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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 OSTI2017

Understanding the Performance of Automotive Catalysts via Spatial Resolution of Reactions inside Honeycomb Monoliths

By directly resolving spatial and temporal species distributions within operating honeycomb monolith catalysts, spatially resolved capillary inlet mass spectrometry (SpaciMS) provides a uniquely enabling perspective for advancing automotive catalysis. Specifically, the ability to follow the spatiotemporal evolution of reactions throughout the catalyst is a significant advantage over inlet-and-effluent-limited analysis. Intracatalyst resolution elucidates numerous catalyst details including the network and sequence of reactions, clarifying reaction pathways; the relative rates of different reactions and impacts of operating conditions and catalyst state; and reaction dynamics and intermediate species that exist only within the catalyst. These details provide a better understanding of how the catalyst functions and have basic and practical benefits; e.g., catalyst system design; strategies for on-road catalyst state assessment, control, and on-board diagnostics; and creating robust and accurate predictive catalyst models. Moreover, such spatiotemporally distributed data provide for critical model assessment, and identification of improvement opportunities that might not be apparent from effluent assessment; i.e., while an incorrectly formulated model may provide correct effluent predictions, one that can accurately predict the spatiotemporal evolution of reactions along the catalyst channels will be more robust, accurate, and reliable. In such ways, intracatalyst diagnostics comprehensively enable improved design and development tools, and faster and lower-cost development of more efficient and durable automotive catalyst systems. Beyond these direct contributions, SpaciMS has spawned and been applied to enable other analytical techniques for resolving transient distributed intracatalyst performance. This chapter focuses on SpaciMS applications and associated catalyst insights and improvements, with specific sections related to lean NOx traps, selective catalytic reduction catalysts, oxidation catalysts, and particulate filters. The objective is to promote broader use and development of intracatalyst analytical methods, and thereby expand the insights resulting from this detailed perspective for advancing automotive catalyst technologies.

Partridge Jr, William↗
DOE OSTI2016

Characteristics of persistent spin current components in a quasi-periodic Fibonacci ring with spin–orbit interactions: Prediction of spin–orbit coupling and on-site energy

In the present work we investigate the behavior of all three components of persistent spin current in a quasi-periodic Fibonacci ring subjected to Rashba and Dresselhaus spin–orbit interactions. Analogous to persistent charge current in a conducting ring where electrons gain a Berry phase in presence of magnetic flux, spin Berry phase is associated during the motion of electrons in presence of a spin–orbit field which is responsible for the generation of spin current. The interplay between two spin–orbit fields along with quasi-periodic Fibonacci sequence on persistent spin current is described elaborately, and from our analysis, we can estimate the strength of any one of two spin–orbit couplings together with on-site energy, provided the other is known. - Highlights: • Determination of Rashba and Dresselhaus spin–orbit fields is discussed. • Characteristics of all three components of spin current are explored. • Possibility of estimating on-site energy is given. • Results can be generalized to any lattice models.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

A PerR-like protein involved in response to oxidative stress in the extreme bacterium Deinococcus radiodurans

Highlights: • We report a novel PerR-like protein of Fur family in D. radiodurans that is not annotated in the current database. • drperR responses to H{sub 2}O{sub 2} and functions as a negative regulator of katE and dps. • We provided implications on how to utilize sequenced genome data and the importance of genome data mining. • This study adds knowledge to complicated regulatory network that responds to ROS stress in D. radiodurans. - Abstract: Response and defense systems against reactive oxygen species (ROS) contribute to the remarkable resistance of Deinococcus radiodurans to oxidative stress induced by oxidants or radiation. However, mechanisms involved in ROS response and defense systems of D. radiodurans are not well understood. Fur family proteins are important in ROS response. Only a single Fur homolog is predicted by sequence similarity in the current D. radiodurans genome database. Our bioinformatics analysis demonstrated an additional guanine nucleotide in the genome of D. radiodurans that is not in the database, leading to the discovery of another Fur homolog DrPerR. Gene disruption mutant of DrPerR showed enhanced resistance to hydrogen peroxide (H{sub 2}O{sub 2}) and increased catalase activity in cell extracts. Real-time PCR results indicated that DrPerR functions as a repressor of the catalase gene katE. Meanwhile, derepression of dps (DNA-binding proteins from starved cells) gene under H{sub 2}O{sub 2} stress by DrPerR point to its regulatory role in metal ions hemostasis. Thus, DrPerR might function as a Fur homolog protein which is involved in ROS response and defense. These results help clarify the complicated regulatory network that responds to ROS stress in D. radiodurans.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Nuclear Data Sheets for A=266,270,274,278,282,286,290,294,298☆

Spectroscopic information such as production, identification, half-lives, decay modes and possible excited states for experimentally known nuclides of mass numbers 266, 270, 274, 278, 282, 286, 290, 294, and 298 are presented together with the recommended values, superseding information and data in the previous ENSDF and NDS evaluation by 2005Gu33. No nuclides have yet been identified for A=302. In the last 14 years, large amounts of new and definitive data on the superheavy nuclides (SHN) have become available, thus changing almost entirely the landscape of nuclear data in this mass region, as also indicated by a number of recent review articles: 2017Og01, 2016Ho09, 2016Ho06 (for fission barriers), 2015Og05, 2015Og07, 2015Mo25, 2015OgZX, 2013Th02, and 2011Og07. See 2016Ka49 for IUPAC technical discussions for the discovery of Z=117 (Ts), Z=115 (Mc), Z=113 (Nh), 2001Ka70 and 2003Ka71 for Z=110-112, 2011Ba54 for Z≥113, 2009Ba62 for Z=112, and 2016Ka50 for Z=118 (Og). A special issue of Nuclear Physics A444 (2015) is devoted to research on superheavy elements (SHE) with 27 articles. In particular, see article by 2015Ko20 on mass spectrometric searches for superheavy elements in terrestrial matter. See also Proceedings of Nobel Symposium NS160 ‘Chemistry and Physics of Heavy and Superheavy Elements’ published in Eur. Phys. Jour. Web of Conferences 131 (2016), in particular 2016UtZZ, 2016DmZZ and 2016HoZY. See also 2016DuZX for future prospects of discovery of elements beyond Z=118 A=266: {sup 266}Db, {sup 266}Sg, {sup 266}Bh, {sup 266}Hs and {sup 266}Mt are the experimentally identified nuclides with A=266. Identification of {sup 266}Lr from α decay of {sup 270}Db has been proposed by 2014Kh04 from experiments at GSI, but complete details and analyses of all the four decay chains reported in this experiment have not yet been published, and discussion in 2015Og05 review article considering their work from Dubna (2013Og04, 2011Og04) and from GSI (2014Kh04) still concluded that {sup 270}Db decayed dominantly by SF mode, in contrast with dominant α decay mode proposed by 2014Kh04. Experiments carried out at FLNR-JINR-Dubna in collaboration with LLNL and ORNL, GSI-SHIP facility, RIKEN, and LBNL facilities: {sup 266}Db from the α-decay of {sup 282}Nh in two correlated decay chains at Dubna; {sup 266}Sg as α-daughter of {sup 270}Hs in 12 correlated decay chains at Dubna and GSI; {sup 266}Bh in α decay of {sup 278}Nh in three correlated decay chains observed at RIKEN, and also directly with one event in {sup 249}Bk({sup 22}Ne,5n) at LBNL, and with four events in {sup 243}Am({sup 26}Mg,3n) at HIRFL-Lanzhou; {sup 266}Hs as α-daughter of {sup 270}Ds at GSI in two different experiments, six correlated decays in the first, and 25 decay chains in the second experiment, the analysis of which has not been fully reported as yet; and {sup 266}Mt directly in {sup 209}Bi({sup 58}Fe,n) reaction at GSI in two different experiments, observing three events in the first experiment and 12 events in the second, also produced in {sup 208}Pb({sup 59}Co,n) reaction at LBNL, observing five correlated decay chains. See also 2000Ho27 for discussion on {sup 266}Sg and {sup 266}Mt. A=270: {sup 270}Db, {sup 270}Bh, {sup 270}Hs, {sup 270}Mt and {sup 270}Ds are the experimentally identified nuclides with A=270 are presented. Experiments carried out at FLNR-JINR-Dubna in collaboration with LLNL and ORNL, GSI-SHIP facility, and RIKEN: {sup 270}Db from the decay of {sup 294}Ts in six correlated decay chains at Dubna and GSI; {sup 270}Bh as α great-granddaughter of {sup 282}Nh in two correlated decay chains observed at Dubna; {sup 270}Hs directly in {sup 248}Cm({sup 26}Mg,4n) reaction at GSI, and in {sup 226}Ra({sup 48}Ca,4n) reaction at Dubna; {sup 270}Mt as granddaughter of {sup 278}Ts in three correlated decay chains at RIKEN; and {sup 270}Ds directly in {sup 207}Pb({sup 64}Ni,n) at GSI in 33 correlated decay chains. A=274: {sup 274}Bh, {sup 274}Mt and {sup 274}Rg are the experimentally identified nuclides with A=274. Search for {sup 274}Ds in {sup 238}U({sup 40}Ar, 4n),E=5.7 MeV/nucleon reaction and subsequent α decays at GSI (1990Sc11) proved negative. Experiments carried out at FLNR-JINR-Dubna in collaboration with LLNL and ORNL, GSI-SHIP facility, and RIKEN: {sup 274}Bh from the decay of {sup 294}Ts in six correlated decay chains at Dubna and GSI, {sup 274}Mt produced as α daughter of {sup 282}Nh in two correlated decay chains observed at Dubna, and {sup 274}Rg as α daughter of {sup 278}Nh produced in three correlated decay chains at RIKEN. A=278: {sup 278}Mt, {sup 278}Rg and {sup 278}Nh are the experimentally identified nuclides with A=278. A very tentative evidence is provided for {sup 278}Bh and {sup 278}Hs from a chain originally observed and assigned to {sup 289}Fl by 1999Og10, but later reassigned by 2004Og10 to {sup 290}Fl, and further discussed in detail by 2016Ho09, where, based on systematics of α decays and SF half-lives, {sup 290}Fl is proposed to decay via ε mode to {sup 290}Nh, which then decays by an α chain, ending in {sup 278}Bh that decays by SF mode. Experiments carried out at FLNR-JINR-Dubna in collaboration with LLNL and ORNL labs in the USA, GSI-SHIP facility, and RIKEN: {sup 278}Mt from the decay of {sup 294}Ts in six correlated decay chains at Dubna and GSI, {sup 278}Rg produced as α daughter of {sup 282}Nh in two correlated decay chains observed at Dubna, and {sup 278}Nh produced directly in three correlated decay chains at RIKEN. A=282: {sup 282}Rg, {sup 282}Cn and {sup 282}Nh are the experimentally identified nuclides with A=282. A very tentative evidence is provided for {sup 282}Mt and {sup 282}Ds from a chain originally observed and assigned to {sup 289}Fl by 1999Og10, but later reassigned by 2004Og10 to {sup 290}Fl, and further discussed in detail by 2016Ho09, where, based on systematics of α decays and SF half-lives, {sup 290}Fl is proposed to decay via ε mode to {sup 290}Nh, which then decays by an α chain, ending in {sup 278}Bh that decays by SF mode. Experiments carried out at FLNR-Dubna, in collaboration with LLNL and ORNL labs in the USA, and at GSI-SHIP facility confirm the identification of these isotopes, {sup 282}Rg in α decay chain of {sup 294}Ts in six correlated decay chains at Dubna and GSI, {sup 282}Cn produced in four ways at Dubna: independently in one correlated decay chain, as α daughter of {sup 286}Lv in 11 correlated decay chains, as α grand-daughter of {sup 290}Lv in 12 correlated decay chains, as α great-grand daughter of {sup 294}Og in four correlated decay chains, and {sup 282}Nh produced at Dubna directly in two correlated decay chains. A=286: {sup 286}Nh and {sup 286}Fl are the only experimentally identified nuclides with A=286. A very tentative evidence is provided for {sup 286}Rg and {sup 286}Cn from a chain originally observed and assigned to {sup 289}Fl by 1999Og10, but later reassigned by 2004Og10 to {sup 290}Fl, and further discussed in detail by 2016Ho09, where, based on systematics of α decays and SF half-lives, {sup 290}Fl is proposed to decay via ε mode to {sup 290}Nh, which then decays by an α chain, ending in {sup 278}Bh that decays by SF mode. 2017Ka66 in experiments at RIKEN using GARIS separator interpret one correlated decay chain in three different ways, one involving possible production of {sup 294}Lv in {sup 248}Cm({sup 48}Ca,2n),E=261.6 MeV, and α decay to {sup 290}Fl which further decays to {sup 286}Cn. Experiments carried out at FLNR-Dubna, in collaboration with LLNL and ORNL labs in the USA, and at GSI-SHIP facility confirm the identification of these isotopes, {sup 286}Nh as α grand-daughter of {sup 294}Ts in six correlated decay chains, and {sup 286}Fl produced in three ways: independently in 11 correlated decay chains, as α daughter of {sup 290}Lv in 12 correlated decay chains, and as α grand-daughter of {sup 294}Og in four correlated decay chains. A=290: {sup 290}Mc and {sup 290}Lv are the only experimentally identified nuclides with A=290. A tentative evidence is provided for {sup 290}Nh and {sup 290}Fl from a chain originally observed and assigned to {sup 289}Fl by 1999Og10, but later reassigned by 2004Og10 to {sup 290}Fl, and further discussed in detail by 2016Ho09, where, based on systematics of α decays and SF half-lives, {sup 290}Fl is proposed to decay via ε mode to {sup 290}Nh, which then decays by an α chain, ending in {sup 278}Bh that decays by SF mode. 2017Ka66 in experiments at RIKEN using GARIS separator interpret one correlated decay chain in three different ways, one involving possible production of {sup 294}Lv in {sup 248}Cm({sup 48}Ca,2n),E=261.6 MeV, and α decay to {sup 290}Fl. Experiments carried out at FLNR-Dubna, in collaboration with LLNL and ORNL labs in the USA, and at GSI-SHIP facility confirm the identification of these isotopes, {sup 290}Mc as α daughter of {sup 294}Ts in six correlated decay chains, and {sup 290}Lv produced in two ways, independently in 14 correlated decay chains, and as α daughter of {sup 294}Og in four correlated decay chains. A=294: {sup 294}Ts and {sup 294}Og are the only experimentally identified nuclides with A=294. Experiments carried out at FLNR-Dubna, in collaboration with LLNL and ORNL labs in the USA, and at GSI-SHIP facility confirm the identification of these isotopes, with a total of six EVR-α-SF correlated decay chains observed for {sup 294}Ts and four for {sup 294}Og. Tentative identification of {sup 294}Lv is provided by 2017Ka66 from the observation one correlated event using GARIS-RIKEN facility, where this event is interpreted in three possible ways, two interpretations lead to production of {sup 293}Lv and successive odd-A nuclides of {sup 289}Fl, {sup 285}Cn and {sup 281}Ds, whereas the third prediction starts with the production of {sup 294}Lv and successive {sup 290}Fl and {sup 286}Cn nuclides. Search for {sup 294}Rg in natural gold materials (2011De03), and for {sup 294}Ds, {sup 294}Fl and {sup 294}Mc in natural Pt, Pb and Bi samples (2011De21) using accelerator mass spectroscopy (AMS) proved negative, with extremely low upper limits established. Also 1980St05 did not see any evidence for {sup 294}Ds in natural Pt sample using AMS. A=298: Search for {sup 298}120 through fusion-evaporation reaction at Dubna, and for {sup 298}Fl and {sup 298}Mc in natural Pt, Pb and Bi samples using accelerator mass spectroscopy (AMS) proved negative. Tentative assignment of three α-α-α decay chains by 2016Ho09 to {sup 299}120 in {sup 248}Cm({sup 54}Cr,3n){sup 299}120 at GSI was refuted by 2017He11, assigning these correlations to random events, instead. A=302: Fluorescent x rays from Z=120 element were observed by 2012Fr03 from compound nucleus {sup 302}120 produced in {sup 238}U({sup 64}Ni,X),E=6.6 MeV/nucleon at GANIL, and x-ray yields were measured, together with minimum average time deduced from x-ray multiplicity. The compound nucleus could decay by 3n- or 4n-channels to produce {sup 299}120 or {sup 298}120. 2012He05 and 2016Ho09 also produced {sup 302}120 compound nucleus in {sup 248}Cm({sup 54}Cr, xn){sup 302}120{sup *},E=6.035 MeV/nucleon; and {sup 238}U({sup 64}Ni,xn){sup 302}120{sup *},E=5.53 MeV/nucleon reactions using UNILAC at GSI. Three α-α-α correlated decays from {sup 248}Cm({sup 54}Cr,xn){sup 302}120{sup *} reaction were tentatively assigned by 2016Ho09 to {sup 299}120 decay, however, a detailed analysis by 2017He11 refuted this claim, ascribing these events to random sequences. There are no data tables for A=302.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

RNA language models predict mutations that improve RNA function

Structured RNA lies at the heart of many central biological processes, from gene expression to catalysis. RNA structure prediction is not yet possible due to a lack of high-quality reference data associated with organismal phenotypes that could inform RNA function. We present GARNET (Gtdb Acquired RNa with Environmental Temperatures), a new database for RNA structural and functional analysis anchored to the Genome Taxonomy Database (GTDB). GARNET links RNA sequences to experimental and predicted optimal growth temperatures of GTDB reference organisms. Using GARNET, we develop sequence- and structure-aware RNA generative models, with overlapping triplet tokenization providing optimal encoding for a GPT-like model. Leveraging hyperthermophilic RNAs in GARNET and these RNA generative models, we identify mutations in ribosomal RNA that confer increased thermostability to the Escherichia coli ribosome. The GTDB-derived data and deep learning models presented here provide a foundation for understanding the connections between RNA sequence, structure, and function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Integral constraints in the study of Richtmyer-Meshkov turbulent mixing

An experimental study of the temporal evolution of the shock-induced Richtmyer-Meshkov instability in the turbulent regime with three-dimensional random interfacial perturbations is carried out. The primary interest is the growth rate of the turbulent mixing layer that develops after an impulsive acceleration of the perturbed interface between two gases (air/SF6) by a weak Ma = 1.2 incident shock wave. Planar Mie scattering is used to visualize the flow, and image sequences are captured using a high-speed video camera. The analysis of the total mixing width has been extended to study the growth behaviors of the bubbles and spikes, separately. A novel definition of the bubble and spike widths is introduced using the mass and linear momentum conservation laws. For the planar incident shock wave the newly defined bubble and spike widths increase in time as hb.s ∝ tθ, with a growth exponent θ = 1/2 that does not depend on either the initial conditions or the physical properties of the gases composing the interface.

Likhachev, Oleg A.↗
DOE OSTI2025

Dynamics of implosion, bounce, and re-implosion of a shell directly driven by a time-shaped laser pulse

Gas-filled plastic spherical shells have been imploded using the 60-beam OMEGA laser. The same laser pulse was used as in a previous experiment, which demonstrated the dynamic formation of a shell by irradiating a homogeneous plastic foam sphere. In the present experiment, the shell initially implodes, bounces, and expands; a new shell then forms and undergoes a second implosion. Analysis of x-ray self-emission-streaked images and sequences of 2D x-ray self-emission framing camera images show shell evolution that is in reasonable agreement with 1D simulations. Shell integrity and symmetry are well maintained until the formation of the new shell. The final implosion, instead, is affected by substantial asymmetries.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2016

Recent Studies on the Asymptotic Convergence of the Spatial Discretization for Two-Dimensional Discrete Ordinates Solutions

In this paper, four types of quadrature schemes are used to define discrete directions in the solution of a two-dimensional fixed-source discrete ordinates problem in Cartesian geometry. Such schemes enable generating numerical results for averaged scalar fluxes over specified regions of the domain with high number (up to 105) of directions per octant. Two different nodal approaches, the ADO and AHOT-N0 methods, are utilized to obtain the numerical results of interest. The AHOT-N0 solutions on a sequence of refined meshes are then used to develop an asymptotic analysis of the spatial discretization error in order to derive a reference solution. It was more clearly observed that the spatial discretization error converges asymptotically with second order for the source region with all four quadratures employed, while for the other regions refined meshes along with tighter convergence criterion must be applied to evidence the same behavior. Although, in that case, some differences among the four quadrature schemes results were found.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Model-based data center cooling controls comparative co-design

This article presents a comparative simulation-based control logic design process. It uses the Control Description Language (CDL) and the ASHRAE Guideline 36 high-performing building control sequences with the Modelica Buildings Library (MBL) to demonstrate a comparative analysis of two control designs for a data center chilled water plant. Details include a description of the closed-loop plant and control design methodology, including sizing and parameterization, base and alternative (Guideline 36) control logic with software implementation structure, and outline of the simulation experimentation process. The selected control designs are paired with comparable chilled water plant configurations. The models include a chiller, a water-side economizer, and an evaporative cooling tower. The plant provides cooling at 27ºC zone supply air temperature to a data center in Sacramento, CA. The comparative simulation results examined the impacts of a selected control logic detail, and present an example model-based design application. Overall, the simulation results showed a 25% annual and a 18% summer energy use reduction for alternative controls. This shows that simulation-based control logic design performance evaluation can improve energy efficiency and resilience aspects of system controls at large.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2015

Ebolavirus comparative genomics

The 2014 Ebola outbreak in West Africa is the largest documented for this virus. We examine the dynamics of this genome, comparing more than one hundred currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms a distinct group from all other sequenced viral genomes. All filovirus genomes sequenced to date encode proteins with similar functions and gene order, although there is considerable divergence in sequences between the three genera Ebolavirus, Cuevavirus, and Marburgvirus within the family Filoviridae. Whereas all ebolavirus genomes are quite similar (multiple sequences of the same strain are often identical), variation is most common in the intergenic regions and within specific areas of the genes encoding the glycoprotein (GP), nucleoprotein (NP), and polymerase (L). We predict regions that could contain epitope-binding sites, which might be good vaccine targets. In conclusion, this information, combined with glycosylation sites and experimentally determined epitopes, can identify the most promising regions for the development of therapeutic strategies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Annotated genome sequence of a fast-growing diploid clone of red alder ( Alnus rubra Bong.)

Abstract Red alder (Alnus rubra Bong.) is an ecologically significant and important fast-growing commercial tree species native to western coastal and riparian regions of North America, having highly desirable wood, pigment, and medicinal properties. We have sequenced the genome of a rapidly growing clone. The assembly is nearly complete, containing the full complement of expected genes. This supports our objectives of identifying and studying genes and pathways involved in nitrogen-fixing symbiosis and those related to secondary metabolites that underlie red alder's many interesting defense, pigmentation, and wood quality traits. We established that this clone is most likely diploid and identified a set of SNPs that will have utility in future breeding and selection endeavors, as well as in ongoing population studies. We have added a well-characterized genome to others from the order Fagales. In particular, it improves significantly upon the only other published alder genome sequence, that of Alnus glutinosa. Our work initiated a detailed comparative analysis of members of the order Fagales and established some similarities with previous reports in this clade, suggesting a biased retention of certain gene functions in the vestiges of an ancient genome duplication when compared with more recent tandem duplications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Bacterial Origin and Reductive Evolution of the CPR Group

The candidate phyla radiation (CPR) is a proposed subdivision within the bacterial domain comprising several candidate phyla. CPR organisms are united by small genome and physical sizes, lack several metabolic enzymes, and populate deep branches within the bacterial subtree of life. Here, these features raise intriguing questions regarding their origin and mode of evolution. In this study, we performed a comparative and phylogenomic analysis to investigate CPR origin and evolution. Unlike previous gene/protein sequence-based reports of CPR evolution, we used protein domain superfamilies classified by protein structure databases to resolve the evolutionary relationships of CPR with non-CPR bacteria, Archaea, Eukarya, and viruses. Across all supergroups, CPR shared maximum superfamilies with non-CPR bacteria and were placed as deep branching bacteria in most phylogenomic trees. CPR contributed 1.22% of new superfamilies to bacteria including the ribosomal protein L19e and encoded four core superfamilies that are likely involved in cell-to-cell interaction and establishing episymbiotic lifestyles. Although CPR and non-CPR bacterial proteomes gained common superfamilies over the course of evolution, CPR and Archaea had more common losses. These losses mostly involved metabolic superfamilies. In fact, phylogenies built from only metabolic protein superfamilies separated CPR and non-CPR bacteria. These findings indicate that CPR are bacterial organisms that have probably evolved in an Archaea-like manner via the early loss of metabolic functions. We also discovered that phylogenies built from metabolic and informational superfamilies gave contrasting views of the groupings among Archaea, Bacteria, and Eukarya, which add to the current debate on the evolutionary relationships among superkingdoms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

SWAP-Assembler 2: Optimization of De Novo Genome Assembler at Large Scale

In this paper, we analyze and optimize the most time-consuming steps of the SWAP-Assembler, a parallel genome assembler, so that it can scale to a large number of cores for huge genomes with the size of sequencing data ranging from terabyes to petabytes. According to the performance analysis results, the most time-consuming steps are input parallelization, k-mer graph construction, and graph simplification (edge merging). For the input parallelization, the input data is divided into virtual fragments with nearly equal size, and the start position and end position of each fragment are automatically separated at the beginning of the reads. In k-mer graph construction, in order to improve the communication efficiency, the message size is kept constant between any two processes by proportionally increasing the number of nucleotides to the number of processes in the input parallelization step for each round. The memory usage is also decreased because only a small part of the input data is processed in each round. With graph simplification, the communication protocol reduces the number of communication loops from four to two loops and decreases the idle communication time. The optimized assembler is denoted as SWAP-Assembler 2 (SWAP2). In our experiments using a 1000 Genomes project dataset of 4 terabytes (the largest dataset ever used for assembling) on the supercomputer Mira, the results show that SWAP2 scales to 131,072 cores with an efficiency of 40%. We also compared our work with both the HipMER assembler and the SWAP-Assembler. On the Yanhuang dataset of 300 gigabytes, SWAP2 shows a 3X speedup and 4X better scalability compared with the HipMer assembler and is 45 times faster than the SWAP-Assembler. The SWAP2 software is available at https://sourceforge.net/projects/swapassembler.

Meng, Jintao↗
DOE OSTI2018

Toward cities without slums: Topology and the spatial evolution of neighborhoods

The world is urbanizing quickly with nearly 4 billion people presently living in urban areas, about 1 billion of them in slums. Achieving sustainable development from rapid urbanization relies critically on creating cities without slums. We show that it is possible to diagnose systematically the central physical problem of slums—the lack of spatial accesses and related services—using a topological analysis of neighborhood maps and resolved by finding solutions to a sequence of constrained optimization problems. We set up the problem by showing that the built environment of any city can be decomposed into two types of networked spaces—accesses and places—and prove that these spaces display universal topological characteristics. We then show that while the neighborhoods of developed cities express the same common topology, urban slums fall into a different topological class. We demonstrate that it is always possible to find solutions that grow a street network in existing slums, providing universal accesses at minimal disruption and cost. We then show how elaborations of this procedure that include local preferences and reduce travel distances between places result from additional access construction. These methods are presently taking effect in neighborhoods in Cape Town (South Africa) and Mumbai (India), demonstrating their practical feasibility and emphasizing their role as a platform to enable communities and local governments to combine technical knowledge with local aspirations into contextually appropriate urban sustainable development solutions.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2024

Expanded genome and proteome reallocation in a novel, robust Bacillus coagulans strain capable of utilizing pentose and hexose sugars

Bacillus coagulans, a Gram-positive thermophilic bacterium, is recognized for its probiotic properties and recent development as a microbial cell factory. Despite its importance for biotechnological applications, the current understanding of B. coagulans’ robustness is limited, especially for undomesticated strains. To fill this knowledge gap, we characterized the metabolic capability and performed functional genomics and systems analysis of a novel, robust strain, B. coagulans B-768. Genome sequencing revealed that B-768 has the largest B. coagulans genome known to date (3.94 Mbp), about 0.63 Mbp larger than the average genome of sequenced B. coagulans strains, with expanded carbohydrate metabolism and mobilome. Functional genomics identified a well-equipped genetic portfolio for utilizing a wide range of C5 (xylose, arabinose), C6 (glucose, mannose, galactose), and C12 (cellobiose) sugars present in biomass hydrolysates, which was validated experimentally. For growth on individual xylose and glucose, the dominant sugars in biomass hydrolysates, B-768 exhibited distinct phenotypes and proteome profiles. Faster growth and glucose uptake rates resulted in lactate overflow metabolism, which makes B. coagulans a lactate overproducer; however, slower growth and xylose uptake diminished overflow metabolism due to the high energy demand for sugar assimilation. Carbohydrate Transport and Metabolism (COG-G), Translation (COG-J), and Energy Conversion and Production (COG-C) made up 60%–65% of the measured proteomes but were allocated differently when growing on xylose and glucose. The trade-off in proteome reallocation, with high investment in COG-C over COG-G, explains the xylose growth phenotype with significant upregulation of xylose metabolism, pyruvate metabolism, and tricarboxylic acid (TCA) cycle. Strain B-768 tolerates and effectively utilizes inhibitory biomass hydrolysates containing mixed sugars and exhibits hierarchical sugar utilization with glucose as the preferential substrate.

carbohydrate metabolism↗
DOE OSTI2023

Inferring microbial co-occurrence networks from amplicon data: a systematic evaluation

Microbes commonly organize into communities consisting of hundreds of species involved in complex interactions with each other. 16S ribosomal RNA (16S rRNA) amplicon profiling provides snapshots that reveal the phylogenies and abundance profiles of these microbial communities. These snapshots, when collected from multiple samples, can reveal the co-occurrence of microbes, providing a glimpse into the network of associations in these communities. However, the inference of networks from 16S data involves numerous steps, each requiring specific tools and parameter choices. Moreover, the extent to which these steps affect the final network is still unclear. In this study, we perform a meticulous analysis of each step of a pipeline that can convert 16S sequencing data into a network of microbial associations. Through this process, we map how different choices of algorithms and parameters affect the co-occurrence network and identify the steps that contribute substantially to the variance. We further determine the tools and parameters that generate robust co-occurrence networks and develop consensus network algorithms based on benchmarks with mock and synthetic data sets. The Microbial Co-occurrence Network Explorer, or MiCoNE (available at https://github.com/segrelab/MiCoNE) follows these default tools and parameters and can help explore the outcome of these combinations of choices on the inferred networks. We envisage that this pipeline could be used for integrating multiple data sets and generating comparative analyses and consensus networks that can guide our understanding of microbial community assembly in different biomes.

16S rRNA↗
DOE OSTI2017

Filamentous ascomycete genomes provide insights into Copia retrotransposon diversity in fungi

The relative scarcity of Copia retrotransposons has been recently characterized in metazoans in comparison with the other superfamilies of LTR elements. Furthermore, Copia retrotransposons have often a particular dynamics that results in a highly predominant single clade of elements within a large host taxon, such as the GalEa-like retrotransposons in crustaceans. Taking advantage of the skyrocketing amount of genomic data available for fungi, we carried out the first large-scale comparative genomic analysis of the Copia clades in filamentous ascomycetes. Screening 30 completely sequenced genomes allowed us to identify more than 2500 Copia copies with conserved LTR, which are distributed in 138 families. Their characterization revealed that fungal Copia diversity is much broader than previously thought with at least 27 clades, 23 of which likely correspond to new ones. While the Copia copy number is low in most species, the two clades GalEa and FunCo1 are widely distributed and highly dominate Copia content as they both account for 80% of the detected sequences. In Fungi, GalEa retrotransposons are restricted to Pezizomycotina in which they can make up an outstandingly high proportion of the genome (up to 10% in Cenococcum geophilum). At last, we revealed that fungal GalEa elements structurally differ from all other Copia elements with an absence of Primer Binding Site. These elements however harbor a Conserved Hairpin Site which is probably essential for their transposition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Homologous expression of the Caldicellulosiruptor bescii CelA reveals that the extracellular protein is glycosylated

Members of the bacterial genus Caldicellulosiruptor are the most thermophilic cellulolytic microbes described with ability to digest lignocellulosic biomass without conventional pretreatment. The cellulolytic ability of different species varies dramatically and correlates with the presence of the multimodular cellulase CelA, which contains both a glycoside hydrolase family 9 endoglucanase and a glycoside hydrolase family 48 exoglucanase known to be synergistic in their activity, connected by three cellulose-binding domains via linker peptides. This architecture exploits the cellulose surface ablation driven by its general cellulase processivity as well as excavates cavities into the surface of the substrate, revealing a novel paradigm for cellulase activity. We recently reported that a deletion of celA in C. bescii had a significant effect on its ability to utilize complex biomass. To analyze the structure and function of CelA and its role in biomass deconstruction, we constructed a new expression vector for C. bescii and were able, for the first time, to express significant quantities of full-length protein in vivo in the native host. The protein, which contains a Histidine tag, was active and excreted from the cell. Expression of CelA protein with and without its signal sequence allowed comparison of protein retained intracellularly to protein transported extracellularly. Analysis of protein in culture supernatants revealed that the extracellular CelA protein is glycosylated whereas the intracellular CelA is not, suggesting that either protein transport is required for this post-translational modification or that glycosylation is required for protein export. The mechanism and role of protein glycosylation in bacteria is poorly understood and the ability to express CelA in vivo in C. bescii will allow the study of the mechanism of protein glycosylation in this thermophile. Finally, it will also allow the study of glycosylation of CelA itself and its role in the structure and function of this important enzyme in biomass deconstruction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗