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At least 433 records · Page 24

Massively-parallel Lagrangian particle code and applications

Massively-parallel, distributed-memory algorithms for the Lagrangian particle hydrodynamic method (Samulyak et al., 2018) have been developed, verified, and implemented. The key component of parallel algorithms is a particle management module that includes a parallel construction of octree databases, dynamic adaptation and refinement of octrees, and particle migration between parallel subdomains. The particle management module is based on the p4est (parallel forest of k-trees) library. The massively-parallel Lagrangian particle code has been applied to a variety of fundamental science and applied problems. A summary of Lagrangian particle code applications to the injection of impurities into thermonuclear fusion devices and to the simulation of supersonic hydrogen jets in support of laser-plasma wakefield acceleration research has also been presented.

97 MATHEMATICS AND COMPUTING↗

Improved solar-driven photocatalytic performance of Ag{sub 2}CO{sub 3}/(BiO){sub 2}CO{sub 3} prepared in-situ

Highlights: • Ag{sub 2}CO{sub 3}/(BiO){sub 2}CO{sub 3} photocatalysts were prepared in-situ. • The photo-induced charge separation rate has been greatly increased. • The photocatalytic activity has been greatly promoted. - Abstract: Ag{sub 2}CO{sub 3}/(BiO){sub 2}CO{sub 3} composites have been fabricated in-situ via a facile parallel flaw co-precipitation method. The specific surface area, structure, morphology, and the separation rate of photo-induced charge pairs of the photocatalysts were characterized by Brunauer–Emmett–Teller (BET) method, X-ray diffraction (XRD), UV–vis diffuse reflectance spectroscopy(DRS), scanning electron microscopy (SEM), high-resolution transmission electron microscopy (HRTEM), and surface photovoltage (SPV) spectroscopy, respectively. XRD patterns and DRS demonstrated that Ag{sub 2}CO{sub 3} has no effect on the crystal phase and bandgap of (BiO){sub 2}CO{sub 3}. The existence of Ag{sub 2}CO{sub 3} in the composites enhances the separation rate of photo-induced charge pairs of the photocatalysts. The photocatalytic performance of Ag{sub 2}CO{sub 3}/(BiO){sub 2}CO{sub 3} was evaluated by the decolorization of methyl orange (MO) aqueous solution under simulated solar irradiation. It was found that the simulated solar-induced photocatalytic activity of Ag{sub 2}CO{sub 3}/(BiO){sub 2}CO{sub 3} copmposites was significantly improved, which was mainly attributed to the enhanced surface area and the separation rate of photo-induced charge pairs.

36 MATERIALS SCIENCE↗

OvAd1, a Novel, Potent, and Selective Chimeric Oncolytic Virus Developed for Ovarian Cancer by 3D-Directed Evolution

Effective therapeutics for ovarian cancer continue to be urgently needed, particularly for chemotherapy-resistant cases. Here we present both a 3D-Matrigel culture-based expansion of our directed evolution method for generation of oncolytic virotherapies and two promising ovarian-cancer targeted oncolytic viruses, OvAd1 and OvAd2. OvAd1 was developed using Matrigel cell cultures, whereas OvAd2 was developed in parallel using traditional monolayer tissue culture methods. Both viruses are potent against a panel of platinum-resistant ovarian cancer cell lines and are attenuated on normal cells in vitro, resulting in therapeutic windows of ~200-fold. We observed two benefits of the use of Matrigel-based cultures for directed evolution of these oncolytics: (1) use of Matrigel generated a bioselected pool that was more strongly attenuated on normal cells while retaining its potency against ovarian cancer cells, and (2) in an ovarian carcinomatosis model, the Matrigel-derived virus OvAd1 suppressed all tumor growth while the non-Matrigelderived virus was 50% effective. Neither virus stimulated formation of peritoneal adhesions as seen for Ad5-based therapies. Consequently, these viruses are novel candidates for development as new effective treatments for aggressive ovarian cancer.

3D cell culture↗

Adaptively Compressed Exchange Operator for Large-Scale Hybrid Density Functional Calculations with Applications to the Adsorption of Water on Silicene

Density functional theory (DFT) calculations using hybrid exchange-correlation functionals have been shown to provide an accurate description of the electronic structures of nanosystems. However, such calculations are often limited to small system sizes due to the high computational cost associated with the construction and application of the Hartree-Fock (HF) exchange operator. Here, we demonstrate that the recently developed adaptively compressed exchange (ACE) operator formulation [J. Chem. Theory Comput. 2016, 12, 2242-2249] can enable hybrid functional DFT calculations for nanosystems with thousands of atoms. The cost of constructing the ACE operator is the same as that of applying the exchange operator to the occupied orbitals once, while the cost of applying the Hamiltonian operator with a hybrid functional (after construction of the ACE operator) is only marginally higher than that associated with applying a Hamiltonian constructed from local and semilocal exchange-correlation functionals. Therefore, this new development significantly lowers the computational barrier for using hybrid functionals in large-scale DFT calculations. We demonstrate that a parallel planewave implementation of this method can be used to compute the ground-state electronic structure of a 1000-atom bulk silicon system in less than 30 wall clock minutes and that this method scales beyond 8000 computational cores for a bulk silicon system containing about 4000 atoms. The efficiency of the present methodology in treating large systems enables us to investigate adsorption properties of water molecules on Ag-supported two-dimensional silicene. Our computational results show that water monomer, dimer, and trimer configurations exhibit distinct adsorption behaviors on silicene. In particular, the presence of additional water molecules in the dimer and trimer configurations induces a transition from physisorption to chemisorption, followed by dissociation on Ag-supported silicene. This is caused by the enhanced effect of hydrogen bonds on charge transfer and proton transfer processes. Lastly, such a hydrogen bond autocatalytic effect is expected to have broad applications for silicene as an efficient surface catalyst for oxygen reduction reactions and water dissociation.

36 MATERIALS SCIENCE↗

The effects of cation–anion clustering on defect migration in MgAl 2 O 4

Magnesium aluminate spinel (MgAl 2 O 4 ), like many other ceramic materials, offers a range of technological applications, from nuclear reactor materials to military body armor. For many of these applications, it is critical to understand both the formation and evolution of lattice defects throughout the lifetime of the material. We use the Speculatively Parallel Temperature Accelerated Dynamics (SpecTAD) method to investigate the effects of di-vacancy and di-interstitial formation on the mobility of the component defects. From long-time trajectories of the state-to-state dynamics, we characterize the migration pathways of defect clusters, and calculate their self-diffusion constants across a range of temperatures. We find that the clustering of Al and O vacancies drastically reduces the mobility of both defects, while the clustering of Mg and O vacancies completely immobilizes them. For interstitials, we find that the clustering of Mg and O defects greatly reduces O interstitial mobility, but has only a weak effect on Mg. Lastly, these findings illuminate important new details regarding defect kinetics relevant to the application of MgAl 2 O 4 in extreme environments.

36 MATERIALS SCIENCE↗

Study of photoluminescence properties of thin films DR1

Fabrication of thin films DR1 have been carried out by the EFA-PDF (Electric Field-Assisted Physical Vapor Deposition) method to obtain films with parallel dipole arrangement. Molecular deposition process is performed by applying an electric field that is placed between the substrate ITO (Indium Tin Oxide) and copper mesh. The resulting films were characterized by using a spectrofluorometer. Analysis of the emission spectrum, indicate that DR1 molecules in the film oriented perpendicular to the substrate and arranged in parallel order (H-aggregate). As an effect, the peak of the emission spectrum appears stronger along with the increase of electric field strength.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Calculated vibrational states of ozone up to dissociation

A new accurate global potential energy surface for the ground electronic state of ozone [R. Dawes et al., J. Chem. Phys. 139, 201103 (2013)] was published fairly recently. The topography near dissociation differs significantly from previous surfaces, without spurious submerged reefs and corresponding van der Waals wells. This has enabled significantly improved descriptions of scattering processes, capturing the negative temperature dependence and large kinetic isotope effects in exchange reaction rates. The exchange reactivity was found to depend on the character of near-threshold resonances and their overlap with reactant and product wavefunctions, which in turn are sensitive to the potential. We present global “three-well” calculations of all bound vibrational states of three isotopic combinations of ozone ( 48 O 3 , 16 O 2 18 O, 16 O 2 17 O) for J = 0 and J = 1 with a focus on the character and density of highly excited states and discuss their impact on the ozone isotopic anomaly. The calculations were done using a parallel symmetry-adapted Lanczos method with the RV3 code. Some comparisons were made with results obtained with the improved relaxation method implemented in the Heidelberg multi-configuration time-dependent Hartree code.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

An accurate and efficient fragmentation approach via the generalized many-body expansion for density matrices

With relevant chemical space growing larger and larger by the day, the ability to extend computational tractability over that larger space is of paramount importance in virtually all fields of science. The solution we aim to provide here for this issue is in the form of the generalized many-body expansion for building density matrices (GMBE-DM) based on the set-theoretical derivation with overlapping fragments, through which the energy can be obtained by a single Fock build. In combination with the purification scheme and the truncation at the one-body level, the DM-based GMBE(1)-DM-P approach shows both highly accurate absolute and relative energies for medium-to-large size water clusters with about an order of magnitude better than the corresponding energy-based GMBE(1) scheme. Simultaneously, GMBE(1)-DM-P is about an order of magnitude faster than the previously proposed MBE-DM scheme [F. Ballesteros and K. U. Lao, J. Chem. Theory Comput. 18, 179 (2022)] and is even faster than a supersystem calculation without significant parallelization to rescue the fragmentation method. For even more challenging systems including ion–water and ion–pair clusters, GMBE(1)-DM-P also performs about 3 and 30 times better than the energy-based GMBE(1) approach, respectively. In addition, this work provides the first overlapping fragmentation algorithm with a robust and effective binning scheme implemented internally in a popular quantum chemistry software package. Thus, GMBE(1)-DM-P opens a new door to accurately and efficiently describe noncovalent clusters using quantum mechanics.

Chemistry↗

Entanglement-enhanced ac magnetometry in the presence of Markovian noise

Entanglement is a resource to improve the sensitivity of quantum sensors. In an ideal case, using an entangled state as a probe to detect target fields, we can beat the standard quantum limit by which all classical sensors are bounded. However, since entanglement is fragile against decoherence, it is unclear whether entanglement-enhanced metrology is useful in a noisy environment. Its benefit is indeed limited when estimating the amplitude of dc magnetic fields under the effect of parallel Markovian decoherence, where the noise operator is parallel to the target field. In this paper, on the contrary, we show an advantage to using an entanglement over the classical strategy under the effect of parallel Markovian decoherence when we try to detect ac magnetic fields. We consider a scenario to induce a Rabi oscillation of the qubits with the target ac magnetic fields. Although we can, in principle, estimate the amplitude of the ac magnetic fields from the Rabi oscillation, the signal becomes weak if the qubit frequency is significantly detuned from the frequency of the ac magnetic field. We show that, by using the Greenberger-Horne-Zeilinger (GHZ) states, we can significantly enhance the signal of the detuned Rabi oscillation even under the effect of parallel Markovian decoherence. Further, our method is based on the fact that the interaction time between the GHZ states and ac magnetic fields scales as 1/L to mitigate the decoherence effect, where L is the number of qubits, which contributes to improving the bandwidth of the detectable frequencies of the ac magnetic fields. Our results pave the way for new applications of entanglement-enhanced ac magnetometry.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Time-dependent density functional theory with twist-averaged boundary conditions

Time-dependent density functional theory is widely used to describe excitations of many-fermion systems. In its many applications, three-dimensional (3D) coordinate-space representation is used, and infinitedomain calculations are limited to a finite volume represented by a spatial box. For finite quantum systems (atoms, molecules, nuclei, hadrons), the commonly used periodic or reflecting boundary conditions introduce spurious quantization of the continuum states and artificial reflections from boundary; hence, an incorrect treatment of evaporated particles. The finite-volume artifacts for finite systems can be practically cured by invoking an absorbing potential in a certain boundary region sufficiently far from the described system. However, such absorption cannot be applied in the calculations of infinite matter (crystal electrons, quantum fluids, neutron star crust), which suffer from unphysical effects stemming from a finite computational box used. Here, twist-averaged boundary conditions (TABC) have been used successfully to diminish the finite-volume effects. In this work, we extend TABC to time-dependent modes. We demonstrate that by using TABC, one can reduce finite-volume effects drastically without adding any additional parameters associated with absorption at large distances. Moreover, TABC are an obvious choice for time-dependent calculations for infinite systems. Furthermore, since TABC calculations for different twists can be performed independently, the method is trivially adapted to parallel computing.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Sci-Fri PM: Radiation Therapy, Planning, Imaging, and Special Techniques - 03: The Potential Benefit Of Esophageal Sparing During Palliative Radiotherapy For Lung Cancer

Puropose: Palliative radiotherapy is an effective technique to alleviate systems of disease burden in late-stage lung cancer patients. Previous randomized controlled studies demonstrated a survival benefit in patients with good performance status at radiation doses of 35Gy10 or greater but with an increased incidence of esophagitis. The objective of this planning study was to assess the potential impact of esophageal-sparing IMRT (ES-IMRT) compared to the current standard of care using parallel-opposed pair beams (POP). Methods: In this study, 15 patients with lung cancer treated to a dose of 30Gy in 10 fractions between August 2015 and January 2016 were identified. Radiation treatment plans were optimized using ES-IMRT by limiting the max esophagus point dose to 24Gy. Using published Lyman-Kutcher-Burman normal tissue complication probabilities (LKB-NTCP) models, both plans were evaluated for the likelihood of esophagitis (≥ grade 2) and pneumonitis (≥ grade 2). Results: Using ES-IMRT, the median esophageal and lung mean doses reduced from 16 and 8Gy to 7 and 7Gy, respectively. Using the LKB models, the theoretical probability of symptomatic esophagitis and pneumonitis reduced from 13 to 1%, and from 5 to 3%, respectively. The median NTD mean for the GTV and PTV of the clinically approved POP plans compared to the ES-IMRT plans were similar. Conclusions: Advanced radiotherapy techniques such as ES-IMRT may have clinical utility in reducing treatment-related toxicity in advanced lung cancer patients. Our data suggests that the rate of esophagitis can be reduced without compromising tumour control.

60 APPLIED LIFE SCIENCES↗

Parallel Element-based Algebraic Multigrid for H (c url ) and H (div) Problems Using the ParELAG Library

This paper presents the use of element-based algebraic multigrid (AMGe) hierarchies, implemented in the ParELAG (Parallel Element Agglomeration Algebraic Multigrid Upscaling and Solvers) library, to produce multilevel preconditioners and solvers for H (c url ) and H (div) formulations. ParELAG constructs hierarchies of compatible nested spaces, forming an exact de Rham sequence on each level. This allows the application of hybrid smoothers on all levels and AMS (Auxiliary-space Maxwell Solver) or ADS (Auxiliary-space Divergence Solver) on the coarsest levels, obtaining complete multigrid cycles. Numerical results are presented, showing the parallel performance of the proposed methods. As a part of the exposition, this paper demonstrates some of the capabilities of ParELAG and outlines some of the components and procedures within the library.

97 MATHEMATICS AND COMPUTING↗

TuckerCompressMPI v. 1.0

As parallel computing trends towards the exascale, scientific data produced by high-fidelity simulations are growing increasingly massive. For instance, a simulation on a three-dimensional spatial grid with 512 points per dimension that tracks 64 variables per grid point for 128 time steps yields 8 TB of data. By viewing the data as a dense five-way tensor, we can compute a Tucker decomposition to find inherent low-dimensional multilinear structure, achieving compression ratios of up to 10000 on real-world data sets with negligible loss in accuracy. So that we can operate on such massive data, we present the first-ever distributed-memory parallel implementation for the Tucker decomposition, whose key computations correspond to parallel linear algebra operations, albeit with nonstandard data layouts. Our approach specifies a data distribution for tensors that avoids any tensor data redistribution, either locally or in parallel. This software provides a method for compressing large-scale multiway data.

Austin, Woody↗

FEL Simulation Using Distributed Computing

While simulation tools are available and have been used regularly for simulating light sources, the increasing availability and lower cost of GPU-based processing opens up new opportunities. This poster highlights a method of how accelerating and parallelizing code processing through the use of COTS software interfaces.

43 PARTICLE ACCELERATORS↗

Real-Time Boundary-Layer Profiling at the Southern Great Plains Field Campaign Report

The National Research Council (NRC 2009, 2010) has argued that the nation needs to establish a boundary-layer profiling network across the conterminous United States (CONUS). These observations would benefit a wide range of applications including short-term severe weather forecasting by providing better initial conditions for weather prediction models (Wulfmeyer et al. 2015). While active remote sensors like Raman lidars (e.g., Turner et al. 2016) and differential absorption lidars (e.g., Spuler et al. 2015) are able to provide high-temporal-and-vertical-resolution profiles of water vapor and temperature from the ground, these systems are not yet available commercially. Passive remote-sensing systems, such as multi-channel microwave radiometers and infrared spectrometers, are commercially available and can provide retrieved profiles of temperature and humidity (e.g., Löhnert et al. 2009; Blumberg et al. 2015). These passive thermodynamic profiling systems are certainly a candidate for a possible boundary-layer network. Radio acoustic sounding systems (RASS), coupled with either a radar or sodar, can provide partial profiles of virtual temperature and are another option. However, the RASS signal is audible and considered by many to be annoying, and strong winds blow the acoustic signal away from the radar and greatly hamper its maximum vertical range. Three basic ground-based remote sensing technologies are used for wind profiling. All of these are active remote sensors that take advantage of a Doppler-shifted signal along different radial directions to determine the wind speed and direction. The three approaches are sodar (which uses pulses of sonic energy), radar (pulses of microwave energy), or lidar (pulses of laser energy). All three methods use either plane-parallel-indicator (PPI; constant elevation) scans that are analyzed with a velocity-azimuth display (VAD) technique or Doppler beam-swinging observing strategies, which are then analyzed to provide the horizontal wind speed and direction profiles as a function of range.

54 ENVIRONMENTAL SCIENCES↗

On ParELAG's Parallel Element-based Algebraic Multigrid and its MFEM Miniapps for H(curl) and H(div) Problems: a report including lowest and next to the lowest order numerical results

This paper presents the utilization of element-based algebraic multigrid (AMGe) hierarchies, implemented in the ParELAG (Parallel Element Agglomeration Algebraic Multigrid Upscaling and Solvers) library, to produce multilevel preconditioners and solvers for H(curl) and H(div) formulations. This involves the construction of hierarchies of compatible nested spaces, forming an exact de Rham sequence on each level. This allows the application of hybrid smoothers on all levels and AMS (Auxiliary-space Maxwell Solver) or ADS (Auxiliary-space Divergence Solver) on the coarsest levels, obtaining complete multigrid cycles. Numerical results are presented, showing the parallel performance of the proposed methods. As a part of the exposition, this paper demonstrates some of the capabilities of ParELAG and outlines some of the components and procedures within the library.

97 MATHEMATICS AND COMPUTING↗

Characterization of flow recirculation zones at the Perdigão site using multi-lidar measurements

Because flow recirculation can generate significant amounts of turbulence, it can impact the success of wind energy projects. This study uses unique Doppler lidar observations to quantify occurrences of flow recirculation on lee sides of ridges. An extensive dataset of observations of flow over complex terrain is available from the Perdigão 2017 field campaign over a period of 3 months. The campaign site was selected because of the unique terrain feature of two nearly parallel ridges with a valley-to-ridge-top height difference of about 200 m and a ridge-to-ridge distance of 1.4 km. Six scanning Doppler lidars probed the flow field in several vertical planes orthogonal to the ridges using range–height indicator scans. With this lidar setup, we achieved vertical scans of the recirculation zone at three positions along two parallel ridges. We construct a method to identify flow recirculation zones in the scans, as well as define characteristics of these zones. According to our data analysis, flow recirculation, with reverse flow wind speeds greater than 0.5 m s -1 , occurs over 50 % of the time when the wind direction is perpendicular to the direction of the ridges. Atmospheric conditions, such as atmospheric stability and wind speed, affect the occurrence of flow recirculation. Flow recirculation occurs more frequently during periods with wind speeds above 8 m s -1 . Recirculation within the valley affects the mean wind and turbulence fields at turbine heights on the downwind ridge in magnitudes significant for wind resource assessment.

17 WIND ENERGY↗