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All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Concurrent coupling of atomistic simulation and mesoscopic hydrodynamics for flows over soft multi-functional surfaces

We develop an e?cient parallel multiscale method that bridges the atomistic and mesoscale regimes, from nanometers to microns and beyond, via concurrent coupling of atomistic simulation and mesoscopic dynamics. In particular, we combine an all-atom molecular dynamics (MD) description for specific atomistic details in the vicinity of the functional surface with a dissipative particle dynamics (DPD) approach that captures mesoscopic hydrodynamics in the domain away from the functional surface. In order to achieve a seamless transition in dynamic properties we endow the MD simulation with a DPD thermostat, which is validated against experimental results by modeling water at di?erent temperatures. We then validate the MD-DPD coupling method for transient Couette and Poiseuille flows, demonstrating that the concurrent MD-DPD coupling can resolve accurately the continuumbased analytical solutions. Subsequently, we simulate shear flows over grafted polydimethylsiloxane (PDMS) surfaces (polymer brushes) for various grafting densities, and investigate the slip flow as a function of the shear stress. We verify that a ‘‘universal’’ power law exists for the slip length, in agreement with published results. Having validated the MD-DPD coupling method, we simulate timedependent flows past an endothelial glycocalyx layer (EGL) in a microchannel. Coupled simulation results elucidate the dynamics of the EGL changing from an equilibrium state to a compressed state under shear by aligning the molecular structures along the shear direction. MD-DPD simulation results agree well with results of a single MD simulation, but with the former more than two orders of magnitude faster than the latter for system sizes above one micron.

Wang, Yuying↗
DOE OSTI2015

Three-Dimensional Assignment of the Structures of Atomic Clusters: an Example of Au 8 M (M=Si, Ge, Sn) Anion Clusters

Identification of different isomer structures of atomic and molecular clusters has long been a challenging task in the field of cluster science. Here we present a three-dimensional (3D) assignment method, combining the energy (1D) and simulated (2D) spectra to assure the assignment of the global minimum structure. This method is more accurate and convenient than traditional methods, which only consider the total energy and first vertical detachment energies (VDEs) of anion clusters. There are two prerequisites when the 3D assignment method is ultilized. First, a reliable global minimum search algorithm is necessary to explore enough valleys on the potential energy surface. Second, trustworthy simulated spectra are necessary, that is to say, spectra that are in quantitative agreement. In this paper, we demonstrate the validity of the 3D assignment method using Au 8 M – (M = Si, Ge, Sn) systems. Results from this study indicate that the global minimum structures of Au 8 Ge – and Au 8 Sn – clusters are different from those described in previous studies.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Three-Dimensional Imaging Lidar for Characterizing Particle Fields and Organisms in the Mesopelagic Zone

The ocean’s mesopelagic zone is largely uncharacterized despite its vital role in sustaining ocean ecosystems. The composition, cycling, and fate of particle fields in the mesopelagic lacks an integrative multi-scale understanding of organism migration patterns, distribution, and diversity. This problem is addressed by combining complementary technologies with overlapping size spectra, including profiler mounted optical scattering sensors, profiler, and ship mounted acoustic devices, and a custom Unobtrusive Multi-Static Lidar Imager (UMSLI). This unique sensor suite can observe distributions of particles including organisms over a six order of magnitude dynamic size range, from microns to meters. Overlapping size ranges between different methods allows for cross-validation. This work focuses on the lidar imaging measurements and optical backscattering and attenuation, covering a combined particle size range of 0.1 mm to several cm. Particles at the small end of this range are sized using an existing backscattering time series inversion method after Briggs et al. (2013). Larger particles are resolved with UMSLI over an expanding volume using three-dimensional photo-realistic laser serial imaging. UMSLI’s image rectifying ability over time allows for derivation of particle concentration, size, and spatial distribution. Technical details on the development and post-processing methods for the novel UMSLI system are provided. Image resolved particle size distributions (PSDs) revealed a size shift from smaller to larger particles (>0.5 mm) as indicated by flatter slopes from dawn (slope = 2.6) to dusk (slope = 3.0). PSD trends are supported by an optical backscatter and transmissometer time series inversion analysis. Size shifts in the particle field are largely attributed to aggregation effects. Images support evidence of temporal variation between dusk and dawn stations through statistical analysis of particle concentrations for particle sizes 0.50–5.41 mm. Spatial analysis of the particle field revealed a dominantly uniform distributed marine snow background. The importance and potential of integrated approaches to studying particle and organism dynamics in ocean environments are discussed.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Optimizing Batch Crystallization with Model-based Design of Experiments

Adaptive and self-optimizing intelligent systems such as digital twins are increasingly important in science and engineering. Digital twins utilize mathematical models to provide added precision to decision-making. However, physics-informed models are challenging to build, calibrate, and validate with existing data science methods. Model-based design of experiments (MBDoE) is a popular framework for optimizing data collection to maximize parameter precision in mathematical models and digital twins. In this work, we apply MBDoE, facilitated by the open-source package Pyomo.DoE, to train and validate mathematical models for batch crystallization. We quantitatively examined the estimability of the model parameters for experiments with different cooling rates. This analysis provides a quantitative explanation for the heuristic of using multiple experiments at different cooling rates.

Lynch, Hailey↗
DOE OSTI2014

Validation of a Monte Carlo model used for simulating tube current modulation in computed tomography over a wide range of phantom conditions/challenges

Purpose: Monte Carlo (MC) simulation methods have been widely used in patient dosimetry in computed tomography (CT), including estimating patient organ doses. However, most simulation methods have undergone a limited set of validations, often using homogeneous phantoms with simple geometries. As clinical scanning has become more complex and the use of tube current modulation (TCM) has become pervasive in the clinic, MC simulations should include these techniques in their methodologies and therefore should also be validated using a variety of phantoms with different shapes and material compositions to result in a variety of differently modulated tube current profiles. The purpose of this work is to perform the measurements and simulations to validate a Monte Carlo model under a variety of test conditions where fixed tube current (FTC) and TCM were used. Methods: A previously developed MC model for estimating dose from CT scans that models TCM, built using the platform of MCNPX, was used for CT dose quantification. In order to validate the suitability of this model to accurately simulate patient dose from FTC and TCM CT scan, measurements and simulations were compared over a wide range of conditions. Phantoms used for testing range from simple geometries with homogeneous composition (16 and 32 cm computed tomography dose index phantoms) to more complex phantoms including a rectangular homogeneous water equivalent phantom, an elliptical shaped phantom with three sections (where each section was a homogeneous, but different material), and a heterogeneous, complex geometry anthropomorphic phantom. Each phantom requires varying levels of x-, y- and z-modulation. Each phantom was scanned on a multidetector row CT (Sensation 64) scanner under the conditions of both FTC and TCM. Dose measurements were made at various surface and depth positions within each phantom. Simulations using each phantom were performed for FTC, detailed x–y–z TCM, and z-axis-only TCM to obtain dose estimates. This allowed direct comparisons between measured and simulated dose values under each condition of phantom, location, and scan to be made. Results: For FTC scans, the percent root mean square (RMS) difference between measurements and simulations was within 5% across all phantoms. For TCM scans, the percent RMS of the difference between measured and simulated values when using detailed TCM and z-axis-only TCM simulations was 4.5% and 13.2%, respectively. For the anthropomorphic phantom, the difference between TCM measurements and detailed TCM and z-axis-only TCM simulations was 1.2% and 8.9%, respectively. For FTC measurements and simulations, the percent RMS of the difference was 5.0%. Conclusions: This work demonstrated that the Monte Carlo model developed provided good agreement between measured and simulated values under both simple and complex geometries including an anthropomorphic phantom. This work also showed the increased dose differences for z-axis-only TCM simulations, where considerable modulation in the x–y plane was present due to the shape of the rectangular water phantom. Results from this investigation highlight details that need to be included in Monte Carlo simulations of TCM CT scans in order to yield accurate, clinically viable assessments of patient dosimetry.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2013

Assessment of Testing Options for the NTR at the INL (Final Report)

One of the main technologies that can be developed to dramatically enhance the human exploration of space is the nuclear thermal rocket (NTR). Several studies over the past thirty years have shown that the NTR can reduce the cost of a lunar outpost, reduce the risk of a human mission to Mars, enable fast transits for most missions throughout the solar system, and reduce the cost and time for robotic probes to deep space. Three separate committees of the National Research Council of the National Academy of Sciences have recommended that NASA develop the NTR. One of the primary issues in development of the NTR is the ability to verify a flight ready unit. Three main methods can be used to validate safe operation of a NTR: 1) Full power, full duration test in an above ground facility that scrubs the rocket exhaust clean of any fission products; 2) Full power , full duration test using the Subsurface Active Filtering of Exhaust (SAFE) technique to capture the exhaust in subsurface strata; 3) Test of the reactor fuel at temperature and power density in a driver reactor with subsequent first test of the fully integrated NTR in space. The first method, the above ground facility, has been studied in the past. The second method, SAFE, has been examined for application at the Nevada Test Site. The third method relies on the fact that the Nuclear Furnace series of tests in 1971 showed that the radioactive exhaust coming from graphite based fuel for the NTR could be completely scrubbed of fission products and the clean hydrogen flared into the atmosphere. Under funding from the MSFC, the Center for Space Nuclear Research (CSNR) at the Idaho National laboratory (INL) has completed a reexamination of Methods 2 and 3 for implementation at the INL site. In short, the effort performed the following: 1) Assess the geology of the INL site and determine a location suitable SAFE testing; 2) Perform calculations of gas transport throughout the geology; 3) Produce a cost estimate of a non-nuclear , sub-scale test using gas injection to validate the computational models; 4) Produce a preliminary cost estimate to build a nuclear furnace equivalent facility to test NTR fuel on a green field location on the INL site. The results show that the INL geology is substantially better suited to the SAFE testing method than the NTS site. The existence of impermeable interbeds just above the sub-surface aquifer ensure that no material from the test, radioactive or not, can enter the water table. Similar beds located just below the surface will prevent any gaseous products from reaching the surface for dispersion. The extremely high permeability of the strata between the interbeds allows rapid dispersion of the rocket exhaust. In addition, the high permeability suggests that a lower back-pressure may develop in the hole against the rocket thrust, which increases safety of operations. Finally, the cost of performing a sub-scale, non-nuclear verification experiment was determined to be $\$$3M. The third method was assessed through discussions with INL staff resident at the site. In essence, any new Category I facility on any DOE site will cost in excess of $\$$250M. Based on the results of this study, a cost estimate for testing a nuclear rocket at the INL site appears to be warranted. Given the fact that a new nuclear fuel may be possible that does not release any fission products, the SAFE testing option appears to be the most affordable.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2022

Automated compatibility checking of prefabricated components using 3D as-built models and BIM

There have been recent efforts to use reality capture technologies to perform remote quality control in construction. However, there is a lack of research efforts in detecting construction incompatibilities in modular construction using reality capture technologies. The construction incompatibilities in modular construction often cause reworks and delays in the project schedule. To address this issue, this paper presents a general compatibility analysis method that propose scanning the modules in manufacturing plant and construction site, and check module-to-module compatibility remotely, prior to the shipment and installation. This study provides three sample module-to-module compatibility scenarios to validate the proposed compatibility analysis. The case study results show that the compatibility analysis method was able to identify the compatibility issues with high accuracy. Lastly, the compatibility analysis method was validated in terms of accuracy and time performance in six scenarios that was defined on the modules.

42 ENGINEERING↗
DOE OSTI2016

Contour interpolated radial basis functions with spline boundary correction for fast 3D reconstruction of the human articular cartilage from MR images

Purpose: The aim of this work is to demonstrate a new image processing technique that can provide a “near real-time” 3D reconstruction of the articular cartilage of the human knee from MR images which is user friendly. This would serve as a point-of-care 3D visualization tool which would benefit a consultant radiologist in the visualization of the human articular cartilage. Methods: The authors introduce a novel fusion of an adaptation of the contour method known as “contour interpolation (CI)” with radial basis functions (RBFs) which they describe as “CI-RBFs.” The authors also present a spline boundary correction which further enhances volume estimation of the method. A subject cohort consisting of 17 right nonpathological knees (ten female and seven male) is assessed to validate the quality of the proposed method. The authors demonstrate how the CI-RBF method dramatically reduces the number of data points required for fitting an implicit surface to the entire cartilage, thus, significantly improving the speed of reconstruction over the comparable RBF reconstruction method of Carr. The authors compare the CI-RBF method volume estimation to a typical commercial package (3D DOCTOR), Carr’s RBF method, and a benchmark manual method for the reconstruction of the femoral, tibial, and patellar cartilages. Results: The authors demonstrate how the CI-RBF method significantly reduces the number of data points (p-value < 0.0001) required for fitting an implicit surface to the cartilage, by 48%, 31%, and 44% for the patellar, tibial, and femoral cartilages, respectively. Thus, significantly improving the speed of reconstruction (p-value < 0.0001) by 39%, 40%, and 44% for the patellar, tibial, and femoral cartilages over the comparable RBF model of Carr providing a near real-time reconstruction of 6.49, 8.88, and 9.43 min for the patellar, tibial, and femoral cartilages, respectively. In addition, it is demonstrated how the CI-RBF method matches the volume estimation of a typical commercial package (3D DOCTOR), Carr’s RBF method, and a benchmark manual method for the reconstruction of the femoral, tibial, and patellar cartilages. Furthermore, the performance of the segmentation method used for the extraction of the femoral, tibial, and patellar cartilages is assessed with a Dice similarity coefficient, sensitivity, and specificity measure providing high agreement to manual segmentation. Conclusions: The CI-RBF method provides a fast, accurate, and robust 3D model reconstruction that matches Carr’s RBF method, 3D DOCTOR, and a manual benchmark method in accuracy and significantly improves upon Carr’s RBF method in data requirement and computational speed. In addition, the visualization tool has been designed to quickly segment MR images requiring only four mouse clicks per MR image slice.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2015

Simulation of elastic wave propagation using cellular automata and peridynamics, and comparison with experiments

Peridynamics is a non-local continuum mechanics formulation that can handle spatial discontinuities as the governing equations are integro-differential equations which do not involve gradients such as strains and deformation rates. This paper employs bond-based peridynamics. Cellular Automata is a local computational method which, in its rectangular variant on interior domains, is mathematically equivalent to the central difference finite difference method. However, cellular automata does not require the derivation of the governing partial differential equations and provides for common boundary conditions based on physical reasoning. Both methodologies are used to solve a half-space subjected to a normal load, known as Lamb’s Problem. The results are compared with theoretical solution from classical elasticity and experimental results. Furthermore, this paper is used to validate our implementation of these methods.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

Model-based approaches to calibration and certification of nondestructive assay systems - 15615

Increasingly, model-based methods founded in physics are employed to calibrate, or extend the calibration of, nondestructive assay (NDA) systems used to characterize materials contaminated with plutonium, uranium, and other radioactive isotopes. In addition, modeling and mathematical methods are used to establish system parameters, correction factors, and measurement uncertainty components in NDA measurements. The methods combine the characteristics of the measurement configuration (detector structure, object shape and dimensions, source-detector distance and orientation, and collimation), generator knowledge of the waste composition, and known physical properties of the system in order to establish these parameters, factors, and components. These methods offer several important benefits over traditional methods used to test, calibrate, operate, and certify radiation measurement systems. First, instruments can be set up and put into service more quickly and correctly using a model-based approach. Second, calibrations can be performed, tested, and modified with reduced use of plutonium and uranium standards when modeling and mathematical methods are employed. Also, modeled approaches avoid calibration error resulting from heterogeneous source distribution. Moreover, the parameters can be installed quickly and simply in an office setting without the need for the safety, security, and safeguards considerations that are present when standards are used. Calibrations can also be tailored to fit unique or nonstandard container configurations (for example, over-packed drums), new container types, or specialized matrices. Finally, when modeling methods are applied, correction factors and measurement uncertainty elements can be developed, tested, and validated relatively quickly and without the need for surrogate matrix materials and a large number of test measurements. A combined gamma and neutron NDA system has recently been moved from Idaho National Laboratory to the TA 55 facility at Los Alamos National Laboratory (LANL). The system will be used to assay transuranic waste packaged in drums. After the move, the system was modified to replace degraded components and improve system performance. Afterwards, it was set up to assay different container types and to extend the calibration range. Model-based approaches were used to adapt the system to its new purpose at LANL. This report will describe the setup, calibration, and certification of the combined system at LANL Included in this discussion will be the measurement applications and details of the measurement methods. The steps in these processes that involved the use of modeling and mathematical calculations to replace or supplement more traditional methods will be identified and discussed. Finally, an overarching discussion of the methods and advantages of model-based methods to establish the properties of NDA systems will be presented. We conclude that validated mathematical methods offer a robust, flexible, and mature approach which is technically defensible from first principle physics. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2014

TU-F-18A-06: Dual Energy CT Using One Full Scan and a Second Scan with Very Few Projections

Purpose: The conventional dual energy CT (DECT) requires two full CT scans at different energy levels, resulting in dose increase as well as imaging errors from patient motion between the two scans. To shorten the scan time of DECT and thus overcome these drawbacks, we propose a new DECT algorithm using one full scan and a second scan with very few projections by preserving structural information. Methods: We first reconstruct a CT image on the full scan using a standard filtered-backprojection (FBP) algorithm. We then use a compressed sensing (CS) based iterative algorithm on the second scan for reconstruction from very few projections. The edges extracted from the first scan are used as weights in the Objectives: function of the CS-based reconstruction to substantially improve the image quality of CT reconstruction. The basis material images are then obtained by an iterative image-domain decomposition method and an electron density map is finally calculated. The proposed method is evaluated on phantoms. Results: On the Catphan 600 phantom, the CT reconstruction mean error using the proposed method on 20 and 5 projections are 4.76% and 5.02%, respectively. Compared with conventional iterative reconstruction, the proposed edge weighting preserves object structures and achieves a better spatial resolution. With basis materials of Iodine and Teflon, our method on 20 projections obtains similar quality of decomposed material images compared with FBP on a full scan and the mean error of electron density in the selected regions of interest is 0.29%. Conclusion: We propose an effective method for reducing projections and therefore scan time in DECT. We show that a full scan plus a 20-projection scan are sufficient to provide DECT images and electron density with similar quality compared with two full scans. Our future work includes more phantom studies to validate the performance of our method.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

X-ray diffraction measurements and pressure determination in nanosecond compression of solids up to 600 GPa

X-ray diffraction measurements under laser-driven dynamic compression now allow us to investigate the atomic structure of matter at TPa pressures and thousands of degree temperatures with broad implications for condensed matter physics, planetary science and astronomy. Furthermore, pressure determination in these experiments often relies on velocimetry measurements coupled with modeling that requires accurate knowledge of the optical and thermo-mechanical properties of a window material, resulting in significant systematic uncertainty. Here we demonstrate different approach applicable to X-ray diffraction experiments under quasi-isentropic ramp-compression based on the use of in-situ pressure calibrants, similar to the methods often adopted in static-compression experiments with diamond anvil cells. Focusing on experiments using a diamond window, we discuss challenges and mitigation strategies for the novel approach. Our study, in addition to providing new structural information of 5 metals up to hundreds of GPa, provides validation to the currently used methods based on time-resolved measurement of the diamond free-surface velocity, and reveals that the use of in-situ calibrants enables a factor of four reduction in the pressure uncertainty in these experiments.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

Incorporating machine learning with building network analysis to predict multi-building energy use

Predicting multi-building energy use at campus or city district scale has recently gained more attention; and more researchers have started to define reference buildings and study inter-impact between building groups. However, how to integrate the relationship to define reference buildings and predict multi-building energy use, using significantly less amount of building data and reducing complexity of prediction models, remains an open research question. To resolve this, this study proposed a novel method to predict multi-building energy use by integrating a social network analysis (SNA) with an Artificial Neural Network (ANN) technique. The SNA method was used to establish a building network (BN) by identifying reference buildings and determine correlations between reference buildings and non-reference buildings. The ANN technique was applied to learn correlations and historical building energy use, and then used to predict multi-building energy use. To validate the SNA-ANN method, 17 buildings in the Southeast University campus, located in Nanjing, China, were studied. These buildings have three years of actual monthly electricity use data and were grouped into four types: office, educational, laboratory, and residential. The results showed the integrated SNA-ANN method achieved average prediction accuracies of 90.67% for the office group, 90.79% for the educational group, 92.34% for the laboratory group, and 83.32% for the residential group. The results demonstrated the proposed SNA-ANN method achieved an accuracy of 90.28% for the predicted energy use for all building groups. Finally, this study provides insights into advancing the interdisciplinary research on multi-building energy use prediction.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2026

Hydrogen Analysis by Gas Chromatography–Mass Spectrometry

The detection of hydrogen in complex gas mixtures is essential for many applications. Conventional approaches such as gas chromatography (GC) with thermal conductivity detection (TCD) and residual gas analyzers (RGAs) face significant limitations: TCD exhibits poor response when helium is used as a carrier gas, whereas RGAs lack chromatographic separation, preventing reliable quantification of hydrogen because of interference from other species. Traditional GC methods rely on dual-column configurations with packed or molecular-sieve porous layer open tubular (PLOT) columns to separate hydrogen from O2, N2, CO, CO2, CH4, and other hydrocarbons, increasing system complexity and limiting compatibility with mass spectrometry (MS) detection. In this work, we developed and validated a robust GC–MS method capable of directly detecting and quantifying hydrogen using electron ionization (EI) without dopants, reagent gases, or ion–molecule reaction schemes. By integrating a modified EI source and a cryogenically cooled single capillary column configuration, we achieved baseline separation of hydrogen from all major permanent gases and hydrocarbons in a refinery gas mixture using helium as the carrier gas. The method demonstrated excellent linearity, high sensitivity, and exceptional reproducibility. Adjustable sample-loop volumes and split ratios enabled optimization of peak shape and signal-to-noise performance for trace-level and percent-level hydrogen concentrations. Beyond hydrogen quantitation, the method provides simultaneous compositional profiling of other gases in a mixture in a single run, making it valuable for a wide range of tasks.

Lobodin, Vlad [ORNL]↗
DOE OSTI2015

The adaptive buffered force QM/MM method in the CP2K and AMBER software packages

The implementation and validation of the adaptive buffered force (AdBF) quantum‐mechanics/molecular‐mechanics (QM/MM) method in two popular packages, CP2K and AMBER are presented. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM‐MM interface errors by discarding forces near the boundary according to the buffered force‐mixing approach. New adaptive thermostats, needed by force‐mixing methods, are also implemented. Different variants of the method are benchmarked by simulating the structure of bulk water, water autoprotolysis in the presence of zinc and dimethyl‐phosphate hydrolysis using various semiempirical Hamiltonians and density functional theory as the QM model. It is shown that with suitable parameters, based on force convergence tests, the AdBF QM/MM scheme can provide an accurate approximation of the structure in the dynamical QM region matching the corresponding fully QM simulations, as well as reproducing the correct energetics in all cases. Adaptive unbuffered force‐mixing and adaptive conventional QM/MM methods also provide reasonable results for some systems, but are more likely to suffer from instabilities and inaccuracies. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

A Versatile System for High-Throughput In Situ X-ray Screening and Data Collection of Soluble and Membrane-Protein Crystals

In recent years, in situ data collection has been a major focus of progress in protein crystallography. Here, we introduce the Mylar in situ method using Mylar-based sandwich plates that are inexpensive, easy to make and handle, and show significantly less background scattering than other setups. A variety of cognate holders for patches of Mylar in situ sandwich films corresponding to one or more wells makes the method robust and versatile, allows for storage and shipping of entire wells, and enables automated crystal imaging, screening, and goniometerbased X-ray diffraction data-collection at room temperature and under cryogenic conditions for soluble and membrane-protein crystals grown in or transferred to these plates. We validated the Mylar in situ method using crystals of the water-soluble proteins hen egg-white lysozyme and sperm whale myoglobin as well as the 7-transmembrane protein bacteriorhodopsin from Haloquadratum walsbyi. In conjunction with current developments at synchrotrons, this approach promises high-resolution structural studies of membrane proteins to become faster and more routine.

automation↗
DOE OSTI2015

Absorption lineshapes of molecular aggregates revisited

Linear absorption is the most basic optical spectroscopy technique that provides information about the electronic and vibrational degrees of freedom of molecular systems. In simulations of absorption lineshapes, often diagonal fluctuations are included using the cumulant expansion, and the off-diagonal fluctuations are accounted for either perturbatively, or phenomenologically. The accuracy of these methods is limited and their range of validity is still questionable. In this work, a systematic study of several such methods is presented by comparing the lineshapes with exact results. It is demonstrated that a non-Markovian theory for off-diagonal fluctuations, termed complex time dependent Redfield theory, gives good agreement with exact lineshapes over a wide parameter range. This theory is also computationally efficient. On the other hand, accounting for the off-diagonal fluctuations using the modified Redfield lifetimes was found to be inaccurate.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Evaluation of machine learning algorithms for prediction of regions of high Reynolds averaged Navier Stokes uncertainty

Reynolds Averaged Navier Stokes (RANS) models are widely used in industry to predict fluid flows, despite their acknowledged deficiencies. Not only do RANS models often produce inaccurate flow predictions, but there are very limited diagnostics available to assess RANS accuracy for a given flow configuration. If experimental or higher fidelity simulation results are not available for RANS validation, there is no reliable method to evaluate RANS accuracy. This paper explores the potential of utilizing machine learning algorithms to identify regions of high RANS uncertainty. Three different machine learning algorithms were evaluated: support vector machines, Adaboost decision trees, and random forests. The algorithms were trained on a database of canonical flow configurations for which validated direct numerical simulation or large eddy simulation results were available, and were used to classify RANS results on a point-by-point basis as having either high or low uncertainty, based on the breakdown of specific RANS modeling assumptions. Classifiers were developed for three different basic RANS eddy viscosity model assumptions: the isotropy of the eddy viscosity, the linearity of the Boussinesq hypothesis, and the non-negativity of the eddy viscosity. It is shown that these classifiers are able to generalize to flows substantially different from those on which they were trained. As a result, feature selection techniques, model evaluation, and extrapolation detection are discussed in the context of turbulence modeling applications.

97 MATHEMATICS AND COMPUTING↗