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At least 289 records · Page 16

Role of Delamination in Zeolite-Catalyzed Aromatic Alkylation: UCB-3 versus 3-D Al-SSZ-70

Delaminated zeolite UCB-3 exhibits 2.4-fold greater catalytic activity relative to its three-dimensional (3D) zeolite counterpart, Al-SSZ-70, and 2.0-fold greater activity (per catalyst mass) when compared with industrial catalyst MCM-22, for the alkylation of toluene with propylene at 523 K. The former increase is nearly equal to the observed relative increase in external surface area and acid sites upon delamination. However, at 423 K for the same reaction, UCB-3 exhibits a 3.5-fold greater catalytic activity relative to 3D Al-SSZ-70. The higher relative rate enhancement for the delaminated material at lower temperature can be elucidated on the basis of increased contributions from internal acid sites. Evidence of possible contributions from such acid sites is obtained by performing catalysis after silanation treatment, which demonstrates that although virtually all catalysis in MCM-22 occurs on the external surface, catalysis also occurs on internal sites for 3D Al-SSZ-70. The additional observed enhancement at low temperatures can therefore be rationalized by greater access to internal active sites as a result of sheet breakage during delamination. Such breakage leads to shorter characteristic internal diffusion paths and was visualized using TEM comparisons of UCB-3 and 3D Al-SSZ-70.

aromatic alkylation↗

eSHAFTS: Integrated and graphical drug design software based on 3D molecular similarity

With the development of computer technology, computer‐aided drug design (CADD) has become an important means for drug research and development, and its representative method is virtual screening. Various virtual screening platforms have emerged in an endless stream and play great roles in the field of drug discovery. With the increasing number of compound molecules, virtual screening platforms face two challenges: low fluency and low visibility of software operations. In this article, we present an integrated and graphical drug design software eSHAFTS based on three‐dimensional (3D) molecular similarity to overcome these shortcomings. Compared with other software, eSHAFTS has four main advantages, which are integrated molecular editing and drawing, interactive loading and analysis of proteins, multithread and multimode 3D molecular similarity calculation, and multidimensional information visualization. Experiments have verified its convenience, usability, and reliability. By using eSHAFTS, various tasks can be submitted and visualized in one desktop software without locally installing any dependent plug‐ins or software. The software installation package can be downloaded for free at http://lilab.ecust.edu.cn/home/resource.html . © 2019 Wiley Periodicals, Inc.

He, Gaoqi↗

Spatial patterns of extracellular enzymes: Combining X-ray computed micro-tomography and 2D zymography

We report that linking the distribution of enzyme activity to the size and properties of soil pores is a necessary prerequisite for mechanistic understanding of soil biochemical processes. In this study we used soil 2D zymography and X-ray computed tomography (μCT) to assess the relationship between enzymes and pores. The objectives of the study were (i) to assess spatial distribution patterns in the activity of six enzymes contributing to C, N and P cycles, namely, cellobiohydrolase, β-glucosidase, xylanase acid phosphatase, leucine aminopeptidase, and N-acetylglucosaminidase, in soils from five long-term land use and management practices, (ii) to study the correlation between enzyme activities and μCT information, i.e., pore characteristics and image grayscale values, and (iii) to explore the potential use of soil 2D zymography in predicting enzyme activities within 3D soil cores. 3D pore-size distributions were obtained from μCT images of 13 intact soil cores and then 8–15 2D zymography maps were taken from each core. Spatial distributions in the activities of all studied enzymes were auto-correlated; the spatial correlation ranges were equal to ~7–8 mm. The relative activity of all enzymes was positively associated within 60–180 μm Ø pores. Combining 3D μCT information with 2D zymography maps visualized the overall patterns of enzyme activity distributions with respect to soil pores and particulate organic matter locations. Based on the findings we propose a conceptual scheme relating localization of microorganisms, enzymes and substrates to pores of different size ranges. Specifically, we suggest that pores in the tens of microns size range represent optimal microbial habitats, and as such are associated with greater microbial abundance, leading to high enzyme production and activity.

59 BASIC BIOLOGICAL SCIENCES↗

In Situ Atomic Scale Visualization Of Surface Kinetics Driven Dynamics Of Oxide Growth On A Ni–Cr Surface

We report in situ atomic-scale visualization of the dynamical three-dimensional (3D) growth of NiO during initial oxidation of Ni-10at%Cr using environmental transmission electron microscopy (ETEM). Despite the thermodynamic preference for Cr2O3 formation, cubic NiO oxides nucleated and grew epitaxially as the dominating oxide phase on the Ni-Cr (100) surface during initial oxidation. The growth of NiO islands proceeds through step-by-step adatom mechanism in 3D, which is sustained by surface diffusion of Ni and O atoms. Although the shapes of oxide islands are controlled by strain energy between oxide and alloy substrate, local surface kinetic variations can lead to the change of surface planes of oxide islands. These results demonstrate that surface diffusion dominates initial oxidation of Ni-Cr in these test conditions.

Environmental Molecular Sciences Laboratory↗

STUDY OF THE THREE-DIMENSIONAL CORONAL MAGNETIC FIELD OF ACTIVE REGION 11117 AROUND THE TIME OF A CONFINED FLARE USING A DATA-DRIVEN CESE-MHD MODEL

We apply a data-driven magnetohydrodynamics (MHD) model to investigate the three-dimensional (3D) magnetic field of NOAA active region (AR) 11117 around the time of a C-class confined flare that occurred on 2010 October 25. The MHD model, based on the spacetime conservation-element and solution-element scheme, is designed to focus on the magnetic field evolution and to consider a simplified solar atomsphere with finite plasma {beta}. Magnetic vector-field data derived from the observations at the photosphere is inputted directly to constrain the model. Assuming that the dynamic evolution of the coronal magnetic field can be approximated by successive equilibria, we solve a time sequence of MHD equilibria based on a set of vector magnetograms for AR 11117 taken by the Helioseismic and Magnetic Imager on board the Solar Dynamic Observatory around the time of the flare. The model qualitatively reproduces the basic structures of the 3D magnetic field, as supported by the visual similarity between the field lines and the coronal loops observed by the Atmospheric Imaging Assembly, which shows that the coronal field can indeed be well characterized by the MHD equilibrium in most cases. The magnetic configuration changes very little during the studied time interval of 2 hr. A topological analysis reveals that the small flare is correlated with a bald patch (BP, where the magnetic field is tangent to the photosphere), suggesting that the energy release of the flare can be understood by magnetic reconnection associated with the BP separatrices. The total magnetic flux and energy keep increasing slightly in spite of the flare, while the computed magnetic free energy drops during the flare by {approx}10{sup 30} erg, which seems to be adequate in providing the energy budget of a minor C-class confined flare.

79 ASTRONOMY AND ASTROPHYSICS↗

Q -score as a reliability measure for protein, nucleic acid and small-molecule atomic coordinate models derived from 3DEM maps

Atomic coordinate models are important for the interpretation of 3D maps produced with cryoEM and cryoET (3D electron microscopy; 3DEM). In addition to visual inspection of such maps and models, quantitative metrics can inform about the reliability of the atomic coordinates, in particular how well the model is supported by the experimentally determined 3DEM map. A recently introduced metric, Q-score, was shown to correlate well with the reported resolution of the map for well fitted models. Here, we present new statistical analyses of Q-score based on its application to ∼10 000 maps and models archived in the EMDB (Electron Microscopy Data Bank) and PDB (Protein Data Bank). Further, we introduce two new metrics based on Q-score to represent each map and model relative to all entries in the EMDB and those with similar resolution. We explore through illustrative examples of proteins, nucleic acids and small molecules how Q-scores can indicate whether the atomic coordinates are well fitted to 3DEM maps and also whether some parts of a map may be poorly resolved due to factors such as molecular flexibility, radiation damage and/or conformational heterogeneity. These examples and statistical analyses provide a basis for how Q-scores can be interpreted effectively in order to evaluate 3DEM maps and atomic coordinate models prior to publication and archiving.

B factors↗

Reservoir Characterization of Bridgeport and Cypress Sandstones in Lawrence Field Illinois to Improve Petroleum Recovery by Alkaline-Surfactant-Polymer Flood

Within the Illinois Basin, most of the oilfields are mature and have been extensively waterflooded with water cuts that range up to 99% in many of the larger fields. In order to maximize production of significant remaining mobile oil from these fields, new recovery techniques need to be researched and applied. The purpose of this project was to conduct reservoir characterization studies supporting Alkaline-Surfactant-Polymer Floods in two distinct sandstone reservoirs in Lawrence Field, Lawrence County, Illinois. A project using alkaline-surfactantpolymer (ASP) has been established in the century old Lawrence Field in southeastern Illinois where original oil in place (OOIP) is estimated at over a billion barrels and 400 million barrels have been recovered leaving more than 600 million barrels as an EOR target. Radial core flood analysis using core from the field demonstrated recoveries greater than 20% of OOIP. While the lab results are likely optimistic to actual field performance, the ASP tests indicate that substantial reserves could be recovered even if the field results are 5 to 10% of OOIP. Reservoir characterization is a key factor in the success of any EOR application. Reservoirs within the Illinois Basin are frequently characterized as being highly compartmentalized resulting in multiple flow unit configurations. The research conducted on Lawrence Field focused on characteristics that define reservoir compartmentalization in order to delineate preferred target areas so that the chemical flood can be designed and implemented for the greatest recovery potential. Along with traditional facies mapping, core analyses and petrographic analyses, conceptual geological models were constructed and used to develop 3D geocellular models, a valuable tool for visualizing reservoir architecture and also a prerequisite for reservoir simulation modeling. Cores were described and potential permeability barriers were correlated using geophysical logs. Petrographic analyses were used to better understand porosity and permeability trends in the region and to characterize barriers and define flow units. Diagenetic alterations that impact porosity and permeability include development of quartz overgrowths, sutured quartz grains, dissolution of feldspar grains, formation of clay mineral coatings on grains, and calcite cementation. Many of these alterations are controlled by facies. Mapping efforts identified distinct flow units in the northern part of the field showing that the Pennsylvanian Bridgeport consists of a series of thick incised channel fill sequences. The sandstones are about 75-150 feet thick and typically consist of medium grained and poorly sorted fluvial to distributary channel fill deposits at the base. The sandstones become indistinctly bedded distributary channel deposits in the main part of the reservoir before fining upwards and becoming more tidally influenced near their top. These channel deposits have core permeabilities ranging from 20 md to well over 1000 md. The tidally influenced deposits are more compartmentalized compared to the thicker and more continuous basal fluvial deposits. Fine grained sandstones that are laterally equivalent to the thicker channel type deposits have permeabilities rarely reaching above 250 md. Most of the unrecovered oil in Lawrence Field is contained in Pennsylvanian Age Bridgeport sandstones and Mississippian Age Cypress sandstones. These reservoirs are highly complex and compartmentalized. Detailed reservoir characterization including the development of 3-D geologic and geocellular models of target areas in the field were completed to identify areas with the best potential to recover remaining reserves including unswept and by-passed oil. This project consisted of tasks designed to compile, interpret, and analyze the data required to conduct reservoir characterization for the Bridgeport and Cypress sandstones in pilot areas in anticipation of expanded implementation of ASP flooding in Lawrence Field. Geologic and geocellular modeling needed for reservoir characterization and reservoir simulation were completed as prerequisites for design of efficient ASP flood patterns. Characterizing the complex reservoir geology that identifies the geologic conditions that will optimize oil recoveries for expansion of the ASP pilots in the Bridgeport and Cypress sandstones to other areas of Lawrence Field is the primary objective of this project. It will permit evaluation of efficiency of oil recovery from Bridgeport and Cypress sandstone reservoirs using ASP technology. Additionally evaluation of similar Pennsylvanian and Chesterian reservoirs shows that it is likely that ASP flood technology can be successfully applied to similar reservoirs in the Illinois Basin as well as to other U.S. reservoirs. Chemical flooding was introduced in stages with the first flood initiated in 2010 and a second offset pilot project initiated during 2011. Rex Energy Corporation is reporting a positive response on its ASP Middagh pilot project in the Pennsylvanian Bridgeport B reservoir, Lawrence Field. Oil response in the 15 acre flood has continued to show an increase in oil cut from 1% to 12%. Total pattern production increased from 16 BOPD and stabilized at a range of 65-75 BOPD in the last three months of 2011. Peak production rose to 100 + BOPD. Oil cut in the pilot increased for 1.0% to ~ 12.0% with an individual well showing oil cuts greater than 20%. A second, 58 acre pilot (Perkins-Smith) adjacent to and likely in communication with the Middagh pilot has been initiated. Preliminary brine injection has been implemented and ASP injection was initiated in mid-2012. Response is expected by mid-2013 with peak recovery expected by late 2013. Rex Energy is projecting full scale expansion with the next step of development being a 351 acre project scheduled to begin in mid-2013. Preliminary development has been initiated in this Delta Unit area located in the south half of section 32, T4N, R12W.

02 PETROLEUM↗

Feasibility Study of Millimeter Wave Radars For Safeguards Applications

Containment and surveillance are fundamental measures in nuclear safeguards. Techniques such as video surveillance and laser curtain for containment provide effective monitoring in areas where maintaining continuity of knowledge is required. These systems, however, can be susceptible to loss of monitoring capabilities under certain environmental conditions such as poor visibility (i.e. low light conditions, smoke, fog, etc.) or extended power loss past the duration that the backup power system is designed for. Brookhaven National Laboratory has been investigating the feasibility of millimeter waves (mmWave) as a new perimeter seal in which radio frequency waves in the range of 60-64 GHz are used to detect and monitor objects of interest. Signals in this frequency range are not susceptible to environmental conditions. For proof-of-concept tests, mmWave sensors from Texas Instruments (TI), specificallyIWR6843, are used in a test bed at BNL's Waste Management facility to simulate the operations at nuclear facilities. The unique design of TI mmWave sensors requires less memory and power consumption compared to counterpart systems. These devices are capable of exporting 3D point-cloud data, which is visualized graphically and compared to videos recorded at the same time to validate the performance of the mmWave sensor. A set of experiments were planned to test the feasibility of the mmWave in this application, including monitoring static containers in a storage area and detecting intrusions at the boundaries of the area. In addition, the experiments also identify potential blind spots relative to sensor position and utilize multiple operating sensors simultaneously to reduce or eliminate such blind spots. The optimal positioning of multiple sensors was determined for the experimental room configuration. In this paper, we will discuss the details of this novel perimeter sealing concept and present the test results.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

Visualization of Jet Impingement and Ignition in a Piston-Cylinder Chamber

The transportation sector accounts for almost a third of the United States energy consumption. We are developing predictive simulations of the complex in-cylinder processes of internal combustion engines to improve performance and decrease pollutant emissions. Using volume rendering, we provide a first look at the jet impingement and ignition inside a piston-cylinder chamber. Through the visualization, we were able to construct a complete 3D picture of the jet impingement on the piston-bowl walls leading to the formation of pockets of auto-ignition of fuel-air mixture. These auto-ignition pockets subsequently lead to flame stabilization releasing the chemical energy for conversion to useful work. A detailed physical picture of flame stabilization as provided by the visualization techniques presented in this study help in the design next-generation internal combustion engines.

91 SC - Advanced Scientific Computing Reseach (ASC↗

SU-E-J-231: Comparison of 3D Angiogram and MRI in Delineating the AVM Target for Frameless Stereotactic Radiosurgery

Purpose: Stereotactic radiation therapy (SRT) provides an excellent alternative to embolization and surgical excision for the management of appropriately selected cerebral arteriovenous malformations (AVMs). The currently accepted standard for delineating AVMs is planar digital subtraction angiography (DSA). DSA can be used to acquire a 3D data set that preserves osseous structures (3D-DA) at the time of the angiography for SRT planning. Magnetic resonance imaging (MRI) provides an alternative noninvasive method of visualizing the AVM nidus with comparable spatial resolution. We utilized 3D-DA and T1 post-contrast MRI data to evaluate the differences in SRT target volumes. Methods: Four patients underwent 3D-DA and high-resolution MRI. 3D T1 post-contrast images were obtained in all three reconstruction planes. A planning CT was fused with MRI and 3D-DA data sets. The AVMs were contoured utilizing one of the image sets at a time. Target volume, centroid, and maximum and minimum dimensions were analyzed for each patient. Results: Targets delineated using post-contrast MRI demonstrated a larger mean volume. AVMs >2 cc were found to have a larger difference between MRI and 3D-DA volumes. Larger AVMs also demonstrated a smaller relative uncertainty in contour centroid position (1 mm). AVM targets <2 cc had smaller absolute differences in volume, but larger differences in contour centroid position (2.5 mm). MRI targets demonstrated a more irregular shape compared to 3D-DA targets. Conclusions: Our preliminary data supports the use of MRI alone to delineate AVM targets >2 cc. The greater centroid stability for AVMs >2 cc ensures accurate target localization during image fusion. The larger MRI target volumes did not result in prohibitively greater volumes of normal brain tissue receiving the prescription dose. The larger centroid instability for AVMs <2 cc precludes the use of MRI alone for target delineation. We recommend incorporating a 3D-DA for these patients.

60 APPLIED LIFE SCIENCES↗

Ascribe XR v0.1.0

Ascribe XR is an immersive visualization software designed for scientists and engineers working with 3D data sets. Its key features include interactive exploration, multi-user collaboration, and flexible data import capabilities, supporting various formats such as meshes, volumes, and terrain maps. The software utilizes Godot, OpenXR and PC-VR technology to provide an immersive experience. Ascribe XR is used for data analysis, visualization, and collaboration in various fields, enabling users to gain deeper insights into complex data sets. Its advantages over similar technologies include its flexibility, customizability, and ease of use. Ascribe XR's interactive and immersive environment facilitates collaboration and accelerates the discovery process. Compared to traditional 2D visualization tools, Ascribe XR offers a more engaging and intuitive experience, allowing users to explore complex data sets in a more natural and interactive way. Its ability to support multi-user collaboration and flexible data import capabilities make it a versatile tool for various applications. Overall, Ascribe XR provides a unique combination of features, usability, and performance, making it an attractive solution for scientists and engineers working with 3D data sets.

Pandolfi, Ronald [Lawrence Berkeley National Labor↗

High-resolution 3D seismic acquisition at the Tomakomai CO2 storage project, offshore Hokkaido, Japan

Monitoring injected CO2 is an important part of assuring permanence of long term storage to mitigate atmospheric emissions. Three-dimensional (3D) seismic has been shown to be an effective technology for visualizing and measuring subsurface geology and fluids. In this study, we demonstrate the successful acquisition, processing and initial interpretation of a high-resolution 3D (HR3D) seismic survey in Tomakomai, offshore Japan, above an active offshore CO2 injection site. The successful deployment of this novel marine seismic monitoring technology validates HR3D as an appropriate characterization and monitoring tool for large- demonstration and commercial-scale offshore Carbon Capture and Storage (CCS) sites.

Carbon Capture and Storage (CCS)↗

BinaryCIF and CIFTools—Lightweight, efficient and extensible macromolecular data management

3D macromolecular structural data is growing ever more complex and plentiful in the wake of substantive advances in experimental and computational structure determination methods including macromolecular crystallography, cryo-electron microscopy, and integrative methods. Efficient means of working with 3D macromolecular structural data for archiving, analyses, and visualization are central to facilitating interoperability and reusability in compliance with the FAIR Principles. We address two challenges posed by growth in data size and complexity. First, data size is reduced by bespoke compression techniques. Second, complexity is managed through improved software tooling and fully leveraging available data dictionary schemas. To this end, we introduce BinaryCIF, a serialization of Crystallographic Information File (CIF) format files that maintains full compatibility to related data schemas, such as PDBx/mmCIF, while reducing file sizes by more than a factor of two versus gzip compressed CIF files. Moreover, for the largest structures, BinaryCIF provides even better compression—factor ten and four versus CIF files and gzipped CIF files, respectively. Herein, we describe CIFTools, a set of libraries in Java and TypeScript for generic and typed handling of CIF and BinaryCIF files. Together, BinaryCIF and CIFTools enable lightweight, efficient, and extensible handling of 3D macromolecular structural data.

59 BASIC BIOLOGICAL SCIENCES↗

An Augmented 3D iPad Mobile Application for Communication, Collaboration, and Learning (CCL) of Building MEP Systems

The goal of this research is to gain better understanding of how BIM models can be used to create mobile 3D game environments for some serious purpose other than entertainment. This project was motivated by the perspective that the capability of BIM creating realistic 3D virtual game environments for collaboration, communication and learning (CCL). The wide dissemination of mobile devices is driving many computer applications toward the direction of ubiquitous mobile accessibility. Considering the popularity of the iPad mobile device, a BIM model of an institutional building was created for this 3D mobile game application on iPad. This game application allows users to visualize and interact with the HVAC BIM components. In this paper, we reported our preliminary findings in developing a BIM-based iPad 3D game application for CCL activities in architecture, engineering, and construction (AEC). Technical barriers of using BIM models to create mobile 3D CCL applications were also discussed. The detailed system architecture and implementation framework were presented in this paper. Differences between the developed program and the existing BIM mobile programs were elaborated to distinguish the developed program from the off-the-shelf BIM mobile programs, such as Vella and Autodesk Inventor mobile viewer. The preliminary results indicated that fairly complex BIM models including multiple building systems can be imported and created through 3D virtual-built environments to conducted CCL activities in the AEC domain.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

X-ray computed tomography of wood-adhesive bondlines: Attenuation and phase-contrast effects

Microscale X-ray computed tomography (XCT) is discussed as a technique for identifying 3D adhesive distribution in wood-adhesive bondlines. Visualization and material segmentation of the adhesives from the surrounding cellular structures require sufficient gray-scale contrast in the reconstructed XCT data. Commercial wood-adhesive polymers have similar chemical characteristics and density to wood cell wall polymers and therefore do not provide good XCT attenuation contrast in their native form. Here, three different adhesive types, namely phenol formaldehyde, polymeric diphenylmethane diisocyanate, and a hybrid polyvinyl acetate, are tagged with iodine such that they yield sufficient X-ray attenuation contrast. However, phase-contrast effects at material edges complicate image quality and segmentation in XCT data reconstructed with conventional filtered backprojection absorption contrast algorithms. A quantitative phase retrieval algorithm, which isolates and removes the phase-contrast effect, was demonstrated. The paper discusses and illustrates the balance between material X-ray attenuation and phase-contrast effects in all quantitative XCT analyses of wood-adhesive bondlines.

36 MATERIALS SCIENCE↗

Elastic and electronic properties of the Ti{sub 5}X{sub 3} (X=Si, Ge, Sn, Pb) compounds from first-principles calculations

The structural stabilities, elastic and electronic properties of Ti{sub 5}X{sub 3} (X=Si, Ge, Sn, Pb) compounds with D8{sub 8} structure have been systematically investigated within the frame work of density functional theory. With increase of atomic number of the element X, the calculated lattice constants of Ti{sub 5}X{sub 3} compounds are found to increase, while stabilities of these compounds decrease because the formation enthalpies increase. Moreover, with exception of C{sub 12}, the calculated elastic constants C{sub ij} are reduced with increase of atomic number of element X, the bulk, shear, Young's modulus and Debye temperature are also lowered, while Poisson's ratio is larger, and the ductility is slightly improved. The elastic anisotropies were further studied, especially the 3D direction dependence of these elastic modulus was visually described. The density of states and charge density distribution reveal bonding feature of Ti{sub 5}X{sub 3}. Especially, the X-X and Ti-X covalent bonding strength is found to decrease with increase of atomic number of element X. - Graphical abstract: The charge density contour plots on the (0 0 0 1) plane for Ti{sub 5}Si{sub 3} (a), Ti{sub 5}Ge{sub 3} (b), Ti{sub 5}Sn{sub 3} (c) and Ti{sub 5}Pb{sub 3} (d). Highlights: Black-Right-Pointing-Pointer The elastic constants except C{sub 12} were lowered with increase of atomic number of X. Black-Right-Pointing-Pointer The bulk and shear modulus as well as Young's modulus was also decreased. Black-Right-Pointing-Pointer The elastic anisotropies of Ti{sub 5}X{sub 3} were further studied visually. Black-Right-Pointing-Pointer The X-X and Ti-X covalent bonding strength was lowered.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗