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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Profiling the BLAST bioinformatics application for load balancing on high-performance computing clusters

Abstract Background The Basic Local Alignment Search Tool (BLAST) is a suite of commonly used algorithms for identifying matches between biological sequences. The user supplies a database file and query file of sequences for BLAST to find identical sequences between the two. The typical millions of database and query sequences make BLAST computationally challenging but also well suited for parallelization on high-performance computing clusters. The efficacy of parallelization depends on the data partitioning, where the optimal data partitioning relies on an accurate performance model. In previous studies, a BLAST job was sped up by 27 times by partitioning the database and query among thousands of processor nodes. However, the optimality of the partitioning method was not studied. Unlike BLAST performance models proposed in the literature that usually have problem size and hardware configuration as the only variables, the execution time of a BLAST job is a function of database size, query size, and hardware capability. In this work, the nucleotide BLAST application BLASTN was profiled using three methods: shell-level profiling with the Unix “time” command, code-level profiling with the built-in “profiler” module, and system-level profiling with the Unix “gprof” program. The runtimes were measured for six node types, using six different database files and 15 query files, on a heterogeneous HPC cluster with 500+ nodes. The empirical measurement data were fitted with quadratic functions to develop performance models that were used to guide the data parallelization for BLASTN jobs. Results Profiling results showed that BLASTN contains more than 34,500 different functions, but a single function, RunMTBySplitDB, takes 99.12% of the total runtime. Among its 53 child functions, five core functions were identified to make up 92.12% of the overall BLASTN runtime. Based on the performance models, static load balancing algorithms can be applied to the BLASTN input data to minimize the runtime of the longest job on an HPC cluster. Four test cases being run on homogeneous and heterogeneous clusters were tested. Experiment results showed that the runtime can be reduced by 81% on a homogeneous cluster and by 20% on a heterogeneous cluster by re-distributing the workload. Discussion Optimal data partitioning can improve BLASTN’s overall runtime 5.4-fold in comparison with dividing the database and query into the same number of fragments. The proposed methodology can be used in the other applications in the BLAST+ suite or any other application as long as source code is available.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

A disk-based dynamical constraint on the mass of the young binary DQ Tau

We present new Atacama Large Millimeter/Submillimeter Array (ALMA) observations of CO J = 2−1 line emission from the DQ Tau circumbinary disk. These data are used to tomographically reconstruct the Keplerian disk velocity field in a forward-modeling inference framework, and thereby provide a dynamical constraint on the mass of the DQ Tau binary of M{sub ∗}=1.27{sub −0.27}{sup +0.46} M{sub ⊙}. Those results are compared with an updated and improved orbital solution for this double-lined system based on long-term monitoring of its stellar radial velocities. Both of these independent dynamical constraints on the binary mass are in excellent agreement: taken together, they demonstrate that the DQ Tau system mass is 1.21 ± 0.26 M{sub ⊙} and that the disk and binary orbital planes are aligned within 3° (at 3σ confidence). The predictions of various theoretical models for pre-main-sequence stellar evolution are also consistent with these masses, though more detailed comparisons are difficult due to lingering uncertainties regarding the photospheric properties of the individual components. DQ Tau is the third, nearly equal-mass, double-lined spectroscopic binary with a circumbinary disk that has been dynamically “weighed” with these two independent techniques: all show consistent results, validating the overall accuracy of the disk-based approach and demonstrating that it can be robustly applied to large samples of young, single stars as ALMA ramps up to operations at full capacity.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Evidence for the Late Arrival of Hot Jupiters in Systems with High Host-star Obliquities

It has been shown that hot Jupiters systems with massive, hot stellar primaries exhibit a wide range of stellar obliquities. On the other hand, hot Jupiter systems with low-mass, cool primaries often have stellar obliquities close to zero. Efficient tidal interactions between hot Jupiters and the convective envelopes present in lower-mass main-sequence stars have been a popular explanation for these observations. If this explanation is accurate, then aligned systems should be older than misaligned systems. Likewise, the convective envelope mass of a hot Jupiter's host star should be an effective predictor of its obliquity. We derive homogeneous stellar parameters—including convective envelope masses—for hot Jupiter host stars with high-quality sky-projected obliquity inferences. Using a thin-disk stellar population's Galactic velocity dispersion as a relative age proxy, we find that hot Jupiter host stars with larger-than-median obliquities are older than hot Jupiter host stars with smaller-than-median obliquities. The relative age difference between the two populations is larger for hot Jupiter host stars with smaller-than-median fractional convective envelope masses and is significant at the 3.6σ level. We identify stellar mass, not convective envelope mass, as the best predictor of stellar obliquity in hot Jupiter systems. The best explanation for these observations is that many hot Jupiters in misaligned systems arrived in the close proximity of their host stars long after their parent protoplanetary disks dissipated. The dependence of observed age offset on convective envelope mass suggests that tidal realignment contributes to the population of aligned hot Jupiters orbiting stars with convective envelopes.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2011

Muon capture for the front end of a muon collider

We discuss the design of the muon capture front end for a {mu}{sup +}-{mu}{sup -} Collider. In the front end, a proton bunch on a target creates secondary pions that drift into a capture transport channel, decaying into muons. A sequence of rf cavities forms the resulting muon beams into strings of bunches of differing energies, aligns the bunches to (nearly) equal central energies, and initiates ionization cooling. The muons are then cooled and accelerated to high energy into a storage ring for high-energy high luminosity collisions. Our initial design is based on the somewhat similar front end of the International Design Study (IDS) neutrino factory.

43 PARTICLE ACCELERATORS↗
DOE OSTI2011

A Compact and High Performance Muon Capture Channel for Muon Accelerators

It is widely believed that a neutrino factory would deliver unparallel performance in studying neutrino mixing and would provide tremendous sensitivity to new physics in the neutrino sector. Here we will describe and simulate the front-end of the neutrino factory system, which plays critical role in determining the number of muons that can be accepted by the downstream accelerators. In this system, a proton bunch on a target creates secondaries that drift into a capture transport channel. A sequence of rf cavities forms the resulting muon beams into strings of bunches of differing energies, aligns the bunches to nearly equal central energies, and initiates ionization cooling. For this, the muon beams are transported through sections containing high-gradient cavities and strong focusing solenoids. In this paper we present results of optimization and variation studies toward obtaining the maximum number of muons for a neutrino factory by using a compact transport channel. It has been suggested computationally and experimentally that the maximum achievable gradient is enhanced by introducing an external magnetic field at right angles to the rf electric field since it suppresses field-emission processes. Here, we have discussed a possible scheme for extending the concept of magnetic insulation to capture, transport, and cool muons in a neutrino factory. We incorporated this idea into a new lattice design where the rf cavities are shaped so that their walls were tangential to the magnetic-field lines. We showed that, with magnetic insulation, the field-emitted electrons impact the cavity surface with energies four orders-of-magnitude less than in conventional pillbox cavities; consequently, damage from field-emission is suppressed significantly. While demanding in terms of power requirements, this neutrino factory lattice showed satisfactory performance in both cooling and collecting the accepted muons within the requirements for the IDSNF. Optimizations were also made to reduce heating on the absorber windows minimizing losses in the accepted muon fluxes. The next step for verifying these ideas should be an experimental demonstration of a single muon accelerator magnetically-insulated rf cavity. A successful demonstration will provide us with a new versatile tool for a future muon accelerator.

43 PARTICLE ACCELERATORS↗
DOE OSTI2010

Muon Capture for the IDS Neutrino Factory

We have developed a new method for capture, bunching and phase-energy rotation of secondary beams from a proton source, using high-frequency rf systems. The method is the baseline for muon capture in the International scoping study for a neutrino factory. In this method, a proton bunch on a target creates secondaries that drift into a capture transport channel. A sequence of rf cavities forms the resulting muon beams into strings of bunches of differing energies, aligns the bunches to (nearly) equal central energies, and initiates ionization cooling. For the International Design Study the method must be optimized for performance and cost, and variations will be explored. In this paper we present results of optimization and variation studies toward obtaining the maximum number of muons for a neutrino factory, as well as for a future muon collider.

43 PARTICLE ACCELERATORS↗
DOE OSTI2023

Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase η and reduces DNA synthesis fidelity

DNA polymerases catalyze DNA synthesis with high efficiency, which is essential for all life. Extensive kinetic and structural efforts have been executed in exploring mechanisms of DNA polymerases, surrounding their kinetic pathway, catalytic mechanisms, and factors that dictate polymerase fidelity. Recent time-resolved crystallography studies on DNA polymerase η (Pol η) and β have revealed essential transient events during the DNA synthesis reaction, such as mechanisms of primer deprotonation, separated roles of the three metal ions, and conformational changes that disfavor incorporation of the incorrect substrate. DNA-embedded ribonucleotides (rNs) are the most common lesion on DNA and a major threat to genome integrity. While kinetics of rN incorporation has been explored and structural studies have revealed that DNA polymerases have a steric gate that destabilizes ribonucleotide triphosphate binding, the mechanism of extension upon rN addition remains poorly characterized. Using steady-state kinetics, static and time-resolved X-ray crystallography with Pol η as a model system, we showed that the extra hydroxyl group on the primer terminus does alter the dynamics of the polymerase active site as well as the catalysis and fidelity of DNA synthesis. During rN extension, Pol η error incorporation efficiency increases significantly across different sequence contexts. Finally, our systematic structural studies suggest that the rN at the primer end improves primer alignment and reduces barriers in C2'-endo to C3'-endo sugar conformational change. Overall, our work provides further mechanistic insights into the effects of rN incorporation on DNA synthesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Opening options for material transfer

Material-transfer agreements (MTAs) underlie the legal frameworks within which biotechnology practitioners define the terms and conditions for sharing biomaterials ranging, for example, from plasmid DNA to patient samples. If MTAs are easy to use and well adapted to the needs of individual researchers, institutions, and broader communities, then more sharing, innovation, and translation can occur. However, the MTA frameworks currently in place were developed in the 1990s—before widespread adoption of the World Wide Web, genome sequencing, and gene synthesis—and are not always well adapted for contemporary research and translation practices or aligned with social objectives.

Kahl, Linda↗
DOE OSTI2014

Omega: an Overlap-graph de novo Assembler for Meta-genomics

Motivation: Metagenomic sequencing allows reconstruction of mi-crobial genomes directly from environmental samples. Omega (overlap-graph metagenome assembler) was developed here for assembling and scaffolding Illumina sequencing data of microbial communities. Results: Omega found overlaps between reads using a prefix/suffix hash table. The overlap graph of reads was simplified by removing transitive edges and trimming small branches. Unitigs were generat-ed based on minimum cost flow analysis of the overlap graph. Obtained unitigs were merged to contigs and scaffolds using mate-pair information. Omega was compared with two de Bruijn graph assemblers, SOAPdenovo and IDBA-UD, using a publically-available Illumina sequencing dataset of a 64-genome mock com-munity. The assembly results were verified by their alignment with reference genomes. The overall performances of the three assem-blers were comparable and each assembler provided best results for a subset of genomes.

Haider, Bahlul↗
DOE OSTI2019

Genomic content of a novel yeast species Hanseniaspora gamundiae sp. nov. from fungal stromata (Cyttaria) associated with a unique fermented beverage in Andean Patagonia, Argentina

A novel yeast species was isolated from the sugar-rich stromata of Cyttaria hariotii collected from two different Nothofagus tree species in the Andean forests of Patagonia, Argentina. Phylogenetic analyses of the concatenated sequence of the rRNA gene sequences and the protein-coding genes for actin and translational elongation factor-1α indicated that the novel species belongs to the genus Hanseniaspora. De novo genome assembly of the strain CRUB 1928 T yielded a 10.2-Mbp genome assembly predicted to encode 4452 protein-coding genes. The genome sequence data were compared to the genomes of other Hanseniaspora species using three different methods, an alignment-free distance measure, K r , and two model-based estimations of DNA-DNA homology values, of which all provided indicative values to delineate species of Hanseniaspora. Given its potential role in a rare indigenous alcoholic beverage in which yeasts ferment sugars extracted from the stromata of Cytarria sp., we searched for the genes that may suggest adaptation of novel Hanseniaspora species to fermenting communities. The SSU1-like gene encoding a sulfite efflux pump, which, among Hanseniaspora, is present only in close relatives to the new species, was detected and analyzed, suggesting that this gene might be one factor that characterizes this novel species. We also discuss several candidate genes that likely underlie the physiological traits used for traditional taxonomic identification. Based on these results, a novel yeast species with the name Hanseniaspora gamundiae sp. nov. is proposed with CRUB 1928 T (ex-types: ZIM 2545 T = NRRL Y-63793 T = PYCC 7262 T ; MycoBank number MB 824091) as the type strain. Furthermore, we propose the transfer of the Kloeckera species, K. hatyaiensis, K. lindneri and K. taiwanica to the genus Hanseniaspora as Hanseniaspora hatyaiensis comb. nov. (MB 828569), Hanseniaspora lindneri comb. nov. (MB 828566) and Hanseniaspora taiwanica comb. nov. (MB 828567).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

High-Density Single Nucleotide Polymorphism Linkage Maps of Lowland Switchgrass using Genotyping-by-Sequencing

Switchgrass (Panicum virgatum L.) is a warm-season perennial grass with promising potential as a bioenergy crop in the United States. However, the lack of genomic resources has slowed the development of plant lines with optimal characteristics for sustainable feedstock production. We generated high-density single nucleotide polymorphism (SNP) linkage maps using a reduced-representation sequencing approach by genotyping 231 F 1 progeny of a cross between two parents of lowland ecotype from the cultivars Kanlow and Alamo. Over 350 million reads were generated and aligned, which enabled identification and ordering of 4611 high-quality SNPs. The total lengths of the resulting framework maps were 1770 cM for the Kanlow parent and 2059 cM for the Alamo parent. These maps show collinearity with maps generated with polymerase chain reaction (PCR)-based simple-sequence repeat (SSR) markers, and new SNP markers were identified in previously unpopulated regions of the genome. Transmission segregation distortion affected all linkage groups (LGs) to differing degrees, and ordering of distorted markers highlighted several regions of unequal inheritance. Framework maps were adversely affected by the addition of distorted markers with varying severity, but distorted maps were of higher marker density and provided additional information for analysis. Alignment of these linkage maps with a draft version of the switchgrass genome assembly demonstrated high levels of collinearity and provides greater confidence in the validity of both resources. This methodology has proven to be a rapid and cost-effective way to generate high-quality linkage maps of an outcrossing species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

CAHS: Context-Aware Homology Search

Protein homology search is foundational to bioinformatics: it supports annotation transfer, structure/function inference, and evolutionary analysis over rapidly expanding sequence repositories (e.g., UniProtKB). Profile hidden Markov models (pHMMs), as implemented in HMMER, remain the most widely trusted approach because they provide statistically calibrated E-values; however, their gap behavior is fixed once a profile is trained, despite biological evidence that insertion/deletion tolerance varies across flexible loops and intrinsically disordered regions. We present CAHS (Context-Aware Homology Search), a lightweight query-time adapter for pHMM search that incorporates learned and biologically motivated signals without changing HMMER's downstream search pipeline or its calibrated E-value reporting. Given a query sequence, CAHS computes per-residue representations from a protein language model and a disorder predictor, maps these to profile coordinates, and modulates only match-state transition rows (gap-open and gap-extension probabilities) while preserving Plan7 constraints. We comprehensively evaluate CAHS across six structurally diverse protein families and multi-domain architectures against a 570k-sequence target corpus. CAHS expands detection capability, retrieving thousands of additional remote homologs at relaxed thresholds by maintaining alignment quality through flexible regions. For multi-domain proteins, context-aware modulation resolves 94% of fragmented alignments. Crucially, CAHS preserves hit-set invariance at stringent operating points (E<10-10), demonstrating increased statistical confidence without inflating false positives. Furthermore, sharper statistical distinction between homologs and background noise during early filter stages yields up to a 3.87× acceleration in end-to-end wall-clock time on high-performance computing clusters. Overall, CAHS illustrates a practical AI-for-science design pattern: augmenting a trusted probabilistic model with query-specific learned signals to improve interpretable, reproducible inference in data-rich biology.

Bhattaram, Swethasree [Georgia Institute of Techno↗
NASA NTRS2013

Development of the Orion Crew-Service Module Umbilical Retention and Release Mechanism

The Orion CSM umbilical retention and release mechanism supports and protects all of the cross-module commodities between the spacecrafts crew and service modules. These commodities include explosive transfer lines, wiring for power and data, and flexible hoses for ground purge and life support systems. The mechanism employs a single separation interface which is retained with pyrotechnically actuated separation bolts and supports roughly two dozen electrical and fluid connectors. When module separation is commanded, either for nominal on-orbit CONOPS or in the event of an abort, the mechanism must release the separation interface and sever all commodity connections within milliseconds of command receipt. There are a number of unique and novel aspects of the design solution developed by the Orion mechanisms team. The design is highly modular and can easily be adapted to other vehiclesmodules and alternate commodity sets. It will be flight tested during Orions Exploration Flight Test 1 (EFT-1) in 2014, and the Orion team anticipates reuse of the design for all future missions. The design packages fluid, electrical, and ordnance disconnects in a single separation interface. It supports abort separations even in cases where aerodynamic loading prevents the deployment of the umbilical arm. Unlike the Apollo CSM umbilical which was a destructive separation device, the Orion design is resettable and flight units can be tested for separation performance prior to flight.Initial development testing of the mechanisms separation interface resulted in binding failures due to connector misalignments. The separation interface was redesigned with a robust linear guide system, and the connector separation and boom deployment were separated into two discretely sequenced events. These changes addressed the root cause of the binding failure by providing better control of connector alignment. The new design was tuned and validated analytically via Monte Carlo simulation. The analytical validation was followed by a repeat of the initial test suite plus test cases at thermal extremes and test cases with imposed mechanical failures demonstrating fault tolerance. The mechanism was then exposed to the qualification vibration environment. Finally, separation testing was performed at full speed with live ordnance.All tests of the redesigned mechanism resulted in successful separation of the umbilical interface with adequate force margins and timing. The test data showed good agreement with the predictions of the Monte Carlo simulation. The simulation proved invaluable due to the number of variables affecting the separation and the uncertainty associated with each. The simulation allowed for rapid assessment of numerous trades and contingency scenarios, and can be easily reconfigured for varying commodity sets and connector layouts.

Separation↗
DOE OSTI2013

Astrophysical tests of modified gravity: the morphology and kinematics of dwarf galaxies

This paper is the third in a series on tests of gravity using observations of stars and nearby dwarf galaxies. We carry out four distinct tests using published data on the kinematics and morphology of dwarf galaxies, motivated by the theoretical work of Hui et al. (2009) and Jain and Vanderplas (2011). In a wide class of gravity theories a scalar field couples to matter and provides an attractive fifth force. Due to their different self-gravity, stars and gas may respond differently to the scalar force leading to several observable deviations from standard gravity. HI gas, red giant stars and main sequence stars can be displaced relative to each other, and the stellar disk can display warps or asymmetric rotation curves aligned with external potential gradients. To distinguish the effects of modified gravity from standard astrophysical phenomena, we use a control sample of galaxies that are expected to be screened from the fifth force. In all cases we find no significant deviation from the null hypothesis of general relativity. The limits obtained from dwarf galaxies are not yet competitive with the limits from cepheids obtained in our first paper, but can be improved to probe regions of parameter space that are inaccessible using other tests. We discuss how our methodology can be applied to new radio and optical observations of nearby galaxies.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2018

Phase diagram of the SU(2) Kondo lattice

We examine the SU(2) Kondo Lattice Model, for simple cubic lattices with various magnitudes of the localized spins j and numbers of conduction electrons, nc. For j=1/2, the system undergoes transitions from the paramagnetic to magnetically ordered states. The sequence of low-temperature magnetic states found on increasing n c is symmetric about half-filling and exhibits a preference for commensurate phases over incommensurate phases. On increasing nc from small values, the sequence of magnetic orderings consists of: ferromagnetic phases, planes of ferromagnetically spins which are sequentially twisted by nc-dependent angles, ferromagnetic planes of spins that are aligned antiferromagnetically, antiferromagnetic planes of spins in which the Neel order parameters are twisted through incommensurate angles. Neel order is most stable around half-filling. Magnetic ordered phases are found to be more stable than the Kondo phase for j=1/2, but larger j values may stabilize the Kondo phase. For j=3/2 the sequence of magnetic ordering with increasing nc is the same but, depending on the value of the strength of the Kondo interaction, the Kondo phase may be stabilized in a window 4 ≥ n c ≥ 2. In accordance with Nozieres’s arguments, we find that magnetic ordering is dominant for almost filled and almost empty bands.

36 MATERIALS SCIENCE↗
DOE OSTI2014

k-merSNP discovery: Software for alignment-and reference-free scalable SNP discovery, phylogenetics, and annotation for hundreds of microbial genomes

With the flood of whole genome finished and draft microbial sequences, we need faster, more scalable bioinformatics tools for sequence comparison. An algorithm is described to find single nucleotide polymorphisms (SNPs) in whole genome data. It scales to hundreds of bacterial or viral genomes, and can be used for finished and/or draft genomes available as unassembled contigs or raw, unassembled reads. The method is fast to compute, finding SNPs and building a SNP phylogeny in minutes to hours, depending on the size and diversity of the input sequences. The SNP-based trees that result are consistent with known taxonomy and trees determined in other studies. The approach we describe can handle many gigabases of sequence in a single run. The algorithm is based on k-mer analysis.

Source record↗
DOE OSTI2021

Predicting Antimicrobial Resistance Using Partial Genome Alignments

Antimicrobial resistance (AMR) is an important global health threat that impacts millions of people worldwide each year. Developing methods that can detect and predict AMR phenotypes can help to mitigate the spread of AMR by informing clinical decision making and appropriate mitigation strategies. Many bioinformatic methods have been developed for predicting AMR phenotypes from whole-genome sequences and AMR genes, but recent studies have indicated that predictions can be made from incomplete genome sequence data. In order to more systematically understand this, we built random forest-based machine learning classifiers for predicting susceptible and resistant phenotypes for Klebsiella pneumoniae (1,640 strains), Mycobacterium tuberculosis (2,497 strains), and Salmonella enterica (1,981 strains). We started by building models from alignments that were based on a reference chromosome for each species. We then subsampled each chromosomal alignment and built models for the resulting subalignments, finding that very small regions, representing approximately 0.1 to 0.2% of the chromosome, are predictive. In K. pneumoniae, M. tuberculosis, and S. enterica, the subalignments are able to predict multiple AMR phenotypes with at least 70% accuracy, even though most do not encode an AMR-related function. We used these models to identify regions of the chromosome with high and low predictive signals. Finally, subalignments that retain high accuracy across larger phylogenetic distances were examined in greater detail, revealing genes and intergenic regions with potential links to AMR, virulence, transport, and survival under stress conditions. IMPORTANCE Antimicrobial resistance causes thousands of deaths annually worldwide. Understanding the regions of the genome that are involved in antimicrobial resistance is important for developing mitigation strategies and preventing transmission. Machine learning models are capable of predicting antimicrobial resistance phenotypes from bacterial genome sequence data by identifying resistance genes, mutations, and other correlated features. They are also capable of implicating regions of the genome that have not been previously characterized as being involved in resistance. In this study, we generated global chromosomal alignments for Klebsiella pneumoniae, Mycobacterium tuberculosis, and Salmonella enterica and systematically searched them for small conserved regions of the genome that enable the prediction of antimicrobial resistance phenotypes. In addition to known antimicrobial resistance genes, this analysis identified genes involved in virulence and transport functions, as well as many genes with no previous implication in antimicrobial resistance.

59 BASIC BIOLOGICAL SCIENCES↗