. Improved understanding of the geology of these provinces has largely been accomplished by improvements in seismic acquisition and processing. In addition, advances in drilling technology have permitted drilling and field development in increasingly greater water depths. The 226 oil and gas fields and discoveries in the northern deep-water Gulf of Mexico are summarized in terms of their exploration and development history, producing facility, ages of reservoirs (Upper Jurassic, upper Paleocene–lower Eocene, Oligocene, lower Miocene–upper Pleistocene), and trap type (structural, combined structural-stratigraphic, and stratigraphic). In addition, the interpreted regional distribution of Upper Jurassic and possible Lower Cretaceous source, source rocks is shown, in part based on the 26 wells that have penetrated these source rocks. The eight papers in this special issue review the geology of the Mississippi Canyon and northern Atwater Valley protraction areas. The first five papers review the subregional structural setting and the evolution of its tectonics and petroleum systems. The final three papers summarize the geologic evolution of two economically important intraslope basins—Thunder Horse and Mensa—in terms of their stratigraphy, structural evolution, and petroleum systems. These two basins contain two of the larger oil and gas fields, respectively, in the northern deep-water Gulf of Mexico.

Description: Thunder Horse and Mensa are two of the largest fields of oil or gas, respectively, in the northern deep-water Gulf of Mexico. The fields are present in adjacent intraslope minibasins, located approximately 12 mi (19 km) apart in Mississippi Canyon. Both fields illustrate important complexities of deep-water sedimentation. Analysis is based on the integration of wire-line logs, biostratigraphy, and a 378-mi 2 (979-km 2 ), three-dimensional seismic data set. Thunder Horse and Mensa reservoirs were deposited during the middle to late Miocene. Changes in paleobathymetry controlled the reservoir deposition, initially as salt withdrawal and later as turtle structures. From 125 to 24 Ma, the lithologies in both intraslope basins are interpreted as dominantly deep-water marls with interbedded shales. From 24 to 14.35 Ma, major input of deep-water siliciclastic sediments began. Sands were deposited in amalgamated sheets and amalgamated channel-fill units within the two major paleobathymetric lows; by contrast, shales were deposited across paleobathymetric highs. Between 14.35 and 13.05 Ma, the Thunder Horse turtle formed, creating a paleobathymetric high. Channelized sands were diverted around and deposited on the flanks of the structure. Meanwhile, to the north at Mensa, thick channel-fill sediments continued to be deposited. From 12.2 to 8.2 Ma, the lithologies throughout the entire area are dominantly overbank shales with thin channel-fill sands, suggesting that large volumes of sand bypassed the study area farther downslope to the south. Finally, at 9.0 Ma, Mensa's sheet-sand reservoir represents a different setting; sands were deposited near the crest of the Mensa turtle, which had subtle bathymetric expression.

Description: The Mensa and Thunder Horse intraslope minibasins in south-central Mississippi Canyon, northern deep-water Gulf of Mexico, had a linked structural evolution from the Early Cretaceous through the late Miocene. Analysis of the two minibasins illustrates the complexities of deep-water sedimentation and salt tectonics in intraslope minibasins. This study is based on the integration of a 378-mi 2 (979-km 2 ) three-dimensional seismic data set, wire-line logs, and biostratigraphic data. These two minibasins comprise several structural features that affected their geologic evolution: basement faults, autochthonous salt, three allochthonous salt systems (top Barremian, top Cretaceous, and Neogene), a growth fault and raft system, three major turtle structures with associated extensive crestal faults, and strike-slip faults. Remnant allochthonous salt pillows are present above the 125 Ma horizon (approximate top Barremian system) and on the 66 Ma horizon (top Cretaceous system) throughout the Mensa minibasin, whereas the top Cretaceous allochthonous salt system is identified regionally by a salt weld in the Thunder Horse area. These allochthonous salt systems formed weld surfaces beneath the Mensa and Thunder Horse turtle structures. Structural features and associated minibasins evolved during several discrete intervals. From the Early Cretaceous through the latest Oligocene (125 to 24 Ma), an extensive allochthonous salt canopy was present within the Mensa and Thunder Horse minibasins. During this interval, sediments loaded the salt, forming thin wedge- and sheet-form deposits in the Mensa area and a thick, northwest-trending trough in the Thunder Horse area. A secondary allochthonous salt system extruded at the Top Cretaceous level, as seen by remnant salt bodies. Salt withdrawal from these allochthonous salt systems provided accommodation for bowl- and trough-shaped external stratigraphic forms to develop during the Miocene. High sedimentation rates produced salt evacuation from these allochthonous salt systems and initiated diapirism that formed the Neogene allochthonous salt level. The prominent turtle structures in the two minibasins, critical to the formation of traps to the two major fields, developed at slightly different times: Thunder Horse at 14.35 and Mensa at 11.4 Ma.

Description: The 86 fields and discoveries in the central Mississippi Canyon, Atwater Valley, western DeSoto Canyon, and Lloyd Ridge protraction areas are summarized with production characteristics and representative seismic profiles and wire-line logs. Three trap styles are recognized: four-way closure, three-way closure, and stratigraphic. The reservoirs in nearly all of the fields are Neogene deep-water sandstones; four are in Upper Jurassic eolian sandstones. Development facilities include a variety of floating platforms and production units and subsea tiebacks.

Description: The petroleum systems of two adjacent Miocene intraslope minibasins in the northern deep-water Gulf of Mexico are modeled to investigate why one of them produces primarily gas but the other produces oil. Specifically, the Mensa field produces gas from a faulted four-way closure that overlies a turtle structure, whereas the adjacent Thunder Horse field produces from a turtle structure with four-way structural closure. To resolve this issue, a three-dimensional petroleum-system model was constructed, whose results indicate that the Lower Cretaceous source interval, comprising type II kerogen, matured significantly earlier in the Mensa basin; the oil window was reached between 11.4 and 9.0 Ma, and the thermogenic gas window was reached between 6.2 and 0.0 Ma. By contrast, within the Thunder Horse basin, the source interval reached the oil window by 10.75 to 9.4 Ma and largely remains in the oil window. The Thunder Horse trap had formed by 13.05 Ma, which was before the end of the oil window. The Mensa trap (9.0–8.2 Ma) was not in place when the source rock passed though the oil window. The primary control on the timing of maturation and charge is related to the original thickness of allochthonous salt that created the accommodation for the thick Miocene deep-water sediments. Originally, the Mensa minibasin contained thicker Cretaceous allochthonous salt than the Thunder Horse minibasin. Consequently, as the salt was loaded with sediment and completely evacuated, the turtle structure (trap) formed earlier in Thunder Horse field than in Mensa. By contrast, the source rocks matured earlier in Mensa, prior to the deposition of reservoir sands and the formation of the trap. The results indicate that turtle structures with similar appearances can have subtle differences in the timing of their petroleum systems, which ultimately control whether the feature is charged and with what fluid. These features must be modeled carefully in evaluating their exploration potential.

Description: The structural framework and evolution from the Middle Jurassic to the present of the Mississippi Canyon, Atwater Valley, western DeSoto Canyon, and western Lloyd Ridge protraction areas consist of a complex history influenced by basement fabric, multiple stages of salt movement, and gravitational gliding. A detailed tectono-stratigraphic interpretation of the study area indicates that three main stages of salt movement controlled sediment dispersal patterns and the formation and evolution of intraslope minibasins. These three stages of salt movement occurred during the Cretaceous, the Paleogene, and the Neogene. Basement structures were the primary control on initial salt kinematics, affecting gravity-driven slope deformation and resulting in a wide variety of structural styles. Basement (acoustic basement) structures (horsts, grabens, and half grabens) formed prior to the deposition of the Middle Jurassic autochthonous Louann Salt. These features are interpreted to have controlled the original thickness of the autochthonous salt layer and subsequent salt-withdrawal patterns. Mesozoic structures, such as extensional-compressional gliding systems and expulsion rollovers, formed above the autochthonous salt. Three levels of allochthonous salt systems are identified: (1) approximate top Barremian, (2) top Cretaceous, and (3) intra-Neogene (between 10 and 4 Ma). Early emplacement of two allochthonous salt layers is present in the northeastern part of the study area, whereas the Neogene allochthonous salt system extends throughout the Mississippi Canyon, western DeSoto Canyon, and northern Atwater Valley protraction areas. Salt from the autochthonous and two deep allochthonous salt layers was expelled vertically and basinward during the Neogene, feeding the younger allochthonous salt systems. The autochthonous and deep allochthonous salt layers were detachments for many of the large Neogene extensional (growth faults and turtles) and contractional (anticlines and thrust faults) structures, whereas the Neogene allochthonous salt system accommodated suprasalt minibasins associated with counterregional and roho salt systems. These three allochthonous salt layers were successively loaded by gravity-flow sediments, resulting in deep (above autochthonous or deep allochthonous salt layers) and shallow (supra-Neogene allochthonous salt) minibasin formations and local development of extensive salt welds. Northwest–southeast-oriented strike-slip structures, active during the Neogene, are present in the salt province within the study area. They are related to basinwide heterogeneities in the salt distribution and are controlled by differential basinward movement of adjacent suprasalt minibasins.

Description: Based on a description of bond valence as a function of valence electron density, a systematic bond softness sensitive approach to determine bond-valence parameters and related quantities such as coordination numbers is elaborated and applied to determine bond-valence parameters for 706 cation–anion pairs. While the approach is closely related to the earlier softBV parameter set, the new softNC1 parameters proposed in this work may be simpler to apply in plausibility checks of crystal structures, as they follow the first coordination shell convention. The performance of this softNC1 bond-valence parameter set is compared with that of the previously derived softBV parameter set that also factors in contributions from higher coordination shells, and with a benchmarking parameter set that has been optimized following the conventional choice of a universal value of the bond-valence parameter b. The results show that a systematic adaptation of the bond-valence parameters to the bond softness leads to a significant improvement in the bond-valence parameters, particularly for bonds involving soft anions, and is safer than individual free refinements of both R0 and b from a limited number of reference cation environments.

Description: The progress in X-ray microbeam applications using synchrotron radiation is beneficial to structure determination from macromolecular microcrystals such as small in meso crystals. However, the high intensity of microbeams causes severe radiation damage, which worsens both the statistical quality of diffraction data and their resolution, and in the worst cases results in the failure of structure determination. Even in the event of successful structure determination, site-specific damage can lead to the misinterpretation of structural features. In order to overcome this issue, technological developments in sample handling and delivery, data-collection strategy and data processing have been made. For a few crystals with dimensions of the order of 10 µm, an elegant two-step scanning strategy works well. For smaller samples, the development of a novel method to analyze multiple isomorphous microcrystals was motivated by the success of serial femtosecond crystallography with X-ray free-electron lasers. This method overcame the radiation-dose limit in diffraction data collection by using a sufficient number of crystals. Here, important technologies and the future prospects for microcrystallography are discussed.

Description: An algorithm for modelling the background for each Bragg reflection in a series of X-ray diffraction images containing Debye–Scherrer diffraction from ice in the sample is presented. The method involves the use of a global background model which is generated from the complete X-ray diffraction data set. Fitting of this model to the background pixels is then performed for each reflection independently. The algorithm uses a static background model that does not vary over the course of the scan. The greatest improvement can be expected for data where ice rings are present throughout the data set and the local background shape at the size of a spot on the detector does not exhibit large time-dependent variation. However, the algorithm has been applied to data sets whose background showed large pixel variations (variance/mean 〉 2) and has been shown to improve the results of processing for these data sets. It is shown that the use of a simple flat-background model as in traditional integration programs causes systematic bias in the background determination at ice-ring resolutions, resulting in an overestimation of reflection intensities at the peaks of the ice rings and an underestimation of reflection intensities either side of the ice ring. The new global background-model algorithm presented here corrects for this bias, resulting in a noticeable improvement in R factors following refinement.

Description: Small-angle X-ray scattering (SAXS) is an established technique that provides low-resolution structural information on macromolecular solutions. Recent decades have witnessed significant progress in both experimental facilities and in novel data-analysis approaches, making SAXS a mainstream method for structural biology. The technique is routinely applied to directly reconstruct low-resolution shapes of proteins and to generate atomistic models of macromolecular assemblies using hybrid approaches. Very importantly, SAXS is capable of yielding structural information on systems with size and conformational polydispersity, including highly flexible objects. In addition, utilizing high-flux synchrotron facilities, time-resolved SAXS allows analysis of kinetic processes over time ranges from microseconds to hours. Dedicated bioSAXS beamlines now offer fully automated data-collection and analysis pipelines, where analysis and modelling is conducted on the fly. This enables SAXS to be employed as a high-throughput method to rapidly screen various sample conditions and additives. The growing SAXS user community is supported by developments in data and model archiving and quality criteria. This review illustrates the latest developments in SAXS, in particular highlighting time-resolved applications aimed at flexible and evolving systems.

Description: Understanding the protein main-chain conformational space forms the basis for the modelling of protein structures and for the validation of models derived from structural biology techniques. Presented here is a novel idea for a three-dimensional distance geometry-based metric to account for the fine details of protein backbone conformations. The metrics are computed for dipeptide units, defined as blocks of Cαi−1—Oi−1—Cαi—Oi—Cαi+1 atoms, by obtaining the eigenvalues of their Euclidean distance matrices. These were computed for ∼1.3 million dipeptide units collected from nonredundant good-quality structures in the Protein Data Bank and subjected to principal component analysis. The resulting new Euclidean orthogonal three-dimensional space (DipSpace) allows a probabilistic description of protein backbone geometry. The three axes of the DipSpace describe the local extension of the dipeptide unit structure, its twist and its bend. By using a higher-dimensional metric, the method is efficient for the identification of Cα atoms in an unlikely or unusual geometrical environment, and its use for both local and overall validation of protein models is demonstrated. It is also shown, for the example of trypsin proteases, that the detection of unusual conformations that are conserved among the structures of this protein family may indicate geometrically strained residues of potentially functional importance.

Description: Serial femtosecond crystallography (SFX) using X-ray free-electron lasers (XFELs) holds enormous potential for the structure determination of proteins for which it is difficult to produce large and high-quality crystals. SFX has been applied to various systems, but rarely to proteins that have previously unknown structures. Consequently, the majority of previously obtained SFX structures have been solved by the molecular replacement method. To facilitate protein structure determination by SFX, it is essential to establish phasing methods that work efficiently for SFX. Here, selenomethionine derivatization and mercury soaking have been investigated for SFX experiments using the high-energy XFEL at the SPring-8 Angstrom Compact Free-Electron Laser (SACLA), Hyogo, Japan. Three successful cases are reported of single-wavelength anomalous diffraction (SAD) phasing using X-rays of less than 1 Å wavelength with reasonable numbers of diffraction patterns (13 000, 60 000 and 11 000). It is demonstrated that the combination of high-energy X-rays from an XFEL and commonly used heavy-atom incorporation techniques will enable routine de novo structural determination of biomacromolecules.

Description: Rieske nonheme iron oxygenases (ROs) are a well studied class of enzymes. Naphthalene 1,2-dioxygenase (NDO) is used as a model to study ROs. Previous work has shown how side-on binding of oxygen to the mononuclear iron provides this enzyme with the ability to catalyze stereospecific and regiospecific cis-dihydroxylation reactions. It has been well documented that ROs catalyze a variety of other reactions, including mono-oxygenation, desaturation, O- and N-dealkylation, sulfoxidation etc. NDO itself catalyzes a variety of these reactions. Structures of NDO in complex with a number of different substrates show that the orientation of the substrate in the active site controls not only the regiospecificity and stereospecificity, but also the type of reaction catalyzed. It is proposed that the mononuclear iron-activated dioxygen attacks the atoms of the substrate that are most proximal to it. The promiscuity of delivering two products (apparently by two different reactions) from the same substrate can be explained by the possible binding of the substrate in slightly different orientations aided by the observed flexibility of residues in the binding pocket.

Description: The flagellated Gram-negative bacterium Escherichia coli is one of the most studied microorganisms. Despite extensive studies as a model prokaryotic cell, the ultrastructure of the cell envelope at the nanometre scale has not been fully elucidated. Here, a detailed structural analysis of the bacterium using a combination of small-angle X-ray and neutron scattering (SAXS and SANS, respectively) and ultra-SAXS (USAXS) methods is presented. A multiscale structural model has been derived by incorporating well established concepts in soft-matter science such as a core-shell colloid for the cell body, a multilayer membrane for the cell wall and self-avoiding polymer chains for the flagella. The structure of the cell envelope was resolved by constraining the model by five different contrasts from SAXS, and SANS at three contrast match points and full contrast. This allowed the determination of the membrane electron-density profile and the inter-membrane distances on a quantitative scale. The combination of USAXS and SAXS covers size scales from micrometres down to nanometres, enabling the structural elucidation of cells from the overall geometry down to organelles, thereby providing a powerful method for a non-invasive investigation of the ultrastructure. This approach may be applied for probing in vivo the effect of detergents, antibiotics and antimicrobial peptides on the bacterial cell wall.

Description: Serial synchrotron-based crystallography using intense microfocused X-ray beams, fast-framing detectors and protein microcrystals held at 300 K promises to expand the range of accessible structural targets and to increase overall structure-pipeline throughputs. To explore the nature and consequences of X-ray radiation damage under microbeam illumination, the time-, dose- and temperature-dependent evolution of crystal diffraction have been measured with maximum dose rates of 50 MGy s−1. At all temperatures and dose rates, the integrated diffraction intensity for a fixed crystal orientation shows non-exponential decays with dose. Non-exponential decays are a consequence of non-uniform illumination and the resulting spatial evolution of diffracted intensity within the illuminated crystal volume. To quantify radiation-damage lifetimes and the damage state of diffracting crystal regions, a revised diffraction-weighted dose (DWD) is defined and it is shown that for Gaussian beams the DWD becomes nearly independent of actual dose at large doses. An apparent delayed onset of radiation damage seen in some intensity–dose curves is in fact a consequence of damage. Intensity fluctuations at high dose rates may arise from the impulsive release of gaseous damage products. Accounting for these effects, data collection at the highest dose rates increases crystal radiation lifetimes near 300 K (but not at 100 K) by a factor of ∼1.5–2 compared with those observed at conventional dose rates. Improved quantification and modeling of the complex spatio-temporal evolution of protein microcrystal diffraction in intense microbeams will enable more efficient data collection, and will be essential in improving the accuracy of structure factors and structural models.

Description: Temporal coherence is one of the most fundamental characteristics of light, connecting to spectral information through the Fourier transform relationship between time and frequency. Interferometers with a variable path-length difference (PLD) between the two branches have widely been employed to characterize temporal coherence properties for broad spectral regimes. Hard X-ray interferometers reported previously, however, have strict limitations in their operational photon energies, due to the specific optical layouts utilized to satisfy the stringent requirement for extreme stability of the PLD at sub-ångström scales. The work presented here characterizes the temporal coherence of hard X-ray free-electron laser (XFEL) pulses by capturing single-shot interferograms. Since the stability requirement is drastically relieved with this approach, it was possible to build a versatile hard X-ray interferometer composed of six separate optical elements to cover a wide photon energy range from 6.5 to 11.5 keV while providing a large variable delay time of up to 47 ps at 10 keV. A high visibility of up to 0.55 was observed at a photon energy of 10 keV. The visibility measurement as a function of time delay reveals a mean coherence time of 5.9 ± 0.7 fs, which agrees with that expected from the single-shot spectral information. This is the first result of characterizing the temporal coherence of XFEL pulses in the hard X-ray regime and is an important milestone towards ultra-high energy resolutions at micro-electronvolt levels in time-domain X-ray spectroscopy, which will open up new opportunities for revealing dynamic properties in diverse systems on timescales from femtoseconds to nanoseconds, associated with fluctuations from ångström to nanometre spatial scales.

Description: Serial femtosecond crystallography is an emerging and promising method for determining protein structures, making use of the ultrafast and bright X-ray pulses from X-ray free-electron lasers. The upcoming X-ray laser sources will produce well above 1000 pulses per second and will pose a new challenge: how to quickly determine successful crystal hits and avoid a high-rate data deluge. Proposed here is a hit-finding scheme based on detecting photons from plasma emission after the sample has been intercepted by the X-ray laser. Plasma emission spectra are simulated for systems exposed to high-intensity femtosecond pulses, for both protein crystals and the liquid carrier systems that are used for sample delivery. The thermal radiation from the glowing plasma gives a strong background in the XUV region that depends on the intensity of the pulse, around the emission lines from light elements (carbon, nitrogen, oxygen). Sample hits can be reliably distinguished from the carrier liquid based on the characteristic emission lines from heavier elements present only in the sample, such as sulfur. For buffer systems with sulfur present, selenomethionine substitution is suggested, where the selenium emission lines could be used both as an indication of a hit and as an aid in phasing and structural reconstruction of the protein.

Description: Geochemical interactions between shale and hydraulic fracturing fluid may affect produced-water chemistry and rock properties. It is important to investigate the rock–water reactions to understand the impacts. Eight autoclave experiments reacting Marcellus and Eagle Ford Shale samples with synthetic brines and a friction reducer were conducted for more than 21 days. To better determine mineral dissolution and precipitation at the rock–water interface, the shale samples were ion milled to create extremely smooth surfaces that were characterized before and after the autoclave experiments using scanning electron microscopy (SEM). This method provides an unprecedented level of detail and the ability to directly compare the same mineral particles before and after the reaction experiments. Dissolution area was quantified by tracing and measuring the geometry of newly formed pores. Changes in porosity and permeability were also measured by mercury intrusion capillary pressure (MICP) tests. Aqueous chemistry and SEM observations show that dissolution of calcite, dolomite, and feldspar and pyrite oxidation are the primary mineral reactions that control the concentrations of Ca, Mg, Sr, Mn, K, Si, and SO 4 in aqueous solutions. Porosity measured by MICP also increased up to 95%, which would exert significant influence on fluid flow in the matrix along the fractures. Mineral dissolution was enhanced and precipitation was reduced in solutions with higher salinity. The addition of polyacrylamide (a friction reducer) to the reaction solutions had small and mixed effects on mineral reactions, probably by plugging small pores and restricting mineral precipitation. The results suggest that rock–water interactions during hydraulic fracturing likely improve porosity and permeability in the matrix along the fractures by mineral dissolution. The extent of the geochemical reactions is controlled by the salinity of the fluids, with higher salinity enhancing mineral dissolution.

Description: This study evaluates the proportion, length, and effective properties of thin (0.003–0.7 m [0.01–2.3 ft]) shale beds and drapes in tidally influenced channels within a compound valley fill with a focus on estimating geologically based effective rock properties. The Cretaceous Ferron Sandstone is an outcrop analog for fluvial–tidal systems with primary reservoirs being deposited as tidally influenced valley filling point bars. The study outcrops expose three valley systems in Neilson Wash of Utah. Light detection and ranging–derived digital outcrop models have been used to characterize shale length, width, thickness, and frequency of each valley fill succession. Long, uncommon, and anisotropic shales in valley 1 (V1) were deposited in a braided setting with little tidal influence. In contrast, shales in valley 2 (V2) were abundant, short, common, and equidimensional, suggesting deposition by more tidally influenced meandering rivers. Short, frequent, and equidimensional shales in valley 3 (V3) were deposited in single-thread meandering rivers with less tidal influence. A sandstone–shale model was used to estimate the effects of shales on vertical to horizontal permeability ratio ( \[{k}_{v}/{k}_{h} \] ). The unique character of each depositional unit was reflected in resultant \[{k}_{v}/{k}_{h} \] distributions. The valley fill deposits, V1, V2, and V3, had average \[{k}_{v}/{k}_{h} \] ratios of 0.11, 0.09, and 0.17, respectively. More tidally influenced reservoirs such as the studied V2 had short but frequent shales, which resulted in low \[{k}_{v}/{k}_{h} \] estimates. Estimates of \[{k}_{v}/{k}_{h} \] for valleys that predominantly contained fluvial point bar deposits with lesser tidal influence (V1 and V3) were higher. The results of this study highlight the link between shale heterogeneity, reservoir architecture, and inferred flow parameters.

Description: The Permian Khuff-C reservoir in Saudi Arabia is known for its lateral and vertical heterogeneity caused mainly by dolomitization. Detailed petrographic analysis of 600 thin sections, from six cored wells, revealed three main replacive dolomite fabrics: (1) fabric-preserving mimetic (FPM), (2) fabric-preserving nonmimetic (FPNM), and (3) fabric-destructive (FD) dolomites. Crystal sizes are mostly less than or equal to 20 μm for FPM dolomite, less than or equal to 50 μm for FPNM dolomite, and less than or equal to 100 μm for FD dolomite. The FPM dolomite decreases in abundance, and FPNM dolomite increases in abundance, with increasing grain content of the facies. The 18 O values of dolostones (although considered an obsolete term, dolostone is used here to mean rock containing ≥80% dolomite) indicate early dolomitization at low temperatures in Permian seawater or evaporated seawater, with landward facies (mudstone and wackestone) generally dolomitized by more evaporated waters and seaward grainy facies generally dolomitized by less evaporated, more normal marine seawaters. Stratigraphic variations in the dolostones’ 18 O values track with facies variations through fourth-order depositional sequences and indicate that different stratigraphic bodies of dolomite formed from seawaters with different degrees of evaporation. The 13 C values of the dolostones exhibit temporal trends inherited from the precursor limestones. Variations in the lateral and vertical abundance of dolomite and dolomite fabrics, in the propensity for each facies to be dolomitized, and in the dolomites’ oxygen isotopic values all suggest that multiple dolomitization events occurred in the Khuff-C reservoir as depositional cycles accumulated, with some dolostones overprinted by younger events. Average porosities of grain-rich dolostones are greater than those of mud-rich dolostones, indicating that depositional facies preordained porosity distribution within the dolostones. However, the more evaporated the dolomitizing fluid, the more likely dolomitization resulted in lower porosity regardless of facies.

Description: Outcrop studies of fracture development, used as analogs for subsurface fracture patterns, are critical because of the importance of fractures as fluid flow pathways and the fact that most fracture networks exist at a smaller resolution than current seismic data can resolve. Fracture networks in carbonate units are typically controlled by the mechanical properties of the unit, indicating that the mechanical stratigraphy, as well as the fracture stratigraphy, should be considered. This study presents the results of a fracture analysis in the Mississippian carbonates of the Ozark Plateau, considering both mechanical and fracture network characteristics. Mechanical characteristics of the succession were defined using a combination of rebound values and thin section petrography. Fracture characteristics included orientation and intensity, together with abutting relationships. Results indicate that fracture orientations show a distinct evolution throughout the measured succession, including the appearance of early systematic sets, followed by pervasive systematic fracture sets related to existing basement features. Fracture orientation changes do not correspond to changes in mechanical stratigraphy. Fracture intensity, however, is related to the thickness of the mechanical unit instead of the bed thickness and is greatest in less competent units. Mechanical control influences the fracture network on a smaller scale than that of regional tectonic stresses. Thus, evaluations of carbonate reservoirs must account for both the large-scale and the small-scale investigations into fracture characteristic controls. Outcrop evaluations are of critical importance to properly assess characteristics that are challenging to recover from conventional subsurface data sets such as core and seismic reflection volumes.

Description: The introduction of direct detectors and the automation of data collection in cryo-EM have led to a surge in data, creating new opportunities for advancing computational processing. In particular, on-the-fly workflows that connect data collection with three-dimensional reconstruction would be valuable for more efficient use of cryo-EM and its application as a sample-screening tool. Here, accelerated on-the-fly analysis is reported with optimized organization of the data-processing tools, image acquisition and particle alignment that make it possible to reconstruct the three-dimensional density of the 70S chlororibosome to 3.2 Å resolution within 24 h of tissue harvesting. It is also shown that it is possible to achieve even faster processing at comparable quality by imposing some limits to data use, as illustrated by a 3.7 Å resolution map that was obtained in only 80 min on a desktop computer. These on-the-fly methods can be employed as an assessment of data quality from small samples and extended to high-throughput approaches.

Description: X-ray free-electron lasers (XFELs) provide new opportunities for structure determination of biomolecules, viruses and nanomaterials. With unprecedented peak brilliance and ultra-short pulse duration, XFELs can tolerate higher X-ray doses by exploiting the femtosecond-scale exposure time, and can thus go beyond the resolution limits achieved with conventional X-ray diffraction imaging techniques. Using XFELs, it is possible to collect scattering information from single particles at high resolution, however particle heterogeneity and unknown orientations complicate data merging in three-dimensional space. Using the Linac Coherent Light Source (LCLS), synthetic inorganic nanocrystals with a core–shell architecture were used as a model system for proof-of-principle coherent diffractive single-particle imaging experiments. To deal with the heterogeneity of the core–shell particles, new computational methods have been developed to extract the particle size and orientation from the scattering data to assist data merging. The size distribution agrees with that obtained by electron microscopy and the merged data support a model with a core–shell architecture.

Description: Understanding published research results should be through one's own eyes and include the opportunity to work with raw diffraction data to check the various decisions made in the analyses by the original authors. Today, preserving raw diffraction data is technically and organizationally viable at a growing number of data archives, both centralized and distributed, which are empowered to register data sets and obtain a preservation descriptor, typically a `digital object identifier'. This introduces an important role of preserving raw data, namely understanding where we fail in or could improve our analyses. Individual science area case studies in crystallography are provided.

Description: Magnetic Heusler compounds (MHCs) have recently attracted great attention since these types of material provide novel functionalities in spintronic and magneto-electronic devices. Among the MHCs, some compounds have been predicted to be spin-filter semiconductors [also called magnetic semiconductors (MSs)], spin-gapless semiconductors (SGSs) or half-metals (HMs). In this work, by means of first-principles calculations, it is demonstrated that rare earth-based equiatomic quaternary Heusler (EQH) compounds with the formula MCoVZ (M = Lu, Y; Z = Si, Ge) are new spin-filter semiconductors with total magnetic moments of 3 µB. Furthermore, under uniform strain, there are physical transitions from spin-filter semiconductor (MS) → SGS → HM for EQH compounds with the formula LuCoVZ, and from HM → SGS → MS → SGS → HM for EQH compounds with the formula YCoVZ. Remarkably, for YCoVZ EQH compounds there are not only diverse physical transitions, but also different types of spin-gapless feature that can be observed with changing lattice constants. The structural stability of these four EQH compounds is also examined from the points of view of formation energy, cohesive energy and mechanical behaviour. This work is likely to inspire consideration of rare earth-based EQH compounds for application in future spintronic and magneto-electronic devices.

Description: Unravelling the interaction of biological macromolecules with ligands and substrates at high spatial and temporal resolution remains a major challenge in structural biology. The development of serial crystallography methods at X-ray free-electron lasers and subsequently at synchrotron light sources allows new approaches to tackle this challenge. Here, a new polyimide tape drive designed for mix-and-diffuse serial crystallography experiments is reported. The structure of lysozyme bound by the competitive inhibitor chitotriose was determined using this device in combination with microfluidic mixers. The electron densities obtained from mixing times of 2 and 50 s show clear binding of chitotriose to the enzyme at a high level of detail. The success of this approach shows the potential for high-throughput drug screening and even structural enzymology on short timescales at bright synchrotron light sources.

Description: The results of petroleum system models (PSM) critically depend on the computed evolution of the temperature field. Because PSM typically only resolve the sedimentary basin and not the entire lithosphere, it is necessary to apply a basement–heat-flow boundary condition inferred from well data, surface–heat-flow measurements, and an assumed tectonic scenario. The purpose of this paper is to assess the use of surface–heat-flow measurements to calibrate basin models. We show that a simple relationship between surface and basement heat flow only exists in thermal steady state and that transient processes such as rifting and sediment deposition will lead to a decoupling. We study this relationship in extensional sedimentary basins with a one-dimensional, lithosphere-scale finite element model. The numerical model was built to capture the large-scale dynamic evolution of the lithosphere and simultaneously solve for transient thermal processes in basin evolution, such as sedimentation, compaction-driven fluid flow, and seafloor temperature variations. Our analysis shows that several corrections need to be applied when using surface–heat-flow information for the calibration of basement heat flow in PSM. Not doing so can lead to significant errors of up to 30°C–50°C (86°F–122°F) at typical petroleum-reservoir and source-rock depths. We further show that resolving sediment-blanketing effects in basin modeling is crucial, with the thermal impact of sediment deposition being at least as important as rifting-induced basement–heat-flow variations.

Description: The Lower Mississippian upper shale member of the Bakken Formation in the Williston Basin, North Dakota, consists of organic-rich, black, siliciclastic mudstones deposited offshore on a low-gradient shelf; 12 fine-grained facies are recognized and grouped into 5 facies associations (FAs). Very fine-grained, massive to faintly laminated mudstone (FA1) records deposition in the deepest, calmest parts of the basin, whereas well-laminated mudstones (FA2a); well-laminated, clay-clast–bearing mudstones (FA2b); burrow-mottled mudstone with shells (FA3); and interlaminated siltstone and mudstone (FA4) suggest deposition in the shallower, less calm, and more proximal offshore environment. These proximal-offshore mudstones (FA2a, FA2b, FA3, and FA4) reflect (1) variation in bottom-water oxygen levels and (2) lateral changes in the input of silt and clay clasts. Ubiquitous Phycosiphon fecal strings, patches of shells, burrows, and rare agglutinated foraminifera indicate dysoxic to suboxic basinal deposition and not a persistently anoxic environment. In all FAs, storm-event laminae are sparse to ubiquitous. Repeated stacking of FAs defines up to 10 coarsening-upward parasequences mostly 0.15–0.60 m (0.49–1.97 ft) thick. Individual parasequences can be correlated for 300 km (180 mi) through the basin. The lower half of the succession (interval 1) represents a transgressive systems tract and shows high radiolarian productivity with minor silt input. The upper half of the succession (interval 2) represents the base of a highstand systems tract. In contrast to interval 1, interval 2 mudstones are characterized by high clay content, low radiolarian productivity, and intermittent colonization of the sea floor during higher-order sea-level lowstands.

Description: The Fort Worth basin in northcentral Texas is a major shale-gas producer, yet its subsidence history and relationship to the Ouachita fold-thrust belt have not been well understood. We studied the depositional patterns of the basin during the late Paleozoic by correlating well logs and constructing structure and isopach maps. We then modeled the one-dimensional (1-D) and two-dimensional subsidence history of the basin and constrained its relationship to the Ouachita orogen. Because the super-Middle Pennsylvanian strata were largely eroded in the region, adding uncertainty to the subsidence reconstruction, we used PetroMod 1-D to conduct thermal-maturation modeling to constrain the post-Middle Pennsylvanian burial and exhumation history by matching the modeled vitrinite reflectance with measured vitrinite reflectance along five depth profiles. Our results of depositional patterns show that the tectonic uplift of the Muenster uplift to the northeast of the basin influenced subsidence as early as the Middle Mississippian, and the Ouachita orogen became the primary tectonic load by the late Middle Pennsylvanian when the depocenter shifted to the east. Our results show that the basin experienced 3.7–5.2 km (12,100–17,100 ft) of burial during the Pennsylvanian, and the burial depth deepens toward the east. We attributed the causes of deep Pennsylvanian burial and its spatial variation to flexural subsidence that continued into the Late Pennsylvanian in response to the growth of the Ouachita orogen and southeastward suturing of Laurentia and Gondwana. The modeling results also suggest that the Mississippian Barnett Shale reached the gas maturation window during the Middle–Late Pennsylvanian.

Description: Compaction disequilibrium is a widely accepted cause of overpressure, especially in clay-rich, rapidly deposited sediments. Clay diagenesis has been associated with the occurrence of overpressure greater than the compaction disequilibrium overpressure. These observations have led to the expectation that overpressure will be greater than the compaction disequilibrium contribution when clay diagenesis occurs within an overpressured mudstone. Clay diagenesis have been reported in a Pliocene section of a well from the Gulf of Mexico, offshore Louisiana. Pressure and log data from that well indicate that despite clay diagenesis, the overpressure can be attributed solely to compaction disequilibrium. This paper examines the whole mudstone and clay mineralogy composition and petrophysical characteristics of the offshore Louisiana well with clay diagenesis, but without a diagenesis contribution to overpressure and contrasts that data with results from other clay diagenesis and petrophysical studies. The comparison suggests that the offshore Louisiana well was relatively smectite poor compared with wells from regions associated with a clay diagenesis contribution to overpressure. The lower smectite content resulted in a lower percentage of reacted volume that was insufficient to allow the load transfer often associated with clay diagenesis. Petrophysical features of the offshore Louisiana well and nearby wells differ from the features associated with clay diagenesis in other Gulf of Mexico wells and a limited number of international wells. Comparison of location, age, depositional package, clay mineralogy, and petrophysical features suggests that provenance may control the occurrence of Gulf of Mexico mudstones that do not experience increased overpressure as a result of clay diagenesis.

Description: Fresh cores from tight-rock samples of subsurface hydrocarbon reservoirs retain mobile fluids. These fluids have complex chemical compositions and a large spectrum of molecules with different diameters and polarities. When investigated using high-resolution field-emission scanning electron microscopy (SEM), the imposed vacuum over hours of time causes pore fluids trapped in the rock sample to flow and interact with the mineral matrix. This paper reports the capillary fluid dynamics effect observed on freshly milled cross sections of tight chalk at high resolution. Multiphase fluid dynamic simulations confirm the aggregation of heavier fluid molecules on the geometrical irregularities of the pore space. As a consequence of this pitfall, the differentiation of solid organic matter versus variably viscous hydrocarbons from SEM data is subject to a fundamental revision.

Description: This study analyzed crude oils from the lower part of the third member of the Eocene Shahejie Formation (Es 3 L ) and three prospective source rocks from the Shulu sag, Bohai Bay basin, eastern China, using a variety of organic geochemical methods. Biomarker characteristics were used to interpret source rock organic matter input and depositional environment, and oil–source rock correlation. The biomarker data indicate that the crude oils originated from the Es 3 L source rock, which contains a mixture of plankton and land plant organic matters deposited in brackish–fresh water under reducing conditions. The oil in the Es 3 L is self-sourced instead of migrated from the overlying source rocks. The petroleum generation potential of the Es 3 L source rock was evaluated using organic geochemistry. Total organic carbon (TOC) values for approximately 100 samples are between 1.02 and 4.92 wt. %, and hydrogen indices range from 285 to 810 mg hydrocarbons/g TOC. The Es 3 L source rock contains mainly type II and III kerogen, and most of the samples are thermally mature. The data show that the Es 3 L source rock has good potential for liquid hydrocarbon generation. The Es 3 L rock also acts as the oil reservoir, having very low bulk porosity and permeability. Various types of storage space in the marlstone and carbonate rudstone in the Es 3 L of the Shulu sag include (1) fractures, (2) intergranular pores, (3) dissolution pores, (4) organic matter pores, (5) intragranular pores, and (6) seams around gravels. Pore size ranges from nanometers to millimeters. Because the oil was generated and stored in Es 3 L strata, which lack any obvious trap and seal and have low permeability, the unit represents a continuous petroleum accumulation.

Description: The characteristics of magnetostructural coupling play a crucial role in the magnetic field-driven behaviour of magnetofunctional alloys. The availability of magnetostructural coupling over a broad temperature range is of great significance for scientific and technological purposes. This work demonstrates that strong magnetostrucural coupling can be achieved over a wide temperature range (222 to 355 K) in Co-doped high Mn-content Mn50Ni42−xCoxSn8 (0 ≤ x ≤ 10) melt-spun ribbons. It is shown that, over a wide composition range with Co content from 3 to 9 at.%, the paramagnetic austenite first transforms into ferromagnetic austenite at TC on cooling, then the ferromagnetic austenite further transforms into a weakly magnetic martensite at TM. Such strong magnetostructural coupling enables the ribbons to exhibit field-induced inverse martensitic transformation behaviour and a large magnetocaloric effect. Under a field change of 5 T, a maximum magnetic entropy change ΔSM of 18.6 J kg−1 K−1 and an effective refrigerant capacity RCeff of up to 178 J kg−1 can be achieved, which are comparable with or even superior to those of Ni-rich Ni–Mn-based polycrystalline bulk alloys. The combination of high performance and low cost makes Mn–Ni–Co–Sn ribbons of great interest as potential candidates for magnetic refrigeration.

Description: Hirshfeld atom refinement (HAR) is a novel X-ray structure refinement technique that employs aspherical atomic scattering factors obtained from stockholder partitioning of a theoretically determined tailor-made static electron density. HAR overcomes many of the known limitations of independent atom modelling (IAM), such as too short element–hydrogen distances, r(X—H), or too large atomic displacement parameters (ADPs). This study probes the accuracy and precision of anisotropic hydrogen and non-hydrogen ADPs and of r(X—H) values obtained from HAR. These quantities are compared and found to agree with those obtained from (i) accurate neutron diffraction data measured at the same temperatures as the X-ray data and (ii) multipole modelling (MM), an established alternative method for interpreting X-ray diffraction data with the help of aspherical atomic scattering factors. Results are presented for three chemically different systems: the aromatic hydrocarbon rubrene (orthorhombic 5,6,11,12-tetraphenyltetracene), a co-crystal of zwitterionic betaine, imidazolium cations and picrate anions (BIPa), and the salt potassium hydrogen oxalate (KHOx). The non-hydrogen HAR-ADPs are as accurate and precise as the MM-ADPs. Both show excellent agreement with the neutron-based values and are superior to IAM-ADPs. The anisotropic hydrogen HAR-ADPs show a somewhat larger deviation from neutron-based values than the hydrogen SHADE-ADPs used in MM. Element–hydrogen bond lengths from HAR are in excellent agreement with those obtained from neutron diffraction experiments, although they are somewhat less precise. The residual density contour maps after HAR show fewer features than those after MM. Calculating the static electron density with the def2-TZVP basis set instead of the simpler def2-SVP one does not improve the refinement results significantly. All HARs were performed within the recently introduced HARt option implemented in the Olex2 program. They are easily launched inside its graphical user interface following a conventional IAM.

Description: Direct observation and structural characterization of a kinetic product and a thermodynamic product for complexes with an NO2S2 macrocycle (L) are reported. L reacts with copper(I) iodide to give a mononuclear complex [Cu(L)]2(Cu2I4)·2CH2Cl2 (1), featuring three separate units. When cadmium(II) iodide was reacted with L, an anion-coordinated complex [Cd(L)I]2(Cd2I6)·4CH3CN (2) with a needle-type crystal shape was formed as the kinetic product. Interestingly, when the needle-type kinetic product was left undisturbed in the mother solution it gradually transformed to the pseudo-dimer complex [Cd2(L)2I2](Cd2I6) (3) with a brick-type crystal shape as the thermodynamic product. The dissolution–recrystallization process resulted in the elimination of the lattice solvent molecules (acetonitrile) in 2 and the contraction of two neighboring macrocyclic complex units [Cd(L)I]+, forming the pseudo-dimer 3 via an intermolecular Cd...I interaction between two monomers. For the entire process from kinetic to thermodynamic products, it was possible to obtain sequential photographic snapshots, single-crystal X-ray structures and powder X-ray diffraction patterns. For the copper(I) and cadmium(II) complexes, competitive NMR results agree with the solid-state data that show copper(I) has a higher affinity for L than does cadmium(II).

Description: This paper shows how nonuniform source–receiver spacing in a three-dimensional (3-D) land acquisition creates footprints that could easily be mistaken for geology. In a 3-D time-migrated seismic volume from the midcontinent United States, amplitude extraction along the top of the Mississippian limestone formation shows a sinkhole-like feature, which is justified from a depositional perspective. However, an inspection of the acquisition layout shows that the sinkhole is a replica of the fold distribution. In land surveys where source and receivers seldom have a regular distribution and for unconventional plays that are not developed through patterned drilling, a thorough review of processing and acquisition parameters is necessary before interpreting amplitude maps.

Description: We use experimental (analog) models to examine the three-dimensional (3-D) fault geometries and interactions that develop during two phases of noncoaxial extension. In the models, a homogeneous layer of wet clay undergoes two phases of extension whose directions differ by 45°. The resulting fault pattern varies significantly with depth. At shallow levels, second-phase normal faults accommodate most second-phase extension. At depth, both second-phase normal faults and reactivated, first-phase faults with oblique slip accommodate most second-phase extension. A variety of interactions occurs between first-phase and second-phase faults. One interaction involves the upward propagation of second-phase faults from tips of reactivated, blind, first-phase faults. These hybrid faults have deep segments that strike subperpendicular to the first-phase extension direction and shallow segments whose strike varies with depth, becoming increasingly subperpendicular to the second-phase extension direction at shallow levels. A second interaction involves the nucleation of second-phase normal faults on the surfaces of reactivated, first-phase faults. These splay faults propagate upward and laterally from their nucleation sites into the hanging walls of the first-phase faults. As they propagate, they commonly encounter and link with different first-phase faults. The resulting composite faults have zigzag geometries in both map and cross-sectional views. A third interaction involves either the termination of second-phase antithetic normal faults against or near first-phase faults or the offset of first-phase faults by second-phase antithetic normal faults. The 3-D fault patterns and interactions within our models closely resemble those within the Taranaki basin of offshore New Zealand and Milne Point on Alaska’s North Slope.

Description: In order to develop transferable and practical avenues for the assembly of coordination complexes into architectures with specific dimensionality, a strategy utilizing ligands capable of simultaneous metal coordination and self-complementary hydrogen bonding is presented. The three ligands used, 2(1H)-pyrazinone, 4(3H)-pyrimidinone and 4(3H)-quinazolinone, consistently deliver the required synthetic vectors in a series of CdII coordination polymers, allowing for reproducible supramolecular synthesis that is insensitive to the different steric and geometric demands from potentially disruptive counterions. In all nine crystallographically characterized compounds presented here, directional intermolecular N—H...O hydrogen bonds between ligands on adjacent complex building blocks drive the assembly and orientation of discrete building blocks into largely predictable topologies. Furthermore, whether the solids are prepared from solution or through liquid-assisted grinding, the structural outcome is the same, thus emphasizing the robustness of the synthetic protocol. The details of the molecular recognition events that take place in this series of compounds have been clearly delineated and rationalized in the context of calculated molecular electrostatic potential surfaces.

Description: Enantiomeric amino acids have specific physiological functions in complex biological systems. Systematic studies focusing on the solid-state properties of d-amino acids are, however, still limited. To shed light on this field, structural and spectroscopic studies of d-alanine using neutron powder diffraction, polarized Raman scattering and ab initio calculations of harmonic vibrational frequencies were carried out. Clear changes in the number of vibrational modes are observed as a function of temperature, which can be directly connected to variations of the N—D bond lengths. These results reveal dissimilarities in the structural properties of d-alanine compared with l-alanine.

Description: Synchrotron-based X-ray structural studies of ligand-bound enzymes are powerful tools to further our understanding of reaction mechanisms. For redox enzymes, it is necessary to study both the oxidized and reduced active sites to fully elucidate the reaction, an objective that is complicated by potential X-ray photoreduction. In the presence of the substrate, this can be exploited to construct a structural movie of the events associated with catalysis. Using the newly developed approach of serial femtosecond rotation crystallography (SF-ROX), an X-ray damage-free structure of the as-isolated copper nitrite reductase (CuNiR) was visualized. The sub-10 fs X-ray pulse length from the SACLA X-ray free-electron laser allowed diffraction data to be collected to 1.6 Å resolution in a `time-frozen' state. The extremely short duration of the X-ray pulses ensures the capture of data prior to the onset of radiation-induced changes, including radiolysis. Unexpectedly, an O2 ligand was identified bound to the T2Cu in a brand-new binding mode for a diatomic ligand in CuNiRs. The observation of O2 in a time-frozen structure of the as-isolated oxidized enzyme provides long-awaited clear-cut evidence for the mode of O2 binding in CuNiRs. This provides an insight into how CuNiR from Alcaligenes xylosoxidans can function as an oxidase, reducing O2 to H2O2, or as a superoxide dismutase (SOD) since it was shown to have ∼56% of the dismutase activity of the bovine SOD enzyme some two decades ago.

Description: The geochemistry and reservoir characteristics of the lacustrine shale in the Eocene Dongying depression are described in detail based on thin-section and field-emission–scanning electron microscope observations of well cores combined with x-ray diffraction, physical property testing, and geochemical indicators. The Eocene Shahejie (Es) Formation Es4s–Es3x shale member is predominantly carbonate, clay minerals, and quartz. Six lithofacies were identified: (1) laminated limestone (organic-rich laminated limestone and organic-poor laminated limestone), (2) laminated marl, (3) laminated calcareous mudstone, (4) laminated dolomite mudstone, (5) laminated gypsum mudstone, and (6) massive mudstone. The Es4s–Es3x shale samples from three cored wells had total organic carbon (TOC) contents in the range of 0.58 to 11.4 wt. %, with an average of 3.17 wt. %. The hydrocarbon generation potential (free hydrocarbons [S1] + the hydrocarbons cracked from kerogen [S2]) values range from 2.53 to 87.68 mg/g, with an average of 24.19 mg/g. The Es4s–Es3x shale of the Dongying depression has a high organic-matter content with very good or excellent hydrocarbon generation potential. The organic maceral composition is predominantly sapropelinite (up to 95%). The hydrogen index (being S2/TOC) versus the maximum yield temperature of pyrolysate ( T max ) indicates that the organic matter is predominantly type I kerogen, which contains a high proportion of convertible organic carbon. The Es4s–Es3x shale is thermally mature and within the oil window, with the vitrinite reflectance values ranging from 0.46% to 0.74% and the T max value ranging from 413°C to 450°C, with the average being 442°C. The shale contains interparticle pores, organic-matter pores, dissolution pores, intracrystalline pores, interlaminar fractures, tectonic fractures, and abnormal-pressure fractures. The primary matrix pore storage is secondary recrystallized intercrystal pores and dissolution pores that formed during thermal maturation of organic matter. The TOC content and effective thickness of the organic-rich shales are the primary factors for hydrocarbon generation. The reservoir capacity is related to the scale, abundance, and connectivity of pore spaces, which are controlled by the characteristics of the lithofacies, mineral composition, TOC content, and microfractures.

Description: A succession of four deep-water lobe complexes deposited within a salt-controlled minibasin have been imaged in unprecedented detail on high-resolution, high-frequency, three-dimensional seismic-reflection data. The ponded interval was deposited over approximately 2.7 m.y. and consists of four discrete sequences, each of which contains one lobe complex. A systematic change exists in the shape and orientation of the lobe complexes through time: the two older lobe complexes are oriented broadly north–south and are up to 10 km (6 mi) long by 5 km (3 mi) wide, whereas the youngest lobe complexes are oriented southeast–northwest and have a rounder shape (9 km [6 mi] long by 8 km [5 mi] wide). The north–to-south migration of the feeder-channel entry point and the change in lobe-complex orientation are attributed to growth of the basin-bounding salt structures. Each lobe complex is composed of a feeder channel, multiple individual lobes formed of a trunk channel, and a diverging network of smaller distributary channels, commonly fringed by a high-amplitude band. The lobes are on average 1.6 km (1 mi) long by 1.3 km (0.8 mi) wide and are fed by trunk channels that range from 60 to 200 m (197 ft to 656 ft) wide, with thicknesses up to 15 m (49 ft). Variations in lobe shape and spatial location are driven by the response of the lobes to topographic growth along the edge of the basin and inherited seabed relief generated by previous lobe growth. In areas where lobe development is constrained by structural growth along the edge of the basin, the lobes become elongated and divert away from the growing topography. Lobe complexes of similar scales have been described in detail in outcrops and in unconfined settings on the sea floor, but this is the first study to describe these systems in such detail in the subsurface, resolving the individual lobes and lobe elements within a ponded intraslope basin. The high-resolution plan-view images help bridge the gap between the fine-scale sedimentological studies that have been carried out on lobe complexes and sheet sands in outcrop for the past 20 yr and more recent research on less well-resolved seismically imaged systems. The sheet sands described in outcrop studies can be correlated with features seen in the plan-view amplitude extraction maps. We record densely channelized lobes passing laterally into more branched, thinner channels and lobe elements then terminating in a high-amplitude fringe. We relate these seismic characteristics to outcrop facies of channelized, amalgamated, and layered sheets.

Description: The limiting factor in protein crystallography is still the production of high-quality crystals. In this regard, the authors have recently introduced hexatungstotellurate(VI) (TEW) as a new crystallization additive, which proved to be successful within the liquid–liquid phase separation (LLPS) zone. Presented here are comparative crystal structure analyses revealing that protein–TEW binding not only induces and stabilizes crystal contacts, but also exhibits a significant impact on the solvent-driven crystallization entropy, which is the driving force for the crystallization process. Upon the formation of TEW-mediated protein–protein contacts, the release of water molecules from the hydration shells of both molecules, i.e. TEW and the protein, causes a reduced solvent-accessible surface area, leading to a significant gain in solvent entropy. Based on the crystal structures of aurone synthase (in the presence and absence of TEW), insights have also been provided into the formation of a metastable LLPS, which is caused by the formation of protein clusters, representing an ideal starting point in protein crystallization. The results strongly encourage the classification of TEW as a valuable crystallization additive.

Description: The design and synthesis of mechanically responsive materials is interesting because they are potential candidates to convert thermal energy into mechanical work. Reported in this paper are thermosalient effects in a series of halogen derivatives of salinazids. The chloro derivative, with higher electronegativity and a weaker inter-halogen bond strength (Cl...Cl) exhibits an excellent thermal response, whereas the response is weaker in the iodo derivative with stronger I...I halogen bonding. 3,5-Dichlorosalinazid (Compound-A) exists in three polymorphic forms, two room-temperature polymorphs (Forms I and II) and one high-temperature modification (Form III). The transformation of Form I to Form III upon heating at 328–333 K is a reversible thermosalient transition, whereas the transformation of Form II to Form III is irreversible and non-thermosalient. 3,5-Dibromo- (Compound-B) and 3-bromo-5-chloro- (Compound-C) salinazid are both dimorphic: the Form I to Form II transition in Compound-B is irreversible, whereas Compound-C shows a reversible thermosalient effect (362–365 K). In the case of 3,5-diiodosalinazid (Compound-D) and 3,5-difluorosalinazid (Compound-E), no phase transitions or thermal effects were observed. The thermosalient behaviour of these halosalinazid molecular crystals is understood from the anisotropy in the cell parameters (an increase in the a axis and a decrease in the b and c axes upon heating) and the sudden release of accumulated strain during the phase transition. The di-halogen salinazid derivatives (chlorine to iodine) show a decrease in thermal effects with an increase in halogen-bond strength. Interestingly, Compound-B shows solid-state photochromism in its polymorphs along with the thermosalient effect, wherein Form I is cyan and Form II is light orange.

Description: Human carbonic anhydrase II (hCA II) is a zinc metalloenzyme that catalyzes the reversible hydration/dehydration of CO2/HCO3−. Although hCA II has been extensively studied to investigate the proton-transfer process that occurs in the active site, its underlying mechanism is still not fully understood. Here, ultrahigh-resolution crystallographic structures of hCA II cryocooled under CO2 pressures of 7.0 and 2.5 atm are presented. The structures reveal new intermediate solvent states of hCA II that provide crystallographic snapshots during the restoration of the proton-transfer water network in the active site. Specifically, a new intermediate water (WI′) is observed next to the previously observed intermediate water WI, and they are both stabilized by the five water molecules at the entrance to the active site (the entrance conduit). Based on these structures, a water network-restructuring mechanism is proposed, which takes place at the active site after the nucleophilic attack of OH− on CO2. This mechanism explains how the zinc-bound water (WZn) and W1 are replenished, which are directly responsible for the reconnection of the His64-mediated proton-transfer water network. This study provides the first `physical' glimpse of how a water reservoir flows into the hCA II active site during its catalytic activity.

Description: Peroxiredoxins (Prxs) are ubiquitous cysteine-based peroxidase enzymes. Recently, a new type of Prx, VvPrx3, was identified in the pathogenic bacterium Vibrio vulnificus as being important for survival in macrophages. It employs only one catalytic cysteine residue to decompose peroxides. Here, crystal structures of VvPrx3 representing its reduced and oxidized states have been determined, together with an H2O2-bound structure, at high resolution. The crystal structure representing the reduced Prx3 showed a typical dimeric interface, called the A-type interface. However, VvPrx3 forms an oligomeric interface mediated by a disulfide bond between two catalytic cysteine residues from two adjacent dimers, which differs from the doughnut-like oligomers that appear in most Prxs. Subsequent biochemical studies showed that this disulfide bond was induced by treatment with nitric oxide (NO) as well as with peroxides. Consistently, NO treatment induced expression of the prx3 gene in V. vulnificus, and VvPrx3 was crucial for the survival of bacteria in the presence of NO. Taken together, the function and mechanism of VvPrx3 in scavenging peroxides and NO stress via oligomerization are proposed. These findings contribute to the understanding of the diverse functions of Prxs during pathogenic processes at the molecular level.

Description: Previous proof-of-concept measurements on single-layer two-dimensional membrane-protein crystals performed at X-ray free-electron lasers (FELs) have demonstrated that the collection of meaningful diffraction patterns, which is not possible at synchrotrons because of radiation-damage issues, is feasible. Here, the results obtained from the analysis of a thousand single-shot, room-temperature X-ray FEL diffraction images from two-dimensional crystals of a bacteriorhodopsin mutant are reported in detail. The high redundancy in the measurements boosts the intensity signal-to-noise ratio, so that the values of the diffracted intensities can be reliably determined down to the detector-edge resolution of 4 Å. The results show that two-dimensional serial crystallography at X-ray FELs is a suitable method to study membrane proteins to near-atomic length scales at ambient temperature. The method presented here can be extended to pump–probe studies of optically triggered structural changes on submillisecond timescales in two-dimensional crystals, which allow functionally relevant large-scale motions that may be quenched in three-dimensional crystals.

Description: Halogen bonds have been identified in a series of ionic compounds involving bromonium and iodonium cations and several different anions, some also containing hypervalent atoms. The hypervalent bromine and iodine atoms in the examined compounds are found to have positive σ-holes on the extensions of their covalent bonds, while the hypervalent atoms in the anions have negative σ-holes. The positive σ-holes on the halogens of the studied halonium salts determine the linearity of the short contacts between the halogen and neutral or anionic electron donors, as usual in halogen bonds.

Description: Confidently defining the trajectory of faults that control structural traps is a recurring challenge for seismic interpreters. In regions with fault-related folds, seismic and well data often constrain the upper fold geometry, but the location and displacement of the controlling fault are unknown. We present a generalized area–depth strain (ADS) analysis method that uses the observed depth variation in deformed horizon areas to directly estimate underlying fault depth, dip, displacement, and layer-parallel strain from a structural interpretation. Previously established ADS methods are only applicable to structures controlled by faults that sole into layer-parallel detachments. The new technique, referred to as the fault-trajectory method, generalizes ADS analysis to contractional and extensional structures controlled by fault ramps that cut across layers and displace the regional. For structures where area is conserved during deformation and shear is minimal, laterally shifting the analysis limits across the structure defines changes in fault orientation. We validate the method by applying it to numerical forward models, analog clay models, and seismically imaged structures from the San Joaquin basin in California, the Sierras Pampeanas in Argentina, and the North Sea. The fault-trajectory method is shown to be robust, because it exactly reproduces the prescribed fault trajectories and displacements used to construct the numerical and analog models. In the natural examples, the ADS-estimated fault trajectories are consistent with independent fault-location constraints such as earthquake focal mechanisms, seismic imaging, and forward modeling.

Description: Well logs such as spontaneous potential and gamma ray historically have been the only tools available for facies evaluation of noncored wells in the McMurray Formation. The addition of microresistivity image logs has greatly improved facies identifications and interpretations, particularly when integrated with core data sets. In the case of McMurray channel complexes, core descriptions provide detail about bedding contacts, sedimentary texture, stratification, bioturbation intensity, and trace fossil diversity. Image logs provide texture, fabric, bedding contact style, dip directions and angles, and bedding architecture information, yielding paleoflow and lateral accretion directions. This study characterizes facies by integrating interpretations from 414 image logs with core-based descriptions from 138 of these wells. The reservoir targets, and most prolific depositional facies in this study, are associated with channel systems and their associated point-bar deposits. Facies identifications are based on several image log criteria. Mud clast breccias display variable dip angles and dip directions. Cross-stratified sands comprise vertical successions of stacked, internally consistent bedsets with high dip angles (〉15°) that indicate paleoflow direction. Lateral accretion beds show consistent dip directions with a progressive change from shallow-to-steep-to-shallow dip angles (e.g., 〈4 to 15° to 〈4°) from the base to the top of the succession, as well as beds that dip toward the thalweg of the paleochannel. Flat-lying (〈4°) mud records vertical accretion associated with point-bar tops or channel abandonment. Although this facies classification is specific to the McMurray Formation in the study area, the principles provided here are applicable to other subsurface studies and demonstrate the enhanced reliability of integrated core–image log data sets.

Description: The development and application of the free-electron X-ray laser (XFEL) to structure and dynamics in biology since its inception in 2009 are reviewed. The research opportunities which result from the ability to outrun most radiation-damage effects are outlined, and some grand challenges are suggested. By avoiding the need to cool samples to minimize damage, the XFEL has permitted atomic resolution imaging of molecular processes on the 100 fs timescale under near-physiological conditions and in the correct thermal bath in which molecular machines operate. Radiation damage, comparisons of XFEL and synchrotron work, single-particle diffraction, fast solution scattering, pump–probe studies on photosensitive proteins, mix-and-inject experiments, caged molecules, pH jump and other reaction-initiation methods, and the study of molecular machines are all discussed. Sample-delivery methods and data-analysis algorithms for the various modes, from serial femtosecond crystallography to fast solution scattering, fluctuation X-ray scattering, mixing jet experiments and single-particle diffraction, are also reviewed.

Description: Crystallogenesis is a longstanding topic that has transformed into a discipline that is mainly focused on the preparation of crystals for practising crystallographers. Although the idiosyncratic features of proteins have to be taken into account, the crystallization of proteins is governed by the same physics as the crystallization of inorganic materials. At present, a diversified panel of crystallization methods adapted to proteins has been validated, and although only a few methods are in current practice, the success rate of crystallization has increased constantly, leading to the determination of ∼105 X-ray structures. These structures reveal a huge repertoire of protein folds, but they only cover a restricted part of macromolecular diversity across the tree of life. In the future, crystals representative of missing structures or that will better document the structural dynamics and functional steps underlying biological processes need to be grown. For the pertinent choice of biologically relevant targets, computer-guided analysis of structural databases is needed. From another perspective, crystallization is a self-assembly process that can occur in the bulk of crowded fluids, with crystals being supramolecular assemblies. Life also uses self-assembly and supramolecular processes leading to transient, or less often stable, complexes. An integrated view of supramolecularity implies that proteins crystallizing either in vitro or in vivo or participating in cellular processes share common attributes, notably determinants and antideterminants that favour or disfavour their correct or incorrect associations. As a result, under in vivo conditions proteins show a balance between features that favour or disfavour association. If this balance is broken, disorders/diseases occur. Understanding crystallization under in vivo conditions is a challenge for the future. In this quest, the analysis of packing contacts and contacts within oligomers will be crucial in order to decipher the rules governing protein self-assembly and will guide the engineering of novel biomaterials. In a wider perspective, understanding such contacts will open the route towards supramolecular biology and generalized crystallogenesis.

Description: A cross-validation method is supplied to judge between various strategies in multipole refinement procedures. Its application enables straightforward detection of whether the refinement of additional parameters leads to an improvement in the model or an overfitting of the given data. For all tested data sets it was possible to prove that the multipole parameters of atoms in comparable chemical environments should be constrained to be identical. In an automated approach, this method additionally delivers parameter distributions of k different refinements. These distributions can be used for further error diagnostics, e.g. to detect erroneously defined parameters or incorrectly determined reflections. Visualization tools show the variation in the parameters. These different refinements also provide rough estimates for the standard deviation of topological parameters.

Description: Crystal structure determination of biological macromolecules using the novel technique of serial femtosecond crystallography (SFX) is severely limited by the scarcity of X-ray free-electron laser (XFEL) sources. However, recent and future upgrades render microfocus beamlines at synchrotron-radiation sources suitable for room-temperature serial crystallography data collection also. Owing to the longer exposure times that are needed at synchrotrons, serial data collection is termed serial millisecond crystallography (SMX). As a result, the number of SMX experiments is growing rapidly, with a dozen experiments reported so far. Here, the first high-viscosity injector-based SMX experiments carried out at a US synchrotron source, the Advanced Photon Source (APS), are reported. Microcrystals (5–20 µm) of a wide variety of proteins, including lysozyme, thaumatin, phycocyanin, the human A2A adenosine receptor (A2AAR), the soluble fragment of the membrane lipoprotein Flpp3 and proteinase K, were screened. Crystals suspended in lipidic cubic phase (LCP) or a high-molecular-weight poly(ethylene oxide) (PEO; molecular weight 8 000 000) were delivered to the beam using a high-viscosity injector. In-house data-reduction (hit-finding) software developed at APS as well as the SFX data-reduction and analysis software suites Cheetah and CrystFEL enabled efficient on-site SMX data monitoring, reduction and processing. Complete data sets were collected for A2AAR, phycocyanin, Flpp3, proteinase K and lysozyme, and the structures of A2AAR, phycocyanin, proteinase K and lysozyme were determined at 3.2, 3.1, 2.65 and 2.05 Å resolution, respectively. The data demonstrate the feasibility of serial millisecond crystallography from 5–20 µm crystals using a high-viscosity injector at APS. The resolution of the crystal structures obtained in this study was dictated by the current flux density and crystal size, but upcoming developments in beamline optics and the planned APS-U upgrade will increase the intensity by two orders of magnitude. These developments will enable structure determination from smaller and/or weakly diffracting microcrystals.

Description: This topical review summarizes the theoretical and experimental findings obtained over the last 20 years on the subject of growth-induced polarity formation driven by a Markov chain process. When entering the growing surface of a molecular crystal, an inorganic–organic composite or a natural tissue, the building blocks may undergo 180° orientational disorder. Driven by configurational entropy, faulted orientations can promote the conversion of a growing non-polar seed into an object showing polar domains. Similarly, orientational disorder at the interface may change a polar seed into a two-domain state. Analytical theory and Monte Carlo simulations were used to model polarity formation. Scanning pyroelectric, piezoresponse force and phase-sensitive second-harmonic microscopies are methods for investigating the spatial distribution of polarity. Summarizing results from different types of materials, a general principle is provided for obtaining growth-induced polar domains: a non-zero difference in the probabilities for 180° orientational misalignments of building blocks, together with uni-directional growth, along with Markov chain theory, can produce objects showing polar domains.