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At least 1,639 records · Page 91

Hydrodeoxygenation of HMF over Pt/C in a continuous flow reactor

The three‐phase hydrodeoxygenation reaction of 5‐hydroxymethylfurfural (HMF) with H 2 was studied over a 10 wt % Pt/C catalyst using both batch and flow reactors, with ethanol, 1‐propanol, and toluene solvents. The reaction is shown to be sequential, with HMF reacting first to furfuryl ethers and other partially hydrogenated products. These intermediate products then form dimethyl furan (DMF), which in turn reacts further to undesired products. Furfuryl ethers were found to react to DMF much faster than HMF, explaining the higher reactivity of HMF when alcohol solvents were used. With the optimal residence time, it was possible to achieve yields approaching 70% in the flow reactor with the Pt/C catalyst. Much higher selectivities and yields were obtained in the flow reactor than in the batch reactor because side products are formed sequentially, rather than in parallel, demonstrating the importance of choosing the correct type of reactor in catalyst screening. © 2014 American Institute of Chemical Engineers AIChE J , 61: 590–597, 2015

Luo, Jing↗

Improved treatment of exact exchange in Quantum ESPRESSO

Here, we present an algorithm and implementation for the parallel computation of exact exchange in Quantum ESPRESSO (QE) that exhibits greatly improved strong scaling. QE is an open-source software package for electronic structure calculations using plane wave density functional theory, and supports the use of local, semi-local, and hybrid DFT functionals. Wider application of hybrid functionals is desirable for the improved simulation of electronic band energy alignments and thermodynamic properties, but the computational complexity of evaluating the exact exchange potential limits the practical application of hybrid functionals to large systems and requires efficient implementations. We demonstrate that existing implementations of hybrid DFT that utilize a single data structure for both the local and exact exchange regions of the code are significantly limited in the degree of parallelization achievable. We present a band-pair parallelization approach, in which the calculation of exact exchange is parallelized and evaluated independently from the parallelization of the remainder of the calculation, with the wavefunction data being efficiently transformed on-the-fly into a form that is optimal for each part of the calculation. For a 64 water molecule supercell, our new algorithm reduces the overall time to solution by nearly an order of magnitude.

97 MATHEMATICS AND COMPUTING↗

Effects of SARS-CoV-2 Main Protease Mutations at Positions L50, E166, and L167 Rendering Resistance to Covalent and Noncovalent Inhibitors

SARS-CoV-2 propagation under nirmatrelvir and ensitrelvir pressure selects for main protease (MPro) drug-resistant mutations E166V (DRM2), L50F/E166V (DRM3), E166A/L167F (DRM4), and L50F/E166A/L167F (DRM5). DRM2-DRM5 undergoes N-terminal autoprocessing to produce mature MPro with dimer dissociation constants (K dimer ) 2–3 times larger than that of the wildtype. Co-selection of L50F restores catalytic activity of DRM2 and DRM4 from ~10 to 30%, relative to that of the wild-type enzyme, without altering K dimer . Binding affinities and thermodynamic profiles that parallel the drug selection pressure, exhibiting significant decreases in affinity through entropy/enthalpy compensation, were compared with GC373. Reorganization of the active sites due to mutations observed in the inhibitor-free DRM3 and DRM4 structures as compared to MPro WT may account for the reduced binding affinities, although DRM2 and DRM3 complexes with ensitrelvir are almost identical to MPro WT -ensitrelvir. In conclusion, chemical reactivity changes of the mutant active sites due to differences in electrostatic and protein dynamics effects likely contribute to losses in binding affinities.

60 APPLIED LIFE SCIENCES↗

Increased Polymer Diffusivity in Thin-Film Confinement

In this work, the behavior of polymer melts under planar confinement was investigated using molecular dynamics simulations. Polymers with a range of lengths, from unentangled to highly entangled (N = 25-400), were confined between two discrete-bead parallel walls to create thin films with thicknesses (h = 3.5-40σ, where σ is the unit length) ranging from much larger to much smaller than the polymer size. These simulations were used to measure polymer-chain conformations, entanglement densities, and center-of-mass diffusion, and the results were compared with previous simulations of polymer melts under cylindrical confinement. Changes to the entanglement density and radius of gyration in thin films follow the same behavior as in cylindrical confinement: decreased entanglements per chain, decreased R g perpendicular to the confining wall, and increased R g parallel to the confining wall, though the deviations from bulklike conformations are smaller. Despite similarities in conformation and entanglement behavior between thin-film and cylindrical confinements, the diffusion behavior differs. Under planar confinement, the diffusion coefficient increases monotonically up to 6 times the bulk diffusivity with decreasing film thickness, while it behaves nonmonotonically in cylinders. This is due to the increased degrees of freedom afforded to the polymer chains in a thin film compared to those in a cylinder, allowing chains to diffuse around one another rather than through, as found in cylindrical confinement. Normalized diffusion coefficients, D norm , can be well described by a master curve with an exponential dependence on confinement after scaling D norm by a thickness dependent term.

36 MATERIALS SCIENCE↗

Twisted-layer boron nitride ceramic with high deformability and strength

Moiré superlattices formed by twisted stacking in van der Waals materials have emerged as a new platform for exploring the physics of strongly correlated materials and other emergent phenomena. However, there remains a lack of research on the mechanical properties of twisted-layer van der Waals materials, owing to a lack of suitable strategies for making three-dimensional bulk materials. Here we report the successful synthesis of a polycrystalline boron nitride bulk ceramic with high room-temperature deformability and strength. This ceramic, synthesized from an onion-like boron nitride nanoprecursor with conventional spark plasma sintering and hot-pressing sintering, consists of interlocked laminated nanoplates in which parallel laminae are stacked with varying twist angles. The compressive strain of this bulk ceramic can reach 14% before fracture, about one order of magnitude higher compared with traditional ceramics (less than 1% in general), whereas the compressive strength is about six times that of ordinary hexagonal boron nitride layered ceramics. The exceptional mechanical properties are due to a combination of the elevated intrinsic deformability of the twisted layering in the nanoplates and the three-dimensional interlocked architecture that restricts deformation from propagating across individual nanoplates. The advent of this twisted-layer boron nitride bulk ceramic opens a gate to the fabrication of highly deformable bulk ceramics.

36 MATERIALS SCIENCE↗

FilDReaMS: II. Application to the analysis of the relative orientations between filaments and the magnetic field in four Herschel fields

Context. Both simulations and observations of the interstellar medium show that the study of the relative orientations between filamentary structures and the magnetic field can bring new insight into the role played by magnetic fields in the formation and evolution of filaments and in the process of star formation. Aims. We provide a first application of FilDReaMS, the new method presented in the companion paper to detect and analyze filaments in a given image. The method relies on a template that has the shape of a rectangular bar with variable width. Our goal is to investigate the relative orientations between the detected filaments and the magnetic field. Methods. We apply FilDReaMS to a small sample of four Herschel fields (G210, G300, G82, G202) characterized by different Galactic environments and different evolutionary stages. First, we look for the most prevalent bar widths, and we examine the networks formed by filaments of different bar widths as well as their hierarchical organization. Second, we compare the filament orientations to the magnetic field orientation inferred from Planck polarization data and, for the first time, we study the statistics of the relative orientation angle as functions of both spatial scale and H2 column density. Results. We find preferential relative orientations in the four Herschel fields: small filaments with low column densities tend to be slightly more parallel than perpendicular to the magnetic field; in contrast, large filaments, which all have higher column densities, are oriented nearly perpendicular (or, in the case of G202, more nearly parallel) to the magnetic field. In the two nearby fields (G210 and G300), we observe a transition from mostly parallel to mostly perpendicular relative orientations at an H 2 column density ≃ 1.1 × 10 21 cm -2 and 1.4 × 10 21 cm -2 , respectively, consistent with the results of previous studies. Conclusions. Our results confirm the existence of a coupling between magnetic fields at cloud scales and filaments at smaller scale. They also illustrate the potential of combining Herschel and Planck observations, and they call for further statistical analyses with our dedicated method.

79 ASTRONOMY AND ASTROPHYSICS↗

Statistical properties of Charney-Hasegawa-Mima zonal flows

A theoretical interpretation of numerically generated probability density functions (PDFs) of intermittent plasma transport events in unforced zonal flows is provided within the Charney-Hasegawa-Mima (CHM) model. The governing equation is solved numerically with various prescribed density gradients that are designed to produce different configurations of parallel and anti-parallel streams. Long-lasting vortices form whose flow is governed by the zonal streams. It is found that the numerically generated PDFs can be matched with analytical predictions of PDFs based on the instanton method by removing the autocorrelations from the time series. In many instances, the statistics generated by the CHM dynamics relaxes to Gaussian distributions for both the electrostatic and vorticity perturbations, whereas in areas with strong nonlinear interactions it is found that the PDFs are exponentially distributed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Near-field radiative heat transfer between doped-Si parallel plates separated by a spacing down to 200 nm

Heat transfer between two objects separated by a nanoscale vacuum gap holds great promise especially in energy harvesting applications such as near-field thermophotovoltaic systems. However, experimental validation of nanoscale radiative heat transfer has been largely limited to tip-plate configurations due to challenges of maintaining small gap spacing over a relatively large area. Here in this paper, we report measurements of heat transfer near room temperature between two 1 cm by 1 cm doped-Si parallel plates, separated by a vacuum gap from about 200 nm to 780 nm. The measured strong near-field radiative transfer is in quantitative agreement with the theoretical prediction based on fluctuational electrodynamics. The largest measured radiative heat flux is 11 times as high as the blackbody limit for the same hot and cold surface temperatures. Our experiments have produced the highest radiative heat transfer rate observed to date across submicron distances between objects near room temperature.

42 ENGINEERING↗

Ghost imaging second harmonic generation microscopy

Second harmonic generation (SHG) microscopy is useful for visualizing interfaces and sub-structures within a wide range of materials due to the propensity for SHG to occur in non-centrosymmetric environments. However, since SHG is a nonlinear process generally necessitating small focal sizes for higher peak powers, a raster scanning approach is usually needed to build an SHG image over a significant sample size. While raster scanning is effective, there is a cost in terms of the time needed to acquire the image and, also, some materials cannot withstand the higher optical intensities within the small focal volume. As such, we describe a SHG microscopy approach based on ghost imaging (GI), which enables imaging data to be collected in parallel rather than sequentially as in raster scanning techniques. We experimentally demonstrate the approach and combine GI-SHG with compressive sensing to make further substantial gains in reducing the amount of sampling required for image reconstruction. Furthermore, GI-SHG is shown to have significant advantages for imaging in highly scattering environments, partly because GI is a background-free approach requiring spatial correlations between photons that travel two paths, with one path entirely devoid of sample interaction. This basic property of GI means that only the photons that travel unimpeded through the sample preserve the spatial correlations needed to reconstruct the image, while more scattered photons do not contribute to the overall GI signal. Finally, we compare the image quality and sampling properties of three different reconstruction algorithms used for compressive sensing.

47 OTHER INSTRUMENTATION↗

Indirect drive ignition at the National Ignition Facility

This paper reviews scientific results from the pursuit of indirect drive ignition on the National Ignition Facility (NIF) and describes the program's forward looking research directions. In indirect drive on the NIF, laser beams heat an x-ray enclosure called a hohlraum that surrounds a spherical pellet. X-ray radiation ablates the surface of the pellet, imploding a thin shell of deuterium/tritium (DT) that must accelerate to high velocity (v > 350 km s –1 ) and compress by a factor of several thousand. Since 2009, substantial progress has been made in understanding the major challenges to ignition: Rayleigh Taylor (RT) instability seeded by target imperfections; and low-mode asymmetries in the hohlraum x-ray drive, exacerbated by laser-plasma instabilities (LPI). Requirements on velocity, symmetry, and compression have been demonstrated separately on the NIF but have not been achieved simultaneously. We now know that the RT instability, seeded mainly by the capsule support tent, severely degraded DT implosions from 2009–2012. Experiments using a 'high-foot' drive with demonstrated lower RT growth improved the thermonuclear yield by a factor of 10, resulting in yield amplification due to alpha particle heating by more than a factor of 2. Furthermore, large time dependent drive asymmetry in the LPI-dominated hohlraums remains unchanged, preventing further improvements. High fidelity 3D hydrodynamic calculations explain these results. Future research efforts focus on improved capsule mounting techniques and on hohlraums with little LPI and controllable symmetry. In parallel, we are pursuing improvements to the basic physics models used in the design codes through focused physics experiments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

PaKman: Scalable Assembly of Large Genomes on Distributed Memory Machines

De novo genome assembly is a fundamental problem in the field of bioinformatics, that aims to assemble the DNA sequence of an unknown genome from numerous short DNA fragments (aka reads) obtained from it. With the advent of high-throughput sequencing technologies, billions of reads can be generated in a matter of hours, necessitating efficient parallelization of the assembly process. While multiple parallel solutions have been proposed in the past, conducting a large- scale assembly at scale remains a challenging problem because of the inherent complexities associated with data movement, and irregular access footprints of memory and I/O operations. In this paper, we present a novel algorithm, called PaKman, to address the problem of performing large-scale genome assemblies on a distributed memory parallel computer. Our approach focuses on improving performance through a combination of novel data structures and algorithmic strategies for reducing the communication and I/O footprint during the assembly process. A key aspect of our algorithm is its graph data structure, which comprises fat nodes (or what we call "macro-nodes") that reduce the communication burden during contig generation. We present an extensive performance and qualitative evaluation of our algorithm, including comparisons to other state-of-the-art parallel assemblers. Our results demonstrate the ability to achieve near-linear speedups on up to 8K cores (tested); outperform state-of-the-art distributed memory and shared memory tools in performance while delivering comparable (if not better) quality; and reduce time to solution significantly. For instance, PaKman is able to complete an assembly of the full human genome in just over a minute on 8K cores.

Ghosh, Priyanka↗

Sub-second State Estimation Implementation and its Evaluation with Real Data

This paper describes the performance of a parallel state estimation (PSE) tool implemented using advanced computing techniques. The developed code is able to solve state estimation of large-size, practical power systems within one second. Benchmark tests against a commercial tool shows that the computational speed is 10 times faster. Benefits brought by the sub-second state estimation are also discussed.

EMS↗

On the Evolution From Micrometer-Scale Inhomogeneity to Global Overheated Structure During the Intense Joule Heating of a z-Pinch Rod

Ultrafast optical microscopy of metal z-pinch rods pulsed with megaampere current is contributing new data and critical insight into what provides the fundamental seed for the magneto-Rayleigh-Taylor (MRT) instability. A two-frame near infrared/visible intensified-charge-coupled device gated imager with 2-ns temporal resolution and 3-μm spatial resolution captured emissions from the nonuniformly Joule heated surfaces of ultrasmooth aluminum (Al) rods. Nonuniform surface emissions are consistently first observed from discrete, 10-μm scale, subelectronvolt spots. Aluminum 6061 alloy, with micrometer-scale nonmetallic resistive inclusions, forms several times more spots than 99.999% pure Al 5N; 5-10 ns later, azimuthally stretched elliptical spots and distinct strata (40-100 μm wide by 10 μm tall) are observed on Al 6061, but not on Al 5N. In such overheat strata, aligned parallel to the magnetic field, we find that they are highly effective seeds for MRT instability growth. Our data give credence to the hypothesis that early nonuniform Joule heating, such as the electrothermal instability, may provide the dominant seed for MRT.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

SU-E-T-301: Dosimetric Comparison Between Adaptive and Rectilinear Template-Based Prostate Seed Implants

Purpose: To compare the dosimetry of a standard rectilinear and an adaptive technique used in I125 prostate seed implants. Methods: To achieve favorable dosimetry in prostate implants we used adaptive needle updates to match actual positions in real-time. The seed locations were optimized based on actual needle locations. The seeds were delivered automatically with a robotic device seedSelectron™ (Elekta Brachytherapy). In this study, we evaluated the former approach against the standard rectilinear technique in which the needles have a parallel distribution. The treatment plans for 10 patients were analyzed. For comparison, the actual treatment plans were revised so each needle was repositioned to its original parallel location through the template. The analysis was performed by comparing the target coverage and dose to the organs at risk. The comparison was done using the following planning goals: the target D90> 90%, V100% > 90%, V50% <70% and V200% <30%; the urethra V125% < 1cm3 and V150%= 0cm3; and the Rectum V100%<1cm3 and V69% < 8cm3. The prescription dose to the target was 145Gy. Results: The average target volume and number of seeds were 44.39cm3(SD=11.14) and 74(SD=12), respectively. The D90 for adaptive and rectilinear plans was 159.9Gy(SD=2.99) and 155.53Gy(SD=4.04) resulting in a 2.74% difference for the average target coverage. A similar difference (1.75%) was noticed in the target V100[%]. No significant difference was noticed in the dose to the urethra and rectum. All planning goals were met with both the adaptive and rectilinear approach for each plan. Conclusion: The study reveals enhanced coverage of the target when using the adaptive needle adjustments as compared to the rectilinear approach for the analyzed cases. However, the differences in dosimetry did not translate to meaningful clinical outcomes.

60 APPLIED LIFE SCIENCES↗

WE-D-BRA-03: Four-Dimensional Dose Reconstruction Through Retrospective Phase Determination Using Cine Images of Electronic Portal Imaging Device

Purpose: To test a method to reconstruct a four-dimensional (4D) dose distribution using the correlation of pre-calculated 4D electronic portal imaging device (EPID) images and measured cine-EPID images. Methods: 1. A phantom designed to simulate a tumor in lung (a polystyrene block with 3.0 cm diameter embedded in cork) was placed on a sinusoidally moving platform with 2 cm amplitude and 4 sec/cycle. Ten-phase 4D CT images were acquired for treatment planning and dose reconstruction. A 6MV photon beam was irradiated on the phantom with static (field size=5×8.5 cm{sup 2}) and dynamic fields (sliding windows, 10×10 cm{sup 2}, X1 MLC closing in parallel with the tumor movement). 2. 4D and 3D doses were calculated forwardly on PTV (1 cm margin). 3. Dose images on EPID under the fields were calculated for 10 phases. 4. Cine EPID images were acquired during irradiation. 5. Their acquisition times were correlated to the phases of the phantom at which irradiation occurred by inter-comparing calculated “reference” EPID images with measured images (2D gamma comparison). For the dynamic beam, the tumor was hidden under MLCs during a portion of irradiation time; the correlation performed when the tumor was visible was extrapolated. 6. Dose for each phase was reconstructed on the 4D CT images and summed over all phases. The summation was compared with forwardly calculated 4D and 3D dose distributions. Monte Carlo methods were used for all calculations. Results: For the open and dynamic beams, the 4D reconstructed doses showed the pass rates of 92.7 % and 100 %, respectively, at the isocenter plane given 3% / 3 mm criteria. The better agreement of the dynamic beam was from its dose gradient which blurred the otherwise sharp difference between forward and reconstructed doses. This also contributed slightly better agreement in DVH of PTV. Conclusion: The feasibility of 4D reconstruction was demonstrated.

60 APPLIED LIFE SCIENCES↗

Symmetry and Topology Code of the Cluster Self-Assembly of Intermetallic Compounds A{sub 2}{sup [16]}B{sub 4}{sup [12]} of the Friauf Families Mg{sub 2}Cu{sub 4} and Mg{sub 2}Zn{sub 4}

A geometrical and topological analysis of intermetallic compounds A{sub 2}{sup [16]}B{sub 4}{sup [12]} of the Friauf families Mg{sub 2}Cu{sub 4} (formed in 273 binary and 775 ternary systems) and Mg{sub 2}Zn{sub 4} (formed in 67 binary and 121 ternary systems) has been performed. Basic 3D nets are determined in the form of a graph, whose sites correspond to the centers of tetrahedral cluster precursors В{sub 4}: Cu-type net with a coordination number (CN) of 12 for Mg{sub 2}Cu{sub 4} and a BN-type net with a CN of 8 for Mg{sub 2}Zn{sub 4}. The symmetry and topology code is determined for the crystal structure self-assembly in the following form: primary chain S{sub 3}{sup 1} → microlayer S{sub 3}{sup 2} → microframework S{sub 3}{sup 3}. An identical mechanism of primary chain S{sub 3}{sup 1} self-assembly from B{sub 4} clusters with participation of large template atoms A{sup [16]} for both families and a mechanism of S{sub 3}{sup 2} microlayer self-assembly from parallel S{sub 3}{sup 1} chains in Mg{sub 2}Cu{sub 4} (basic 2D net 4{sup 4}) and shifted chains in Mg{sub 2}Zn{sub 4} (basic 2D net 3{sup 6}) have been determined for the first time. The constant chemical composition of intermetallic compounds A{sub 2}{sup [16]}B{sub 4}{sup [12]} is related to the functional difference between the B atoms forming 3D frameworks and template atoms А. The numbers of chemically different В{sub 4} clusters for the Mg{sub 2}Cu{sub 4} and Mg{sub 2}Zn{sub 4} families are found to be 25 and 19, respectively.

36 MATERIALS SCIENCE↗

Exploiting variability for energy optimization of parallel programs

Here in this paper we present optimizations that use DVFS mechanisms to reduce the total energy usage in scientific applications. Our main insight is that noise is intrinsic to large scale parallel executions and it appears whenever shared resources are contended. The presence of noise allows us to identify and manipulate any program regions amenable to DVFS. When compared to previous energy optimizations that make per core decisions using predictions of the running time, our scheme uses a qualitative approach to recognize the signature of executions amenable to DVFS. By recognizing the "shape of variability" we can optimize codes with highly dynamic behavior, which pose challenges to all existing DVFS techniques. We validate our approach using offline and online analyses for one-sided and two-sided communication paradigms. We have applied our methods to NWChem, and we show best case improvements in energy use of 12% at no loss in performance when using online optimizations running on 720 Haswell cores with one-sided communication. With NWChem on MPI two-sided and offline analysis, capturing the initialization, we find energy savings of up to 20%, with less than 1% performance cost.

97 MATHEMATICS AND COMPUTING↗

Performance analysis of emerging data analytics and HPC workloads

Supercomputers are increasingly being used to run a data analytics workload in addition to a traditional simulation science workload. This mixed workload must be rigorously characterized to ensure that appropriately balanced machines are deployed. In this paper we analyze a suite of applications representing the simulation science and data workload at the NERSC supercomputing center. We show how time is spent in application compute, library compute, communication and I/O, and present application performance on both the Intel Xeon and Intel Xeon-Phi partitions of the Cori supercomputer. We find commonality in the libraries used, I/O motifs and methods of parallelism, and obtain similar node-to-node performance for the base application configurations. We demonstrate that features of the Intel Xeon-Phi node architecture and a Burst Buffer can improve application performance, providing evidence that an exascale-era energy-efficient platform can support a mixed workload.

Daley, Christopher S.↗