Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “lack”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Role of glucuronoxylomannan and steryl glucosides in protecting against cryptococcosis

The development of vaccines for fungal diseases, including cryptococcosis, is an emergent line of research and development. In previous studies, we showed that a Cryptococcus mutant lacking the SGL1 gene (∆sgl1) accumulates certain glycolipids called steryl glucosides (SGs) on the fungal capsule, promoting an effective immunostimulation that totally protects the host from a secondary cryptococcal infection. However, this protection is lost when the cryptococcal capsule is absent in the ∆sgl1 background. The cryptococcal capsule is mainly composed of glucuronoxylomannan (GXM), a polysaccharide microfiber consisting of glucuronic acid, xylose, and mannose linked by glycosidic bonds forming specific triads. In this study, we engineered cells to lack each of the GXM components and tested the effect of these deletions on protection under the condition of SG accumulation. We found that glucuronic acid and xylose are required for protection, and their absence abrogates the production of IFNγ and IL-17A by γδ T cells, which are necessary stimulants for the protective phenotype of the ∆sgl1. We analyzed the structure of the GXM microfibers and found that although the deletion of SGL1 only slightly affects the size and distribution of these microfibers, it significantly changes the ratio of mannose to other components. In conclusion, this study identifies the structural modifications that the deletion of SGL1 and the consequent accumulation of SGs impart to the GXM structure of C. neoformans. This provides significant insights into the protective mechanisms mediated by SG accumulation on the capsule, with important implications for the future development of an efficacious cryptococcal vaccine.

Cryptococcus neoformans↗
DOE OSTI2024

Structure and identification of the native PLP synthase complex from Methanosarcina acetivorans lysate

Many protein-protein interactions behave differently in biochemically purified forms as compared to their in vivo states. As such, determining native protein structures may elucidate structural states previously unknown for even well-characterized proteins. Here, we apply the bottom-up structural proteomics method, cryoID , toward a model methanogenic archaeon. While they are keystone organisms in the global carbon cycle and active members of the human microbiome, there is a general lack of characterization of methanogen enzyme structure and function. Through the cryoID approach, we successfully reconstructed and identified the native Methanosarcina acetivorans pyridoxal 5′-phosphate (PLP) synthase (PdxS) complex directly from cryogenic electron microscopy (cryo-EM) images of fractionated cellular lysate. We found that the native PdxS complex exists as a homo-dodecamer of PdxS subunits, and the previously proposed supracomplex containing both the synthase (PdxS) and glutaminase (PdxT) was not observed in cellular lysate. Our structure shows that the native PdxS monomer fashions a single 8α/8β TIM-barrel domain, surrounded by seven additional helices to mediate solvent and interface contacts. A density is present at the active site in the cryo-EM map and is interpreted as ribose 5-phosphate. In addition to being the first reconstruction of the PdxS enzyme from a heterogeneous cellular sample, our results reveal a departure from previously published archaeal PdxS crystal structures, lacking the 37-amino-acid insertion present in these prior cases. This study demonstrates the potential of applying the cryoID workflow to capture native structural states at atomic resolution for archaeal systems, for which traditional biochemical sample preparation is nontrivial.

Methanosarcina acetivorans↗
DOE OSTI2023

Exploring novel alkane-degradation pathways in uncultured bacteria from the North Atlantic Ocean

Microbes play a significant role in the degradation of petroleum hydrocarbons in the oceans, yet little is known about the native bacteria that metabolize hydrocarbons before an oil spill. The Faroe-Shetland Channel (FSC) is a deepwater subarctic region of the North Atlantic with prominent oil production and a diverse microbial community associated with the degradation of petroleum. Here, we combine DNA-based stable-isotope probing (DNA-SIP) with metagenomics to elucidate the metabolic underpinnings of native alkane-degrading bacteria from the FSC. From two 13C n-hexadecane SIP experiments using seawater from 5 and 700 m depths in the FSC, we obtained 42 metagenome-assembled genomes (MAGs) belonging to 19 genera, including two previously overlooked hydrocarbon-degrading bacteria, Lentibacter (Alphaproteobacteria) and Dokdonia (Bacteroidetes). Diversity surveys indicated Lentibacter were dominant members of the FSC, constituting up to 17% of these communities. Many of the SIP-enriched MAGs (20/42) encoded a complete alkane oxidation pathway, including alkane monooxygenase (AlkB), rubredoxin reductase (AlkT), and rubredoxin-2 (AlkG). Fourteen Aphaproteobacteria MAGs lacked AlkG for electron transfer. Instead, they encoded novel disulfide isomerases with iron-binding cysteine motifs conserved across rubredoxins. Dokdonia lacked AlkT and AlkG, however, their central alkane-degradation catabolic pathways were complete. We describe previously unrecognized bacteria capable of hydrocarbon degradation, including the dominant genera Lentibacter, which may continuously purge hydrocarbons released from oil exploration activities in the FSC. This advances the understanding of the diversity and physiologies of alkane degradation in the North Atlantic and provides evidence of new mechanisms used to metabolize alkanes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Distinguishing Leptothrix and Sphaerotilus genera by an integrated genomic-phenotypic analysis supported by new Leptothrix genomes

The Sphaerotilus-Leptothrix group of bacteria includes one of the first described microorganisms, Leptothrix ochracea, an uncultured type strain, plus isolates of Leptothrix and Sphaerotilus. This group is unified by the ability to form sheaths and oxidize metals, although L. ochracea exhibits obvious ecological, morphological, and functional differences from the rest of Sphaerotilus-Leptothrix. Recently, there have been calls to combine the group into one genus, Sphaerotilus; however, these studies lacked adequate genomic representation of L. ochracea. Here, we present a comprehensive comparative genomic analysis of the Sphaerotilus-Leptothrix group, including expanded representation of L. ochracea, a closely related novel species, Leptothrix toolikensis, and two new isolates (Leptothrix mechoopdaensis). Analysis of 38 genomes resolves three phylogenetic and functional groups: the ochracea-type Leptothrix (Group 1), the mobilis-type Leptothrix (Group 2), and Sphaerotilus (Group 3). Group 1 genomes form a separate genus based on average nucleotide identity and alignment fraction. The genomes clearly diverge from the rest of Sphaerotilus-Leptothrix in phylogeny, size, and metabolic potential. Group 1 genomes are much smaller (2.59–3.04 Mb) than those of Groups 2 (4.55–6.06 Mb) and 3 (3.94–5.07 Mb), while encoding more metal oxidases and fewer carbohydrate-active enzymes. Group 2 clusters with Group 3 phylogenetically and is similar in organic carbon metabolisms but maintains more metal oxidation genes. Group 2 members lack homogeneity in phenotype and genotype, suggesting that additional isolates and genomes are needed for confident classification. However, Group 1 genomes (L. ochracea and L. toolikensis) show clear divergence, precluding their inclusion in Sphaerotilus and supporting the retention of the genus Leptothrix.

Leptothrix↗
DOE OSTI2024

Versatile allelic replacement and self-excising integrative vectors for plasmid genome mutation and complementation

ABSTRACT The ability to better understand the function of proteins expressed by bacteria has typically relied upon the development of genetic mutant strains. This approach has been especially challenging for plasmid-encoded genes, as most of the previously described allelic replacement vectors are inefficient for plasmid genome mutation as they either rely on plasmid-derived counterselection toxins or depend on other strategies suchsacB,tetA, andrpsLwhich have been proven to be less efficient for mutant selection. Integrative vectors lack chromophore indicators, thus requiring laborious screening or excision of the vector’s backbone relies on the introduction of a flippase (FLP)-expressing plasmid. The allelic replacement vector, designated here as pDG1, expresses an X-Gal hydrolyzing enzyme (BgaB) that can be used for blue/white screening allowing identification of colonies that integrated and successfully removed the mutagenesis plasmid without a bias for those still carrying it. pDG1 was further improved by including the rhamnose-inducible Tse2 toxin as a potent counterselection system. The efficacy of pDG1 was validated by deleting portions of the plasmid-encoded VirB4/D4 type IV secretion system and aerobactin-synthesizing operons inSalmonella enterica. The integrative vectors, which contain an ΦC31attPsite and genes encoding ΦC31 integrase (int), can seamlessly integrate to target ΦC31attBonSalmonellaplasmids or chromosome. These vectors were improved by insertingbgaBand FLP-encoding genes so that, following integration, most of the vector’s backbone encompassingint,bgaB, and FLP genes can be excised by FLP, without the need for another FLP-expressing vector, creating white colonies carrying a stably integrated target gene. As such, we were able to integrate a 9.3-kb DNA fragment toSalmonellachromosome and flipped out most of the integrated vector in one step, leaving the target fragment in the chromosome. IMPORTANCE In spite of the dissemination of multidrug-resistant plasmids among Gram-negative pathogens, including those carrying virulence genes, vector tools for studying plasmid-born genes are lacking. The allelic replacement vectors can be used to generate plasmid or chromosomal mutations including markless point mutations. This is the first report describing a self-excising integrative vector that can be used as a stable single-copy complementing tool to study medically important pathogens includingin vivostudies without the need for antibiotic selection. Overall, our newly developed vectors can be applied for the assessment of the function of plasmid-encoded genes by specifically creating mutations, moving large operons between plasmids and to/from the chromosome, and complementing phenotypes associated with gene mutation. Furthermore, the vectors express chromophores for the detection of target gene modification or colony isolation, avoiding time-consuming screening procedures.

Microbiology↗
DOE OSTI2024

Drug providers’ perspectives on antibiotic misuse practices in eastern Ethiopia: a qualitative study

Objective Antibiotic misuse includes using them to treat colds and influenza, obtaining them without a prescription, not finishing the prescribed course and sharing them with others. Although drug providers are well positioned to advise clients on proper stewardship practices, antibiotic misuse continues to rise in Ethiopia. It necessitates an understanding of why drug providers failed to limit such risky behaviours. This study aimed to explore drug providers’ perspectives on antibiotic misuse practices in eastern Ethiopia. Setting The study was conducted in rural Haramaya district and Harar town, eastern Ethiopia. Design and participants An exploratory qualitative study was undertaken between March and June 2023, among the 15 drug providers. In-depth interviews were conducted using pilot-tested, semistructured questions. The interviews were transcribed verbatim, translated into English and analysed thematically. The analyses considered the entire dataset and field notes. Results The study identified self-medication pressures, non-prescribed dispensing motives, insufficient regulatory functions and a lack of specific antibiotic use policy as the key contributors to antibiotic misuse. We found previous usage experience, a desire to avoid extra costs and a lack of essential diagnostics and antibiotics in public institutions as the key drivers of non-prescribed antibiotic access from private drug suppliers. Non-prescribed antibiotic dispensing in pharmacies was driven by client satisfaction, financial gain, business survival and market competition from informal sellers. Antibiotic misuse in the setting has also been linked to traditional and ineffective dispensing audits, inadequate regulatory oversights and policy gaps. Conclusion This study highlights profits and oversimplified access to antibiotics as the main motivations for their misuse. It also identifies the traditional antibiotic dispensing audit as an inefficient regulatory operation. Hence, enforcing specific antibiotic usage policy guidance that entails an automated practice audit, a responsible office and insurance coverage for persons with financial limitations can help optimise antibiotic use while reducing resistance consequences.

General & Internal Medicine↗
DOE OSTI2024

Diffeomorphism invariance and quantum mechanical paradoxes

Paradoxes in gravitational physics, such as grandfather paradoxes with closed timelike curves or the AMPS paradox, are often constructed in a weak gravity regime but upon further examination engender strong gravitational responses such as unstable Cauchy horizons or firewalls. In contrast, some proposed paradoxes in nonrelativistic quantum mechanics ignore gravity completely. Such nonrelativistic proposed paradoxes are often not gauge invariant — they use local operators which should be forbidden by diffeomorphism-invariant quantum gravity. Ignoring this complication is reasonable if there is a consistent weak gravity regime where the paradox can be formulated with gauge invariant observables up to some order in Newton’s constant. Here, we show that this approach remains inconsistent due to a lack of analyticity of the necessary solutions. As a consequence, there is no consistent weak gravity, diffeomorphism invariant embedding of such paradoxes—just as in other gravitational paradoxes they generate a strong gravitational response and are in principle sensitive to quantum gravity.

quantum gravity↗
DOE OSTI2021

Neuromorphic Computing for Autonomous Racing

Neuromorphic computing has many opportunities in future autonomous systems, especially those that will operate at the edge. However, there are relatively few demonstrations of neuromorphic implementations on real-world applications, partly because of the lack of availability of neuromorphic hardware and software, but also because of the lack of availability of an accessible demonstration platform. In this work, we propose utilizing the F1Tenth platform as an evaluation task for neuromorphic computing. F1Tenth is a competition wherein one tenth scale cars compete in an autonomous racing task; there are significant open source resources in both software and hardware for realizing this task. We present a workflow with neuromorphic hardware, software, and training that can be used to develop a spiking neural network for neuromorphic hardware deployment to perform autonomous racing. We present initial results on utilizing this approach for this small-scale, real-world autonomous vehicle task.

Patton, Robert↗
DOE OSTI2022

Pit Stability Predictions of Additively Manufactured SS316 Surfaces Using Finite Element Analysis

Stainless steels are susceptible to localized forms of corrosion attack, such as pitting. The size and lifetime of a nucleated pit can vary, depending on a critical potential or current density criterion, which determines if the pit repassivates or continues growing. This work uses finite element method (FEM) modeling to compare the critical pit radii predicted by thermodynamic and kinetic repassivation criteria. Experimental electrochemical boundary conditions are used to capture the active pit kinetics. Geometric and environmental parameters, such as the pit shape and size (analogous to additively manufactured lack-of-fusion pores), solution concentration, and water layer thickness were considered to assess their impact on the pit repassivation criterion. The critical pit radius (the transition point from stable growth to repassivation) predicted for a hemispherical pit was larger when using the repassivation potential (E rp ) criteria, as opposed to the current density criteria (pit stability product). Including both the pit stability product and E rp into its calculations, the analytical maximum pit model predicted a critical radius two times more conservative than the FEA approach, under the conditions studied herein. The complex pits representing lack-of-fusion pores were shown to have minimal impact on the critical radius in atmospheric conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

A new mud shrimp of the genus Paragourretia Sakai, 2004, from the Gulf of Mexico (Crustacea: Decapoda: Ctenochelidae)

A new western Atlantic member of the ctenochelid genus Paragourretia Sakai, 2004 is described to accommodate a single unique specimen collected by dredge on muddy rubble substrates of the continental shelf in the southwestern Gulf of Mexico. Paragourretia sandrae n. sp. closely resembles Paragourretia biffari, another regionally reported species for which photographs and additional illustrations are herein provided. While P. biffari and P. sandrae n. sp. are similar in habitus and known habitat o the more commonly encountered confamilial Dawsonius latispina, the third maxillipeds in Paragourretia bear distinct exopods that are absent in Dawsonius. As in eight other world congeners, P. sandrae n. sp. differs from both P. biffari and Dawsonius in lacking triangular ventrolateral projections on the sixth pleomere. It is further distinguished from P. biffari by lacking a distinctly incised notch in the anterodistal margin of the uropodal exopod and by absence of a median terminal spine on the telson. Additional sequence-quality specimens of P. sandrae n. sp. are required to clarify its relationships within the polyphyletic genus Paragourretia on a molecular genetic basis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

T cell activation is insufficient to drive SIV disease progression

Resolution of T cell activation and inflammation is a key determinant of the lack of SIV disease progression in African green monkeys (AGMs). Although frequently considered together, T cell activation occurs in response to viral stimulation of acquired immunity, while inflammation reflects innate immune responses to mucosal injury. We dissociated T cell activation from inflammation through regulatory T cell (Treg) depletion with Ontak (interleukin-2 coupled with diphtheria toxin) during early SIV infection of AGMs. This intervention abolished control of T cell immune activation beyond the transition from acute to chronic infection. Ontak had no effect on gut barrier integrity, microbial translocation, inflammation, and hypercoagulation, despite increasing T cell activation. Ontak administration increased macrophage counts yet decreased their activation. Persistent T cell activation influenced SIV pathogenesis, shifting the ramp-up in viral replication to earlier time points, prolonging the high levels of replication, and delaying CD4 + T cell restoration yet without any clinical or biological sign of disease progression in Treg-depleted AGMs. Thus, by inducing T cell activation without damaging mucosal barrier integrity, we showed that systemic T cell activation per se is not sufficient to drive disease progression, which suggests that control of systemic inflammation (likely through maintenance of gut integrity) is the key determinant of lack of disease progression in natural hosts of SIVs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

An Observational Evaluation of RKW Theory over the U.S. Southern Great Plains

The theory of Rotunno et al. (“RKW” theory) addresses the behavior of squall-line cold pools in vertically sheared flows. It predicts that, within a given thermodynamic environment, a balance between baroclinic vorticity generation by the cold pool and low-level environmental vertical wind shear induces an upright updraft along the gust front that maximizes the initiation of new convective cells. Although this theory has been evaluated numerically, its applicability to observed systems remains unclear and is limited by a lack of critical measurements, including high-frequency thermodynamic and wind profiles across the gust front. Herein, observations from the Atmospheric Radiation Measurement Southern Great Plains (ARM-SGP) observatory near Lamont, Oklahoma, are used to evaluate RKW theory for 10 well-observed squall lines over a 11-yr period. For this evaluation, RKW parameters including cold-pool intensity (c), low-level ambient, line-normal vertical shear (ΔV n ), subcloud and cloud-layer updraft tilts, and multiple measures of system intensity are estimated. Furthermore, the c estimates rely on thermodynamic retrievals from the Atmosphere Emitted Radiance Interferometer (AERI), which are uncertain but verify reasonably well against independent observations. As predicted by the theory, for c/ΔV n ≥ 1, c/ΔV n correlates positively with updraft tilt and negatively with system intensity, but these results are not always statistically significant and are also sensitive to the method by which ΔV n is evaluated. Specifically, ΔV n evaluations that extend above the cold-pool top yield greater consistency with RKW predictions. Also, some measures of intensity correlate more strongly with standard moist instability metrics than with RKW parameters.

Cold pools↗
DOE OSTI2021

Are 100 Ensemble Members Enough to Capture the Remote Atmospheric Response to +2°C Arctic Sea Ice Loss?

This study presents results from the Polar Amplification Multimodel Intercomparison Project (PAMIP) single-year time-slice experiments that aim to isolate the atmospheric response to Arctic sea ice loss at global warming levels of +2°C. Using two general circulation models (GCMs), the ensemble size is increased up to 300 ensemble members, beyond the recommended 100 members. After partitioning the response in groups of 100 ensemble members, the reproducibility of the results is evaluated, with a focus on the response of the midlatitude jet streams in the North Atlantic and North Pacific. Both atmosphere-only and coupled ocean–atmosphere PAMIP experiments are analyzed. Substantial differences in the midlatitude response are found among the different experiment subsets, suggesting that 100-member ensembles are still significantly influenced by internal variability, which can mislead conclusions. Despite an overall stronger response, the coupled ocean–atmosphere runs exhibit greater spread due to additional ENSO-related internal variability when the ocean is interactive. The lack of consistency in the response is true for anomalies that are statistically significant according to Student’s t and false discovery rate tests. This is problematic for the multimodel assessment of the response, as some of the spread may be attributed to different model sensitivities whereas it is due to internal variability. Here, we propose a method to overcome this consistency issue that allows for more robust conclusions when only 100 ensemble members are used.

58 GEOSCIENCES↗
DOE OSTI2023

Near-Cloud Atmospheric Ingredients for Deep Convection Initiation

A lack of routine environmental observations located near deepening cumulus congestus clouds limits verification of important theorized and simulated updraft–environment interaction processes occurring during deep convection initiation (CI). We analyze radiosonde profiles collected during several hundred CI events near a mountain range in central Argentina during the CACTI field campaign. Statistical analyses illustrate environmental conditions supporting radar-observed CI outcomes that span a spectrum of convective cell depths, widths, and durations, as well as events lacking precipitating convection. Tested environmental factors include a large variety of sounding-derived measurements of CAPE, CIN, moisture, terrain-relative winds, vertical shear, and lifted parcel properties, with supplemental model reanalysis of background larger-scale vertical motion. CAPE and CIN metrics do not consistently differentiate CI success from failure. Only a few environmental factors contain consistent monotonic relationships among the spectrum of cloud depths achieved during CI: (i) the depth and strength of background ascent, and (ii) the component of low-level flow oriented parallel to the ridgeline. These metrics suggest that the ability of the surrounding flow to lift parcels to their LFC and terrain-modified flow are consistently relevant processes for CI. Low- to midlevel relative humidity strongly discriminated between CI and non-CI events, likely reflecting entrainment-driven dilution processes. However, we could not confidently conclude that relative humidity similarly discriminated robust from marginal CI events. Circumstantial evidence was found linking cell width, an important cloud property governing the probability of CI, to LCL height, boundary layer depth, depth and magnitude of the CIN layer, and ambient wind shear.

Storm environments↗
DOE OSTI2024

Exploration of Factors That Influence Willingness to Consider Pooled Rideshare

Ridesharing has become an increasingly prevalent form of transportation. Although transportation network companies such as Uber and Lyft initially started as a personal rideshare service where individuals ride alone or with people they know, rideshare services have been expanded to pooled rideshare—a dynamic rideshare system where an individual rides with passengers they do not know. Despite the growth in rideshare services worldwide, the use of pooled rideshare in the U.S.A. is relatively low compared to other forms of transportation. A national U.S. survey (N = 5385) was conducted to investigate reasons why individuals are willing or unwilling to consider pooled rideshare. Exploratory and confirmatory factor analyses were performed, where the exploratory factor analysis suggests five factors, specifically,service experience,time/cost,traffic/environment,privacy, andsafety. Model fit indices of the confirmatory factor analysis verified that these five factors can represent the factors behind riders’ willingness to consider pooled rideshare. Furthermore, a binomial logistic regression was conducted to explore how the five factors influence riders’ willingness to consider pooled rideshare. The three factors that influence riders’ willingness to consider pooled rideshare wereservice experience(B = 1.05),traffic/environment(B = .38), andtime/cost(B = .26), while a lack ofprivacy(B = −1.46) can be a deterrent for pooled rideshare.Safetyis important for those who are both willing and unwilling to consider the use of pooled rideshare. Understanding these factors is important for the future of pooled rideshare services in the U.S.A.

Engineering↗
DOE OSTI2020

Reducing communication in algebraic multigrid with multi-step node aware communication

Algebraic multigrid (AMG) is often viewed as a scalable [Formula: see text] solver for sparse linear systems. Yet, AMG lacks parallel scalability due to increasingly large costs associated with communication, both in the initial construction of a multigrid hierarchy and in the iterative solve phase. This work introduces a parallel implementation of AMG that reduces the cost of communication, yielding improved parallel scalability. It is common in Message Passing Interface (MPI), particularly in the MPI-everywhere approach, to arrange inter-process communication, so that communication is transported regardless of the location of the send and receive processes. Performance tests show notable differences in the cost of intra- and internode communication, motivating a restructuring of communication. In this case, the communication schedule takes advantage of the less costly intra-node communication, reducing both the number and the size of internode messages. Node-centric communication extends to the range of components in both the setup and solve phase of AMG, yielding an increase in the weak and strong scaling of the entire method.

Computer Science↗
DOE OSTI2021

Numerical investigation of a fueled pre-chamber spark-ignition natural gas engine

Pre-chamber spark-ignition (PCSI) is a leading advanced ignition concept for internal combustion engines with the potential to enable diesel-like efficiency in medium-duty/heavy-duty (MD/HD) natural gas (NG) engines. By leveraging distributed ignition sources from multiple turbulent jets, the PCSI technology can deliver extremely short combustion duration in ultra-lean mixtures and significantly improve the engine thermal efficiency. However, in the automotive industry there is a lack of adequate science base and predictive simulation tools required for commercial development of PCSI engines. Here, in this study, Reynolds-Average Navier-Stokes simulations are carried out to describe the combustion process in lean-burn NG engines, focusing on the combustion modeling approach. Two combustion models, multi-zone well-stirred reactor (MZ-WSR) and G-equation, are used to simulate the combustion process in an MD NG engine equipped with a fueled-PCSI system for four operating conditions close to the lean operating limit. A skeletal chemical mechanism and a laminar flame speed tabulation are used to compute the combustion accurately. Simulation results are compared with experimental data regarding measured cylinder pressure, heat release rate, and combustion duration. By dividing the PCSI combustion process into four distinct phases, the difference between the two models’ results for each phase is analyzed in detail. The MZ-WSR model overestimates the combustion duration for early flame kernel growth in the pre-chamber due to the lack of a specific formulation to take turbulence-chemistry interaction into account. Despite the prolonged combustion duration and low pressure built-up inside the pre-chamber, the model matches the combustion rate in the main-chamber. In contrast, the G-equation model delivers good agreements for the pre-chamber combustion and turbulent jet-driven combustion processes. However, the model starts to underestimate the combustion rate in the main-chamber, especially under ultra-lean mixture conditions. Finally, improvements are needed for both models to simulate the later combustion stage that occurred in the near-wall regions.

33 ADVANCED PROPULSION SYSTEMS↗
DOE OSTI2020

Decoy selection for protein structure prediction via extreme gradient boosting and ranking

Background: Identifying one or more biologically-active/native decoys from millions of non-native decoys is one of the major challenges in computational structural biology. The extreme lack of balance in positive and negative samples (native and non-native decoys) in a decoy set makes the problem even more complicated. Consensus methods show varied success in handling the challenge of decoy selection despite some issues associated with clustering large decoy sets and decoy sets that do not show much structural similarity. Recent investigations into energy landscape-based decoy selection approaches show promises. However, lack of generalization over varied test cases remains a bottleneck for these methods. Results: We propose a novel decoy selection method, ML-Select, a machine learning framework that exploits the energy landscape associated with the structure space probed through a template-free decoy generation. The proposed method outperforms both clustering and energy ranking-based methods, all the while consistently offering better performance on varied test-cases. Moreover, ML-Select shows promising results even for the decoy sets consisting of mostly low-quality decoys. Conclusions: ML-Select is a useful method for decoy selection. This work suggests further research in finding more effective ways to adopt machine learning frameworks in achieving robust performance for decoy selection in template-free protein structure prediction.

59 BASIC BIOLOGICAL SCIENCES↗