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At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Technical note: A modified formulation of dynamic energy budget theory for faster computation of biological growth

Abstract. The mass conservation equation in the presence of boundary fluxes and chemical reactions from non-equilibrium thermodynamics is used to derive a modified dynamic energy budget (mDEB) model. Compared to the standard dynamic energy budget (sDEB) model (Kooijman, 2009), this modified formulation does not place the dilution effect in the mobilization kinetics of reserve biomass, and it maintains the partition principle for reserve mobilization dynamics for both linear and non-linear kinetics. Overall, the mDEB model shares most features with the sDEB model. However, for biological growth that requires multiple nutrients, the mDEB model is computationally much more efficient by not requiring numerical iterations for obtaining the specific growth rate. In an example of modeling the growth of Thalassiosira weissflogii in a nitrogen-limiting chemostat, the mDEB model was found to have almost the same accuracy as the sDEB model while requiring almost half of the computing time of the sDEB model. Since the sDEB model has been successfully applied in numerous studies, we believe that the mDEB model can help improve the modeling of biological growth and the associated ecosystem processes in various contexts.

Tang, Jinyun↗
DOE OSTI2022

Beyond carbon flux partitioning: Carbon allocation and nonstructural carbon dynamics inferred from continuous fluxes

Carbon (C) allocation and nonstructural carbon (NSC) dynamics play essential roles in plant growth and survival under stress and disturbance. However, quantitative understanding of these processes remains limited. Here, in this work, we propose a framework where we connect commonly measured carbon cycle components (eddy covariance fluxes of canopy CO 2 exchange, soil CO 2 efflux, and allometry-based biomass and net primary production) by a simple mass balance model to derive ecosystem-level NSC dynamics (NSC i ), C translocation (dC i ), and the biomass production efficiency (BPE i ) in above- and belowground plant (i = agp and bgp) compartments. We applied this framework to two long-term monitored loblolly pine (Pinus taeda) plantations of different ages in North Carolina and characterized the variations of NSC and allocation in years under normal and drought conditions. The results indicated that the young stand did not have net NSC flux at the annual scale, whereas the mature stand stored a near-constant proportion of new assimilates as NSC every year under normal conditions, which was comparable in magnitude to new structural growth. Roots consumed NSC in drought and stored a significant amount of NSC post drought. The above- and belowground dC i and BPE i varied more from year to year in the young stand and approached a relatively stable pattern in the mature stand. The belowground BPE bgp differed the most between the young and mature stands and was most responsive to drought. With the internal C dynamics quantified, this framework may also improve biomass production estimation, which reveals the variations resulting from droughts. Overall, these quantified ecosystem-scale dynamics were consistent with existing evidence from tree-based manipulative experiments and measurements and demonstrated that combining the continuous fluxes as proposed here can provide additional information about plant internal C dynamics. Given that it is based on broadly available flux data, the proposed framework is promising to improve the allocation algorithms in ecosystem C cycle models and offers new insights into observed variability in soil–plant–climate interactions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Adaptive_Evolution_2026

Thermoanaerobacterium saccharolyticum, an anaerobic and thermophilic bacterium capable of metabolizing sugar monomers and soluble oligomers into ethanol, has been proposed for use in consolidated bioprocessing in coculture with compatible cellulolytic bacteria such asClostridium thermocellum. Although the mixed acid fermentation of both of these strains has been engineered to produce ethanol as the major fermentation product, the maximum titer produced thus far byC. thermocellum, about 3% (w/v) ethanol, is half that produced byT. saccharolyticum. There is thus motivation to understand the mechanistic basis of the robust ethanol pathway inT. saccharolyticumso that key features can be recapitulated inC. thermocellumand other organisms.Previously, we characterized theindividualrole of the main genes responsible for electron transfer in the ethanol production ofT. saccharolyticum. However, the consequences of thecombinedloss of function of all these genes have not been investigated, nor has the way in which fermentative metabolism adapts to such constraints. In this work, we combined knockouts of ferredoxin nicotinamide oxidoreductase (fnor) genes (nfnAandnfnB) and hydrogenase genes (hydAandhfsD) and studied their effects on fermentation and grow. We showed that these genetic modifications together impair growth and decrease electron transfer from reduced ferredoxin, thereby redirecting flux from the pyruvate ferredoxin oxidoreductase enzyme to the pyruvate formate lyase enzyme. We also performed adaptive evolution of these mutants to rescue their growth, and most notably, we observed a single nucleotide variation in the alcohol dehydrogenaseadhAgene. Through molecular dynamics simulations and enzymatic assays, we determined that this point mutation causes a structural change that impairs the AdhA specificity for the NADPH cofactor and increases NADH-linked activity to restore redox balance. These findings consolidate our understanding of the functioning of electron transfer pathways in this organism.

alcohol dehydrogenase↗
DOE OSTI2026

Modification of ion-temperature-gradient turbulence by impurities in stellarator plasmas

Recent nonlinear gyrokinetic simulations have shown that impurities can strongly modify the turbulent heat flux in stellarator plasmas. Here, the ion-temperature-gradient (ITG) dispersion relation in a plasma containing impurities is analytically solved in certain limits and an expression for the modification of the ITG growth rate by impurities is derived. The analytical expression is the sum of three terms corresponding to three different physical causes (impurity density gradient, impurity temperature gradient and dilution) of the change in the growth rate. The scalings predicted analytically for the modification of the growth rate are shown to be reproduced by linear gyrokinetic simulations. The conditions for reduction or increase of the ITG growth by impurities are also correctly predicted by the analytical solution to the dispersion relation. Finally, a remarkable correlation is found between the analytical expression for the modification of the growth rate and the modification of the turbulent heat flux obtained from nonlinear gyrokinetic simulations.

Calvo, Iván [Research Centre for Energy, Environme↗
DOE OSTI2025

Growth of Hexagonal Boron Nitride from Molten Nickel Solutions: A Reactive Molecular Dynamics Study

Metal flux methods are excellent for synthesizing high-quality hexagonal boron nitride (hBN) crystals, but the atomic mechanisms of hBN nucleation and growth in these systems are poorly understood and difficult to probe experimentally. Here, we harness classical reactive molecular dynamics (ReaxFF) to unravel the mechanisms of hBN synthesis from liquid nickel solvent over time scales up to 30 ns. These simulations mimic experimental conditions by including relatively large liquid nickel slabs containing dissolved boron and a molecular nitrogen gas phase. Overall, the reaction takes place almost exclusively on the surface of the liquid nickel, owing to the low solubility of nitrogen in bulk nickel and the intermediate species’ preference for the metal–gas interface. The formation of hBN invariably begins by reaction of dinitrogen with nickel-solvated boron atoms at the surface, forming intermediate N–N–B species, which typically evolve into B–N–B units through a short-lived intermediate where a single nitrogen atom is coordinated by one nitrogen and two boron atoms. The resulting B–N–B units, in turn, coalesce with growing hBN nuclei and carry nitrogen between hBN nanocrystals in an Ostwald ripening process. The amount of hBN produced on the tens of nanosecond time scale depends critically on the boron concentration, while having a much weaker dependence on the N 2 pressure for the regime considered (N 2 pressures of 2.5–10 MPa, Ni–B solutions with 6–12% boron by atom fraction). The highest rate of hBN formation occurs at the lowest temperature considered (1750 K, just above the melting point of nickel), while no hBN sheets are formed at 2000 K or above. An analysis of the transition pathways for nitrogen atoms shows that the final step, incorporation of small B–N motifs into larger hBN sheets, is the rate-limiting step in the regimes considered. While raising the temperature from 1750 to 2000 K has little effect on the formation of intermediates (N–N–B, B–N–B, etc.), the lack of large hBN sheets at temperatures >1900 K is explained by decreased probability of the final step and increased probability of breakup of hBN into B–N motifs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Morning boundary layer conditions for shallow to deep convective cloud evolution during the dry season in the central Amazon

Observations of the boundary layer (BL) processes are analyzed statistically for dry seasons of 2 years and in detail, as case studies, for 4 shallow convective days (ShCu) and 4 shallow-to-deep convective days (ShDeep) using a suite of ground-based measurements from the Observation and Modeling of the Green Ocean Amazon (GoAmazon 2014/5) Experiment. The BL stages in ShDeep days, from the nighttime to the cloudy mixing layer stage, are then described in comparison with ShCu days. Atmospheric thermodynamics and dynamics, environmental profiles, and surface turbulent fluxes were employed to compare these two distinct situations for each stage of the BL evolution. Particular attention is given to the morning transition stage, in which the BL changes from stable to unstable conditions in the early morning hours. Results show that the decrease in time duration of the morning transition on ShDeep days is associated with high humidity and well-established vertical wind shear patterns. Higher humidity since nighttime not only contributes to lowering the cloud base during the rapid growth of the BL but also contributes to the balance between radiative cooling and turbulent mixing during nighttime, resulting in higher sensible heat flux in the early morning. The sensible heat flux promotes rapid growth of the well-mixed layer, thus favoring the deeper BL starting from around 08:00 LST (UTC-4 h). Under these conditions, the time duration of morning transition is used to promote convection, having an important effect on the convective BL strength and leading to the formation of shallow cumulus clouds and their subsequent evolution into deep convective clouds. Statistical analysis was used to validate the conceptual model obtained from the case studies. Despite the case-to-case variability, the statistical analyses of the processes in the BL show that the described processes are very representative of cloud evolution during the dry season.

54 ENVIRONMENTAL SCIENCES↗
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 OSTI2023

Phase Discovery and Selected Synthesis of Subvalent Niobium Tellurides Using a Polytelluride Flux Strategy

Transition metal subchalcogenides involve electron-rich metals and can facilitate an in-depth understanding of the relationships among quantum properties such as superconductivity, charge density wave, and topological band structures. However, effective experimental routes toward synthesizing transition metal subchalcogenides are still lacking, hindering the development of new quantum materials. Herein, we propose a eutectic polytelluride flux strategy as an excellent solution to address phase discovery and crystal growth in transition metal subtelluride systems. We report new phases easily and selectively synthesized using a eutectic “K 3 Te 4 ” polytelluride flux upon adjusting the ratio of Nb metal to flux in the starting materials (K/Nb/Te = 3:x:4). Using a high Nb content in the solvent (x = 2 and 1), crystals of KNb 3 Te 3 O 0.38 and K 0.9 Nb 3 Te 4 are obtained. Both subtellurides exhibit diverse Nb clusters, including face-sharing and edge-sharing Nb 6 octahedral columns and zig-zag Nb chains. Reducing the Nb content to x = 0.33 leads to the formation of a layered compound, K 1.06 NbTe 2 . This compound comprises a NbTe 6 trigonal prism with K intercalated between the layers. Single crystals of known binary Nb tellurides can also be grown using another eutectic flux “KTe 3 . 2 ”, and the obtained NbTe 2 exhibits a new polymorphism with extra trimerization along the b-axis in the Nb–Nb bonded double zig-zag cluster. Finally, precise control over the structural dimensionality and oxidation state, combined with the facile crystal growth process, makes our synthetic strategy an efficient route to explore quantum materials in transition metal subchalcogenides.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Molecular beam epitaxy growth of IrO 2 using plasma-only oxidation

Growth of IrO 2 films via molecular beam epitaxy (MBE) using an oxygen plasma as the sole oxidant is demonstrated for the first time. We investigate the oxidizing conditions required for IrO 2 by characterizing the species present in the plasma using optical emission spectroscopy and comparing the thermodynamic equilibrium between Ir/IrO 2 under atomic and molecular oxygen. Across the pressure range accessible, monatomic oxygen was the primary reactive species present in the plasma. IrO 2 films were grown under varying Ir flux, oxygen pressure, and substrate temperature to understand growth thermodynamics and kinetics. Structural characterization assessed film phase and composition, crystallinity, strain, and surface morphology. The optimized films from this study validate plasma-only reactive growth by MBE as a successful method for growing IrO 2 .

36 MATERIALS SCIENCE↗
DOE OSTI2022

Plasma-Assisted Epitaxy of Piezoelectric Sc x Al 1-x N Films on Sapphire for Use in Harsh-Environment Microwave Acoustic Sensors

The Sc x Al 1-x N wurtzite structure has been shown theoretically and experimentally to exhibit significantly higher piezoelectric coupling compared to pure AlN. In this work, a plasma-assisted epitaxial growth method has been used to synthesize epitaxial (0002) Sc x Al 1-x N films on c-sapphire substrates from x = 0.07 to 0.30 by co-evaporating high-purity Sc and Al sources in the presence of a nitrogen plasma generated by an RF plasma source. Epitaxial Sc x Al 1-x N films with highly oriented (0002) grains and in-plane registry were produced on c-sapphire substrates that were pre-exposed to the nitrogen plasma to form an oxynitride seed layer. Growth of Sc x Al 1-x N films was carried out at 930°C under both metal-rich and N-rich conditions using precisely controlled Sc, Al, and N-plasma fluxes. Metal-rich depositions yielded non-(0002)-oriented Sc x Al 1-x N grains and intermetallic ScAl grains. Nitrogen-rich growth with a Sc/Al flux ratio of 1/3 produced the best (0002) epitaxy as determined by x-ray diffraction analysis. Surface acoustic wave resonator (SAWR) devices were fabricated from 500-nm-thick Sc x Al 1-x N and AlN films to extract their electromechanical coupling coefficients, k 2 . As the Sc concentration in the films increases, the degree of (0002) epitaxy is reduced, yet the value of k 2 increases becasue there is more Sc in the wurzite lattice despite the decreased level of (0002) grain alignment. As a result, the use of a 10-nm-thick Si x N y capping layer on top of the Sc x Al 1-x N films aids in preventing etching during SAWR device photolithography and also helps hinder film oxidation up to 800°C.

36 MATERIALS SCIENCE↗
DOE OSTI2021

A Bi-Layer Dense/Porous Solid Electrolyte Interphase for Enhanced Lithium-Metal Stability

Due to its high theoretical capacity and low electrochemical potential, lithium metal is a highly investigated anode for next-generation high-energy batteries. However, the unstable chemical and topographical heterogeneous surface of lithium gives rise to safety and efficiency concerns that prevent it from being utilized in practical applications. Exposure to electrolyte leads to non-uniform, mixed organic-inorganic solid-electrolyte interphase (SEI) formation, starting a cascading to non-uniform flux distribution, consumption of active materials, and dendrite growth. The SEI is the key feature that will lead to harnessing the capabilities possible with lithium metal. In this work, the formation of a closed-host bi-layer solid electrolyte interphase (SEI) improves the stability of lithium anode. This is successfully realized by forming an interconnected porous LiF-rich artificial SEI in contact with Li metal, and a dense, stable in-situ formed upper layer SEI. The porous layer increases the number of Li/LiF interfaces, which reduces local volume fluctuations and improves Li+ diffusion along these interfaces. Additionally, the tortuous porous structure guides uniform Li+ flux distribution and mechanically suppresses dendrite propagation. The dense upper layer of the SEI accomplishes a closed-host design through reaction with LiNO3 additive and prevents continuous consumption of active materials seen without the additive included in the electrolyte. The duality of a dense top layer with porous bottom layer led to extended cycle life and improved rate performance, evidenced with symmetric cell testing, as well as full cell testing paired with sulfur and LiFePO4 (LFP) cathodes. This work is a good example of a rational design of the SEI, based on comprehensive consideration of various critical factors to improve Li-metal anode stability, and highlights a new pathway to improve cycling and rate performances of Li metal batteries.

25 ENERGY STORAGE↗
DOE OSTI2026

Implementing belowground controls on nutrient uptake in ELMv2-SPRUCE improves representation of a boreal peatland ecosystem

Boreal peatlands store 13 %–32 % of the global soil carbon (C) stock, a service dependent on plant-mycorrhizal fungi associations. In these nutrient poor systems, ectomycorrhizal and ericoid mycorrhizal fungi supply up to >80 % of the nutrient requirements of their plant hosts, partly with mined nitrogen (N) and phosphorus (P) from soil organic matter that are otherwise inaccessible to plants. Despite the ecological significance, mycorrhizal associations are only represented in a few land surface or ecosystem models. We modify the peatland branch of version 2 of the Energy Exascale Earth System Land Model (ELMv2-SPRUCE) to replace the default photosynthesis-driven inorganic N and P (NP) uptake process with a more realistic representation of the process via three pathways: (1) direct inorganic NP uptake by uncolonized fine roots, (2) indirect inorganic NP acquisition and (3) indirect NP acquisition from organic sources by mycorrhizal roots. We systematically evaluated the performance of the default and modified models with field observations from a whole ecosystem warming and carbon dioxide fertilization experimental site: Spruce and Peatland Responses Under Changing Environment (SPRUCE), in northern Minnesota, USA. The modified model reduces the underestimation of the growth response of shrubs in the default model to warming from 40 %–80 % to 17 %–35 % and reduces the overall relative absolute error on C fluxes from 1.61 to 1.54 in calibration. Improvements on modeled shrub growths and shrub-moss community net ecosystem exchanges are also seen in validation. The improved growth response of shrubs to warming is accompanied by several-fold increase in direct inorganic NP uptake and decrease in fungal colonization rate. The modified model simulates a smaller magnitude of transition of the ecosystem from C sink to C source under warming due to alleviation of plant nutrient limitation. Equifinality analysis shows the newly added parameters in the modified model can be constrained by the observed C fluxes. Sensitivity analysis shows the newly added parameters have stronger statistical interactions than the preexisting parameters in the default model. Overall, the modified model is an improvement over the default ELMv2-SPRUCE and will be a useful tool for understanding boreal peatland change.

Wang, Yaoping [Oak Ridge National Laboratory (ORNL↗
DOE OSTI2024

Safety First: Stability and Dissipation of Line-tied Force-free Flux Tubes in Magnetized Coronae

Abstract Magnetized plasma columns and extended magnetic structures with both footpoints anchored to a surface layer are an important building block of astrophysical dissipation models. Current loops shining in X-rays during the growth of plasma instabilities are observed in the corona of the Sun and are expected to exist in highly magnetized neutron star magnetospheres and accretion disk coronae. For varying twist and system sizes, we investigate the stability of line-tied force-free flux tubes and the dissipation of twist energy during instabilities using linear analysis and time-dependent force-free electrodynamics simulations. Kink modes ( m = 1) and efficient magnetic energy dissipation develop for plasma safety factors q ≲ 1, where q is the inverse of the number of magnetic field line windings per column length. Higher-order fluting modes ( m > 1) can distort equilibrium flux tubes for q > 1 but induce significantly less dissipation. In our analysis, the characteristic pitch μ ˜ 0 of flux-tube field lines determines the growth rate ( ∝ μ ˜ 0 3 ) and minimum wavelength of the kink instability ( ∝ μ ˜ 0 − 1 ). We use these scalings to determine a minimum flux tube length for the growth of the kink instability for any given μ ˜ 0 . By drawing analogies to idealized magnetar magnetospheres with varying regimes of boundary shearing rates, we discuss the expected impact of the pitch-dependent growth rates for magnetospheric dissipation in magnetar conditions.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

TEM turbulence in simulation and experiment in quasisymmetric and degraded-symmetry configurations of the HSX stellarator

The Helically Symmetric Experiment (HSX) has demonstrated reduced neoclassical transport and flow damping with quasisymmetry, but the difference of turbulent transport between quasisymmetric and degraded-symmetry configurations has not been definitively assessed. Profile analysis presented here shows that anomalous transport at the mid-radius is larger with degraded quasisymmetry when temperature and density profiles are matched. An initial comparison (${T_\mathrm{i}/T_\mathrm{e}} = 1$) between the quasisymmetric and degraded symmetry configurations finds that trapped-electron mode (TEM) turbulence can support larger heat fluxes in the degraded symmetry configuration despite smaller linear growth rates. However, further simulations at the experimental temperature ratio ($T_\mathrm{i}/T_\mathrm{e} = 0.2$) do not reproduce this effect. Experimental measurements of heat transport and density fluctuation amplitude are compared to nonlinear gyrokinetic simulations at the experimental temperature ratio. The heat flux and density fluctuation amplitude in simulation reproduce a substantial dependence on the density gradient, and the simulated heat flux matches measurements within experimental uncertainties, indicating that TEM turbulence is responsible for the anomalous transport at the steep density gradient in HSX.

HSX↗
DOE OSTI2022

Vapor transport growth of MnBi 2 Te 4 and related compounds

Motivated by fine tuning of the magnetic and topological properties of MnBi 2 Te 4 via defect engineering, in this work, we report the crystal growth of MnBi 2 Te 4 and related compounds using vapor transport method and crystal characterization by measuring elemental ratio, magnetic and transport properties, and scanning tunneling microscopy. For the growth of MnBi 2 Te 4 single crystals, I 2 , MnI 2 , MnCl 2 , TeCl 4 , and MoCl 5 are all effective transport agents; chemical transportation occurs faster in the presence of iodides than chlorides. We further successfully grow MnSb 2 Te 4 , MnBi 2-x Sb x Te 4 , and Sb-doped MnBi 4 Te 7 crystals. A small temperature gradient< 20°C between the hot and cold ends of the growth ampoule is critical for the successful crystal growth of MnBi 2 Te 4 and related compounds. Compared to flux grown crystals, vapor transported crystals tend to be Mn stoichiometric, and Sb-bearing compositions have more Mn/Sb site mixing. The vapor transport growth provides a new materials synthesis approach to fine tune the magnetic and topological properties of these intrinsic magnetic topological insulators where controlling defects is vital.

36 MATERIALS SCIENCE↗
DOE OSTI2025

A dynamic protein interactome drives energy conservation and electron flux in Thermococcus kodakarensis

ABSTRACT Life is supported by energy gains fueled by catabolism of a wide range of substrates, each reliant on the selective partitioning of electrons through redox ( red uction and ox idation) reactions. Electron flux through tunable and regulated protein interactions provides dynamic routes for energy conservation, but how electron flux is regulated in vivo , particularly for archaeal metabolisms that support rapid growth at the thermodynamic limits of life, is poorly understood. Identification of bona fide in vivo protein assemblies and how such assemblies dictate the totality of electron flux is critical to our understanding of the regulation imposed on metabolism, energy production, and energy conservation. Here, 25 key proteins in central metabolic redox pathways in the model, genetically accessible, hyperthermophilic archaeon Thermococcus kodakarensis , were purified to reveal an extensive, dynamic, and tightly interconnected network of protein interactions that responds to environmental cues (such as the availability of various reductive sinks) to direct electron flux to maximize energetic gains. Interactions connecting disparate functions suggest many catabolic and anabolic activities occur in spatial proximity in vivo , and while protein complexes have been historically defined under optimal conditions, many of these complexes appear to maintain alternative partnerships in changing conditions. The totality of the results obtained redefines our understanding of in vivo assemblies driving ancient metabolic strategies supporting the growth of modern Archaea. IMPORTANCE Given the potential for rational genetic manipulations of biofuel- and biotech-promising archaea to yield transformative results for major markets, it is a priority to define how the metabolisms of such species are controlled, at least in part, by in vivo protein assemblies, and from such, define routes of energy flux that can be most efficiently altered toward biofuel or biotechnological gains. Proteinaceous electron carriers (PECs, such as ferredoxins) offer the potential for specific protein–protein interactions to coordinate selective reductive flow. Employing the model, genetically accessible, hyperthermophilic archaeon, Thermococcus kodakarensis , we establish the metabolic protein interactome of 25 key redox proteins, revealing that each redox active protein has a dynamic partnership profile, suggesting catabolic and anabolic activities may occur in concert and in temporal and spatial proximity in vivo . These results reveal critical importance in evaluating the newly identified partnerships and their role and utility in providing regulated redox flux in T. kodakarensis .

Williams, Sere A. (ORCID:0000000235509590)↗
DOE OSTI2021

Self-assembled nanocolumns in Bi 2 Se 3 grown by molecular beam epitaxy

Layered van der Waals (vdW) materials grown by physical vapor deposition techniques are generally assumed to have a weak interaction with the substrate during growth. This leads to films with relatively small domains that are usually triangular and a terraced morphology. In this paper, we demonstrate that Bi 2 Se 3 , a prototypical vdW material, will form a nano-column morphology when grown on GaAs(001) substrates. This morphology is explained by a relatively strong film/substrate interaction, long adatom diffusion lengths, and a high reactive selenium flux. In conclusion, this discovery paves the way toward growth of self-assembled vdW structures even in the absence of strain.

36 MATERIALS SCIENCE↗