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At least 973 records · Page 54
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Distinct Composition‐Dependent Topological Hall Effect in Mn 2‐x Zn x Sb

Abstract Spintronics, an evolving interdisciplinary field at the intersection of magnetism and electronics, explores innovative applications of electron charge and spin properties for advanced electronic devices. The topological Hall effect (THE), a key component in spintronics, has gained significance due to emerging theories surrounding noncoplanar chiral spin textures. This study focuses on Mn 2‐x Zn x Sb, a material crystalizing in centrosymmetric space group with rich magnetic phases tunable by Zn contents. Through comprehensive magnetic and transport characterizations, we found that the high‐Zn ( x > 0.6) samples display THE which is enhanced with decreasing temperature, while THE in the low‐Zn ( x < 0.6) samples show an opposite trend. The coexistence of those distinct temperature dependencies for THE suggests very different magnetic interactions/structures for different compositions and underscores the strong coupling between magnetism and transport in Mn 2‐x Zn x Sb. The findings contribute to understanding topological magnetism in centrosymmetric tetragonal lattices, establishing Mn 2‐x Zn x Sb as a unique platform for exploring tunable transport effects and opening avenues for further exploration in the realm of spintronics.

Nabi, Md Rafique Un↗
DOE OSTI2020

Briquetting characteristics of woody and herbaceous biomass blends: Impact on physical properties, chemical composition, and calorific value

Abstract Intercropping (or polyculture) is gaining a lot of interest as it increases yields, allows better utilization of resources (water and nutrients), and provides better land management. The objective of this study is to understand the briquetting characteristics of woody and herbaceous biomass blends, which might result from intercropping. Tests were conducted on blends of lodgepole pine, switchgrass, and corn stover biomass using three hammer mill screen sizes (i.e., 4.8, 12.7, and 19.05 mm), three blend moistures (12%, 15%, and 18%, w.b.), and two‐ and three‐blend ratios (i.e., 1:1 and 1:1:1) using a pilot‐scale hydraulic briquette press. The briquette properties, such as unit and bulk density, durability rating after 5 days of storage (as they tend to attain stable density), and the energy consumption of the process were measured. The results indicate that moisture content of 12% and 15% (w.b.) and smaller hammer mill screen size of 4.8 mm increased the unit and bulk densities to >750 and >430 kg/m 3 and moisture content (15% and 18% (w.b.)) and hammer mill screen size of 12.7 and 19.05 mm produced briquettes with durability rating values of >95%. The higher moisture content of 18% (w.b.) and the hammer mill screen size of 12.7 and 19.05 mm had the highest energy consumption. The proximate and ultimate analysis showed that energy content improved by blending lodgepole pine with both corn stover and switchgrass and also showed increased calorific value and reduced ash content. Scanning electron microscopy micrographs showed interlocking of particles and cracks in the briquettes. © 2020 Society of Chemical Industry and John Wiley & Sons, Ltd

Tumuluru, Jaya Shankar↗
DOE OSTI2020

Restoration and Modification of Magnetosome Biosynthesis by Internal Gene Acquisition in a Magnetotactic Bacterium

We report that the Integration of a large-sized DNA fragment into a chromosome is an important strategy for characterization of cellular functions in microorganisms. Magnetotactic bacteria synthesize intracellular organelles comprising membrane-bound single crystalline magnetite, also referred to as magnetosomes. Magnetosomes have gained interest in both scientific and engineering sectors as they can be utilized as a material for biomedical and nanotechnological applications. Although genetic engineering of magnetosome biosynthesis mechanism has been investigated, the current method requires cumbersome gene preparation processes. Here, the chromosomal integration of a plasmid containing ≈27 magnetosome genes (≈26 kbp region) in a non-magnetic mutant of Magnetospirillum magneticum AMB-1 using a broad-host-range plasmid is shown. The genome sequencing of gene-complemented strains reveals the chromosomal integration of the plasmid with magnetosome genes at a specific site, most likely by catalysis of an endogenous transposase. Magnetosome production is successfully enhanced by integrating a variation of magnetosome gene operons in the chromosome. This chromosomal integration mechanism will allow the design of functional magnetosomes de novo and M. magneticum AMB-1 may be used as a chassis for the designed magnetosome production.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Kinetic modeling of microbial growth, enzyme activity, and gene deletions: An integrated model of β-glucosidase function in Cellvibrio japonicus

Understanding the complex growth and metabolic dynamics in microorganisms requires advanced kinetic models containing both metabolic reactions and enzymatic regulation to predict phenotypic behaviors under different conditions and perturbations. Most current kinetic models lack gene expression dynamics and are separately calibrated to distinct media, which consequently makes them unable to account for genetic perturbations or multiple substrates. This challenge limits our ability to gain a comprehensive understanding of microbial processes towards advanced metabolic optimizations that are desired for many biotechnology applications. Here, we present an integrated computational and experimental approach for the development and optimization of mechanistic kinetic models for microbial growth and metabolic and enzymatic dynamics. Our approach integrates growth dynamics, gene expression, protein secretion, and gene-deletion phenotypes. We applied this methodology to build a dynamic model of the growth kinetics in batch culture of the bacterium Cellvibrio japonicus grown using either cellobiose or glucose media. The model parameters were inferred from an experimental data set using an evolutionary computation method. The resulting model was able to explain the growth dynamics of C. japonicus using either cellobiose or glucose media and was also able to accurately predict the metabolite concentrations in the wild-type strain as well as in β-glucosidase gene deletion mutant strains. We validated the model by correctly predicting the non-diauxic growth and metabolite consumptions of the wild-type strain in a mixed medium containing both cellobiose and glucose, made further predictions of mutant strains growth phenotypes when using cellobiose and glucose media, and demonstrated the utility of the model for designing industrially-useful strains. Importantly, the model is able to explain the role of the different β-glucosidases and their behavior under genetic perturbations. Here, this integrated approach can be extended to other metabolic pathways to produce mechanistic models for the comprehensive understanding of enzymatic functions in multiple substrates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Engineering Clostridium cellulovorans for highly selective n ‐butanol production from cellulose in consolidated bioprocessing

Abstract Cellulosic n ‐butanol from renewable lignocellulosic biomass has gained increased interest. Previously, we have engineered Clostridium cellulovorans , a cellulolytic acidogen, to overexpress the bifunctional butyraldehyde/butanol dehydrogenase gene adh E2 from C. acetobutylicum for n ‐butanol production from crystalline cellulose. However, butanol production by this engineered strain had a relatively low yield of approximately 0.22 g/g cellulose due to the coproduction of ethanol and acids. We hypothesized that strengthening the carbon flux through the central butyryl‐CoA biosynthesis pathway and increasing intracellular NADH availability in C. cellulovorans adh E2 would enhance n ‐butanol production. In this study, thiolase ( thl A CA ) from C. acetobutylicum and 3‐hydroxybutyryl‐CoA dehydrogenase ( hbd CT ) from C. tyrobutyricum were overexpressed in C. cellulovorans adh E2 to increase the flux from acetyl‐CoA to butyryl‐CoA. In addition, ferredoxin‐NAD(P) + oxidoreductase ( fnr ), which can regenerate the intracellular NAD(P)H and thus increase butanol biosynthesis, was also overexpressed. Metabolic flux analyses showed that mutants overexpressing these genes had a significantly increased carbon flux toward butyryl‐CoA, which resulted in increased production of butyrate and butanol. The addition of methyl viologen as an electron carrier in batch fermentation further directed more carbon flux towards n ‐butanol biosynthesis due to increased reducing equivalent or NADH. The engineered strain C. cellulovorans adh E2‐ fnr CA ‐ thl A CA ‐ hbd CT produced n ‐butanol from cellulose at a 50% higher yield (0.34 g/g), the highest ever obtained in batch fermentation by any known bacterial strain. The engineered C. cellulovorans is thus a promising host for n ‐butanol production from cellulosic biomass in consolidated bioprocessing.

Bao, Teng↗
DOE OSTI2023

Reductive amination cascades in cell‐free and resting whole cell formats for valorization of lignin deconstruction products

Abstract The selective introduction of amine groups within deconstruction products of lignin could provide an avenue for valorizing waste biomass while achieving a green synthesis of industrially relevant building blocks from sustainable sources. Here, we built and characterized enzyme cascades that create aldehydes and subsequently primary amines from diverse lignin‐derived carboxylic acids using a carboxylic acid reductase (CAR) and an ω‐transaminase (TA). Unlike previous studies that have paired CAR and TA enzymes, here we examine multiple homologs of each of these enzymes and a broader set of candidate substrates. In addition, we compare the performance of these systems in cell‐free and resting whole‐cell biocatalysis formats using the conversion of vanillate to vanillyl amine as model chemistry. We also demonstrate that resting whole cells can be recycled for multiple batch reactions. We used the knowledge gained from this study to produce several amines from carboxylic acid precursors using one‐pot biocatalytic reactions, several of which we report for the first time. These results expand our knowledge of these industrially relevant enzyme families to new substrates and contexts for environmentally friendly and potentially low‐cost synthesis of diverse aryl aldehydes and amines.

Biotechnology & Applied Microbiology↗
DOE OSTI2024

Oleaginous Yeast Biology Elucidated With Comparative Transcriptomics

ABSTRACT Extremophilic yeasts have favorable metabolic and tolerance traits for biomanufacturing‐ like lipid biosynthesis, flavinogenesis, and halotolerance – yet the connection between these favorable phenotypes and strain genotype is not well understood. To this end, this study compares the phenotypes and gene expression patterns of biotechnologically relevant yeasts Yarrowia lipolytica , Debaryomyces hansenii , and Debaryomyces subglobosus grown under nitrogen starvation, iron starvation, and salt stress. To analyze the large data set across species and conditions, two approaches were used: a “network‐first” approach where a generalized metabolic network serves as a scaffold for mapping genes and a “cluster‐first” approach where unsupervised machine learning co‐expression analysis clusters genes. Both approaches provide insight into strain behavior. The network‐first approach corroborates that Yarrowia upregulates lipid biosynthesis during nitrogen starvation and provides new evidence that riboflavin overproduction in Debaryomyces yeasts is overflow metabolism that is routed to flavin cofactor production under salt stress. The cluster‐first approach does not rely on annotation; therefore, the coexpression analysis can identify known and novel genes involved in stress responses, mainly transcription factors and transporters. Therefore, this work links the genotype to the phenotype of biotechnologically relevant yeasts and demonstrates the utility of complementary computational approaches to gain insight from transcriptomics data across species and conditions.

Weintraub, Sarah J. [Department of Bioinformatics ↗
DOE OSTI2021

Activity-based protein profiling of chitin catabolism

Microbial catabolism of chitin, a highly abundant component of polymeric organic matter worldwide, is a fundamental cog in the carbon and nitrogen cycles that govern CO2 emissions, nutrient dynamics in aquatic systems, and soil vitality. Despite this critical biogeochemical function, we have a poor understanding of the synergy between various microbial chitinases and key accessory enzymes involved in chitin catabolism. We designed and synthesized activity-based probes (ABPs) for profiling active chitinolytic enzymes by modifying the chitin derivatives N-acetyl glucosamine and chitotriose. The ABPs were used to determine the active complement of chitinolytic enzymes produced over time by the soil bacterium Cellvibrio japonicus treated with various C substrates. This approach allowed us to demonstrate the utility of these ABPs in determining the intricate synergy between chitinases and other glycoside hydrolases that microbes employ to catabolize chitin. The strategy can be used to gain molecular level insights that can be used to better understand microbial roles in soil C and N cycling in the face of a changing climate.

Zegeye, Elias↗
DOE OSTI2022

Fluxionality of Subnano Clusters Reshapes the Activity Volcano of Electrocatalysis

The Sabatier activity volcano provides intuitive guide for catalyst design, but also imposes fundamental limitations on the composition and maximal activity of catalysts. Here we show that the ORR activity volcano is shifted and reshaped by the potential-dependent fluxionality of subnano cluster catalysts. Fluxionality causes the typically under-binding Ag/Au to gain optimal activity in the cluster form, and surpass Pt/Pd. Furthermore, isomerization of clusters as a function of the potential breaks linear scaling relationships, enabling surpassing the volcano “apex” relative to the bulk. The effect is likely general for fluxional cluster catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Radiation‐Induced Defects in Uranyl Trinitrate Solids

Abstract Actinides are inherently radioactive; thus, ionizing radiation is emitted by these elements can have profound effects on its surrounding chemical environment through the formation of free radical species. While previous work has noted that the presence of free radicals in the system impacts the redox state of the actinides, there is little atomistic understanding of how these metal cations interact with free radicals. Herein, we explore the effects of radiation (UV and γ) on three U(VI) trinitrate complexes, M[UO 2 (NO 3 ) 3 ] (where M=K + , Rb + , Cs + ), and their respective nitrate salts in the solid state via electron paramagnetic resonance (EPR) and Raman spectroscopy paired with Density Functional Theory (DFT) methods. We find that the alkali salts form nitrate radicals under UV and γ irradiation, but also note the presence of additional degradation products. M[UO 2 (NO 3 ) 3 ] solids also form nitrate radicals and additional DFT calculations indicate the species corresponds to a change from the bidentate bound nitrate anion into a monodentate NO 3 • radical. Computational studies also highlight the need to include the second sphere coordination environment around the [UO 2 (NO 3 ) 3 ] 0,1 species to gain agreement between the experimental and predicted EPR signatures.

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

Quantifying the Long‐Range Coupling of Electronic Properties in Proteins with ab initio Molecular Dynamics**

Abstract The delicate interplay of covalent and non‐covalent interactions in proteins is inherently quantum mechanical and highly dynamic in nature. To directly interrogate the evolving nature of the electronic structure of proteins, we carry out 100‐ps‐scale ab initio molecular dynamics simulations of three representative small proteins with range‐separated hybrid density functional theory. We quantify the nature and length‐scale of the coupling of residue‐specific charge probability distributions in these proteins. While some nonpolar residues exhibit expectedly narrow charge distributions, most polar and charged residues exhibit broad, multimodal distributions. Even for nonpolar residues, we observe sequence‐specific deviations corresponding to charge accumulation or depletion that would be challenging to capture in a fixed charge force field. We quantify the effect of residue‐residue interactions on charge distributions first with linear cross‐correlations. We then show how additional insight can be gained from evaluating the mutual information of charge distributions. We show that a significant number of residues couple most strongly with residues that are distant in both sequence and space over a range of secondary structures including α‐helical, β‐sheet, disulfide bridging, and lasso motifs. The mutual information analysis is necessary to capture coupling between some polar and charged residues that would be otherwise missed.

Yang, Zhongyue↗
DOE OSTI2020

Runtime power allocation approach for GAMESS hybrid CPU‐GPU implementation

Summary To improve power consumption of applications at the runtime, modern processors provide frequency scaling capabilities, which along with workload optimization, are also available on GPU accelerators. In this work, a runtime strategy is proposed to distribute a given power allocation among the host components and the GPU according to the current application performance and power usage, such that GPU execution is prioritized over CPU for power allocation to maximize application performance. Next, the strategy is tailored to an application, a quantum‐chemistry package GAMESS for ab initio electronic structure calculations. Specifically, GAMESS hybrid CPU–GPU implementation as provided in the Libcchem library is considered. Experiments, performed on a 28‐core node with a Kepler GPU, resulted in performance gains of up to 50% under the proposed strategy and the largest power allocation considered here as compared with the scenario when this allocation was equally distributed among the computing‐platform components.

Sundriyal, Vaibhav↗
DOE OSTI2021

Indirectly Detected DNP-Enhanced 17 O NMR Spectroscopy: Observation of Non-Protonated Near-Surface Oxygen at Naturally Abundant Silica and Silica-Alumina

Recent studies have shown that dynamic nuclear polarization (DNP) can be used to detect 17 O solid-state NMR spectra of naturally abundant samples within a reasonable experimental time. Observations using indirect DNP, which relies on 1 H mediation in transferring electron hyperpolarization to 17 O, are currently limited mostly to hydroxyls. Direct DNP schemes can hyperpolarize non-protonated oxygen near the radicals; however, they generally offer much lower signal enhancements. In this study, we demonstrate the detection of signals from non-protonated 17 O in materials containing silicon. The sensitivity boost that made the experiment possible originates from three sources: indirect DNP excitation of 29 Si via protons, indirect detection of 17 O through 29 Si nuclei using two-dimensional 29 Si{ 17 O} D-HMQC, and Carr-Purcell-Meiboom-Gill refocusing of 29 Si magnetization during acquisition. This 29 Si-detected scheme enabled, for the first time, 2D 17 O– 29 Si heteronuclear correlation spectroscopy in mesoporous silica and silica-alumina surfaces at natural abundance. In contrast to the silanols showing motion-averaged 17 O signals, the framework oxygens exhibit unperturbed powder patterns as unambiguous fingerprints of surface sites. Furthermore, along with hydroxyl oxygens, detection of these moieties will help in gaining more atomistic-scale insights into surface chemistry.

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

UV Excitation of Carotenoid Binding Proteins OCP and HCP: Excited‐State Dynamics and Product Formation

Abstract Over the last decade the orange carotenoid protein (OCP) gained attention due to its role in photoprotection in cyanobacteria. Recently, other carotenoid binding proteins such as helical carotenoid proteins (HCPs) have been identified and characterized, although the function of the HCPs is not yet clarified. Here we have examined OCP1 and two HCPs, HCP2 and HCP3, from Tolypothrix PCC 7601 by ultrafast spectroscopy after excitation of both carotenoid canthaxanthin and amino acids tryptophan and tyrosine in UV at 275 nm. We find that the canthaxanthin S 1 lifetime remains the same 3.5 ps as for excitation of the carotenoid S 2 state, but the S* signal is significantly amplified by UV excitation. In contrast to the S 2 excitation, we observe a formation of the canthaxanthin radical cation at 900 nm for all three proteins after 275 nm excitation. In OCP1, UV light also enhances the amplitude of spectral band centered at 550 nm at longer delays. This band likely corresponds to the first photoproduct of the OCP photocycle, suggesting that excess energy excitation and/or direct excitation of amino acids can enhance the product formation.

Khan, Tuhin↗
DOE OSTI2022

Electrochemical Oxidation of HMF via Hydrogen Atom Transfer and Hydride Transfer on NiOOH and the Impact of NiOOH Composition

Abstract A great deal of attention has been directed toward studying the electrochemical oxidation of 5‐hydroxymethylfurfural (HMF), a molecule that can be obtained from biomass‐derived cellulose and hemicellulose, to 2,5‐furandicarboxylic acid (FDCA), a molecule that can replace the petroleum‐derived terephthalic acid in the production of widely used polymers such as polyethylene terephthalate. NiOOH is one of the best and most well studied electrocatalysts for achieving this transformation; however, the mechanism by which it does so is still poorly understood. This study quantitatively examines how two different dehydrogenation mechanisms on NiOOH impact the oxidation of HMF and its oxidation intermediates on the way to FDCA. The first mechanism is a well‐established indirect oxidation mechanism featuring chemical hydrogen atom transfer to Ni 3+ sites while the second mechanism is a newly discovered potential‐dependent (PD) oxidation mechanism involving electrochemically induced hydride transfer to Ni 4+ sites. The composition of NiOOH was also tuned to shift the potential of the Ni(OH) 2 /NiOOH redox couple and to investigate how this affects the rates of indirect and PD oxidation as well as intermediate accumulation during a constant potential electrolysis. The new insights gained by this study will allow for the rational design of more efficient electrochemical dehydrogenation catalysts.

2,5-furandicarboxylic acid↗
DOE OSTI2022

Probing the Kinetic Origin of Varying Oxidative Stability of Ethyl- vs. Propyl-spaced Amines for Direct Air Capture

Amine-based adsorbents are promising for direct air capture of CO 2 , yet oxidative degradation remains a key unmitigated risk hindering wide-scale deployment. Borrowing wisdom from the basic auto-oxidation scheme, insights are gained into the underlying degradation mechanisms of polyamines by quantum chemical, advanced sampling simulations, adsorbent synthesis, and accelerated degradation experiments. The reaction kinetics of polyamines are contrasted with that of typical aliphatic polymers and they elucidate for the first time the critical role of aminoalkyl hydroperoxide decomposition in the oxidative degradation of amino-oligomers. The experimentally observed variation in oxidative stability of polyamines with different backbone structures is explained by the relationship between the local chemical structure and the free energy barrier of aminoalkyl hydroperoxide decomposition, suggesting that its energetics can be used as a descriptor to screen and design new polyamines with improved stability. In conclusion, the developed computational capability sheds light on radical-induced degradation chemistry of other organic functional materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Electrolyte Engineering Stabilizes Photoanodes Decorated with Molecular Catalysts

Molecular catalysts are promising oxygen evolution promoters in conjunction with photoanodes for solar water splitting. Maintaining the stability of both photoabsorber and cocatalyst is still a prime challenge, with many efforts tackling this issue through sophisticated material designs. Such approaches often mask the importance of the electrode-electrolyte interface and overlook easily tunable system parameters, such as the electrolyte environment, to improve efficiency. We provide a systematic study on the activity-stability relationship of a prominent Fe 2 O 3 photoanode modified with Ir molecular catalysts using in situ mass spectroscopy. After gaining detailed insights into the dissolution behavior of the Ir cocatalyst, a comprehensive pH study is conducted to probe the impact of the electrolyte on the performance. An inverse trend in Fe and Ir stability is found, with the best activity-stability synergy obtained at pH 9.7. The results bring awareness to the overall photostability and electrolyte engineering when advancing catalysts for solar water splitting.

14 SOLAR ENERGY↗