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DOE SBIR phase II final report GSM
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The Generalized Spallation Model
The Generalized Spallation Model (GSM) event generator is an advanced, robust, and scalable Fortran code developed from an extended and improved version of the earlier event generator codes CEM03.03 and LAQGSM03.03. The GSM implements its algorithms within the context of cascade exciton, particle equilibration, particle evaporation, and particle disintegration models sampled via Monte-Carlo techniques. Coalescence of particles is also considered. The GSM assumes the incident particles has sufficient energy to satisfy the assumptions utilized in the GSM. The GSM calculates reactions induced by hadrons and nuclei incident on nuclear targets at incident energies ranging from ~20 MeV up to several TeV per nucleon. Usage of GSM is recommended however for particles with incident energies exceeding ~100 MeV to ensure model-assumptions are satisfied. The GSM additionally provides its clients with sub-model libraries to allow them to model desired physics within their own physical models.
How threshold effects in spectroscopic factors influence heavy-ion knockout reactions
A two-decade-old puzzle in heavy-ion one-nucleon knockout reactions is the strong correlation between the reduction factor R S = σ exp /σ t h and the Fermi surface asymmetry ΔS. Theoretical cross sections typically rely on spectroscopic factors (SFs) from shell model (SM) calculations, which neglect continuum coupling effects. Here, we employ the Gamow shell model (GSM), which explicitly incorporates continuum coupling, to compute SFs for p-shell nuclei and predict corresponding theoretical cross sections. Systematic calculations demonstrate that using GSM-derived SFs substantially reduces discrepancies between theoretical and experimental results. This improvement is particularly significant for deeply bound nucleon knockout in nuclei near the dripline, where traditional SM-based calculations fall short. As a result, using GSM SFs, the ratio R s exhibits no pronounced dependence on ΔS. Furthermore, both the ratio of GSM SFs to SM SFs and their corresponding reaction cross sections ratios exhibit a strong ΔS dependence. We have also compared GSM SFs and cross sections with those from the no-core shell model calculations, giving a similar pronounced sensitivity to ΔS. Detailed analysis attributes these correlations to threshold effects for SFs in weakly bound systems. Overall, incorporating continuum coupling via GSM enhances the reliability of SF predictions for exotic, weakly bound nuclei and provides key insights toward resolving the enduring puzzle in heavy-ion knockout reactions from a nuclear structure perspective.
Dissecting the metabolic reprogramming of maize root under nitrogen-deficient stress conditions
The growth and development of maize (Zea mays L.) largely depends on its nutrient uptake through the root. Hence, studying its growth, response, and associated metabolic reprogramming to stress conditions is becoming an important research direction. A genome-scale metabolic model (GSM) for the maize root was developed to study its metabolic reprogramming under nitrogen stress conditions. The model was reconstructed based on the available information from KEGG, UniProt, and MaizeCyc. Transcriptomics data derived from the roots of hydroponically grown maize plants were used to incorporate regulatory constraints in the model and simulate nitrogen-non-limiting (N+) and nitrogen-deficient (N-) condition. Model-predicted flux-sum variability analysis achieved 70% accuracy compared with the experimental change of metabolite levels. In addition to predicting important metabolic reprogramming in central carbon, fatty acid, amino acid, and other secondary metabolism, maize root GSM predicted several metabolites (l-methionine, l-asparagine, l-lysine, cholesterol, and l-pipecolate) playing a regulatory role in the root biomass growth. Furthermore, this study revealed eight phosphatidylcholine and phosphatidylglycerol metabolites which, even though not coupled with biomass production, played a key role in the increased biomass production under N-deficient conditions. Overall, the omics-integrated GSM provides a promising tool to facilitate stress condition analysis for maize root and engineer better stress-tolerant maize genotypes.
Toward scalable many-body calculations for nuclear open quantum systems using the Gamow Shell Model
Drip-line nuclei have very different properties from those of the valley of stability, as they are weakly bound and resonant. Therefore, the models devised for stable nuclei can no longer be applied therein. Hence, a new theoretical tool, the Gamow Shell Model (GSM), has been developed to study the many-body states occurring at the limits of the nuclear chart. GSM is a configuration interaction model based on the use of the so-called Berggren basis, which contains bound, resonant and scattering states, so that inter-nucleon correlations are fully taken into account and the asymptotes of extended many-body wave functions are precisely handled. However, large complex symmetric matrices must be diagonalized in this framework, therefore the use of very powerful parallel machines is needed therein. So, in order to fully take advantage of their power, a 2D partitioning scheme using hybrid MPI/OpenMP parallelization has been developed in our GSM code. The specificities of the 2D partitioning scheme in the GSM framework will be described and illustrated with numerical examples. It will then be shown that the introduction of this scheme in the GSM code greatly enhances its capabilities.
An accurate perturbative approach to redshift space clustering of biased tracers in modified gravity
We extend the scale-dependent Gaussian Streaming Model (GSM) to produce analytical predictions for the anisotropic redshift-space correlation function for biased tracers in modified gravity models. Employing the Convolution Lagrangian Perturbation Theory (CLPT) re-summation scheme, with a local Lagrangian bias schema provided by the peak-background split formalism, we predict the necessary ingredients that enter the GSM, the real-space halo pairwise velocity and the pairwise velocity dispersion. We further consider effective field theory contributions to the pairwise velocity dispersion in order to model correctly its large scale behavior. We apply our method on two widely-considered modified gravity models, the chameleon-screened ƒ(R) Hu-Sawicki model and the nDGP Vainshtein model and compare our predictions against state-of-the-art N-body simulations for these models. We demonstrate that the GSM approach to predict the monopole and the quadrupole of the redshift-space correlation function for halos, gives very good agreement with the simulation data, for a wide range of screening mechanisms, levels of screening and halo masses at z = 0.5 and z = 1. Our work shows the applicability of the GSM, for cosmologies beyond GR, demonstrating that it can serve as a powerful predictive tool for the next stage of cosmological surveys like DESI, Euclid, LSST and WFIRST.
Distinguishing the gapped and Weyl semimetal scenario in ZrTe 5 : insights from an effective two-band model
In this work, we study the static and dynamic transport properties of a low-energy two-band model proposed previously in Martino et al. [PRL 122, 217402 (2019)], with an anisotropic in-plane linear momentum dependence and a parabolic out-of-plane dispersion. The model is extended to include a negative band gap, which leads to the emergence of a Weyl semimetal (WSM) state, as opposed to the gapped semimetal (GSM) state when the band gap is positive. Furthermore, we calculate and compare the zero- and finite-frequency transport properties of the GSM and WSM cases. The DC properties that are calculated for the GSM and WSM cases are Drude spectral weight, mobility, and resistivity. We determine their dependence on the Fermi energy and crystal direction. The in- and out-of-plane optical conductivities are calculated in the limit of the vanishing interband relaxation rate for both semimetals. The main common features are an ω 1/2 in-plane and ω 3/2 out-of-plane frequency dependence of the optical conductivity. We seek particular features related to the charge transport that could unambiguously point to one ground state over the other, based on the comparison with the experiment. Differences between the WSM and GSM are in principle possible only at extremely low carrier concentrations and at low temperatures.
Genome-scale model development and genomic sequencing of the oleaginous clade Lipomyces
The Lipomyces clade contains oleaginous yeast species with advantageous metabolic features for biochemical and biofuel production. Limited knowledge about the metabolic networks of the species and limited tools for genetic engineering have led to a relatively small amount of research on the microbes. Here, a genome-scale metabolic model (GSM) of Lipomyces starkeyi NRRL Y-11557 was built using orthologous protein mappings to model yeast species. Phenotypic growth assays were used to validate the GSM (66% accuracy) and indicated that NRRL Y-11557 utilized diverse carbohydrates but had more limited catabolism of organic acids. The final GSM contained 2,193 reactions, 1,909 metabolites, and 996 genes and was thus named iLst996. The model contained 96 of the annotated carbohydrate-active enzymes. iLst996 predicted a flux distribution in line with oleaginous yeast measurements and was utilized to predict theoretical lipid yields. Twenty-five other yeasts in the Lipomyces clade were then genome sequenced and annotated. Sixteen of the Lipomyces species had orthologs for more than 97% of the iLst996 genes, demonstrating the usefulness of iLst996 as a broad GSM for Lipomyces metabolism. Pathways that diverged from iLst996 mainly revolved around alternate carbon metabolism, with ortholog groups excluding NRRL Y-11557 annotated to be involved in transport, glycerolipid, and starch metabolism, among others. Overall, this study provides a useful modeling tool and data for analyzing and understanding Lipomyces species metabolism and will assist further engineering efforts in Lipomyces .
Metabolic engineering of Synechococcus elongatus 7942 for enhanced sucrose biosynthesis
The capability of cyanobacteria to produce sucrose from CO 2 and light has a remarkable societal and biotechnological impact since sucrose can serve as a carbon and energy source for a variety of heterotrophic organisms and can be converted into value-added products. However, most metabolic engineering efforts have focused on understanding local pathway alterations that drive sucrose biosynthesis and secretion in cyanobacteria rather than analyzing the global flux re-routing that occurs following induction of sucrose production by salt stress. Here, we investigated global metabolic flux alterations in a sucrose-secreting (cscB-overexpressing) strain relative to its wild-type Synechococcus elongatus 7942 parental strain. Here we used targeted metabolomics, 13 C metabolic flux analysis (MFA), and genome-scale modeling (GSM) as complementary approaches to elucidate differences in cellular resource allocation by quantifying metabolic profiles of three cyanobacterial cultures - wild-type S. elongatus 7942 without salt stress (WT), wild-type with salt stress (WT/NaCl), and the cscB-overexpressing strain with salt stress (cscB/NaCl) - all under photoautotrophic conditions. We quantified the substantial rewiring of metabolic fluxes in WT/NaCl and cscB/NaCl cultures relative to WT and identified a metabolic bottleneck limiting carbon fixation and sucrose biosynthesis. This bottleneck was subsequently mitigated through heterologous overexpression of glyceraldehyde-3-phosphate dehydrogenase in an engineered sucrose-secreting strain. Our study also demonstrates that combining 13 C-MFA and GSM is a useful strategy to both extend the coverage of MFA beyond central metabolism and to improve the accuracy of flux predictions provided by GSM.
Modification and analysis of context-specific genome-scale metabolic models: methane-utilizing microbial chassis as a case study
ABSTRACT Context-specific genome-scale model (CS-GSM) reconstruction is becoming an efficient strategy for integrating and cross-comparing experimental multi-scale data to explore the relationship between cellular genotypes, facilitating fundamental or applied research discoveries. However, the application of CS modeling for non-conventional microbes is still challenging. Here, we present a graphical user interface that integrates COBRApy, EscherPy, and RIPTiDe, Python-based tools within the BioUML platform, and streamlines the reconstruction and interrogation of the CS genome-scale metabolic frameworks via Jupyter Notebook. The approach was tested using -omics data collected for Methylotuvimicrobium alcaliphilum 20Z R , a prominent microbial chassis for methane capturing and valorization. We optimized the previously reconstructed whole genome-scale metabolic network by adjusting the flux distribution using gene expression data. The outputs of the automatically reconstructed CS metabolic network were comparable to manually optimized i IA409 models for Ca-growth conditions. However, the CS model questions the reversibility of the phosphoketolase pathway and suggests higher flux via primary oxidation pathways. The model also highlighted unresolved carbon partitioning between assimilatory and catabolic pathways at the formaldehyde-formate node. Only a very few genes and only one enzyme with a predicted function in C1 metabolism, a homolog of the formaldehyde oxidation enzyme ( fae1-2 ), showed a significant change in expression in La-growth conditions. The CS-GSM predictions agreed with the experimental measurements under the assumption that the Fae1-2 is a part of the tetrahydrofolate-linked pathway. The cellular roles of the tungsten (W)-dependent formate dehydrogenase ( fdhAB ) and fae homologs ( fae1-2 and fae3 ) were investigated via mutagenesis. The phenotype of the f dhAB mutant followed the model prediction. Furthermore, a more significant reduction of the biomass yield was observed during growth in La-supplemented media, confirming a higher flux through formate. M. alcaliphilum 20Z R mutants lacking fae1-2 did not display any significant defects in methane or methanol-dependent growth. However, contrary to fae1, the fae1-2 homolog failed to restore the formaldehyde-activating enzyme function in complementation tests. Overall, the presented data suggest that the developed computational workflow supports the reconstruction and validation of CS-GSM networks of non-model microbes. IMPORTANCE The interrogation of various types of data is a routine strategy to explore the relationship between genotype and phenotype. An efficient approach for integrating and cross-comparing experimental multi-scale data in the context of whole-genome-based metabolic network reconstruction becomes a powerful tool that facilitates fundamental and applied research discoveries. The present study describes the reconstruction of a context-specific (CS) model for the methane-utilizing bacterium, Methylotuvimicrobium alcaliphilum 20Z R . M. alcaliphilum 20Z R is becoming an attractive microbial platform for the production of biofuels, chemicals, pharmaceuticals, and bio-sorbents for capturing atmospheric methane. We demonstrate that this pipeline can help reconstruct metabolic models that are similar to manually curated networks. Furthermore, the model is able to highlight previously overlooked pathways, thus advancing fundamental knowledge of non-model microbial systems or promoting their development toward biotechnological or environmental implementations.
Gamow-shell-model description of Li isotopes and their mirror partners
Background: Weakly bound and unbound nuclei close to particle drip lines are laboratories of new nuclear structure physics at the extremes of neutron/proton excess. The comprehensive description of these systems requires an open quantum system framework that is capable of treating resonant and nonresonant many-body states on equal footing. Purpose: In this work, we develop the complex-energy configuration interaction approach to describe binding energies and spectra of selected 5 ≤ $\textit{A}$ ≤ 11 nuclei. Method: We employ the complex-energy Gamow shell model (GSM) assuming a rigid 4 He core. The effective Hamiltonian, consisting of a core-nucleon Woods-Saxon potential and a simplified version of the Furutani-Horiuchi-Tamagaki interaction with the mass-dependent scaling, is optimized in the $\textit{sp}$ space. To diagonalize the Hamiltonian matrix, we employ the Davidson method and the Density Matrix Renormalization Group technique. Results: We report our optimized GSM Hamiltonian offers a good reproduction of binding energies and spectra with the root-mean-square (rms) deviation from experiment of 160 keV. Since the model performs well when used to predict known excitations that have not been included in the fit, it can serve as a reliable tool to describe poorly known states. A case in point is our prediction for the pair of unbound mirror nuclei 10 Li – 10 N in which a huge Thomas-Ehrman shift dramatically alters the pattern of low-energy excitations. Conclusion: The new model will enable comprehensive studies of structure and reactions aspects of light drip-line nuclei.
Neutron-rich calcium isotopes within realistic Gamow shell model calculations with continuum coupling
Based on the realistic nuclear force of the high-precision CD-Bonn potential, we have performed comprehensive calculations for neutron-rich calcium isotopes using the Gamow shell model (GSM) which includes resonance and continuum. The realistic GSM calculations produce well binding energies, one- and two-neutron separation energies, predicting that 57 Ca is the heaviest bound odd isotope and 70 Ca is the dripline nucleus. Resonant states are predicted, which provides useful information for future experiments on particle emissions in neutron-rich calcium isotopes. Shell evolutions in the calcium chain around neutron numbers $\textit{N}$ = 32, 34, and 40 are understood by calculating effective single-particle energies, the excitation energies of the first 2 + states and two-neutron separation energies. The calculations support shell closures at 52 Ca ($\textit{N}$ = 32) and 54 Ca ($\textit{N}$ = 34) but show a weakening of shell closure at 60 Ca ($\textit{N}$ = 40). Finally, the possible shell closure at 70 Ca ($\textit{N}$ = 50) is predicted.
New narrow resonances observed in the unbound nucleus F 15
The structure of the unbound 15 F nucleus is investigated using the inverse kinematics resonant scattering of a radioactive 14 O beam impinging on a CH 2 target. The analysis of 1 H( 14 O,p) 14 O and 1 H( 14 O,2p) 13 N reactions allowed the confirmation of the previously observed narrow 1/2 - resonance, near the two-proton decay threshold, and the identification of two new narrow 5/2 - and 3/2 - resonances. The newly observed levels decay by 1p emission to the ground of 14 O, and by sequential 2p emission to the ground state (g.s.) of 13 N via the 1 - resonance of 14 O. Gamow shell model (GSM) analysis of the experimental data suggests that the wave functions of the 5/2 - and 3/2 - resonances may be collectivized by the continuum coupling to nearby 2p- and 1p- decay channels. Finally, the observed excitation function 1 H( 14 O, p) 14 O and resonance spectrum in 15 F are well reproduced in the unified framework of the GSM.
MOSIQS: Persistent Memory Object Storage With Metadata Indexing and Querying for Scientific Computing
Scientific applications often require high-bandwidth shared storage to perform joint simulations and collaborative data analytics. Shared memory pools provide a chance to satisfy such needs. Recently, a high-speed network such as Gen-Z utilizing persistent memory (PM) offers an opportunity to create a shared memory pool connected to compute nodes. However, there are several challenges to use scientific applications on the shared memory pool directly such as scalability, failure-atomicity, and lack of scientific metadata-based search and query. In this paper, we propose MOSIQS, a persistent memory object storage framework with metadata indexing and querying for scientific computing. We design MOSIQS based on the key idea that memory objects on PM pool can live beyond the application lifetime and can become the sharing currency for applications and scientists. MOSIQS provides an aggregate memory pool atop an array of persistent memory devices to store and access memory objects to accelerate scientific computing. MOSIQS uses a lightweight persistent memory key-value store to manage the metadata of memory objects, which enables memory object sharing. To facilitate metadata search and query over millions of memory objects resident on memory pool, we introduce Group Split and Merge (GSM), a novel persistent index data structure designed primarily for scientific datasets. GSM splits and merges dynamically to minimize the query search space and maintains low query processing time while overcoming the index storage overhead. MOSIQS is implemented on top of PMDK. We evaluate the proposed approach on many-core server with an array of real PM devices. Experimental results show that MOSIQS gains a 100% write performance improvement and executes multi-attribute queries efficiently with 2.7× less index storage overhead offering significant potential to speed up scientific computing applications.
Test and Validate Distributed Coaxial Cable Sensors for in situ Condition Monitoring of Coal-Fired Boiler Tubes
This project aims to test, validate, and advance the technology readiness level (from TRL5 to TRL7) of a novel low-cost distributed stainless-steel/ceramic coaxial cable sensing (SSC-CCS) technology for in situ monitoring of the boiler tube temperature in existing coal-fired power plants. The novel SSC-CCS sensing technology and associated condition-based monitoring (CBM) software to be demonstrated in this project will lead to an improved understanding of the boiler tube failure mechanisms and a prognostic system to improve the overall performance, reliability, and flexibility of the nation’s coal-fired power plant fleet. A boiler tube monitoring system with distributed coaxial cable temperature sensors and a sensor acquisition system was constructed. The high-temperature coaxial cable sensor with a length of 1.3m was made by using a quartz tube (1mm inner diameter (ID) and 6mm outer diameter (OD)) to concentrically separate a 304 stainless-steel (SS) rod (1mm OD) and SS tube (7.94mm OD and 6.16mm ID). The sensor acquisition system includes a vector network analyzer (VNA), a radio frequency (RF) power amplifier, multiple switches and a USB hub. The distributed stainless-steel quartz coaxial cable sensor (SSQ-CCS) had a linear response to temperature with a resolution uncertainty of σ = 0.77℃. To withstand the harsh conditions of 3,300 steam pressures and 800℃ high temperatures, the sensor was shielded by a protective tube made of the same material as the boiler tube. The protection tube had an OD of 1.5 inches and a thickness of 0.25 inches. In the laboratory tests, the sensor showed good sensitivity and fast response. The drift was bounded between +0.33% and -0.67% during a test at 600℃ for 350 hours, indicating good stability of the sensor. A field test was conducted where four sensors were welded on four superheat tubes (SH-Ts) at a coal-fired power station over 400 days. Conventional thermocouples were welded to the superheater tubes alongside the coaxial cable sensors for the purpose of comparison. Two sensors were capable of distributed sensing, with three multiplexed sensing sections. The other two sensors were single section. During the 400-day test period, the power plant experienced startups and shutdowns. At the steady state operations, the temperature of the boiler tube is about 600℃ (1112°F). The sensors recorded the entire coal-firing processes (start-up, steady state, and shut-down) and the glitch event. A GSM modem and a Watchdog were added to the system to ensure reliable data recording. The GSM modem sent daily messages to plant managers and Clemson team to inform the status of the sensor system. If the system was not normally working, the Watchdog would reboot the system automatically. The new coaxial cable based distributed sensing technology has been proven to be successful in both laboratory and field tests. A comprehensive four-stage multi-physics computational framework has been developed to assist the design, optimization, installation, and operation of SSQ-CCS. With the consideration of various operation conditions, we predict the distributions of flue gas temperatures within coal-fired boilers, the temperature correlation between the boiler tube and SSQ-CCS, and the safety of SSQ-CCS. A conditional-based monitoring system is implemented as well. The computational framework developed in this work can guide the future operation of coal-fired plants and other power plants for the safety prediction of boiler operations.
A Genome-Scale Metabolic Model of Anabaena 33047 to Guide Genetic Modifications to Overproduce Nylon Monomers
Nitrogen fixing-cyanobacteria can significantly improve the economic feasibility of cyanobacterial production processes by eliminating the requirement for reduced nitrogen. Anabaena sp. ATCC 33047 is a marine, heterocyst forming, nitrogen fixing cyanobacteria with a very short doubling time of 3.8 h. We developed a comprehensive genome-scale metabolic (GSM) model, iAnC892, for this organism using annotations and content obtained from multiple databases. iAnC892 describes both the vegetative and heterocyst cell types found in the filaments of Anabaena sp. ATCC 33047. iAnC892 includes 953 unique reactions and accounts for the annotation of 892 genes. Comparison of iAnC892 reaction content with the GSM of Anabaena sp. PCC 7120 revealed that there are 109 reactions including uptake hydrogenase, pyruvate decarboxylase, and pyruvate-formate lyase unique to iAnC892. iAnC892 enabled the analysis of energy production pathways in the heterocyst by allowing the cell specific deactivation of light dependent electron transport chain and glucose-6-phosphate metabolizing pathways. The analysis revealed the importance of light dependent electron transport in generating ATP and NADPH at the required ratio for optimal N2 fixation. When used alongside the strain design algorithm, OptForce, iAnC892 recapitulated several of the experimentally successful genetic intervention strategies that over produced valerolactam and caprolactam precursors.