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DOE OSTI2025

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.

Kulyashov, M. A.↗

DOE OSTI2022

merlin , an improved framework for the reconstruction of high-quality genome-scale metabolic models

Abstract Genome-scale metabolic models have been recognised as useful tools for better understanding living organisms’ metabolism. merlin (https://www.merlin-sysbio.org/) is an open-source and user-friendly resource that hastens the models’ reconstruction process, conjugating manual and automatic procedures, while leveraging the user's expertise with a curation-oriented graphical interface. An updated and redesigned version of merlin is herein presented. Since 2015, several features have been implemented in merlin, along with deep changes in the software architecture, operational flow, and graphical interface. The current version (4.0) includes the implementation of novel algorithms and third-party tools for genome functional annotation, draft assembly, model refinement, and curation. Such updates increased the user base, resulting in multiple published works, including genome metabolic (re-)annotations and model reconstructions of multiple (lower and higher) eukaryotes and prokaryotes. merlin version 4.0 is the only tool able to perform template based and de novo draft reconstructions, while achieving competitive performance compared to state-of-the art tools both for well and less-studied organisms.

Capela, João (ORCID:0000000212352922)↗

DOE OSTI2022

Support Effect and Surface Reconstruction in In 2 O 3 / m- ZrO 2 Catalyzed CO 2 Hydrogenation

Here, we investigate the chemical and structural dynamics at the interface of In 2 O 3 /m-ZrO 2 and their consequences on the CO 2 hydrogenation reaction (CO 2 HR) under reaction conditions. While acting to enrich CO 2 , monoclinic zirconia (m-ZrO 2 ) was also found to serve as a chemical and structural modifier of In 2 O 3 that directly governs the outcome of the CO 2 HR. These modifying effects include the following: (1) Under reaction conditions (above 623 K), partially reduced In 2 O 3 , i.e., InO x (0 < x < 1.5), was found to migrate in and out of the subsurface of m-ZrO 2 in a semireversible manner, where m-ZrO 2 accommodates and stabilizes InO x by serving as a reservoir. The decreased concentration of surface InO x under elevated temperatures coincides with significantly decreased selectivity toward methanol and a sharp increase of the reverse water–gas shift reaction. The reconstruction-induced variation of InO x concentration appears to be one of the most important factors contributing to the altered catalytic performance of CO 2 HR at different reaction conditions. (2) The strong interactions and reactions between m-ZrO 2 and In 2 O 3 result in the activation of a pool of In–O bonds at the In 2 O 3 /m-ZrO 2 interface to form oxygen vacancies. On the other hand, the high dispersity of In 2 O 3 nanostructures onto m-ZrO 2 prevents their over-reduction under catalytically relevant conditions (up to 673 K), when bare In 2 O 3 is unavoidably reduced into the metallic phase (In 0 ). The relationship between the extent of reduction of In 2 O 3 and catalytic performance (CO 2 conversion, CH 3 OH selectivity, or yield of CH 3 OH) suggests the presence of an optimum coverage of surface InO x and oxygen vacancies under reaction conditions. The conventional model that links catalytic performance solely to the coverage of oxygen vacancies appears invalid in the present case. In situ analysis also allows the observation of surface reaction intermediates and their interconversions, including the reduction of CO 3 * into formate, a precursor for the formation of methanol and CO. The combinative ex situ and in situ study sheds light on the reaction mechanism of the CO 2 HR on In 2 O 3 /m-ZrO 2 -based catalysts. Our findings on the large-scale surface reconstructions, support effect, and the reaction mechanism of In 2 O 3 /m-ZrO 2 for CO 2 HR may apply to other related metal oxide catalyzed CO 2 reduction reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS2011

Reconstruction of Ares I-X Integrated Vehicle Rollout Loads

The measurements taken during the Ares I-X test flight provided a unique opportunity to assess the accuracy of the models and methods used to analyze the loads and accelerations present in the planned Ares I vehicle. During the rollout of the integrated vehicle from the Vehicle Assembly Building (VAB) to the launch pad, the vehicle and its supporting structure are subjected to wind loads and the vibrations produced by the crawler-transporter (CT) that is carrying it. While the loads induced on the vehicle during this period are generally low relative to those experienced in flight, the rollout is a period of operation of primary interest to those designing both the ground support equipment and the interfaces between the launch vehicle and its supporting structure. In this paper, the methods used for reconstructing the loads during the rollout phase are described. The results generated are compared to measured values, leading to insight into the accuracy of the Ares I assessment techniques.

Chamberlain, Matthew K.↗

NASA NTRS2011

Reconstruction of Ares I-X Integrated Vehicle Rollout Loads

Chamberlain, Matthew K.↗

DOE OSTI2021

Effect of interfacial structures on phonon transport across atomically precise Si/Al heterojunctions

Phonons are important carriers of energy and information in many cryogenic devices used for quantum information science and in fundamental physics experiments such as dark matter detectors. In these systems phonon behavior can be dominated by interfaces, hence there is increasing demand for a more detailed understanding of interfacial phonon transport in relevant material systems. Previous studies have focused on understanding thermal transport over the entire phonon spectrum at and above room temperature. At ultra-low temperatures, however, knowledge is missing regarding athermal phonon behavior due to the challenge in modeling the extreme conditions in micro-scale, heterogeneous cryogenic systems, as well as extracting single-phonon information from a large ensemble. In this work, we delineate interfacial phonon transport using a combination of classical molecular dynamics (MD) and phonon wave packet simulations, to illustrate the consistency and differences between the ensemble- and single-phonon dynamics. We consider three single-crystal Si surface reconstructions --- (1×1), (v3×v3) and (7×7) --- and model both experimentally observed Si(1×1)/Al interfaces and hypothesized Si(v3×v3)/Al and Si(7×7)/Al interfaces. The overall interfacial thermal conductance calculated from non-equilibrium MD shows that for the Si(1×1)/Al system, the presence of Al twin grain boundaries can hinder phonon transport and reduce thermal conductance by 2--12% relative to single-crystal Al; whereas the Si (v3×v3) and (7×7) reconstructions can enhance it by 6--19%. Normal mode decomposition reveals that both the increase and decrease in conductance are related to inelastic phonon scattering. Single-phonon wave packet simulations show results consistent with NEMD, while further suggesting that phonon polarization conversion is significant even when elastic transmission dominates, and that the interfacial structures have anisotropic impacts on atomic vibrations along different lattice directions. Our findings suggest alternative perspectives in achieving selective phonon transport through controlling interfacial structures of materials with atomically-precise fabrication techniques, and that the phonon wave packet formalism is a potentially powerful method for developing a detailed understanding of non-equilibrium phenomena in the low-temperature limit.

Lu, Zexi↗

DOE OSTI2024

Microstructural Underpinnings of Giant Intrinsic Exchange Bias in Epitaxial NiCo 2 O 4 Thin Films

Understanding intrinsic exchange bias in nominally single-component ferromagnetic or ferrimagnetic materials is crucial for simplifying related device architectures. However, the mechanisms behind this phenomenon and its tunability remain elusive, which hinders the efforts to achieve unidirectional magnetization for widespread applications. Inspired by the high tunability of ferrimagnetic inverse spinel NiCo 2 O 4 , the origin of intrinsic exchange bias in NiCo 2 O 4 (111) films deposited on Al 2 O 3 (0001) substrates are investigated. The comprehensive characterizations, including electron diffraction, X-ray reflectometry and spectroscopy, and polarized neutron reflectometry, reveal that intrinsic exchange bias in NiCo 2 O 4 (111)/Al 2 O 3 (0001) arises from a reconstructed antiferromagnetic rock-salt Ni x Co 1-x O layer at the interface between the film and the substrate due to a significant structural mismatch. Remarkably, by engineering the interfacial structure under optimal growth conditions, it can achieve exchange bias larger than coercivity, leading to unidirectional magnetization. Such giant intrinsic exchange bias can be utilized for realistic device applications. This work establishes a new material platform based on NiCo 2 O 4 , an emergent spintronics material, to study tunable interfacial magnetic and spintronic properties.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Three-dimensional visualization of nanoparticle lattices and multi-material frameworks

We report advances in nanoscale self-assembly have enabled the formation of complex nanoscale architectures. However, the development of self-assembly strategies toward bottom-up nanofabrication is impeded by challenges in revealing these structures volumetrically at the single-component level and with elemental sensitivity. Leveraging advances in nano-focused hard x-rays, DNA-programmable nanoparticle assembly, and nanoscale inorganic templating, we demonstrate nondestructive three-dimensional imaging of complexly organized nanoparticles and multimaterial frameworks. In a three-dimensional lattice with a size of 2 micrometers, we determined the positions of about 10,000 individual nanoparticles with 7-nanometer resolution, and identified arrangements of assembly motifs and a resulting multimaterial framework with elemental sensitivity. The real-space reconstruction permits direct three-dimensional imaging of lattices, which reveals their imperfections and interfaces and also clarifies the relationship between lattices and assembly motifs.

36 MATERIALS SCIENCE↗

DOE OSTI2022

The His-tag as a decoy modulating preferred orientation in cryoEM

The His-tag is a widely used affinity tag that facilitates purification by means of affinity chromatography of recombinant proteins for functional and structural studies. We show here that His-tag presence affects how coproheme decarboxylase interacts with the air-water interface during grid preparation for cryoEM. Depending on His-tag presence or absence, we observe significant changes in patterns of preferred orientation. Our analysis of particle orientations suggests that His-tag presence can mask the hydrophobic and hydrophilic patches on a protein’s surface that mediate the interactions with the air-water interface, while the hydrophobic linker between a His-tag and the coding sequence of the protein may enhance other interactions with the air-water interface. Our observations suggest that tagging, including rational design of the linkers between an affinity tag and a protein of interest, offer a promising approach to modulating interactions with the air-water interface.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1997

Accurate Monotonicity - Preserving Schemes With Runge-Kutta Time Stepping

A new class of high-order monotonicity-preserving schemes for the numerical solution of conservation laws is presented. The interface value in these schemes is obtained by limiting a higher-order polynominal reconstruction. The limiting is designed to preserve accuracy near extrema and to work well with Runge-Kutta time stepping. Computational efficiency is enhanced by a simple test that determines whether the limiting procedure is needed. For linear advection in one dimension, these schemes are shown as well as the Euler equations also confirm their high accuracy, good shock resolution, and computational efficiency.

Suresh, A.↗

NASA NTRS2010

Propulsion Design With Freeform Fabrication (PDFF)

The nation is challenged to decrease the cost and schedule to develop new space transportation propulsion systems for commercial, scientific, and military purposes. Better design criteria and manufacturing techniques for small thrusters are needed to meet current applications in missile defense, space, and satellite propulsion. The requirements of these systems present size, performance, and environmental demands on these thrusters that have posed significant challenges to the current designers and manufacturers. Designers are limited by manufacturing processes, which are complex, costly, and time consuming, and ultimately limited in their capabilities. The PDFF innovation vastly extends the design opportunities of rocket engine components and systems by making use of the unique manufacturing freedom of solid freeform rapid prototype manufacturing technology combined with the benefits of ceramic materials. The unique features of PDFF are developing and implementing a design methodology that uses solid freeform fabrication (SFF) techniques to make propulsion components with significantly improved performance, thermal management, power density, and stability, while reducing development and production costs. PDFF extends the design process envelope beyond conventional constraints by leveraging the key feature of the SFF technique with the capability to form objects with nearly any geometric complexity without the need for elaborate machine setup. The marriage of SFF technology to propulsion components allows an evolution of design practice to harmonize material properties with functional design efficiency. Reduced density of materials when coupled with the capability to honeycomb structure used in the injector will have significant impact on overall mass reduction. Typical thrusters in use for attitude control have 60 90 percent of its mass in the valve and injector, which is typically made from titanium. The combination of material and structure envisioned for use in an SFF thruster design could reduce thruster weight by a factor of two or more. The thrust-to-weight ratios for such designs can achieve 1,000:1 or more, depending on chamber pressure. The potential exists for continued development in materials, size, speed, accuracy of SFF techniques, which can lead to speculative developments of PDFF processes such as fabrication of custom human interface devices like masks, chairs, and clothing, and advanced biomedical application to human organ reconstruction. Other potential applications are: higher fidelity lower cost test fixtures for probes and inspection, disposable thrusters, and ISRU (in situ resource utilization) for component production in space or on Lunar and Martian missions, and application for embedding MEMS (microelectromechanical systems) during construction process of form changing aerostructure/dynamic structures.

Barnes, Daudi↗

NASA NTRS1997

Instability Mechanisms of Thermally-Driven Interfacial Flows in Liquid-Encapsulated Crystal Growth

During the past year, a great deal of effort was focused on the enhancement and refinement of the computational tools developed as part of our previous NASA grant. In particular, the interface mollification algorithm developed earlier was extended to incorporate the effects of surface-rheological properties in order to allow the study of thermocapillary flows in the presence of surface contamination. These tools will be used in the computational component of the proposed research in the remaining years of this grant. A detailed description of the progress made in this area is provided elsewhere. Briefly, the method developed allows for the convection and diffusion of bulk-insoluble surfactants on a moving and deforming interface. The novelty of the method is its grid independence: there is no need for front tracking, surface reconstruction, body-fitted grid generation, or metric evaluations; these are all very expensive computational tasks in three dimensions. For small local radii of curvature there is a need for local grid adaption so that the smearing thickness remains a small fraction of the radius of curvature. A special Neumann boundary condition was devised and applied so that the calculated surfactant concentration has no variations normal to the interface, and it is hence truly a surface-defined quantity. The discretized governing equations are solved subsequently using a time-split integration scheme which updates the concentration and the shape successively. Results demonstrate excellent agreement between the computed and exact solutions.

Haj-Hariri, Hossein↗

DOE OSTI2022

Regulation of Surface Defect Chemistry toward Stable Ni-Rich Cathodes

Surface reconstruction of Ni-rich layered oxides (NLO) degrades the cycling stability and safety of high-energy-density lithium-ion batteries (LIBs), which challenges typical surface-modification approaches to build a robust interface with electrochemical activity. Here, a strategy of leveraging the low-strain analogues of Li- and Mn-rich layered oxides (LMR) to reconstruct a stable surface on the Ni-rich layered cathodes is proposed. The new surface structure not only consists of a gradient chemical composition but also contains a defect-rich structure regarding the formation of oxygen vacancies and cationic ordering, which can simultaneously facilitate lithium diffusion and stabilize the crystal structure during the (de)lithiation. These features in the NLO lead to a dramatic improvement in electrochemical properties, especially the cyclability under high voltage cycling, exhibiting the 30% increase in capacity retention after 200 cycles at the current density of 1 C (3.0-4.6 V). We report the findings offer a facile and effective way to regulate defect chemistry and surface structure in parallel on Ni-rich layered structure cathodes to achieve high-energy density LIBs.

25 ENERGY STORAGE↗

DOE OSTI2021

Distance‐based reconstruction of protein quaternary structures from inter‐chain contacts

Abstract Predicting the quaternary structure of protein complex is an important problem. Inter‐chain residue‐residue contact prediction can provide useful information to guide the ab initio reconstruction of quaternary structures. However, few methods have been developed to build quaternary structures from predicted inter‐chain contacts. Here, we develop the first method based on gradient descent optimization (GD) to build quaternary structures of protein dimers utilizing inter‐chain contacts as distance restraints. We evaluate GD on several datasets of homodimers and heterodimers using true/predicted contacts and monomer structures as input. GD consistently performs better than both simulated annealing and Markov Chain Monte Carlo simulation. Starting from an arbitrarily quaternary structure randomly initialized from the tertiary structures of protein chains and using true inter‐chain contacts as input, GD can reconstruct high‐quality structural models for homodimers and heterodimers with average TM‐score ranging from 0.92 to 0.99 and average interface root mean square distance from 0.72 Å to 1.64 Å. On a dataset of 115 homodimers, using predicted inter‐chain contacts as restraints, the average TM‐score of the structural models built by GD is 0.76. For 46% of the homodimers, high‐quality structural models with TM‐score ≥ 0.9 are reconstructed from predicted contacts. There is a strong correlation between the quality of the reconstructed models and the precision and recall of predicted contacts. Only a moderate precision or recall of inter‐chain contact prediction is needed to build good structural models for most homodimers. Moreover, GD improves the quality of quaternary structures predicted by AlphaFold2 on a Critical Assessment of Techniques for Protein Structure Prediction–Critical Assessments of Predictions of Interactions dataset.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Surface Reconstruction in Hydrated Amphiphilic Block Copolymer Thin Films Probed by Fluid Cell Atomic Force Microscopy

In many thin film materials, nuanced interplays of interfacial energies control the surface morphology and rearrangement. This work evaluates polymer−solvent interactions and solvent-driven surface reconstructions via ex situ and in situ fluid cell Atomic Force Microscopy (fc-AFM) analysis of amphiphilic block copolymer (BCP) thin films upon exposure to deionized (DI) water. We examine the differences in surface morphology, whole-film swelling, and force response in thin films of polystyrene-block-poly(ethylene oxide) (PS-b-PEO) and polystyrene- block-poly[(allyl glycidyl ether)-co-(ethylene oxide)] (PS-b- P[AGE-co-EO]) processed into standing-up cylinder morphologies perpendicular to a silicon substrate (⊥C). Using Amplitude Modulation AFM (AM-AFM) and Amplitude-Phase Distance (APD) force spectroscopy, this work probes the mechanoresponsive nature of the dynamic surface layers of these films, unveiling surface layer stratification and surface chain rearrangement via minimal tip−sample stimulation. To help rationalize the observed reconfigurations, the energetic driving forces were estimated using the harmonic mean approximations of interfacial energies. Given the nonionizable nature of the minority P(AGE-co-EO) block and the energetic driving forces for chain mobility, this work shows how the elimination of unfavorable PS−water interfaces drives chain rearrangement and coverage of the PS surface by chains of the hydrophilic block. This work highlights considerations for increasing the heterogeneity and complexity of BCP thin films via random blocks and how those changes to local interfacial energies may drive larger scale film morphology reconstructions, with broader implications for tuning interface hydrophilicity.

Copolymers↗

DOE OSTI2025

Wide‐Field Bond Quality Evaluation Using Frequency Domain Thermoreflectance with Deep Neural Network Feature Reconstruction

Heterogeneous integration of microelectronic components provides a pathway to improve circuit/component performance; however, this comes with assembly challenges, in particular due to complex interfaces via subsurface bump bonds. The ability of these bonds to transmit electrical signals and conduct heat to the carrier substrate limits component performance. In this work, hyperspectral frequency‐domain thermoreflectance (FDTR) imaging is demonstrated as a robust technique for evaluating the quality of subsurface indium bump bonds in a surrogate microelectronic sample. By performing microscale FDTR imaging with coarse motion image stitching, thermal phase maps that cover a 4 mm by 4 mm field‐of‐view with subsurface feature sensitivity at depths greater than 50 µm are obtained. The resulting FDTR hyperspectral data contains more than three million pixels and reveal the quality of subsurface microbump arrays. Wide‐field analysis of bonded versus gap regions is enabled by deep neural network feature reconstruction, that after training, rapidly provides an interpretable representation of bond quality. Utility of noisy higher frequency FDTR phase maps, i.e., near the computationally predicted sensing depth limit, results in an average prediction error of 11%. Taken together, FDTR with neural network‐based analysis demonstrates subsurface bond monitoring at length scales relevant for heterogeneously integrated microelectronics.

FDTR↗

NASA NTRS2010

Ultrasonic Characterization of Interfaces in Composite Bonds

The inverse determination of imperfect interfaces from reflection spectra of normal and oblique incident ultrasonic waves in adhesive bonds of multidirectional composites is investigated. The oblique measurements are complicated by the highly dispersed nature of oblique wave spectra at frequencies above 3MHz. Different strategies for bond property reconstruction, including a modulation method, are discussed. The relation of measured interfacial spring density to the physico-chemical model of a composite interface described by polymer molecular bonds to emulate loss of molecular strength on an adhesive composite interface is discussed. This potentially relates the interfacial (adhesion) strength (number of bonds at the adhesive substrate interface) to the spring constant (stiffness) area density (flux), which is an ultrasonically measurable parameter.

Wang, N.↗

NASA NTRS1984

Ceramic microstructure and adhesion

When a ceramic is brought into contact with a ceramic, a polymer, or a metal, strong bond forces can develop between the materials. The bonding forces will depend upon the state of the surfaces, cleanliness and the fundamental properties of the two solids, both surface and bulk. Adhesion between a ceramic and another solid are discussed from a theoretical consideration of the nature of the surfaces and experimentally by relating bond forces to interface resulting from solid state contact. Surface properties of ceramics correlated with adhesion include, orientation, reconstruction and diffusion as well as the chemistry of the surface specie. Where a ceramic is in contact with a metal their interactive chemistry and bond strength is considered. Bulk properties examined include elastic and plastic behavior in the surficial regions, cohesive binding energies, crystal structures and crystallographic orientation. Materials examined with respect to interfacial adhesive interactions include silicon carbide, nickel zinc ferrite, manganese zinc ferrite, and aluminum oxide. The surfaces of the contacting solids are studied both in the atomic or molecularly clean state and in the presence of selected surface contaminants.

Buckley, D. H.↗