Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “time sequence analysis”

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

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

At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Real-time PCR assays that detect genes for botulinum neurotoxin A–G subtypes

The role of Real-Time PCR assays for surveillance and rapid screening for pathogens is garnering more and more attention because of its versatility and ease of adoption. The goal of this study was to design, test, and evaluate Real-Time TaqMan PCR assays for the detection of botulinum neurotoxin (bont/A-G) genes from currently recognized BoNT subtypes. Assays were computationally designed and then laboratory tested for sensitivity and specificity using DNA preparations containing bont genes from 82 target toxin subtypes, including nine bivalent toxin types; 31 strains representing other clostridial species; and an extensive panel that consisted of DNA from a diverse set of prokaryotic (bacterial) and eukaryotic (fungal, protozoan, plant, and animal) species. In addition to laboratory testing, the assays were computationally evaluated using in silico analysis for their ability to detect bont gene sequences from recently identified toxin subtypes. Seventeen specific assays (two for each of the bont/C, bont/D, bont/E, and bont/G subtypes and three for each of the bont/A, bont/B, and bont/F subtypes) were designed and evaluated for their ability to detect bont genes encoding multiple subtypes from all seven serotypes. These assays could provide an additional tool for the detection of botulinum neurotoxins in clinical, environmental and food samples that can complement other existing methods used in clinical diagnostics, regulatory, public health, and research laboratories.

59 BASIC BIOLOGICAL SCIENCES↗
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 OSTI2024

High throughput automated characterization of enamel microstructure using synchrotron tomography and optical flow imaging

The remarkable damage-tolerance of enamel has been attributed to its hierarchical microstructure and the organized bands of decussated rods. A thorough characterization of the microscale rod evolution within the enamel is needed to elucidate this complex structure. While prior efforts in this area have made use of single particle tracking to track a single rod evolution to various degrees of success, such a process can be both computationally and labor intensive, limited to the evolution path of a single rod, and is therefore prone to error from potentially tracking outliers. Particle image velocimetry (PIV) is a well-established algorithm to derive field information from image sequences for processes that are time-dependent, such as fluid flows and structural deformation. In this work, we demonstrate the use of PIV in extracting the full-field microstructural distribution of rods within the enamel. Further, enamel samples from a wild African lion were analyzed using high-energy synchrotron X-ray micro-tomography. Results from the PIV analysis provide sufficient full-field information to reconstruct the growth of individual rods that can potentially enable rapid analysis of complex microstructures from high resolution synchrotron datasets. Such information can serve as a template for designing damage-tolerant bioinspired structures for advanced manufacturing.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Modeling and Simulation of Xe-100-type Pebble Bed Gas-Cooled Reactor with SCALE

The US Department of Energy (DOE) announced the Advanced Reactor Demonstration Program (ARDP) to accelerate the deployment of advanced reactor concepts. Awardees of ARDP funds are expected to demonstrate the operation of an advanced reactor within 7 years of receiving the award. X-Energy’s advanced reactor concept, the Xe-100, was selected as one of two advanced reactor concepts to receive funding to demonstrate the operation of its high-temperature gas-cooled pebble-bed reactor before the end of this decade. As a result of this push to bring advanced reactors to maturation and commercialization, transition and deployment scenario studies are being performed under the Systems Analysis and Integration (SA&I) campaign within the DOE Office of Nuclear Energy (DOE-NE) to evaluate the transition of the current US commercial fleet of light-water reactors (LWRs) to a future fleet of advanced reactors consisting of a mix of ARDP type reactor concepts and advanced LWRs. To accurately evaluate the front- and back-end resource requirements, it is important to perform reactor physics calculations to determine the discharge burnup and isotopic content, fuel residence time, as well as other parameters. For this purpose, a summer project funded by the SA&I campaign allowed for the setup of SCALE models for full-core Xe-100 type high-temperature gas-cooled pebble-bed reactor and a Xe-100 type slice using publicly available information. The core-averaged equilibrium compositions and zone-wise equilibrium compositions for the slice and 3D models, respectively, were obtained following an iterative depletion method developed by Bostelmann et al. using SCALE’s reactor physics sequence TRITON. The slice model was used with TRITON to generate burnup-dependent cross section libraries at different temperatures which can be used with SCALE’s ORIGAMI code to rapidly determine fuel inventory and therefore to perform quick sensitivity studies on parameters such as the pebble location in the core. The SCALE/TRITON transport and depletion calculation for the Xe-100 type slice model indicates that the isotopic concentrations are in good agreement at 1,300 effective full power days (EFPD) for 235 U. An analysis of 236 U results match 239 Pu results would seem to indicate a typographical error in Mulder and Boyes wherein the reported results of 236 U and 239 Pu are reversed. In addition to SCALE/TRITON calculations, a new capability within SCALE/ORIGAMI for the simulation of pebble-bed reactors was used to study the burnup sensitivity with respect to the pebble pathway through the core. The SCALE/ORIGAMI results show that pebbles that travel closer to the reflector for the entire depletion history have a higher burnup than pebbles that travel through the middle of the core because of the higher thermal to fast flux ratio near the reflector. Consequently, a pebble’s burnup is strongly affected by the pebble’s pathway for each pass. Additional phenomena such as temperature distributions in the core and different travel times of the pebbles in the individual radial zones further affect the burnup distribution. The sensitivity of the discharge vector to the pebble pathways taken during each pass can be evaluated in the future using SCALE/ORIGAMI now that the SCALE inputs have been established.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2024

Machine learning analysis of RB-TnSeq fitness data predicts functional gene modules in Pseudomonas putida KT2440

ABSTRACT There is growing interest in engineering Pseudomonas putida KT2440 as a microbial chassis for the conversion of renewable and waste-based feedstocks, and metabolic engineering of P. putida relies on the understanding of the functional relationships between genes. In this work, independent component analysis (ICA) was applied to a compendium of existing fitness data from randomly barcoded transposon insertion sequencing (RB-TnSeq) of P. putida KT2440 grown in 179 unique experimental conditions. ICA identified 84 independent groups of genes, which we call fModules (“functional modules”), where gene members displayed shared functional influence in a specific cellular process. This machine learning-based approach both successfully recapitulated previously characterized functional relationships and established hitherto unknown associations between genes. Selected gene members from fModules for hydroxycinnamate metabolism and stress resistance, acetyl coenzyme A assimilation, and nitrogen metabolism were validated with engineered mutants of P. putida . Additionally, functional gene clusters from ICA of RB-TnSeq data sets were compared with regulatory gene clusters from prior ICA of RNAseq data sets to draw connections between gene regulation and function. Because ICA profiles the functional role of several distinct gene networks simultaneously, it can reduce the time required to annotate gene function relative to manual curation of RB-TnSeq data sets. IMPORTANCE This study demonstrates a rapid, automated approach for elucidating functional modules within complex genetic networks. While Pseudomonas putida randomly barcoded transposon insertion sequencing data were used as a proof of concept, this approach is applicable to any organism with existing functional genomics data sets and may serve as a useful tool for many valuable applications, such as guiding metabolic engineering efforts in other microbes or understanding functional relationships between virulence-associated genes in pathogenic microbes. Furthermore, this work demonstrates that comparison of data obtained from independent component analysis of transcriptomics and gene fitness datasets can elucidate regulatory-functional relationships between genes, which may have utility in a variety of applications, such as metabolic modeling, strain engineering, or identification of antimicrobial drug targets.

09 BIOMASS FUELS↗
DOE OSTI2024

Phylometagenomics of cycad coralloid roots reveals shared symbiotic signals

Cycads are known to host symbiotic cyanobacteria, includingNostocalesspecies, as well as other sympatric bacterial taxa within their specialized coralloid roots. Yet, it is unknown if these bacteria share a phylogenetic origin and/or common genomic functions that allow them to engage in facultative symbiosis with cycad roots. To address this, we obtained metagenomic sequences from 39 coralloid roots sampled from diverse cycad species and origins in Australia and Mexico. Culture-independent shotgun metagenomic sequencing was used to validate sub-community co-cultures as an efficient approach for functional and taxonomic analysis. Our metanalysis shows a host-independent microbiome core consisting of seven bacterial orders with high species diversity within the identified taxa. Moreover, we recovered 43 cyanobacterial metagenome-assembled genomes, and in addition toNostocspp., symbiotic cyanobacteria of the genusAulosirawere identified for the first time. Using this robust dataset, we used phylometagenomic analysis to reveal three monophyletic cyanobiont clades, two host-generalist and one cycad-specific that includesAulosiraspp. Although the symbiotic clades have independently arisen, they are enriched in certain functional genes, such as those related to secondary metabolism. Furthermore, the taxonomic composition of associated sympatric bacterial taxa remained constant. Our research quadruples the number of cycad cyanobiont genomes and provides a robust framework to decipher cyanobacterial symbioses, with the potential of improving our understanding of symbiotic communities. This study lays a solid foundation to harness cyanobionts for agriculture and bioprospection, and assist in conservation of critically endangered cycads.

Genetics & Heredity↗
DOE OSTI2020

Detection and Diagnosis of Data Integrity Attacks in Solar Farms Based on Multilayer Long Short-Term Memory Network

Photovoltaic (PV) systems are becoming more vulnerable to cyber threats. In response to this emerging concern, developing cyber-secure power electronics converters has received increased attention from the IEEE Power Electronics Society that recently launched a cyber-physical-security initiative. Here this letter proposes a deep sequence learning based diagnosis solution for data integrity attacks on PV systems in smart grids, including dc–dc and dc–ac converters. The multilayer long short-term memory networks are used to leverage time-series electric waveform data from current and voltage sensors in PV systems. The proposed method has been evaluated in a PV smart grid benchmark model with extensive quantitative analysis. As a comparison, we have evaluated classic data-driven methods, including K-nearest neighbor, decision tree, support vector machine, artificial neural network, and convolutional neural network. Comparison results verify performances of the proposed method for detection and diagnosis of various data integrity attacks on PV systems.

42 ENGINEERING↗
DOE OSTI2024

Communication Lower Bounds and Optimal Algorithms for Multiple Tensor-Times-Matrix Computation

Multiple tensor-times-matrix (Multi-TTM) is a key computation in algorithms for computing and operating with the Tucker tensor decomposition, which is frequently used in multidimensional data analysis. Here, we establish communication lower bounds that determine how much data movement is required (under mild conditions) to perform the Multi-TTM computation in parallel. The crux of the proof relies on analytically solving a constrained, nonlinear optimization problem. We also present a parallel algorithm to perform this computation that organizes the processors into a logical grid with twice as many modes as the input tensor. We show that, with correct choices of grid dimensions, the communication cost of the algorithm attains the lower bounds and is therefore communication optimal. Finally, we show that our algorithm can significantly reduce communication compared to the straightforward approach of expressing the computation as a sequence of tensor-times-matrix operations when the input and output tensors vary greatly in size.

HBL-inequalities↗
DOE OSTI2026

Near-Optimal Performance of Stochastic Model Predictive Control

Here, this article presents a regret analysis for stochastic model predictive control (SMPC) in linear systems with quadratic performance index and additive and multiplicative uncertainties. Under a finite support assumption, the problem can be cast as a finite-dimensional quadratic program, but the problem becomes quickly intractable as the problem size grows exponentially in the horizon length. SMPC aims to compute approximate solutions by solving a sequence of problems with truncated prediction horizons and committing the solution in a receding-horizon fashion. Although this approach is widely used in practice, its performance relative to the optimal solution is not well understood. This article reports for the first time a rigorous near-optimal performance guarantee of SMPC: under stabilizability and detectability conditions, the regret of SMPC is exponentially small in the prediction horizon length, allowing SMPC to achieve near-optimal performance at a substantially reduced computational expense.

93E20, 93B45↗
DOE OSTI2024

Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake

Abstract Background Protists, single-celled eukaryotic organisms, are critical to food web ecology, contributing to primary productivity and connecting small bacteria and archaea to higher trophic levels. Lake Mendota is a large, eutrophic natural lake that is a Long-Term Ecological Research site and among the world’s best-studied freshwater systems. Metagenomic samples have been collected and shotgun sequenced from Lake Mendota for the last 20 years. Here, we analyze this comprehensive time series to infer changes to the structure and function of the protistan community and to hypothesize about their interactions with bacteria. Results Based on small subunit rRNA genes extracted from the metagenomes and metagenome-assembled genomes of microeukaryotes, we identify shifts in the eukaryotic phytoplankton community over time, which we predict to be a consequence of reduced zooplankton grazing pressures after the invasion of a invasive predator (the spiny water flea) to the lake. The metagenomic data also reveal the presence of the spiny water flea and the zebra mussel, a second invasive species to Lake Mendota, prior to their visual identification during routine monitoring. Furthermore, we use species co-occurrence and co-abundance analysis to connect the protistan community with bacterial taxa. Correlation analysis suggests that protists and bacteria may interact or respond similarly to environmental conditions. Cryptophytes declined in the second decade of the timeseries, while many alveolate groups (e.g., ciliates and dinoflagellates) and diatoms increased in abundance, changes that have implications for food web efficiency in Lake Mendota. Conclusions We demonstrate that metagenomic sequence-based community analysis can complement existing efforts to monitor protists in Lake Mendota based on microscopy-based count surveys. We observed patterns of seasonal abundance in microeukaryotes in Lake Mendota that corroborated expectations from other systems, including high abundance of cryptophytes in winter and diatoms in fall and spring, but with much higher resolution than previous surveys. Our study identified long-term changes in the abundance of eukaryotic microbes and provided context for the known establishment of an invasive species that catalyzes a trophic cascade involving protists. Our findings are important for decoding potential long-term consequences of human interventions, including invasive species introduction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Mongooses ( Urva auropunctata ) as reservoir hosts of Leptospira species in the United States Virgin Islands, 2019–2020

During 2019–2020, the Virgin Islands Department of Health investigated potential animal reservoirs of Leptospira spp., the bacteria that cause leptospirosis. In this cross-sectional study, we investigated Leptospira spp. exposure and carriage in the small Indian mongoose (Urva auropunctata, syn: Herpestes auropunctatus), an invasive animal species. This study was conducted across the three main islands of the U.S. Virgin Islands (USVI), which are St. Croix, St. Thomas, and St. John. We used the microscopic agglutination test (MAT), fluorescent antibody test (FAT), real-time polymerase chain reaction (lipl32 rt-PCR), and bacterial culture to evaluate serum and kidney specimens and compared the sensitivity, specificity, positive predictive value, and negative predictive value of these laboratory methods. Mongooses (n = 274) were live-trapped at 31 field sites in ten regions across USVI and humanely euthanized for Leptospira spp. testing. Bacterial isolates were sequenced and evaluated for species and phylogenetic analysis using the ppkgene. Anti-Leptospira spp. antibodies were detected in 34% (87/256) of mongooses. Reactions were observed with the following serogroups: Sejroe, Icterohaemorrhagiae, Pyrogenes, Mini, Cynopteri, Australis, Hebdomadis, Autumnalis, Mankarso, Pomona, and Ballum. Of the kidney specimens examined, 5.8% (16/270) were FAT-positive, 10% (27/274) were culture-positive, and 12.4% (34/274) were positive by rt-PCR. Of the Leptospira spp. isolated from mongooses, 25 were L. borgpetersenii, one was L. interrogans, and one was L. kirschneri. Positive predictive values of FAT and rt-PCR testing for predicting successful isolation of Leptospira by culture were 88% and 65%, respectively. The isolation and identification of Leptospira spp. in mongooses highlights the potential role of mongooses as a wildlife reservoir of leptospirosis; mongooses could be a source of Leptospira spp. infections for other wildlife, domestic animals, and humans.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Quantitative Analysis of the Effects of Natural and Human Factors on a Hydrological System in Zhangweinan Canal Basin

Drought is a water deficit state caused by large-scale climate change that cannot be avoided by a water resource management system. Water scarcity refers to the unsustainable utilization of water resources over a long time, which is the result of water management policies. However, water deficits caused by drought and water scarcity often occur simultaneously and are indistinguishable. This study proposes a model-based simulation framework that can quantitatively distinguish natural factors (drought) from human factors (water scarcity) in a hydrological system. The simulation was applied to the Zhangweinan Canal Basin, based on the runoff sequences from 1950 to 2004. The results show that the runoff curve number, soil depth, soil available water, soil evaporation compensation coefficient, base runoff α coefficient and the maximum canopy interception have the highest sensitivity to runoff, and that the calibrated and validated SWAT model can effectively simulate the runoff process in the Zhangweinan Canal Basin and similar areas. Abrupt changes in human activities in 1975 and water scarcity led to the disappearance of the summer peak runoff period in both wet and dry years. Human factors are the main reason for the change in the hydrological system in the study area; the runoff loss caused by human factors is four times that caused by natural factors according to the proposed variable threshold. This study proposes a model-based simulation framework that can help water resource managers to distinguish the effects of drought and water scarcity in water-stressed areas and adjust management accordingly.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Cross-reactive immunogenicity of group A streptococcal vaccines designed using a recurrent neural network to identify conserved M protein linear epitopes

The M protein of group A streptococci (Strep A) is a major virulence determinant and protective antigen. The N-terminal sequence of the protein defines the more than 200 M types of Strep A and also contains epitopes that elicit opsonic antibodies, some of which cross-react with heterologous M types. Current efforts to develop broadly protective M protein-based vaccines are directed at identifying potential cross-protective epitopes located in the N-terminal regions of cluster-related M proteins for use as vaccine antigens. In this study, we have used a comprehensive approach using the recurrent neural network ABCpred and IEDB epitope conservancy analysis tools to predict 16 residue linear B-cell epitopes from 117 clinically relevant M types of Strep A (~88% of global Strep A infections). Furthermore, to examine the immunogenicity of these epitope-based vaccines, nine peptides that together shared ≥60% sequence identity with 37 heterologous M proteins were incorporated into two recombinant hybrid protein vaccines, in which the epitopes were repeated 2 or 3 times, respectively. The combined immune responses of immunized rabbits showed that the vaccines elicited significant levels of antibodies against all nine vaccine epitopes present in homologous N-terminal 1–50 amino acid synthetic M peptides, as well as cross-reactive antibodies against 16 of 37 heterologous M peptides predicted to contain similar epitopes. The epitope-specificity of the cross-reactive antibodies was confirmed by ELISA inhibition assays and functional opsonic activity was assayed in HL-60-based bactericidal assays. The results provide important information for the future design of broadly protective M protein-based Strep A vaccines.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Genomics and physiology of Catenibacillus, human gut bacteria capable of polyphenol C-deglycosylation and flavonoid degradation

The genusCatenibacillus(familyLachnospiraceae, phylumBacillota) includes only one cultivated species so far,Catenibacillus scindens,isolated from human faeces and capable of deglycosylating dietary polyphenols and degrading flavonoid aglycones. Another human intestinalCatenibacillusstrain not taxonomically resolved at that time was recently genome-sequenced. We analysed the genome of this novel isolate, designatedCatenibacillus decagia, and showed its ability to deglycosylateC-coupled flavone and xanthone glucosides andO-coupled flavonoid glycosides. Most of the resulting aglycones were further degraded to the corresponding phenolic acids. Including the recently sequenced genome ofC. scindensand ten faecal metagenome-assembled genomes assigned to the genusCatenibacillus, we performed a comparative genome analysis and searched for genes encoding potentialC-glycosidases and other polyphenol-converting enzymes. According to genome data and physiological characterization, the core metabolism ofCatenibacillusstrains is based on a fermentative lifestyle with butyrate production and hydrogen evolution. BothC. scindensandC. decagiaencode a flavonoidO-glycosidase, a flavone reductase, a flavanone/flavanonol-cleaving reductase and a phloretin hydrolase. Several gene clusters encode enzymes similar to those of the flavonoidC-deglycosylation system ofDoreastrain PUE (DgpBC), while separately located genes encode putative polyphenol-glucoside oxidases (DgpA) required forC-deglycosylation. The diversity ofdgpAanddgpBCgene clusters might explain the broadC-glycoside substrate spectrum ofC. scindensandC. decagia. The otherCatenibacillusgenomes encode only a few potential flavonoid-converting enzymes. Our results indicate that severalCatenibacillusspecies are well-equipped to deglycosylate and degrade dietary plant polyphenols and might inhabit a corresponding, specific niche in the gut.

Genetics & Heredity↗
DOE OSTI2026

Diagnosing Ghost Bunches with the Upstream Extinction Monitor in the Mu2e Experiment

The Mu2e experiment has a stringent requirement for extinction of the pulsed proton beam, referring to the elimination of particles between proton bunches to a relative level of 10$^-10$, which means a single out-of-time particle in the inter-pulse gaps for every 250 complete proton pulses. As the construction of the Mu2e experiment nears completion, it is crucially important to make an early measurement of the beam extinction in its current condition. Hence the upstream extinction monitor was constructed and operated to probe for problems in the proton pulse structure or a higher than expected incidence rate of out-of-time particles. The analysis in this work comes from data taken in March 2026. The long data run showed a significant presence of out-of-time particles from ghost bunches in the Delivery Ring approximately 388 ns after the centers of the main proton pulses. These are hypothesized to be the result of a combination of a RF frequency mismatch, particle space charge, and machine impedance during the rebunching sequence in the Recycler Ring, which can lead to particles leaking into adjacent buckets, but further studies and simulations are needed to confirm this

Hensley, R. [UC, Davis] (ORCID:0000000216064485)↗
DOE OSTI2025

SynopFrame: Multiscale time-dependent visual abstraction framework for analyzing DNA nanotechnology simulations

We present an open-source framework, SynopFrame, that allows DNA nanotechnology (DNA-nano) experts to analyze and understand molecular dynamics simulation trajectories of their designs. We use a multiscale multi-dimensional abstraction space, connect the representations to a projected conformational space plot of the structure’s temporal sequence, and thus enable experts to analyze the dynamics of their structural designs and, specifically, failure cases of the assembly. In addition, our time-dependent abstraction representation allows the biologists, for the first time in a smooth and structurally clear way, to identify and observe temporal transitions of a DNA-nano design from one configuration to another, and to highlight important periods of the simulation for further analysis. We realize SynopFrame as a dashboard of the different synchronized 3D spatial and 2D schematic visual representations, with a color overlay to show essential properties such as the status of hydrogen bonds. The linking of the spatial, schematic, and abstract views ensures that users can effectively analyze the high-frequency motion. We also categorize the status of the hydrogen bonds into a new format to allow us to color-encode it and overlay it on the representations. To demonstrate the utility of SynopFrame, we describe example usage scenarios and report user feedback.

Abstraction space↗
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↗
DOE OSTI2023

Catalytic Upgrading of Carbohydrates in Waste Streams to Hydrocarbons: Paper Sludge to Fuel Project (PStF)

This research, funded by the Department of Energy Bioenergy Technologies Office (DOE BETO), aims to understand the barriers and assess opportunities for transforming carbohydrates in paper sludge, a solid lignocellulosic residue from the pulp and paper industry. The goal is to turn the paper sludge into a liquid hydrocarbon product that can be blended into jet fuel, both economically and sustainably. Research groups at North Carolina State University, National Renewable Energy Laboratory, and Yale University collaborated synergistically, leveraging their expertise in pulp and paper operations, biomass deconstruction, and catalytic upgrading to propose a pathway that efficiently captures the energy in paper sludge. Findings from this study could potentially contribute to advancing biomass conversion technologies, aligning with the efforts of the U.S. DOE BETO. This report documents the experimental and simulation results of a biochemical and catalytic pathway designed to transform paper sludge into a liquid hydrocarbon product. The process involves a sequence of seven steps, including ash removal, carbohydrate enzymatic hydrolysis, sugar dehydration, solvent recovery, aldol-condensation between furans and ketone, hydrogenation, and hydrodeoxygenation to obtain a hydrocarbon blend in the ~C10 range. The experimental efforts from the initiation of the project were guided by techno-economic analysis (TEA) and sensitivity analysis results including around seventy-eight operational parameters. This methodology facilitated the efficient use of resources over time. This study relies on detailed process simulations and TEA to determine the minimum fuel selling price (MFSP) for the hydrocarbon fuel product. Preliminary TEA results led to the evaluation of eight case studies considering alternative dehydration co-solvents, operational settings, and biorefinery layouts. Finally, the life cycle assessment of twenty-eight scenarios, comparing various dehydration co-solvents, fuel sources, chemical feedstock sources, side product utilization, and other process settings, was conducted. Landfilling scenarios with and without landfill gas recovery were also estimated, analyzed, and compared.

09 BIOMASS FUELS↗