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At least 1,189 records · Page 66

Synthetic Foveal Imaging Technology

Apparatuses and methods are disclosed that create a synthetic fovea in order to identify and highlight interesting portions of an image for further processing and rapid response. Synthetic foveal imaging implements a parallel processing architecture that uses reprogrammable logic to implement embedded, distributed, real-time foveal image processing from different sensor types while simultaneously allowing for lossless storage and retrieval of raw image data. Real-time, distributed, adaptive processing of multi-tap image sensors with coordinated processing hardware used for each output tap is enabled. In mosaic focal planes, a parallel-processing network can be implemented that treats the mosaic focal plane as a single ensemble rather than a set of isolated sensors. Various applications are enabled for imaging and robotic vision where processing and responding to enormous amounts of data quickly and efficiently is important.

Monacos, Steve P.↗

Acceleration and sensitivity analysis of lattice kinetic Monte Carlo simulations using parallel processing and rate constant rescaling

Kinetic Monte Carlo (KMC) simulation provides insights into catalytic reactions unobtainable with either experiments or mean-field microkinetic models. Sensitivity analysis of KMC models assesses the robustness of the predictions to parametric perturbations and identifies rate determining steps in a chemical reaction network. Stiffness in the chemical reaction network, a ubiquitous feature, demands lengthy run times for KMC models and renders efficient sensitivity analysis based on the likelihood ratio method unusable. We address the challenge of efficiently conducting KMC simulations and performing accurate sensitivity analysis in systems with unknown time scales by employing two acceleration techniques: rate constant rescaling and parallel processing. We develop statistical criteria that ensure sufficient sampling of non-equilibrium steady state conditions. Our approach provides the twofold benefit of accelerating the simulation itself and enabling likelihood ratio sensitivity analysis, which provides further speedup relative to finite difference sensitivity analysis. As a result, the likelihood ratio method can be applied to real chemistry. We apply our methodology to the water-gas shift reaction on Pt(111).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Compile-time estimation of communication costs in multicomputers

An important problem facing numerous research projects on parallelizing compilers for distributed memory machines is that of automatically determining a suitable data partitioning scheme for a program. Any strategy for automatic data partitioning needs a mechanism for estimating the performance of a program under a given partitioning scheme, the most crucial part of which involves determining the communication costs incurred by the program. A methodology is described for estimating the communication costs at compile-time as functions of the numbers of processors over which various arrays are distributed. A strategy is described along with its theoretical basis, for making program transformations that expose opportunities for combining of messages, leading to considerable savings in the communication costs. For certain loops with regular dependences, the compiler can detect the possibility of pipelining, and thus estimate communication costs more accurately than it could otherwise. These results are of great significance to any parallelization system supporting numeric applications on multicomputers. In particular, they lay down a framework for effective synthesis of communication on multicomputers from sequential program references.

Gupta, Manish↗

Experimental Analysis of File Transfer Rates over Wide-Area Dedicated Connections

File transfers over dedicated connections, supported by large parallel file systems, have become increasingly important in high-performance computing and big data workflows. It remains a challenge to achieve peak rates for such transfers due to the complexities of file I/O, host, and network transport subsystems, and equally importantly, their interactions. We present extensive measurements of disk-to-disk file transfers using Lustre and XFS file systems mounted on multi-core servers over a suite of 10 Gbps emulated connections with 0-366 ms round trip times. Our results indicate that large buffer sizes and many parallel flows do not always guarantee high transfer rates. Furthermore, large variations in the measured rates necessitate repeated measurements to ensure confidence in inferences based on them. We propose a new method to efficiently identify the optimal joint file I/O and network transport parameters using a small number of measurements. We show that for XFS and Lustre with direct I/O, this method identifies configurations achieving 97% of the peak transfer rate while probing only 12% of the parameter space.

Rao, Nageswara S.↗

Numerical solutions of Navier-Stokes equations for a Butler wing

The flow field is simulated on the surface of a given delta wing (Butler wing) at zero incident in a uniform stream. The simulation is done by integrating a set of flow field equations. This set of equations governs the unsteady, viscous, compressible, heat conducting flow of an ideal gas. The equations are written in curvilinear coordinates so that the wing surface is represented accurately. These equations are solved by the finite difference method, and results obtained for high-speed freestream conditions are compared with theoretical and experimental results. In this study, the Navier-Stokes equations are solved numerically. These equations are unsteady, compressible, viscous, and three-dimensional without neglecting any terms. The time dependency of the governing equations allows the solution to progress naturally for an arbitrary initial initial guess to an asymptotic steady state, if one exists. The equations are transformed from physical coordinates to the computational coordinates, allowing the solution of the governing equations in a rectangular parallel-piped domain. The equations are solved by the MacCormack time-split technique which is vectorized and programmed to run on the CDC VPS 32 computer.

Abolhassani, J. S.↗

EOS: A project to investigate the design and construction of real-time distributed Embedded Operating Systems

Project EOS is studying the problems of building adaptable real-time embedded operating systems for the scientific missions of NASA. Choices (A Class Hierarchical Open Interface for Custom Embedded Systems) is an operating system designed and built by Project EOS to address the following specific issues: the software architecture for adaptable embedded parallel operating systems, the achievement of high-performance and real-time operation, the simplification of interprocess communications, the isolation of operating system mechanisms from one another, and the separation of mechanisms from policy decisions. Choices is written in C++ and runs on a ten processor Encore Multimax. The system is intended for use in constructing specialized computer applications and research on advanced operating system features including fault tolerance and parallelism.

Campbell, R. H.↗

Progressive Hedging Decomposition for Solutions of Large-Scale Process Family Design Problems

Rapid, wide-scale deployment of green process systems, such as carbon capture or water desalination systems, is essential for combatting climate change. Methods relying on traditional design or modularity fail to capture the benefits of both economies of numbers and economies of scale. We have proposed process family design, which designs a family of processes simultaneously exploiting opportunities for common elements. In previous work, we explored different optimization formulations to solve this problem. In this work, we develop a decomposition approach to tackle larger problems efficiently. We solve a water desalination case study, which is too large to solve within a reasonable timeframe with the discretization formulation. We exploit the block angular structure of the discretization problem to decompose and solve using Progressive Hedging (PH). We use the open-source Python package mpi-sppy to execute PH which allows us to leverage parallelization and a HPC cluster to further improve solution time.

Stinchfield, Georgia↗

Nur77 inhibits oxLDL induced apoptosis of macrophages via the p38 MAPK signaling pathway

The interaction between macrophages and oxLDL plays a crucial role in the initiation and progression of atherosclerosis. As a key initiator in a number of plaque promoting processes, oxLDL induces variable effects such as cell apoptosis or proliferation. Orphan nuclear receptor Nur77 is potently induced in macrophages by diverse stimuli, suggesting that it is of importance in vascular inflammation resulting in atherosclerosis, but whether Nur77 induction is detrimental or protective is unclear. In our study, we explore the role of Nur77 in the regulation of oxLDL-induced macrophage apoptosis and the signaling pathways that are involved. We found that oxLDL induced Nur77 expression in a dose and time dependent fashion, and cell viability was decreased in parallel. To determine whether Nur77 induction contributes to the loss of cell viability or is a protective mechanism, the effect of Nur77 overexpression was examined. Importantly, Nur77 overexpression inhibited the oxLDL-induced decrease of cell viability, inhibited the production of apoptotic bodies and restored DNA synthesis following oxLDL exposure. Furthermore, we found that Nur77 induction is mediated through the p38 MAPK signaling pathway. After pretreatment with SB203580, cell viability was decreased, the expression of CyclinA2 and PCNA was attenuated and the percentage of cell apoptosis was enhanced. Likewise, Nur77 overexpression increased the expression of the cell cycle genes PCNA and p21, and attenuated the increase in caspase-3. On the other hand, knockdown of Nur77 expression by specific siRNA resulted in the increased expression of caspase 3. The results demonstrate that Nur77 is induced by oxLDL via the p38 MAPK signaling pathway, which is involved in the regulation of cell survival. Nur77 enhanced cell survival via suppressing apoptosis, without affecting cell proliferation of activated macrophages, which may be beneficial in patients with atherosclerosis. - Highlights: • oxLDL could induce Nur77 expression. • Nur77 overexpression inhibited oxLDL-induced cell viability, production of apoptotic bodies and restored DNA synthesis. • Cell viability, CyclinA2 and PCNA expression and cell apoptosis were mediated through the p38 MAPK signaling pathway. • Nur77 overexpression mediated the expression of genes PCNA, p21, and caspase-3.

60 APPLIED LIFE SCIENCES↗

A Case Study of Truncated Electrostatics for Simulation of Polyelectrolyte Brushes on GPU Accelerators

Numerous issues have disrupted the trend for increasing computational performance with faster CPU clock frequencies. In order to exploit the potential performance of new computers, it is becoming increasingly desirable to re-evaluate computational physics methods and models with an eye towards towards approaches that allow for increased concurrency and data locality. The evaluation of long-range Coulombic interactions is a common bottleneck for molecular dynamics simulations. Enhanced truncation approaches have been proposed as an alternative method and are particularly well suited for many-core architectures and GPUs due to the inherent fine-grain parallelism that can be exploited. In this paper, we compare efficient truncation-based approximations to evaluation of electrostatic forces with the more traditional particle-particle particle-mesh (P3M) method for molecular dynamics simulation of polyelectrolyte brush layers. We show that with the use of GPU accelerators, large parallel simulations using P3M can be greater than 3 times faster due to a reduction in the mesh-size required. Alternatively, using a truncation-based scheme can improve performance even further. This approach can be up to 3.9 times faster than GPU-accelerated P3M for many polymer systems and results in accurate calculation of shear velocities and disjoining pressures for brush layers. For configurations with highly non-uniform charge distributions, however, we find that it is more efficient to use P3M; for these systems, computationally efficient parameterizations of the truncation-based approach do not produce accurate counterion density profiles or brush morphologies.

Nguyen, Trung D↗

Observations of Subduction, Downward Heat Flux and Dense Filament Collapse in the Northern Gulf of Mexico

Submesoscale processes are important contributors to the global heat budget and generally support upward heat transport through restratification. However, in salinity‐stratified regions, such as the northern Gulf of Mexico with its influx of freshwater from the Mississippi‐Atchafalaya river system, temperature can act like a passive tracer and submesoscale processes can contribute to downward heat transport. Oceanic heat content is a factor in many environmental risks the region faces, for example, hurricane intensification, and marine heatwaves. During the 2022 field campaign of the Submesoscales Under Near‐Resonant Inertial Shear Experiment, a sampling plan was developed to study such submesoscale processes in high resolution. Over 31 hr, four assets (two research ships and two remotely controlled boats) drove in parallel across a dense filament, capturing its evolution in time and space. The observations show that surface waters, warmed by daytime solar radiation, were subducted and that the associated overturning circulation transported heat below the surface layer where it was later irreversibly mixed away. The estimated downward heat flux was as strong as the concurrent net air‐sea heat flux into the ocean. The filament was then observed to rapidly collapse which we attribute to boundary layer turbulence and the breakdown of geostrophic balance. The collapsing fronts display behaviors indicative of gravity currents. These observations highlight how in salinity‐stratified regions, frontal dynamics can be associated with downward heat flux and how the submesoscale can play an important role in the oceanic heat budget.

58 GEOSCIENCES↗

Real-space grids and the Octopus code as tools for the development of new simulation approaches for electronic systems

Real-space grids are a powerful alternative for the simulation of electronic systems. One of the main advantages of the approach is the flexibility and simplicity of working directly in real space where the different fields are discretized on a grid, combined with competitive numerical performance and great potential for parallelization. These properties constitute a great advantage at the time of implementing and testing new physical models. Based on our experience with the Octopus code, in this article we discuss how the real-space approach has allowed for the recent development of new ideas for the simulation of electronic systems. Among these applications are approaches to calculate response properties, modeling of photoemission, optimal control of quantum systems, simulation of plasmonic systems, and the exact solution of the Schrödinger equation for low-dimensionality systems.

97 MATHEMATICS AND COMPUTING↗

Lower hybrid instability driven by mono-energy {alpha}-particles with finite pitch angle spread in a plasma

A kinetic formalism of lower hybrid wave instability, driven by mono-energy {alpha}-particles with finite pitch angle spread, is developed. The instability arises through cyclotron resonance interaction with high cyclotron harmonics of {alpha}-particles. The {alpha}-particles produced in D-T fusion reactions have huge Larmor radii ({approx}10 cm) as compared to the wavelength of the lower hybrid wave, whereas their speed is an order of magnitude smaller than the speed of light in vacuum. As a result, large parallel phase velocity lower hybrid waves, suitable for current drive in tokamak, are driven unstable via coupling to high cyclotron harmonics. The growth rate decreases with increase in pitch angle spread of the beam. At typical electron density of {approx}10{sup 19} m{sup -3}, magnetic field {approx}4 Tesla and {alpha}-particle concentration {approx}0.1%, the large parallel phase velocity lower hybrid wave grows on the time scale of 20 ion cyclotron periods. The growth rate decreases with plasma density.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Electromagnetic nonlinear gyrokinetics with polarization drift

A set of new nonlinear electromagnetic gyrokinetic Vlasov equation with polarization drift and gyrokinetic Maxwell equations is systematically derived by using the Lie-transform perturbation method in toroidal geometry. For the first time, we recover the drift-kinetic expression for parallel acceleration [R. M. Kulsrud, in Basic Plasma Physics, edited by A. A. Galeev and R. N. Sudan (North-Holland, Amsterdam, 1983)] from the nonlinear gyrokinetic equations, thereby bridging a gap between the two formulations. This formalism should be useful in addressing nonlinear ion Compton scattering of intermediate-mode-number toroidal Alfvén eigenmodes for which the polarization current nonlinearity [T. S. Hahm and L. Chen, Phys. Rev. Lett. 74, 266 (1995)] and the usual finite Larmor radius effects should compete.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Alkali metal mediated C–C bond coupling reaction

Metal catalyzed carbon-carbon (C–C) bond formation is one of the important reactions in pharmacy and in organic chemistry. In the present study, the electron and hole capture dynamics of a lithium-benzene sandwich complex, expressed by Li(Bz){sub 2}, have been investigated by means of direct ab-initio molecular dynamics method. Following the electron capture of Li(Bz){sub 2}, the structure of [Li(Bz){sub 2}]{sup −} was drastically changed: Bz–Bz parallel form was rapidly fluctuated as a function of time, and a new C–C single bond was formed in the C{sub 1}–C{sub 1}′ position of Bz–Bz interaction system. In the hole capture, the intermolecular vibration between Bz–Bz rings was only enhanced. The mechanism of C–C bond formation in the electron capture was discussed on the basis of theoretical results.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Plasmon resonant amplification of hot electron-driven photocatalysis

We discuss plasmon resonant excitation of hot electrons in a metal based photocatalyst in the oxygen evolution half reaction in aqueous solution. In this report, the photocatalyst consists of a 100-nm thick Au film deposited on a corrugated silicon substrate. Here, hot electrons photoexcited in the metal are injected into the solution, ultimately reversing the water oxidation reaction (O 2 +4H + +4e–⇌2H 2 O) and producing a photocurrent. In order to amplify this process, the gold electrode is patterned into a plasmon resonant grating structure with a pitch of 500 nm. The photocurrent (i.e., charge transfer rate) is measured as a function of incident angle using 633 nm wavelength light. We observe peaks in the photocurrent at incident angles of ±9° from normal when the light is polarized parallel to the incident plane (p-polarization) and perpendicular to the lines on the grating. Due to these peaks, we estimate an overall plasmonic gain (or amplification) factor of 2.1× in the charge transfer rate. At these same angles, we also observe sharp dips in the photoreflectance, corresponding to the condition when there is wavevector matching between the incident light and the plasmon mode in the grating. No angle dependence is observed in the photocurrent or photoreflectance when the incident light is polarized perpendicular to the incident plane (s-polarization) and parallel to the lines on the grating. Finite difference time domain simulations also predict sharp dips in the photoreflectance at ±9°, and the electric field intensity profiles show clear excitation of a plasmon-resonant mode when illuminated at those angles with p-polarized light.

42 ENGINEERING↗

Transport of cosmic-ray protons in intermittent heliospheric turbulence: Model and simulations

The transport of charged energetic particles in the presence of strong intermittent heliospheric turbulence is computationally analyzed based on known properties of the interplanetary magnetic field and solar wind plasma at 1 astronomical unit. The turbulence is assumed to be static, composite, and quasi-three-dimensional with a varying energy distribution between a one-dimensional Alfvénic (slab) and a structured two-dimensional component. The spatial fluctuations of the turbulent magnetic field are modeled either as homogeneous with a Gaussian probability distribution function (PDF), or as intermittent on large and small scales with a q-Gaussian PDF. Simulations showed that energetic particle diffusion coefficients both parallel and perpendicular to the background magnetic field are significantly affected by intermittency in the turbulence. This effect is especially strong for parallel transport where for large-scale intermittency results show an extended phase of subdiffusive parallel transport during which cross-field transport diffusion dominates. The effects of intermittency are found to depend on particle rigidity and the fraction of slab energy in the turbulence, yielding a perpendicular to parallel mean free path ratio close to 1 for large-scale intermittency. Investigation of higher order transport moments (kurtosis) indicates that non-Gaussian statistical properties of the intermittent turbulent magnetic field are present in the parallel transport, especially for low rigidity particles at all times.

79 ASTRONOMY AND ASTROPHYSICS↗

Pump and ionizing-probe dynamics in a simultaneous treatment of electronic and nuclear motion in LiH

The dissociative single ionization of the LiH molecule using a two-color UV-UV pump-probe scheme is simulated in ab initio calculations demonstrating how the dynamics initiated on intermediate Rydberg states of diatomic molecules can be imaged by such experiments. The theoretical treatment combines nuclear motion with highly correlated descriptions of electronic continua and bound electronic states. Nuclear dynamics on Rydberg states are only weakly reflected by changes in photoelectron energies ejected by time-delayed ionizing pulses if the Rydberg potential curves parallel those of the ion states being produced. However, coincidence measurements guided by knowledge of the photoionization amplitudes as a function of internuclear distance can still reveal intermediate-state dynamics in pump-probe experiments.

74 ATOMIC AND MOLECULAR PHYSICS↗

Electronic Excitation Response of DNA to High-Energy Proton Radiation in Water

The lack of molecular-level understanding for the electronic excitation response of DNA to charged particle radiation, such as high-energy protons, remains a fundamental scientific bottleneck in advancing proton and other ion beam cancer therapies. In particular, the dependence of different types of DNA damage on high-energy protons represents a significant knowledge void. Here, in this work, we employ first-principles real-time time-dependent density functional theory simulation, using a massively parallel supercomputer, to unravel the quantum-mechanical details of the energy transfer from high-energy protons to DNA in water. The calculations reveal that protons deposit significantly more energy onto the DNA sugar-phosphate side chains than onto the nucleobases, and greater energy transfer is expected onto the DNA side chains than onto water. As a result of this electronic stopping process, highly energetic holes are generated on the DNA side chains as a source of oxidative damage.

74 ATOMIC AND MOLECULAR PHYSICS↗