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At least 1,153 records · Page 64

On Eliminating Synchronous Communication in Molecular Simulations to Improve Scalability

Molecular dynamics simulation, as a complementary tool to experimentation, has become an important methodology for the understanding and design of molecular systems as it provides access to properties that are difficult, impossible or prohibitively expensive to obtain experimentally. Many of the available software packages have been parallelized to take advantage of modern massively concurrent processing resources. The challenge in achieving parallel efficiency is commonly attributed to the fact that molecular dynamics algorithms are communication intensive. This paper illustrates how an appropriately chosen data distribution and asynchronous one-sided communication approach can be used to effectively deal with the data movement within the Global Arrays/ARMCI programming model framework. A new put_notify capability is presented here, allowing the implementation of the molecular dynamics algorithm without any explicit global or local synchronization or global data reduction operations. In addition, this push-data model is shown to very effectively allow hiding data communication behind computation. Rather than data movement or explicit global reductions, the implicit synchronization of the algorithm becomes the primary challenge for scalability. Without any explicit synchronous operations, the scalability of molecular simulations is shown to depend only on the ability to evenly balance computational load.

Straatsma, TP↗

A study of model parameters associated with the urban climate using HCMM data

Progress in the study of the intensity of the urban heat island is reported. The intensity of the heat island is commonly defined as the temperature difference between the center of the city and the surrounding suburban and rural regions. The intensity is considered as a function of changes in the season and changes in meteorological conditions in order to derive various parameters which may be used in numerical models for urban climate. Twelve case studies were selected and CCT's were ordered. In situ data was obtained from sixteen stations scattered about the city of St. Louis. Upper-air meteorological data were obtained and the water vapor and the temperature data were processed. Atmospheric transmissivities were computed for each of the case studies.

Source record↗

Assessment of impingement effects in the isentropic core of a small satellite control thruster plume

Two computational techniques commonly employed in the calculation of rocket and thruster expansion plumes are assessed. These are the method of characteristics (MOC), which is derived from the continuum Euler equations, and the direct simulation Monte Carlo (DSMC) method, which adopts a discrete particle approach. These techniques vary both in the computational expense and in the accuracy and detail of the solutions that they provide, depending upon the regime of application. The assessment is made with reference to the plume expanding from a small monopropellant hydrazine thruster and concentrates on the isentropic core of the jet for the flow regime lying between the continuum and free molecular limits. It is found that the more numerically intensive DSMC method offers the better correspondence to the available experimental data. In addition, large differences in typical impingement effects such as drag force and heat transfer are found at the free molecular limit of the plume expansion for the two predictive techniques. It is concluded that accurate estimation of impingement potential may only be achieved through application of the discrete particle method.

Boyd, I. D.↗

Diabatic forcing and initialization with assimilation of cloud and rain water in a forecast model: Methodology

The focus of this part of the investigation is to find one or more general modeling techniques that will help reduce the time taken by numerical forecast models to initiate or spin-up precipitation processes and enhance storm intensity. If the conventional data base could explain the atmospheric mesoscale flow in detail, then much of our problem would be eliminated. But the data base is primarily synoptic scale, requiring that a solution must be sought either in nonconventional data, in methods to initialize mesoscale circulations, or in ways of retaining between forecasts the model generated mesoscale dynamics and precipitation fields. All three methods are investigated. The initialization and assimilation of explicit cloud and rainwater quantities computed from conservation equations in a mesoscale regional model are examined. The physical processes include condensation, evaporation, autoconversion, accretion, and the removal of rainwater by fallout. The question of how to initialize the explicit liquid water calculations in numerical models and how to retain information about precipitation processes during the 4-D assimilation cycle are important issues that are addressed. The explicit cloud calculations were purposely kept simple so that different initialization techniques can be easily and economically tested. Precipitation spin-up processes associated with three different types of weather phenomena are examined. Our findings show that diabatic initialization, or diabatic initialization in combination with a new diabatic forcing procedure, work effectively to enhance the spin-up of precipitation in a mesoscale numerical weather prediction forecast. Also, the retention of cloud and rain water during the analysis phase of the 4-D data assimilation procedure is shown to be valuable. Without detailed observations, the vertical placement of the diabatic heating remains a critical problem.

Raymond, William H.↗

Neural Network and Regression Approximations in High Speed Civil Transport Aircraft Design Optimization

Nonlinear mathematical-programming-based design optimization can be an elegant method. However, the calculations required to generate the merit function, constraints, and their gradients, which are frequently required, can make the process computational intensive. The computational burden can be greatly reduced by using approximating analyzers derived from an original analyzer utilizing neural networks and linear regression methods. The experience gained from using both of these approximation methods in the design optimization of a high speed civil transport aircraft is the subject of this paper. The Langley Research Center's Flight Optimization System was selected for the aircraft analysis. This software was exercised to generate a set of training data with which a neural network and a regression method were trained, thereby producing the two approximating analyzers. The derived analyzers were coupled to the Lewis Research Center's CometBoards test bed to provide the optimization capability. With the combined software, both approximation methods were examined for use in aircraft design optimization, and both performed satisfactorily. The CPU time for solution of the problem, which had been measured in hours, was reduced to minutes with the neural network approximation and to seconds with the regression method. Instability encountered in the aircraft analysis software at certain design points was also eliminated. On the other hand, there were costs and difficulties associated with training the approximating analyzers. The CPU time required to generate the input-output pairs and to train the approximating analyzers was seven times that required for solution of the problem.

Patniak, Surya N.↗

A Synthesis of Star Calibration Techniques for Ground-Based Narrowband Electron-Multiplying Charge-Coupled Device Imagers Used in Auroral Photometry

A technique is presented for the periodic and systematic calibration of ground-based optical imagers. It is important to have a common system of units (Rayleighs or photon flux) for cross comparison as well as self-comparison over time. With the advancement in technology, the sensitivity of these imagers has improved so that stars can be used for more precise calibration. Background subtraction, flat fielding, star mapping, and other common techniques are combined in deriving a calibration technique appropriate for a variety of ground-based imager installations. Spectral (4278, 5577, and 8446 A ) ground-based imager data with multiple fields of view (19, 47, and 180 deg) are processed and calibrated using the techniques developed. The calibration techniques applied result in intensity measurements in agreement between different imagers using identical spectral filtering, and the intensity at each wavelength observed is within the expected range of auroral measurements. The application of these star calibration techniques, which convert raw imager counts into units of photon flux, makes it possible to do quantitative photometry. The computed photon fluxes, in units of Rayleighs, can be used for the absolute photometry between instruments or as input parameters for auroral electron transport models.

Grubbs, Guy II↗

Do You See What I See? Interactive Visualization of Mission Design and Navigation

Mission Design and Navigation (MDNav) is an intensive process requiring advanced computational resources, expert human intuition, and many successive human-in-the-loop iterations to converge on acceptable trajectory designs or navigation solutions. The current bottleneck in MDNav is not the underlying computational algorithms but the human cognitive capacity to prune through a multitude of simulated results to select high-value candidates. One approach to alleviate this burden is through the judicious application of visualizations that allow humans to interactively filter data in multiple dimensions to reveal salient patterns and highlight divergences. When designed efficiently, such interactive visualizations should aid human operators to get familiar with data faster, visually observe correlations, and communicate findings more effortlessly. In this work, we present three visualization case studies that have the potential to increase human operator efficiency in MDNav. While identifying the most critical “pain points” that operators face, and also working on potential solutions, we followed a human-centered design approach. We started with a series of interviews with potential users, and then rapidly created prototypes for alternative solutions, validated outcomes with feedback from users through out development of these proof of concept visualizations. With this survey of our current efforts, we demonstrate the transformative capability of interactive data visualizations for improving mission development and operations, enabling operators to grow intuition, and communicating key concepts across diverse mission teams.

Arora, Nitin↗

Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography

A systematic approach to the scaling and merging of data from multiple crystals in macromolecular crystallography is introduced and explained. The availability of intense microbeam macromolecular crystallography beamlines at third-generation synchrotron sources has enabled data collection and structure solution from microcrystals of <10 µm in size. The increased likelihood of severe radiation damage where microcrystals or particularly sensitive crystals are used forces crystallographers to acquire large numbers of data sets from many crystals of the same protein structure. The associated analysis and merging of multi-crystal data is currently a manual and time-consuming step. Here, a computer program, BLEND, that has been written to assist with and automate many of the steps in this process is described. It is demonstrated how BLEND has successfully been used in the solution of a novel membrane protein.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Provenance–aware workflow for data quality management and improvement for large continuous scientific data streams

Data quality assessment, management and improvement is integral part of any big data intensive scientific research to ensure accurate, reliable and reproducible science discoveries. The task of maintaining the quality of data, however, is non-trivial and pose a challenge for a program like Department of Energy’s Atmospheric Radiation Measurement (ARM) that collects data from hundreds of instruments across the world,and distributes thousands of streaming data products that are continuously growing in near-real-time in an archive 1.7 Petabyte in size and growing. We present a computational data processing workflow to collect the data quality issue via an easy and intuitive web-based portal that allows reporting of any quality issues for any site, facility or instruments at a granularity down to individual variable in the data files. Portal allows instrument specialists and scientists to provide corrective actions in form of symbolic equation. A parallel processing framework applies the data improvement to large volume of data in efficient parallel environment, while optimizing data transfer and file I/O operations. Corrected files are systematically versioned and archived. A provenance tracking module tracks and records any change made to the data during its entire life cycle which are communicated transparently to the scientific users. Developed in Python using open source technologies, software architecture enables efficient and fast management and improvement of data in an operational data center environment.

Kumar, Jitendra↗

A Hard X-ray Study of a Manganese-Terpyridine Dimer Catalyst in a Chromium-Based Metal Organic Framework

Much of today’s scientific research is geared toward discovering clean energy from renewable sources. A promising approach is to split water into its fundamental elements – hydrogen and oxygen. The hydrogen produced from this process is a source of clean energy. Plants carry out this water splitting routinely as a part of photosynthesis, but we cannot do this readily as the reaction requires a lot of energy, negating the value of cleaner and plentiful energy from hydrogen. Adding a catalyst provides an alternative pathway for the reaction so that it can proceed with lower energy input. Many such catalysts have been developed; the one used in this study is manganese based and is called manganese-terpyridine dimer (MnTD). The problem is that when individual molecules of MnTD interact they destroy each other, which limits practical use of the catalyst. However, by placing the catalyst in a Metal Organic Framework (MOF), the molecules of MnTD can be separated so that, in principle, they do not interact with each other and only interact with water. The MOF is essentially a repetition of boxes, and each box should contain one MnTD molecule. However, preliminary studies showed that a different molecule, not MnTD, may be inside the boxes. My research focused on identifying which molecules are present in the MOF. The primary method of analysis used was x-ray powder diffraction, a technique in which x-rays are scattered by a sample, and the intensity of the scattered radiation is measured as a function of scattering angle. Three samples were analyzed; one contained only the MOF, one contained the MOF and catalyst before catalysis, and one contained the MOF and catalyst during catalysis. The diffraction experiments were carried out at the Stanford Synchrotron Radiation Lightsource (SSRL) at SLAC National Accelerator Laboratory. Initial results revealed that the MOF structure falls apart during catalysis. To further analyze the data, I used several computer programs, including GSAS II, FOX, and VESTA. These programs allowed me to create maps that showed regions of electron density within the MOF and gave me clues as to which molecules were present. I found that MnTD was not the catalytic molecule in the MOF. The preliminary studies showed that manganese oxide is likely present, which is consistent with by data. However, the catalytic rate for this system is much higher than that reported for manganese oxide, and thus future studies are needed to verify the identity of the catalytic molecule and determine the reasons for its unusually high rate of catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A numerical method for the prediction of high-speed boundary-layer transition using linear theory

A method is described of estimating the location of transition in an arbitrary laminar boundary layer on the basis of linear stability theory. After an examination of experimental evidence for the relation between linear stability theory and transition, a discussion is given of the three essential elements of a transition calculation: (1) the interaction of the external disturbances with the boundary layer; (2) the growth of the disturbances in the boundary layer; and (3) a transition criterion. The computer program which carried out these three calculations is described. The program is first tested by calculating the effect of free-stream turbulence on the transition of the Blasius boundary layer, and is then applied to the problem of transition in a supersonic wind tunnel. The effects of unit Reynolds number and Mach number on the transition of an insulated flat-plate boundary layer are calculated on the basis of experimental data on the intensity and spectrum of free-stream disturbances. Reasonable agreement with experiment is obtained in the Mach number range from 2 to 4.5.

Mack, L. M.↗

Dynamics and structure of turbulent premixed flames

In earlier work (Mantel & Bilger, 1994) the structure of the turbulent premixed flame was investigated using statistics based on conditional averaging with the reaction progress variable as the conditioning variable. The DNS data base of Trouve and Poinsot (1994) was used in this investigation. Attention was focused on the conditional dissipation and conditional axial velocity in the flame with a view to modeling these quantities for use in the conditional moment closure (CMC) approach to analysis of kinetics in premixed flames (Bilger, 1993). Two remarkable findings were made: there was almost no acceleration of the axial velocity in the flame front itself; and the conditional scalar dissipation remained as high, or higher, than that found in laminar premixed flames. The first finding was surprising since in laminar flames all the fluid acceleration occurs through the flame front, and this could be expected also for turbulent premixed flames at the flamelet limit. The finding gave hope of inventing a new approach to the dynamics of turbulent premixed flames through use of rapid distortion theory or an unsteady Bernoulli equation. This could lead to a new second order closure for turbulent premixed flames. The second finding was contrary to our measurements with laser diagnostics in lean hydrocarbon flames where it is found that conditional scalar dissipation drops dramatically below that for laminar flamelets when the turbulence intensity becomes high. Such behavior was not explainable with a one-step kinetic model, even at non-unity Lewis number. It could be due to depletion of H2 from the reaction zone by preferential diffusion. The capacity of the flame to generate radicals is critically dependent on the levels of H2 present (Bilger, et al., 1991). It seemed that a DNS computation with a multistep reduced mechanism would be worthwhile if a way could be found to make this feasible. Truly innovative approaches to complex problems often come only when there is the opportunity to work close at hand with the (in this case numerical) experimental data. Not only can one spot patterns and relationships in the data which could be important, but one can also get to know the limitations of the technique being used, so that when the next experiment is being designed it will address resolvable questions. A three-year grant from the Australian Research Council has enabled us to develop a small capability at the University of Sydney to work on DNS of turbulent reacting flow, and to analyze data bases generated at CTR. Collaboration between the University of Sydney and CTR is essential to this project and finding a workable modus operandum for this collaboration, given the constraints involved, has been a major objective of the past year's effort. The overall objectives of the project are: (1) to obtain a quantitative understanding of the dynamics of turbulent premixed flames at high turbulence levels with a view to developing improved second order closure models; and (2) to carry out new DNS experiments on turbulent premixed flames using a carefully chosen multistep reduced mechanism for the chemical kinetics, with a view to elucidating the laser diagnostic findings that are contrary to the findings for DNS using one-step kinetics. In this first year the objectives have been to make the existing CTR data base more accessible to coworkers at the University of Sydney, to make progress on understanding the dynamics of the flame in this existing CTR data base, and to carefully construct a suitable multistep reduced mechanism for use in a new set of DNS experiments on turbulent premixed flames.

Bilger, R. W.↗

Mass Spectrometer Transient Analysis

This software implements a complete preprocessing pipeline for transient mass spectrometry (MS) data collected during TAP (Temporal Analysis of Products) experiments. It is designed to extract chemically meaningful fluxes from overlapping ion signals by applying a calibrated defragmentation matrix and solving the resulting linear system using non-negative least squares (NNLS) regression. The core script, preprocess_mass_spec.py, performs the following operations: Gain correction: Applies amplifier gain scalars derived from inert-packed calibration pulses to normalize signal intensities across AMUs and acquisition settings. Background subtraction: Removes experiment baselines using user-defined time windows, ensuring compatibility with slow-diffusing species and preventing negative values that would interfere with NNLS. Options to subtract before and after defragmentation. Defragmentation: Constructs a fragmentation matrix A from zeroth moments of calibration pulses (equal molar gas:inert mixtures) and solves Ax=b at each time point, where b is the raw MS signal and x is the estimated species flux. The matrix is normalized to inert signals and accounts for instrument-specific fragmentation behavior. Pulse-mode handling: Supports both averaged and individual pulse modes, enabling statistical treatment of fluxes and calculation of standard deviations. Integration and output: Computes zeroth moments (integrated fluxes) and exports time-resolved and integrated data in CSV format, suitable for downstream kinetic modeling. The software is validated using both virtual TAP simulations (VTAP) and experimental data from propane dehydrogenation (PDH) on CrOx/Al2O3 catalysts. It preserves temporal resolution by applying NNLS point-by-point across the pulse duration (typically 6,000+ time slices per pulse), leveraging the linear superposition principle to reconstruct full flux profiles. The defragmented outputs are compatible with kinetic extraction methods such as the G and Y procedures, which are used to derive rate–concentration relationships from TAP data. The details of these validations are discussed in detail in the supporting manuscript and supporting information. Example data and output files are also included. The methodology is robust to experimental noise and drift, with calibration protocols that account for pulse size effects, MS aging, and inert gas normalization. The software is modular, reproducible, and tailored for high-throughput TAP-MS workflows in catalysis research.

Kristy, Stephen [Idaho National Laboratory (INL), ↗

Predictability of Malaria Transmission Intensity in the Mpumalanga Province, South Africa, Using Land Surface Climatology and Autoregressive Analysis

There has been increasing effort in recent years to employ satellite remotely sensed data to identify and map vector habitat and malaria transmission risk in data sparse environments. In the current investigation, available satellite and other land surface climatology data products are employed in short-term forecasting of infection rates in the Mpumalanga Province of South Africa, using a multivariate autoregressive approach. The climatology variables include precipitation, air temperature and other land surface states computed by the Off-line Land-Surface Global Assimilation System (OLGA) including soil moisture and surface evaporation. Satellite data products include the Normalized Difference Vegetation Index (NDVI) and other forcing data used in the Goddard Earth Observing System (GEOS-1) model. Predictions are compared to long- term monthly records of clinical and microscopic diagnoses. The approach addresses the high degree of short-term autocorrelation in the disease and weather time series. The resulting model is able to predict 11 of the 13 months that were classified as high risk during the validation period, indicating the utility of applying antecedent climatic variables to the prediction of malaria incidence for the Mpumalanga Province.

Grass, David↗

Simulating Collisions for Hydrokinetic Turbines

Evaluations of blade-strike on an axial-flow Marine Hydrokinetic turbine were conducted using a conventional methodology as well as an alternative modeling approach proposed in the present document. The proposed methodology integrates the following components into a Computational Fluid Dynamics (CFD) model: (i) advanced eddy-resolving flow simulations, (ii) ambient turbulence based on field data, (iii) moving turbine blades in highly transient flows, and (iv) Lagrangian particles to mimic the potential fish pathways. The sensitivity of blade-strike prob- ability to the following conditions was also evaluated: (i) to the turbulent environment, (ii) to fish size and (iii) to mean stream flow velocity. The proposed methodology provided fraction of collisions and offered the capability of analyzing the causal relationships between the flow environment and resulting strikes on rotating blades. Overall, the conventional methodology largely overestimates the probability of strike, and lacks the ability to produce potential fish and aquatic biota trajectories as they interact with the rotating turbine. By using a set of experimental correlations of exposure-response of living fish colliding on moving blades, the occurrence, frequency and intensity of the particle collisions was next used to calculate the survival rate of fish crossing the MHK turbine. This step indicated survival rates always greater than 98%. Although the proposed CFD framework is computationally more expensive, it provides the advantage of evaluating multiple mechanisms of stress and injury of hydrokinetic turbine devices on fish.

CFD↗

A computationally efficient P 1 radiation model for modern combustion systems utilizing pre-conditioned conjugate gradient methods

The iterative convergence of the P 1 radiation model can be slow in optically thin scenarios when employing classical iterative methods. In order to remedy this shortcoming, an in-house P 1 radiation model was interfaced with high performance, scalable, linear solver libraries. Next, the accuracies of P 1 radiation model calculations was assessed by comparing its predictions against discrete ordinates (DO) model calculations for prototypical problems representative of modern combustion systems. Corresponding benchmark results were also included for comparison. Utilizing Pre-Conditioners (PC) to the Conjugate Gradients (CG) method, the convergence time of the P 1 radiation model reduced by a factor of 30 for modest problem sizes and a factor of 70 for larger sized problems when compared against classical Gauss Seidel sweeps. Additionally, PC provided 50% computational savings compared to employing CG in a standalone mode. The P 1 model calculation times were about 25–30% of the DO model calculation time. The time to solution also scaled linearly with an increase in problem size. The weighted sum of gray gases model employed in this study in conjunction with the P 1 model provided good agreement against benchmark data with L 2 error norms (defined relative to corresponding DO calculations) improving when isotropic intensities were prevalent.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Toward Magnetic Resonance–Only Simulation: Segmentation of Bone in MR for Radiation Therapy Verification of the Head

Purpose: To develop a practical method to localize bones in magnetic resonance (MR) images, to create “computed tomography–like” MR images (ctMRI) that could be used for radiation therapy verification, and to generate MR-based digitally reconstructed radiographs (DRR). Methods and Materials: Using T1-weighted MR images, an air mask was derived from the manual contouring of all airways within the head and neck region using axial images at 6 anatomic levels. Compact bone, spongy bone, and soft tissue masks were then automatically generated using the statistical data derived from MR intensities and the air mask. ctMRI were then generated by mapping the MR intensities of the voxels within these masks into the CT number ranges of corresponding tissues. MR-based DRRs created from ctMRI were quantitatively evaluated using the co-registered MR and CT head images of 20 stereotactic radiosurgery patients. Ten anatomical points, positioned on the skull segmented using a threshold of 300 HU, in CT and ctMRI, were used to determine the differences in distance between MR-based DRRs and CT-based DRRs, and to evaluate the geometric accuracy of ctMRI and MR-based DRRs. Results: The bony structures were identified on ctMRI and were visible in the MR-based DRRs. From the 20 patient cases, the mean geometric difference and standard deviation between the 10 anatomical points on MR-based and CT-based DRRs was −0.05 ± 0.85 mm, respectively. This included uncertainty in image fusion. The maximum distance difference was 1.88 mm. Conclusions: A practical method was developed to segment bone from MR images. The ctMRI created can be used for radiation treatment verification when MR-only simulation is performed. MR-based DRRs can be used in place of CT-based DRRs.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Implementing intensity modulated radiotherapy to the prostate bed: Dosimetric study and early clinical results

Salvage intensity modulated radiotherapy (IMRT) to the prostate bed has hardly been studied so far. We present here a feasibility study and early clinical results for 10 patients. These patients were selected on the basis of having either a biochemical relapse or high risk histology after prostatectomy. They were treated using “sliding-window” IMRT to 68 Gy in 34 fractions. Three-dimensional conformal radiotherapy (3D-CRT) plans were generated using the same planning computed tomography data set. Dose coverage of planning target volumes (PTVs) and of organs-at-risk (OAR, namely: rectum, bladder, and femoral heads) were compared. Acute toxicity and chronic toxicity were measured using the Common Toxicity Criteria for Adverse Events version 3.0 scale. IMRT significantly reduces the dose above the prescription dose given to the PTV1 (mean dose: IMRT 67.2 Gy vs 3D-CRT 67.7 Gy (p = 0.0137)), without altering dose coverage for PTV2 (mean dose: IMRT 68.1 Gy vs 3D-CRT 68.0 Gy (p = 0.3750)). Doses to OAR were lower with IMRT and differences were statistically significant (mean dose: IMRT 51.4 Gy vs 3D-CRT 56.6 Gy for rectum (p = 0.002), IMRT 45.1 Gy vs 3D-CRT 53.1 Gy for bladder (p = 0.002), and IMRT 26.1 Gy vs 3D-CRT 28.4 Gy for femoral heads (p = 0.0059)). There was no acute or chronic genitourinary or gastrointestinal toxicity >1 with a median follow-up of 38 months. IMRT to the prostatic fossa is feasible and reduces dose to OAR, with consequential limited toxicity.

61 RADIATION PROTECTION AND DOSIMETRY↗