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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Genetic Predictive Factors for Nonsusceptible Phenotypes and Multidrug Resistance in Expanded-Spectrum Cephalosporin-Resistant Uropathogenic Escherichia coli from a Multicenter Cohort: Insights into the Phenotypic and Genetic Basis of Coresistance

Antimicrobial resistance in urinary tract infections (UTIs) is a major public health concern. This study aims to characterize the phenotypic and genetic basis of multidrug resistance (MDR) among expanded-spectrum cephalosporin-resistant (ESCR) uropathogenic Escherichia coli (UPEC) causing UTIs in California patient populations. Between February and October 2019, 577 ESCR UPEC isolates were collected from patients at 6 clinical laboratory sites across California. Lineage and antibiotic resistance genes were determined by analysis of whole-genome sequence data. The lineages ST131, ST1193, ST648, and ST69 were predominant, representing 46%, 5.5%, 4.5%, and 4.5% of the collection, respectively. Overall, 527 (91%) isolates had an expanded-spectrum β-lactamase (ESBL) phenotype, with bla CTX-M-15 , bla CTX-M-27 , bla CTX-M-55 , and bla CTX-M-14 being the most prevalent ESBL genes. In the 50 non-ESBL phenotype isolates, 40 (62%) contained bla CMY-2 , which was the predominant plasmid-mediated AmpC (pAmpC) gene. Narrow-spectrum β-lactamases, bla TEM-1B and bla OXA-1 , were also found in 44.9% and 32.1% of isolates, respectively. Among ESCR UPEC isolates, isolates with an ESBL phenotype had a 1.7-times-greater likelihood of being MDR than non-ESBL phenotype isolates (P < 0.001). The cooccurrence of bla CTX-M-15 , bla OXA-1 , and aac(6')-Ib-cr within ESCR UPEC isolates was strongly correlated. Cooccurrence of bla CTX-M-15 , bla OXA-1 , and aac(6')-Ib-cr was associated with an increased risk of nonsusceptibility to piperacillin-tazobactam, cefepime, fluoroquinolones, and amikacin as well as MDR. Multivariate regression revealed the presence of bla CTX-M-55 , bla TEM-1B , and the ST131 genotype as predictors of MDR.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Field expedient stool collection methods for gut microbiome analysis in deployed military environments

ABSTRACT Field expedient devices and protocols for the collection, storage, and shipment of stool samples in deployed settings are needed for the advancement of microbiome research in military health. Relevant assessments include the evaluation of microbiome signatures associated with susceptibility to travelers’ diarrhea and recovery of gut function following infection. However, inherent biases in microbial measurements due to preservatives and sampling methods are unclear and should be assessed for an accurate evaluation of the microbiome. We performed shotgun metagenomic sequencing and compared the microbiome composition in paired fecal samples collected using Flinters Technology Associates (FTA) cards and OMNIgene (OG) Gut tubes, prior to and during international travel, from 49 adult participants, 39 of whom remained asymptomatic and 10 experienced travelers’ diarrhea. Higher concentrations of nucleic acid and sequencing libraries were observed in OG samples. A majority of genera (82.9%) were detected with both methods, and detections of genera limited to one collection method were not highly prevalent across samples and were present in extremely low relative abundances (<0.01%). Differences in beta diversity were largely explained by inter-individuality of microbiome composition, followed by the effect of collection method and timepoint-disease states. Differential abundance analysis indicated that Corynebacterium and Blautia were consistently higher in abundance across all groups with FTA and OG collection, respectively. The observed differences in microbiome composition between methods suggest the need for consistent and standardized protocols within a study. Overall, the data presented here could help guide the future design of fecal microbiome study protocols in field and military deployment settings. IMPORTANCE The assessment of field-deployable methods for fecal sample collection and storage is required to reliably capture samples collected in remote and austere locations. This study describes a comparative metagenomics analysis between samples collected by two different commercially available methods in a military-deployed setting. The results presented here are foundational for the future design of fecal microbiome study protocols in an operational context.

field study↗
DOE OSTI2023

Identification of hidden N4-like viruses and their interactions with hosts

The N4-like viruses, which were recently assigned to the novel viral family Schitoviridae in 2021, belong to a podoviral-like viral lineage and possess conserved genomic characteristics and a unique replication mechanism. Despite their significance, our understanding of N4-like viruses is primarily based on viral isolates. To address this knowledge gap, this study has established a comprehensive N4-like viral data sets comprising 342 high-quality N4-like viruses/proviruses (144 viral isolates, 158 uncultured viruses, and 40 integrated N4-like proviruses). These viruses were classified into 97 subfamilies (89 of which are newly identified), 148 genera (100 of which are newly identified), and 253 species (177 of which are newly identified). The study reveals that N4-like viruses inhibit the polar region, oligotrophic open oceans, and the human gut, where they infect various bacterial lineages, such as Alpha/Beta/Gamma/Epsilon-proteobacteria in the Proteobacteria phylum. Although N4-like viral endogenization appears to be prevalent in Proteobacteria, it has also been observed in Firmicutes. Additionally, the phylogenetic analysis has identified evolutionary divergence within the hallmark genes of N4-like viruses, indicating a complex origin of the different conserved parts of viral genomes. Moreover, 1,101 putative auxiliary metabolic genes (AMGs) were identified in the N4-like viral pan-proteome, which mainly participate in nucleotide and cofactor/vitamin metabolisms. Of these AMGs, 27 were found to be associated with virulence, suggesting their potential involvement in the spread of bacterial pathogenicity. The findings of this study are significant, as N4-like viruses represent a unique viral lineage with a distinct replication mechanism and a conserved core genome. This work has resulted in a comprehensive global map of the entire N4-like viral lineage, including information on their distribution in different biomes, evolutionary divergence, genomic diversity, and the potential for viral-mediated host metabolic reprogramming. As such, this work significantly contributes to our understanding of the ecological function and viral-host interactions of bacteriophages.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

A bloom of a single bacterium shapes the microbiome during outdoor diatom cultivation collapse

Algae-dominated ecosystems are fundamentally influenced by their microbiome. We lack information on the identity and function of bacteria that specialize in consuming algal-derived dissolved organic matter in high algal density ecosystems such as outdoor algal ponds used for biofuel production. Here, we describe the metagenomic and metaproteomic signatures of a single bacterial strain that bloomed during a population-wide crash of the diatom, Phaeodactylum tricornutum, grown in outdoor ponds. 16S rRNA gene data indicated that a single Kordia sp. strain (family Flavobacteriaceae) contributed up to 93% of the bacterial community during P. tricornutum demise. Kordia sp. expressed proteins linked to microbial antagonism and biopolymer breakdown, which likely contributed to its dominance over other microbial taxa during diatom demise. Analysis of accompanying downstream microbiota (primarily of the Rhodobacteraceae family) provided evidence that cross-feeding may be a pathway supporting microbial diversity during diatom demise. In situ and laboratory data with a different strain suggested that Kordia was a primary degrader of biopolymers during algal demise, and co-occurring Rhodobacteraceae exploited degradation molecules for carbon. An analysis of 30 Rhodobacteraceae metagenome assembled genomes suggested that algal pond Rhodobacteraceae commonly harbored pathways to use diverse carbon and energy sources, including carbon monoxide, which may have contributed to the prevalence of this taxonomic group within the ponds. These observations further constrain the roles of functionally distinct heterotrophic bacteria in algal microbiomes, demonstrating how a single dominant bacterium, specialized in processing senescing or dead algal biomass, shapes the microbial community of outdoor algal biofuel ponds.

Kordia↗
DOE OSTI2021

Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance

To our knowledge, this is the first study to identify the bacteriophage distribution in a groundwater ecosystem shedding light on their prevalence and distribution across metal-contaminated and background sites. Our study is uniquely based on selective sequencing of solely the extrachromosomal elements of a microbiome followed by analysis for viral signatures, thus establishing a more focused approach for phage identifications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Native Plasmid-Encoded Mercury Resistance Genes Are Functional and Demonstrate Natural Transformation in Environmental Bacterial Isolates

Plasmid-mediated horizontal gene transfer (HGT) is a major driver of genetic diversity in bacteria. We experimentally validated the function of a putative mercury resistance operon present on an abundant 8-kbp native plasmid found in groundwater samples without detectable levels of mercury. Phylogenetic analyses of the plasmid-encoded mercury reductases from the studied groundwater site show them to be distinct from those reported in proximal metal-contaminated sites. We synthesized the entire native plasmid and demonstrated that the plasmid was sufficient to confer functional mercury resistance in Escherichia coli . Given the possibility that natural transformation is a prevalent HGT mechanism in the low-cell-density environments of groundwaters, we also assayed bacterial strains from this environment for competence. We used the native plasmid-encoded metal resistance to design a screen and identified 17 strains positive for natural transformation. We selected 2 of the positive strains along with a model bacterium to fully confirm HGT via natural transformation. From an ecological perspective, the role of the native plasmid population in providing advantageous traits combined with the microbiome’s capacity to take up environmental DNA enables rapid adaptation to environmental stresses. Horizontal transfer of mobile genetic elements via natural transformation has been poorly understood in environmental microbes. Here, we confirm the functionality of a native plasmid-encoded mercury resistance operon in a model microbe and then query for the dissemination of this resistance trait via natural transformation into environmental bacterial isolates. We identified 17 strains including Gram-positive and Gram-negative bacteria to be naturally competent. These strains were able to successfully take up the plasmid DNA and obtain a clear growth advantage in the presence of mercury. Our study provides important insights into gene dissemination via natural transformation enabling rapid adaptation to dynamic stresses in groundwater environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Comprehensive characterization of extracellular vesicles produced by environmental (Neff) and clinical (T4) strains of Acanthamoeba castellanii

We conducted a comprehensive comparative analysis of extracellular vesicles (EVs) from two Acanthamoeba castellanii strains, Neff (environmental) and T4 (clinical). Morphological analysis via transmission electron microscopy revealed slightly larger Neff EVs (average = 194.5 nm) compared to more polydisperse T4 EVs (average = 168.4 nm). Nanoparticle tracking analysis (NTA) and dynamic light scattering validated these differences. Proteomic analysis of the EVs identified 1,352 proteins, with 1,107 common, 161 exclusive in Neff, and 84 exclusively in T4 EVs. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) mapping revealed distinct molecular functions and biological processes and notably, the T4 EVs enrichment in serine proteases, aligned with its pathogenicity. Lipidomic analysis revealed a prevalence of unsaturated lipid species in Neff EVs, particularly triacylglycerols, phosphatidylethanolamines (PEs), and phosphatidylserine, while T4 EVs were enriched in diacylglycerols and diacylglyceryl trimethylhomoserine, phosphatidylcholine and less unsaturated PEs, suggesting differences in lipid metabolism and membrane permeability. Metabolomic analysis indicated Neff EVs enrichment in glycerolipid metabolism, glycolysis, and nucleotide synthesis, while T4 EVs, methionine metabolism. Furthermore, RNA-seq of EVs revealed differential transcript between the strains, with Neff EVs enriched in transcripts related to gluconeogenesis and translation, suggesting gene regulation and metabolic shift, while in the T4 EVs transcripts were associated with signal transduction and protein kinase activity, indicating rapid responses to environmental changes. In this novel study, data integration highlighted the differences in enzyme profiles, metabolic processes, and potential origins of EVs in the two strains shedding light on the diversity and complexity of A. castellanii EVs and having implications for understanding host-pathogen interactions and developing targeted interventions for Acanthamoeba-related diseases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The Microbial Community and Functional Potential in the Midland Basin Reveal a Community Dominated by Both Thiosulfate and Sulfate-Reducing Microorganisms

The Permian Basin is the highest producing oil and gas reservoir in the United States. Hydrocarbon resources in this region are often accessed by unconventional extraction methods, including horizontal drilling and hydraulic fracturing. Despite the importance of the Permian Basin, there is no publicly available microbiological data from this region. We completed an analysis of Permian produced water samples to understand the dynamics present in hydraulically fractured wells in this region. We analyzed produced water samples taken from 10 wells in the Permian region of the Midland Basin using geochemical measurements, 16S rRNA gene sequencing, and metagenomic sequencing. Compared to other regions, we found that Permian Basin produced water was characterized by higher sulfate and lower total dissolved solids (TDS) concentrations, with a median of 1,110 mg/L and 107,000 mg/L. Additionally, geochemical measurements revealed the presence of frac hits, or interwell communication events where an established well is affected by the pumping of fracturing fluid into a new well. The occurrence of frac hits was supported by correlations between the microbiome and the geochemical parameters. Our 16S rRNA gene sequencing identified a produced water microbiome characterized by anaerobic, halophilic, and sulfur reducing taxa. Interestingly, sulfate and thiosulfate reducing taxa including Halanaerobium, Orenia, Marinobacter, and Desulfohalobium were the most prevalent microbiota in most wells. We further investigated the metabolic potential of microorganisms in the Permian Basin with metagenomic sequencing. We recovered 15 metagenome assembled genomes (MAGs) from seven different samples representing 6 unique well sites. These MAGs corroborated the high presence of sulfate and thiosulfate reducing genes across all wells, especially from key taxa including Halanaerobium and Orenia. The observed microbiome composition and metabolic capabilities in conjunction with the high sulfate concentrations demonstrate a high potential for hydrogen sulfide production in the Permian Basin. Additionally, evidence of frac hits suggests the possibility for the exchange of microbial cells and/or genetic information between wells. This exchange would increase the likelihood of hydrogen sulfide production and has implications for the oil and gas industry.

16S RNA↗
DOE OSTI2023

Targeted metagenomic assessment reflects critical colonization in battlefield injuries

Current diagnostics and clinical management strategies for combat wounds are based on decisions made by expert clinicians. However, even in the hands of experienced surgeons, wounds from combat injuries can exhibit failed healing and complications related to limitations in the rapid and comprehensive generation of diagnostic information. Previous studies have demonstrated the possible use of genomic sequencing approaches to detect microbial signatures involved in combat casualty care. While effective, whole metagenome sequencing is limited by the depth required to confidently detect all relevant signatures. To address this, we developed a targeted capture sequencing panel to detect microbial signatures relevant to wound healing. These targets include known microbial nosocomial pathogens, wound colonizers, and genes involved in virulence and antimicrobial resistance. A bioinformatics pipeline was built to identify genomic regions of interest and over 8,000 oligonucleotide probes were designed for capture. The panel was synthesized and validated using control reference genomes in human background and on wound-effluent samples from a cohort of combat-injured U.S. service members. Our panel was sensitive against wound-colonizing species, Acinetobacter baumannii and Pseudomonas aeruginosa, and was specific in detecting corresponding virulence and antimicrobial-resistance genes as well as other pathogenic species present in microflora mixtures. Random forest feature permutation confirmed the prevalence of Acinetobacter and Pseudomonas in critically colonized wounds and wounds that failed to heal, respectively. Our results demonstrate the capability of targeted sequencing tools and analysis platforms to profile and deliver information on pathogenic factors influencing wound progression, thereby guiding therapeutic intervention.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Characterization of Pseudomonas aeruginosa and Acinetobacter calcoaceticus-baumannii complex traumatic wound isolates

Healing of traumatic wounds is complicated by infecting pathogens, with Pseudomonas aeruginosa and members of the Acinetobacter calcoaceticus-baumannii complex among the most common infectious agents. However, a full understanding of genotypic and phenotypic differences between circulating wound isolates is lacking. To address this, traumatic wounds were sampled at Emory University Hospital, and 24 isolates were characterized; we focused on P. aeruginosa and Acinetobacter due to their prevalence and tendency for antibiotic resistance. Even though these species are renowned for antibiotic resistance, only two of the tested isolates could be classified as multidrug resistant. Whole-genome sequencing and analysis revealed that isolates from different patients were genetically distinct; however, longitudinal isolates from the same patient were closely related and appeared to represent chronic colonization by the same strain. Phylogenetic analysis revealed that laboratory strains (PAO1 and AB5075) that were isolated decades previously and from different locations grouped closely to subsets of the recent wound isolates. Given the importance of biofilm formation in infection, the ability of the isolates to form biofilms was assessed; all isolates formed biofilms but showed temporal and magnitude differences. Analysis of a subset of isolates revealed that planktonic P. aeruginosa was resistant to human serum-mediated killing. While the same was true for the majority of Acinetobacter isolates, one showed planktonic sensitivity that was abrogated when grown in a biofilm. Taken together, these data reveal genotypic and phenotypic differences in circulating isolates of P. aeruginosa and A. baumannii.

Acinetobacter↗
DOE OSTI2023

Dating submarine landslides using the transient response of gas hydrate stability

Abstract Submarine landslides are prevalent on the modern-day seafloor, yet an elusive problem is constraining the timing of past slope failure. We present a novel age-dating technique based on perturbations to underlying gas hydrate stability caused by slide-impacted seafloor changes. Using three-dimensional (3-D) seismic data, we mapped an irregular bottom simulating reflection (BSR) underneath a submarine landslide in the Orca Basin, Gulf of Mexico. The irregular BSR mimics the pre-slide seafloor geometry rather than the modern bathymetry. Therefore, we suggest that the gas hydrate stability zone (GHSZ) is still adjusting to the post-slide sediment temperature. We applied transient conductive heat-flow modeling to constrain the response of the GHSZ to the slope failure, which yielded a most likely age of ca. 8 ka, demonstrating that gas hydrate can respond to landslides even on multimillennial time scales. We further provide a generalized analytical solution that can be used to remotely date submarine slides in the absence of traditional dating techniques.

Geology↗
DOE OSTI2020

The relatively young and rural population may limit the spread and severity of COVID-19 in Africa: a modelling study

A novel coronavirus disease 2019 (COVID-19) has spread to all regions of the world. There is great uncertainty regarding how countries’ characteristics will affect the spread of the epidemic; to date, there are few studies that attempt to predict the spread of the epidemic in African countries. In this paper, we investigate the role of demographic patterns, urbanisation and comorbidities on the possible trajectories of COVID-19 in Ghana, Kenya and Senegal. We use an augmented deterministic Susceptible-Infected-Recovered model to predict the true spread of the disease, under the containment measures taken so far. We disaggregate the infected compartment into asymptomatic, mildly symptomatic and severely symptomatic to match observed clinical development of COVID-19. We also account for age structures, urbanisation and comorbidities (HIV, tuberculosis, anaemia). In our baseline model, we project that the peak of active cases will occur in July, subject to the effectiveness of policy measures. When accounting for the urbanisation, and factoring in comorbidities, the peak may occur between 2 June and 17 June (Ghana), 22 July and 29 August (Kenya) and, finally, 28 May and 15 June (Senegal). Successful containment policies could lead to lower rates of severe infections. While most cases will be mild, we project in the absence of policies further containing the spread, that between 0.78% and 1.03%, 0.61% and 1.22%, and 0.60% and 0.84% of individuals in Ghana, Kenya and Senegal, respectively, may develop severe symptoms at the time of the peak of the epidemic. Compared with Europe, Africa’s younger and rural population may modify the severity of the epidemic. The large youth population may lead to more infections but most of these infections will be asymptomatic or mild, and will probably go undetected. The higher prevalence of underlying conditions must be considered.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Efficient Parallel Sparse Symmetric Tucker Decomposition for High-Order Tensors

Tensor based methods are receiving renewed attention in recent years due to their prevalence in diverse real-world applications. There is considerable literature on tensor representations and algorithms for tensor decompositions, both for dense and sparse tensors. Many applications in hypergraph analytics, machine learning, psychometry, and signal processing result in tensors that are both sparse and symmetric, making it an important class for further study. Similar to the critical Tensor Times Matrix chain operation (TTMc) in general sparse tensors, the Sparse Symmetric Tensor Times Same Matrix chain (S3TTMc) operation is compute and memory intensive due to high tensor order and the associated factorial explosion in the number of non-zeros. In this work, we present a novel compressed storage format CSS for sparse symmetric tensors, along with an efficient parallel algorithm for the S3TTMc operation. We theoretically establish that S3TTMc on CSS achieves a better memory versus run-time trade-off compared to state-of-the-art implementations. We demonstrate experimental findings that confirm these results and achieve up to 2.9× speedup on synthetic and real datasets.

Shivakumar, Shruti↗
DOE OSTI2022

Optimal Experimental Design for Inverse Problems in the Presence of Observation Correlations

Optimal experimental design (OED) is the general formalism of sensor placement and decisions on the data collection strategy for engineered or natural experiments. This problem is prevalent in many critical fields such as battery design, numerical weather prediction, geosciences, environmental and urban studies. State-of-the-art computational methods for experimental design do not accommodate correlation structure in observational errors produced by many expensive-to-operate devices such as X-ray machines, radars, and satellites. Discarding evident data correlations leads to biased results, higher expenses, and waste of valuable resources. We present a general formulation of the OED formalism for model-constrained large-scale Bayesian linear inverse problems, where measurement errors are generally correlated. The proposed approach utilizes the Hadamard product of matrices to formulate the weighted-likelihood, and is valid for both finite as well as infinite-dimensional Bayesian inverse problems. Extensive numerical experiments are carried out for empirical verification of the proposed approach using an advection-diffusion model, where the objective is to optimally place a small set of sensors, under a limited budget, to predict the concentration of a contaminant in a closed and bounded domain.

Correlated observations↗
DOE OSTI2024

A study of nuclear structure of light nuclei at the electron–ion collider

Understanding the substructure of atomic nuclei, particularly the clustering of nucleons inside them, is essential for comprehending nuclear dynamics. Various cluster configurations can emerge depending on excitation energy, the number and types of core clusters, and the presence of excess neutrons. Despite the prevalence of tightly bound cluster formations in low-lying states, understanding the correlation between clusters and their formation mechanisms remains incomplete. This exploring study investigates nuclear clustering at the electron–ion collider (EIC) using simulations based on the modified BeAGLE model. By simulating collisions involving e+ 9 Be, e+ 12 C, and e+ 16 O nuclei, we find that the average energy of particles and the system size ratios of particles at forward rapidity exhibit sensitivity to alpha clustering and its various configurations. These findings offer valuable insights into the dynamics of nuclear clustering and its implications for future studies at the EIC.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Evaluating Automated Face Identity-Masking Methods with Human Perception and a Deep Convolutional Neural Network

Face de-identification (or “masking”) algorithms have been developed in response to the prevalent use of video recordings in public places. Here, we evaluated the success of face identity masking for human perceivers and a deep convolutional neural network (DCNN). Eight de-identification algorithms were applied to videos of drivers’ faces, while they actively operated a motor vehicle. These masks were pre-selected to be applicable to low-quality video and to maintain coarse information about facial actions. Humans studied high-resolution images to learn driver identities and were tested on their recognition of active drivers in low-resolution videos. Faces in the videos were either unmasked or were masked by one of the eight algorithms. When participants were tested immediately after learning (Experiment 1), all masks reduced identification, with six of eight masks reducing identification to extremely poor performance. In a second experiment, two of the most effective masks were tested after a delay of 7 or 28 days. The delay did not further reduce identification of the masked faces. In all masked conditions, participants maintained stringent decision criteria, with low confidence in recognition, further indicating the effectiveness of the masks. Next, the DCNN performed an identity-matching task between high-resolution images and masked videos—a task analogous to that done by humans. The pattern of accuracy for the DCNN mirrored some, but not all, aspects of human performance, highlighting the need to test the effectiveness of identity masking for both humans and machines. The DCNN was also tested on its ability to match identity between masked and unmasked versions of the same video, based only on the face. DCNN performance for the eight masks offers insight into the nature of the information in faces that is coded in these networks.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Implementing Arbitrary/Common Concurrent Writes of CRCW PRAM

The Parallel Random Access Machines (PRAM) abstraction is the simplest and most elegant algorithmic model for the design and analysis of parallel algorithms. It consists of different models categorized based on the underlying memory access mode used, the most powerful of which is the Concurrent Read Concurrent Write (CRCW) model. A PRAM algorithm describes a series of rounds, each of which consists of a collection of operations that can be executed concurrently within the same time step. However, the lack of support for concurrent memory accesses and the prevalence of asynchronous programming models led to the belief that implementing CRCW PRAM algorithms is unattainable and prompted many to avoid this model except for theoretical studies of optimal performance.In this work, we study the arbitrary and common concurrent writes in the CRCW PRAM model and explore implementation challenges on general-purpose systems. Moreover, we examine current practices for implementing common/arbitrary concurrent writes and propose a new efficient lightweight and thread-safe method to implement concurrent writes through leveraging atomic instructions. To demonstrate the efficacy of our method, we developed OpenMP kernels for classical CRCW PRAM algorithms and provide experimental results and comparisons based on run time performance measured over the x86 multicore architecture. Our results show a performance speedup compared to current practices up to 4.5x across all our benchmarks.

Ghanim, Fady↗