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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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DOE OSTI2018

A Review of Interface Microstructures in Electronic Packaging Applications: Soldering Technology

Here, this report examines the role of interfaces in electronic packaging applications with the focus placed on soldering technology. Materials and processes are described with respect to their roles on the performance and reliability of associated interfaces. The discussion will also include interface microstructures created by coatings and finishes that are frequently used in packaging applications. Numerous examples are cited to illustrate the importance of interfaces in physical and mechanical metallurgy as well as the engineering function of interconnections. Regardless of the specific application, interfaces are non-equilibrium structures , which has important ramifications for the long-term reliability of electronic packaging.

42 ENGINEERING↗
DOE OSTI2018

Multiphase flow studies for microscale hydrodynamics in the structured packed column

Post combustion carbon capture by solvent absorption in a structured packed column is a promising technology for mitigating greenhouse gas emissions. Computational fluid dynamic (CFD) modelling of such a column is a challenging multiscale problem due to the range in length and time scales. The microscale hydrodynamics play a key role in the overall column efficiency with the interfacial area significantly influencing the mass transfer between the gas and liquid phases. In this context, multiphase flow simulations using the volume of fluid (VOF) method in a representative elementary unit (REU) of the packed column can provide fundamental insights into the microscale hydrodynamics, such as, interfacial area and liquid holdup. The present paper systematically examines the impact of various factors (e.g., physical properties and contact angle) on the interfacial area. The results are compared with existing correlations and a scaling analysis is also performed. The solvent physical properties are characterized by the Kapitza number (Ka), a dimensionless number that depends only on fluid properties. So that the Ka number decreases with increasing viscosity. At a fixed liquid load, the interfacial area and liquid holdup are observed to increase with decreasing Ka number. The impact of contact angle (i.e., solid surface characteristics) is effectively investigated by modifying the wall boundary conditions. The interfacial area and liquid holdup are found to decrease with increasing contact angle. Subsequently, a phenomenological correlation for interfacial area is proposed that includes the impact of these parameters. Finally, this correlation may be used to predict the interfacial area for gas-liquid flow in a structured packing for rivulet to fully wetted flow regimes.

42 ENGINEERING↗
DOE OSTI2022

Editorial: Nanotechnology for natural products

Humans around the globe have lived through an unprecedented time. The emergence and rapid spread of coronavirus disease 2019 (COVID-19) have resulted in the loss of millions of lives, and this number is still climbing every day and hour. As a consequence, there have been drastic changes over the past two years in how we live, communicate, and work, some of which may have changed forever: remote conferencing has become a new norm for businesses, schools, and academia; work-from-home and hybrid working is now more than just acceptable in many industries; most importantly, COVID-19 has raised global awareness of infectious diseases and pandemic responses to an exceptional level. Certainly, COVID-19 is not the only disease that is causing human suffering at this moment. Other highly contagious and lethal viruses, such as the human immunodeficiency virus (HIV), Ebola, and the recent addition to the list, Monkeypox, pose extraordinary challenges to modern civilizations. On the other hand, non-communicable diseases, such as heart disease, stroke, and cancer, are still claiming the majority of deaths on a global level (World Health Organization, 2020). Before the availability of synthetic drugs, civilizations worldwide relied on natural products extracted from the environment and various organisms for healthcare. Natural products and their derivatives continue to be critical components in the drug library available today. Indeed, almost a quarter of the new drugs approved by the US Food and Drug Administration (FDA) since 1981 are natural products, botanical mixtures, or their derivatives (Newman and Cragg, 2020). Recent developments in analytical characterization, genome mining, and engineering have further increased interest in drug discovery from the pool of natural products (Atanasov et al., 2021). This Research Topic celebrates a collection of studies at the intersection of natural product research and nanotechnological advances. As a successor and extension of the Research Topic in “Nanotechnology in Traditional Medicines and Natural Products” published last year (Zhang et al., 2021), the present collection focused more on recent developments in employing the synthesis and characterization of nanostructures for the delivery of functional natural products. Specifically, the use of carrier nanostructures to conjugate or encapsulate therapeutically active natural products with carrier nanostructures could enable their robust, targeted delivery tailored to either tackle a specific disease or unlock a drug administration pathway. Over the last decade, nanostructures such as liposomes (Pattni et al., 2015) and lipid nanoparticles (Hou et al., 2021) have been developed as versatile platforms for the inclusion and delivery of a wide range of therapeutical compounds; a significant advance in this aspect is the stabilization of mRNA strands for COVID-19 vaccination recently produced by Pfizer/BioNTech and Moderna (Tenchov et al., 2021). Such engineered nanomaterials are now widely used in the development of new drugs, while regulatory forces, such as the US FDA, remain cautious with the evaluation of each product on a case-by-case basis (Wang and Grainger, 2022). In this collection, Zeng et al. provided a timely review of natural products conjugated to and contained within nanomaterials for the ongoing COVID-19 pandemic. Natural products that are potentially useful in the mitigation of this disease, such as chloroquine and curcumin, supported in nanocarrier systems, have been discussed in detail. More broadly, Cheng et al. comprehensively reviewed the use of liposomes as a nanocarrier for natural products. This article provides a summary of natural product compounds and extracts used to form liposomal structures. Readers can further enjoy the practical aspects of these engineered drugs for the treatment of specific diseases as well as insights into future directions in this field.

peptides↗
DOE OSTI2021

Importance of Engineered and Learned Molecular Representations in Predicting Organic Reactivity, Selectivity, and Chemical Properties

Machine-readable chemical structure representations are foundational in all attempts to harness machine learning for the prediction of reactivities, selectivities, and chemical properties directly from molecular structure. The featurization of discrete chemical structures into a continuous vector space is a critical phase undertaken before model selection, and the development of new ways to quantitatively encode molecules is an active area of research. Here, we highlight the application and suitability of different representations, from expert-guided “engineered” descriptors to automatically “learned” features, in different prediction tasks relevant to organic and organometallic chemistry, where differing amounts of training data are available. These tasks include statistical models of stereo- and enantioselectivity, thermochemistry, and kinetics developed using experimental and quantum chemical data. The use of expert-guided molecular descriptors provides an opportunity to incorporate chemical knowledge, domain expertise, and physical constraints into statistical modeling. In applications to stereoselective organic and organometallic catalysis, where data sets may be relatively small and 3D-geometries and conformations play an important role, mechanistically informed features can be used successfully to obtain predictive statistical models that are also chemically interpretable. We provide an overview of several recent applications of this approach to obtain quantitative models for reactivity and selectivity, where topological descriptors, quantum mechanical calculations of electronic and steric properties, along with conformational ensembles, all feature as essential ingredients of the molecular representations used. Alternatively, more flexible, general-purpose molecular representations such as attributed molecular graphs can be used with machine learning approaches to learn the complex relationship between a structure and prediction target. This approach has the potential to out-perform more traditional representation methods such as “hand-crafted” molecular descriptors, particularly as data set sizes grow. One area where this is particularly relevant is in the use of large sets of quantum mechanical data to train quantitative structure–property relationships. A general approach toward curating useful data sets and training highly accurate graph neural network models is discussed in the context of organic bond dissociation enthalpies, where this strategy outperforms regression using precomputed descriptors. Finally, we describe how graph neural network predictions can be incorporated into mechanistically informed statistical models of chemical reactivity and selectivity. Once trained, this approach avoids the expensive computational overhead associated with quantum mechanical calculations, while maintaining chemical interpretability. We illustrate examples for which fast predictions of bond dissociation enthalpy and of the identities of radicals formed through cleavage of a molecule’s weakest bond are used in simple physical models of site-selectivity and reactivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

A High Specific Output Gasoline Low Temperature Combustion Engine

This report summarizes activities conducted in support of the project “A High Specific Output Gasoline Low Temperature Combustion Engine” under COOPERATIVE AGREEMENT NUMBER DE-EE0007788. This cooperative agreement was structured as a 51%/49% recipient/DOE NETL cost share with two Go / no-Go decision gates spanning three budget periods. The primary objective of the program is the development and demonstration of a downsized boosted, lean, low temperature gasoline combustion engine system capable of demonstrating a 15-17% fuel economy improvement relative to a contemporary naturally aspirated stoichiometric combustion engine consistent with relevant emissions constraints and the use of marketplace gasolines. The program focused on maximizing internal combustion engine fuel economy potential by combining the benefits of downsized boosted engine technology with next generation gasoline lean-burn, low temperature combustion and novel low temperature plasma ignition. The project achieved a 20.5% improvement from hot FTP cycle test and 18.9% improvement from cold FTP cycle test while meeting stringent SULEV30 emissions regulation for both test cycles (HOT FTP: 15.37 mg of NOx+HC; 0.16 g/mile of CO, COLD FTP: 23.1 mg of NOx+HC; 0.33 g/mile of CO).

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2021

Excitonic structure and charge separation in the heliobacterial reaction center probed by multispectral multidimensional spectroscopy

Photochemical reaction centers are the engines that drive photosynthesis. The reaction center from heliobacteria (HbRC) has been proposed to most closely resemble the common ancestor of photosynthetic reaction centers, motivating a detailed understanding of its structure-function relationship. The recent elucidation of the HbRC crystal structure motivates advanced spectroscopic studies of its excitonic structure and charge separation mechanism. We perform multispectral two-dimensional electronic spectroscopy of the HbRC and corresponding numerical simulations, resolving the electronic structure and testing and refining recent excitonic models. Through extensive examination of the kinetic data by lifetime density analysis and global target analysis, we reveal that charge separation proceeds via a single pathway in which the distinct A 0 chlorophyll a pigment is the primary electron acceptor. In addition, we find strong delocalization of the charge separation intermediate. Our findings have general implications for the understanding of photosynthetic charge separation mechanisms, and how they might be tuned to achieve different functional goals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Detailed Compositional Comparison of Hydrogenated Vegetable Oil with Several Diesel Fuels and Their Effects on Engine-Out Emissions

The Coordinating Research Council (CRC) is actively involved in developing and applying advanced analytical techniques to the chemical characterization of transportation fuels. Here, this article complements a 2017 CRC project to quantify and compare the effects of a commercially available renewable diesel fuel (hydrotreated vegetable oil [HVO]) and an ultralow sulfur diesel (ULSD) fuel on engine-out gaseous and particulate matter (PM) emissions from a light-duty vehicle. Results showed that the combustion of HVO fuel had an advantage over ULSD in terms of lowering engine-out emissions (THC, CO, NO x , etc.). Furthermore, this advantage is strongly related to the fuel composition. This article summarizes the results of advanced and comprehensive analytical tests on the same ULSD and HVO fuels and attempts to connect some of the engine-out emissions results to fuel composition and specific chemical structures. A variety of test methods, generally unavailable in combination, were employed, such as one-dimensional (1D) and two-dimensional (2D) gas chromatography (GC), nuclear magnetic resonance spectroscopy (NMR), and high-pressure solid-liquid phase transition experiments. In summary, the ULSD sample was found to have representation across the expected set of hydrocarbon classes typical for the sample type. Interestingly, a high content of cycloparaffins (>50 wt%) and a very low content of diaromatics (~2 wt%) were present. While not without precedent, these are higher and lower, respectively, than typically found for commercial ULSD compositions. In contrast, HVO was found to consist of only two hydrocarbon classes: n-paraffins (~10 wt%) and iso-paraffins (~90 wt%), both predominantly in a narrow carbon atom number range (i.e., C14–C18). HVO engine-out emissions results for the LA-92 and steady-state testing can be tracked to the narrow carbon atom number range of the n-paraffins and iso-paraffins, which result in a high cetane number fuel having a narrow distillation range. Previously, the low-temperature operability of HVO has been a concern, but that appears not be the case for this particular HVO. HVO and ULSD were evaluated at pressures up to ~275 MPa and found to have comparable solid-liquid equilibria despite significant compositional differences.

09 BIOMASS FUELS↗
DOE OSTI2020

On the regeneration of fish scales: structure and mechanical behavior

Fish scales serve as a dermal armor that provides protection from physical injury. Owing to a number of outstanding properties, fish scales are inspiring new concepts for layered engineered materials and next-generation flexible armors. Although past efforts have primarily focused on the structure and mechanical behavior of ontogenetic scales, the structure–property relationships of regenerated scales have received limited attention. In the present study, common carp ( Cyprinus carpio ) acquired from the wild were held live in an aquatic laboratory at 10°C and 20°C. Ontogenetic scales were extracted from the fish for analysis, as well as regenerated scales after approximately 1 year of development and growth. Their microstructure was characterized using microscopy and Raman spectroscopy, and the mechanical properties were evaluated in uniaxial tension to failure under hydrated conditions. We note the strength, strain to fracture and toughness of the regenerated scales were significantly lower than those of ontogenetic scales from the same fish, regardless of the water temperature. Scales that regenerated at 20°C exhibited significantly higher strength, strain to fracture and toughness than those regenerated at 10°C. The regenerated scales exhibited a highly mineralized outer layer, but no distinct limiting layer or external elasmodine; they also possessed a significantly lower number of plies in the basal layer than the ontogenetic scales. The results suggest that a mineralized layer develops preferentially during scale regeneration with the topology needed for protection, prior to the development of other qualities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Fast ion conductivity in strained defect-fluorite structure created by ion tracks in Gd 2 Ti 2 O 7

The structure and ion-conducting properties of the defect-fluorite ring structure formed around amorphous ion-tracks by swift heavy ion irradiation of Gd 2 Ti 2 O 7 pyrochlore are investigated. High angle annular dark field imaging complemented with ion-track molecular dynamics simulations show that the atoms in the ring structure are disordered, and have relatively larger cation-cation interspacing than in the bulk pyrochlore, illustrating the presence of tensile strain in the ring region. Density functional theory calculations show that the non-equilibrium defect-fluorite structure can be stabilized by tensile strain. The pyrochlore to defect-fluorite structure transformation in the ring region is predicted to be induced by recrystallization during a melt-quench process and stabilized by tensile strain. Static pair-potential calculations show that planar tensile strain lowers oxygen vacancy migration barriers in pyrochlores, in agreement with recent studies on fluorite and perovskite materials. Lastly, in view of these results, it is suggested that strain engineering could be simultaneously used to stabilize the defect-fluorite structure and gain control over its high ion-conducting properties.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Computational Analysis of Hydraulic Efficiency of Michigan DOT Cover C

Drainage structures are used to capture stormwater runoff in streets and highways in urban environments. These drainage structures, which typically consist of catch basins with grates, inlets, or combination grates/inlets, collect stormwater runoff and discharge through buried conveyance systems. They are strategically placed for public safety in curb and gutter systems to provide efficient drainage of water from roadways and thus reduce the risk of hydroplaning. The performance of drainage structures is measured in terms of hydraulic efficiency, which is defined as the percentage of flow captured by the basin as compared to the total flow drainage to the structure. Understanding of the performance of these drainage structures helps designers properly space inlets to promote an economic design that ensures the safety of the traveling public. The current design methodology used to determine drainage structure follows guidelines established in the current Michigan Department of Transportation (MDOT) Drainage Manual (2006). The guidelines in the MDOT Drainage Manual were modeled after the Federal Highway Administration’s (FHWA) Hydraulic Engineering Circular 22 “Urban Drainage Design” (HEC-22). HEC-22 includes empirically derived equations to calculate the interception capacity of drainage structures for several commonly used grate configurations, such as the parallel bar, curved vane and tilt bar grates, which are based on a research study performed by Burgi et al. in the 1970s. MDOT uses several drainage structures to capture runoff that are detailed as Standard Plans. Many of these drainage structures utilize sinusoidal type grates that are not described in HEC-22. Physical modeling of these structures has been limited, posing the need to have them analyzed to verify their capture efficiency. Current MDOT practice is to assume a similar sized reticuline grate, as described in HEC-22, for capture efficiencies. Until recently, evaluating the hydraulic performance of drainage structures was limited to physical modeling in a hydraulics laboratory. With advances in engineering software and computing power, computational fluid dynamics (CFD) modeling has become a more cost-effective alternative. The Federal Highway Administration (FHWA) provides states the option to evaluate their drainage structures using CFD through the Transportation Pooled Fund Program. This study, “Computational Analysis of Hydraulic Efficiency of Michigan DOT Cover C,” was carried out using the pooled fund. MDOT’s Cover C was chosen as the first test candidate, given its similar sinusoidal pattern to other MDOT grates, but it is typically used for high-volume, higher speed applications. A similar version, Cover CX, is used on interstate highways but does not have traverse bars for bicycle safety. Additional grates may be considered for evaluation in the future.

42 ENGINEERING↗
DOE OSTI2016

Interfacial Octahedral Rotation Mismatch Control of the Symmetry and Properties of SrRuO 3

We can use epitaxial strain to tune the properties of complex oxides with perovskite structure. Beyond just lattice mismatch, the use of octahedral rotation mismatch at heterointerfaces could also provide a route to manipulate material properties. We examine the evolution of the lattice (i.e., parameters, symmetry, and octahedral rotations) of SrRuO 3 films grown on substrates engineered to have the same lattice parameters, but 2 different octahedral rotations. SrRuO 3 films grown on SrTiO 3 (001) (no octahedral rotations) and GdScO 3 -buffered SrTiO 3 (001) (with octahedral rotations) substrates are found to exhibit monoclinic and tetragonal symmetry, respectively. Electrical transport and magnetic measurements reveal that the tetragonal films exhibit higher resistivity, lower magnetic Curie temperatures, and more isotropic magnetism as compared to those with monoclinic structure. Synchrotron-based half-order Bragg peak analysis reveals that the octahedral rotation pattern in both film variants is the same (albeit with slightly different magnitudes of in-plane rotation angles). Furthermore, the abnormal rotation pattern observed in tetragonal SrRuO 3 indicates a possible decoupling between the internal octahedral rotation and lattice symmetry, which could provide new opportunities to engineer thin-film structure and properties.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Structural Basis of Substrate Specificity and Regiochemistry in the MycF/TylF Family of Sugar O -Methyltransferases.

Sugar moieties in natural products are frequently modified by O-methylation. In the biosynthesis of the macrolide antibiotic mycinamicin, methylation of a 6'-deoxyallose substituent occurs in a stepwise manner first at the 2'- and then the 3'-hydroxyl groups to produce the mycinose moiety in the final product. The timing and placement of the O-methylations impact final stage C-H functionalization reactions mediated by the P450 monooxygenase MycG. The structural basis of pathway ordering and substrate specificity is unknown. A series of crystal structures of MycF, the 3'-O-methyltransferase, including the free enzyme and complexes with S-adenosyl homocysteine (SAH), substrate, product, and unnatural substrates, show that SAM binding induces substantial ordering that creates the binding site for the natural substrate, and a bound metal ion positions the substrate for catalysis. A single amino acid substitution relaxed the 2'-methoxy specificity but retained regiospecificity. The engineered variant produced a new mycinamicin analog, demonstrating the utility of structural information to facilitate bioengineering approaches for the chemoenzymatic synthesis of complex small molecules containing modified sugars. Using the MycF substrate complex and the modeled substrate complex of a 4'-specific homolog, active site residues were identified that correlate with the 3'- or 4'- specificity of MycF family members and define the protein and substrate features that direct the regiochemistry of methyltransfer. Lastly, this classification scheme will be useful in the annotation of new secondary metabolite pathways that utilize this family of enzymes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

ECAR-6580 Rev 0 ASME Section III, Division 5 Analysis of the MARVEL PCS and GVS Top Corner

The purpose of this Engineering Calculations and Analysis Report (ECAR) is to document the structural evaluation for part of the Microreactor Applications Research Validation and Evaluation (MARVEL) Primary Coolant System (PCS) and Guard Vessel System (GVS). For the PCS this relates specifically to the Distribution Plenum (DP), The Intermediate Heat Exchanger (IHX), and the Upper Downcomer (UD). For the GVS, this will include only the top corner that is machined into the DP Top Plate. These components will be evaluated using the 2021 version of ASME Section III, Division 5 [1] which is a design code that governs the construction of vessels, storage tanks, piping, pumps, valves, supports, core support structures and nonmetallic core components for use in high temperature reactor systems and their supporting systems. Materials at high temperature are subject to creep and fatigue mechanisms that require additional analyses that aren’t covered in ASME Section III, Division 1 rules. Division 5 contains two approaches: elastic or inelastic, however, additional Code Cases specific to Division 5, allow for an Elastic-Perfectly Plastic (EPP) approach. The components analyzed in this ECAR will use a combination of the elastic and EPP approach. Only Design and Service Levels A and B are evaluated in this ECAR. Service Level D evaluations for the entire PCS are documented in ECAR-6564, “MARVEL Project Primary Coolant System Pressure Vessel Stress Documentation” [2] and for the entire GVS are documented in ECAR-6574, “MARVEL Guard Vessel System FEA and ASME Analysis” [3]. The Design and Service Level A and B analyses for the PCS Downcomer piping and Core Barrel are documented in ANL-24/36, "Engineering Calculations and Analysis of the Core Barrel and Downcomer Piping in the MARVEL PCS” [4], and the GVS (except for the top corner) is in ECAR-6574, “MARVEL Guard Vessel System FEA and ASME Analysis.” See Section 2.0 for more detail on the analysis boundaries.

21 - SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLAN↗
DOE OSTI2023

Characteristics and selection of near-fault simulated earthquake ground motions for nonlinear analysis of buildings

Earthquake-induced ground shaking near rupturing faults is highly sensitive to the rupture characteristics, seismic wave propagation patterns and site conditions, and field recordings of near-fault shaking are relatively sparse. These challenges complicate the assessment of the seismic performance of near-fault structures. A common approach to representing near-fault ground motion in engineering analysis is to explicitly consider and select records with strong directivity pulses (pulse records). We use three-dimensional high-resolution physics-based earthquake simulations to test this approach in the context of scenario-based ground motion record selection, and to study the important characteristics of near-fault ground shaking. We highlight the deficiencies associated with classifying near-fault simulated records as “pulse” or “non-pulse,” based on the presence of a single dominating pulse in the velocity time history. We show that this approach is inadequate for characterizing near-fault shaking on soft soils which can be dominated by both forward rupture directivity and basin amplification effects. We conduct ground motion selection experiments for the analysis of near-fault structures with and without explicit classification of the pulse features in the records, and evaluate the bias in the predicted structural demands. We find that the maximum interstory drift demands on building structures imposed by unscaled site-specific simulated ground motion records selected based on relevant spectral shape features are not sensitive to the classification of records as pulse/non-pulse. Therefore, with regard to predicting the maximum interstory drifts in near-fault buildings, we do not find justification for the binary pulse classification of near-fault records.

42 ENGINEERING↗
DOE OSTI2017

Efficient Machine Learning Approach for Optimizing Scientific Computing Applications on Emerging HPC Architectures

Efficient parallel implementations of scientific applications on multi-core CPUs with accelerators such as GPUs and Xeon Phis is challenging. This requires - exploiting the data parallel architecture of the accelerator along with the vector pipelines of modern x86 CPU architectures, load balancing, and efficient memory transfer between different devices. It is relatively easy to meet these requirements for highly structured scientific applications. In contrast, a number of scientific and engineering applications are unstructured. Getting performance on accelerators for these applications is extremely challenging because many of these applications employ irregular algorithms which exhibit data-dependent control-ow and irregular memory accesses. Furthermore, these applications are often iterative with dependency between steps, and thus making it hard to parallelize across steps. As a result, parallelism in these applications is often limited to a single step. Numerical simulation of charged particles beam dynamics is one such application where the distribution of work and memory access pattern at each time step is irregular. Applications with these properties tend to present significant branch and memory divergence, load imbalance between different processor cores, and poor compute and memory utilization. Prior research on parallelizing such irregular applications have been focused around optimizing the irregular, data-dependent memory accesses and control-ow during a single step of the application independent of the other steps, with the assumption that these patterns are completely unpredictable. We observed that the structure of computation leading to control-ow divergence and irregular memory accesses in one step is similar to that in the next step. It is possible to predict this structure in the current step by observing the computation structure of previous steps. In this dissertation, we present novel machine learning based optimization techniques to address the parallel implementation challenges of such irregular applications on different HPC architectures. In particular, we use supervised learning to predict the computation structure and use it to address the control-ow and memory access irregularities in the parallel implementation of such applications on GPUs, Xeon Phis, and heterogeneous architectures composed of multi-core CPUs with GPUs or Xeon Phis. We use numerical simulation of charged particles beam dynamics simulation as a motivating example throughout the dissertation to present our new approach, though they should be equally applicable to a wide range of irregular applications. The machine learning approach presented here use predictive analytics and forecasting techniques to adaptively model and track the irregular memory access pattern at each time step of the simulation to anticipate the future memory access pattern. Access pattern forecasts can then be used to formulate optimization decisions during application execution which improves the performance of the application at a future time step based on the observations from earlier time steps. In heterogeneous architectures, forecasts can also be used to improve the memory performance and resource utilization of all the processing units to deliver a good aggregate performance. We used these optimization techniques and anticipation strategy to design a cache-aware, memory efficient parallel algorithm to address the irregularities in the parallel implementation of charged particles beam dynamics simulation on different HPC architectures. Experimental result using a diverse mix of HPC architectures shows that our approach in using anticipation strategy is effective in maximizing data reuse, ensuring workload balance, minimizing branch and memory divergence, and in improving resource utilization.

Arumugam, Kamesh↗
DOE OSTI2019

Engineering a conserved RNA regulatory protein repurposes its biological function in vivo

PUF (PUmilio/FBF) RNA-binding proteins recognize distinct elements. In C. elegans, PUF-8 binds to an 8-nt motif and restricts proliferation in the germline. Conversely, FBF-2 recognizes a 9-nt element and promotes mitosis. To understand how motif divergence relates to biological function, we first determined a crystal structure of PUF-8. Comparison of this structure to that of FBF-2 revealed a major difference in a central repeat. We devised a modified yeast 3-hybrid screen to identify mutations that confer recognition of an 8-nt element to FBF-2. We identified several such mutants and validated structurally and biochemically their binding to 8-nt RNA elements. Using genome engineering, we generated a mutant animal with a substitution in FBF-2 that confers preferential binding to the PUF-8 element. The mutant largely rescued overproliferation in animals that spontaneously generate tumors in the absence of puf-8. This work highlights the critical role of motif length in the specification of biological function.

Bhat, Vandita D.↗
DOE OSTI2015

Are X-rays the key to integrated computational materials engineering?

The ultimate dream of materials science is to predict materials behavior from composition and processing history. Owing to the growing power of computers, this long-time dream has recently found expression through worldwide excitement in a number of computation-based thrusts: integrated computational materials engineering, materials by design, computational materials design, three-dimensional materials physics and mesoscale physics. However, real materials have important crystallographic structures at multiple length scales, which evolve during processing and in service. Moreover, real materials properties can depend on the extreme tails in their structural and chemical distributions. This makes it critical to map structural distributions with sufficient resolution to resolve small structures and with sufficient statistics to capture the tails of distributions. For two-dimensional materials, there are high-resolution nondestructive probes of surface and near-surface structures with atomic or near-atomic resolution that can provide detailed structural, chemical and functional distributions over important length scales. Furthermore, there are no nondestructive three-dimensional probes with atomic resolution over the multiple length scales needed to understand most materials.

36 MATERIALS SCIENCE↗
DOE OSTI2021

An FEM-Based Peridynamic Model for Failure Analysis of Unidirectional Fiber-Reinforced Laminates

To predict the mixed damage modes of unidirectional fiber-reinforced polymer (FRP) laminates under dynamic loading, an FEM-based peridynamic model is introduced in this paper. Based on its geometric structure and material composition, a long fiber lamina is considered a transversely isotropic medium as a result of homogenization at the meso-scale. The laminated structure is modeled by stacking surface mesh layers with arbitrary fiber angles along the thickness direction. The peridynamic bonds between Gauss points connect the separated elements. These bonds are classified as inner-layer bonds and inter-layer bonds. To represent the anisotropy of a laminate, the micro-elastic modulus of the inner-layer and inter-layer bonds is calculated from the anisotropic engineering material constants separately. To capture complex failure behaviors of laminate structures, an empirical damage model is proposed for the tension/ compression breakage of peridynamic bonds. This damage model can control the in-plane and delamination failure process. Finally, benchmark tests are conducted to validate the elastic response of laminates under dynamic loading. In terms of damage analysis, the proposed model can capture the complex damage modes and resistive force of laminate structures.

36 MATERIALS SCIENCE↗