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

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At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Membrane synthesis via in-situ pore formation in silica gels through dynamic miscibility with soybean oil

The dynamic immiscibility between vegetable oil and organic silica precursors during sol-gel synthesis was used to tailor the microstructure of gels made with tetraethoxysilane (TEOS) or tetraethoxysilane+methyltrimethoxysilane (MTMS). Vegetable oil was investigated as an environmentally friendly and cheaper alternative to many other porogens. Oil concentrations of 9.09 v/v% and 33.33 v/v% were studied. For both TEOS and TEOS+MTMS gels, the miscibility of the oil and precursor decreases as the silica gel network forms, leading to oil-rich regions within the silica matrix. Gels containing MTMS maintained partial miscibility with the oil during gel formation due to the non-hydrolysable methyl groups on the MTMS. The pore structure of MTMS gels appeared more interconnected compared to the isolated pores observed in gels made with only TEOS. To create membranes with hierarchical pore structures, solvent exchanges were performed on gels or dried gels (i.e., xerogels) were calcined. The effect of the methyl group was also observed in the results of the time sweep rheology, as the addition of oil to the TEOS+MTMS gels caused an increase in the time to form the spanning gel. The trend was the opposite for oil additions to TEOS gels, which only contained polar groups. Xerogel membranes made with TEOS+MTMS had higher specific surface areas (SSAs) than those made with TEOS. For oil concentrations of 33.33 v/v%, xerogels made from TEOS+MTMS had an average SSA of 1068 + 113 m2 g-1, an order of magnitude higher than the average SSA of 103 + 6 m2 g-1 for xerogels made with TEOS.

sol-gel, dynamic immiscibility, oil-alkoxide inter↗
DOE OSTI2020

Effects of solvent formulations in electrolytes on fast charging of Li-ion cells

Improving the fast charging performance of lithium ion batteries (LIBs) has the promise to increase the widespread adoption of electric vehicles (EVs). Electrolyte development plays an important role in enabling fast charging. In this study, fast charging performance of LIBs is studied with different electrolytes of 1.2 M LiPF 6 in Ethylene Carbonate (EC)/Ethyl Methyl Carbonate (EMC)/co-solvents at 30/50/20 wt%. The co-solvents are methyl acetate (MA), ethyl acetate (EA), ethyl formate (EF), dimethyl carbonate (DMC) and EMC. Long term cycling performance under fast charging shows different capacity retention behaviors for different co-solvents. The structural changes in the electrode material are studied by X-ray absorption spectroscopy (XAS) and X-ray diffraction (XRD). The molarity changes in electrolyte is investigated by inductively coupled plasma-optical emission spectroscopy (ICP-OES). The electrode/electrolyte interfaces before and after fast charging are analyzed by X-ray photoemission spectroscopy (XPS). The characterization results are in good agreement with the long-term cycling performance. DMC shows the highest fast-charging capability among the five studied co-solvents due to its increased conductivity, improved electrode/electrolyte interface and stable electrode structural integrity.

25 ENERGY STORAGE↗
DOE OSTI2021

Formation of Benzene and Naphthalene through Cyclopentadienyl-Mediated Radical–Radical Reactions

Resonantly stabilized free radicals (RSFRs) have been contemplated as fundamental molecular building blocks and reactive intermediates in molecular mass growth processes leading to polycyclic aromatic hydrocarbons (PAHs) and carbonaceous nanoparticles on Earth and in deep space. Here, by combining molecular beams and computational fluid dynamics simulations, we provide compelling evidence on the formation of benzene via the cyclopentadienyl-methyl reaction and of naphthalene through the cyclopentadienyl self-reaction, respectively. These systems offer benchmarks for the conversion of a five-membered ring to the 6π-aromatic (benzene) and the generation of the simplest 10π-PAH (naphthalene) at elevated temperatures. These results uncover molecular mass growth processes from the “bottom up” via RSFRs in high temperature circumstellar environments and combustion systems expanding our fundamental knowledge of the organic, hydrocarbon chemistry in our universe.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Shock tube and laser absorption study of CO time-histories during combustion of branched alkenes

Combustion experiments of the three isomers of methyl butene compound - 2-methyl-1-butene (2M1B), 2-methyl-2-butene (2M2B), and 3-methyl-1-butene (3M1B), have been carried out in a shock tube using laser absorption technique. Carbon monoxide (CO) time-histories are obtained behind reflected shockwaves over the temperature range of 1350–1630 K near 9.3 atm with stoichiometric mixtures of 0.075% fuel in O2/Ar. Comparative study of CO time-histories reveals different rates of CO formation indicating different ignition delay time of the methyl butene isomers.

09 BIOMASS FUELS↗
DOE OSTI2024

The ICF syndrome protein CDCA7 harbors a unique DNA binding domain that recognizes a CpG dyad in the context of a non-B DNA

CDCA7, encoding a protein with a carboxyl-terminal cysteine-rich domain (CRD), is mutated in immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome, a disease related to hypomethylation of juxtacentromeric satellite DNA. How CDCA7 directs DNA methylation to juxtacentromeric regions is unknown. Here, we show that the CDCA7 CRD adopts a unique zinc-binding structure that recognizes a CpG dyad in a non-B DNA formed by two sequence motifs. CDCA7, but not ICF mutants, preferentially binds the non-B DNA with strand-specific CpG hemi-methylation. The unmethylated sequence motif is highly enriched at centromeres of human chromosomes, whereas the methylated motif is distributed throughout the genome. At S phase, CDCA7, but not ICF mutants, is concentrated in constitutive heterochromatin foci, and the formation of such foci can be inhibited by exogenous hemi-methylated non-B DNA bound by the CRD. Binding of the non-B DNA formed in juxtacentromeric regions during DNA replication provides a mechanism by which CDCA7 controls the specificity of DNA methylation.

Science & Technology - Other Topics↗
DOE OSTI2020

Base pairing, structural and functional insights into N 4 -methylcytidine (m 4 C) and N 4 ,N 4 -dimethylcytidine (m 4 2 C) modified RNA

The N 4 -methylation of cytidine (m 4 C and m 4 2 C) in RNA plays important roles in both bacterial and eukaryotic cells. In this work, we synthesized a series of m 4 C and m 4 2 C modified RNA oligonucleotides, conducted their base pairing and bioactivity studies, and solved three new crystal structures of the RNA duplexes containing these two modifications. Our thermostability and X-ray crystallography studies, together with the molecular dynamic simulation studies, demonstrated that m 4 C retains a regular C:G base pairing pattern in RNA duplex and has a relatively small effect on its base pairing stability and specificity. By contrast, the m 4 2 C modification disrupts the C:G pair and significantly decreases the duplex stability through a conformational shift of native Watson-Crick pair to a wobble-like pattern with the formation of two hydrogen bonds. This double-methylated m 4 2 C also results in the loss of base pairing discrimination between C:G and other mismatched pairs like C:A, C:T and C:C. The biochemical investigation of these two modified residues in the reverse transcription model shows that both mono- or di-methylated cytosine bases could specify the C:T pair and induce the G to T mutation using HIV-1 RT. In the presence of other reverse transcriptases with higher fidelity like AMV-RT, the methylation could either retain the normal nucleotide incorporation or completely inhibit the DNA synthesis. These results indicate the methylation at N 4 -position of cytidine is a molecular mechanism to fine tune base pairing specificity and affect the coding efficiency and fidelity during gene replication.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Directed Gas-Phase Formation of The Propargyl Family of Resonance-Stabilized Radicals in The Reactions of Ground-State Carbon Atoms (C; 3 P j ) with Butene Isomers (C 4 H 8 ): Dimethylpropargyl and Ethylpropargyl

The propargyl radical (C 3 H 3 ) is the simplest resonance-stabilized free radical (RSFR), but how does stepwise methyl substitution in the alkene reactant affect its dynamics of their formation? We report a crossed molecular beam study of the reactions of atomic carbon (C, 3 P j ) with four butene isomers (C 4 H 8 ) under single collision conditions at a collision energy of 28 ± 2 kJ mol −1 . Barrierless addition of atomic carbon to the alkene C=C bond triggers ring opening to triplet substituted allenes—a de facto insertion mechanism—followed by unimolecular decomposition via atomic hydrogen (H), methyl (CH 3 ) or ethyl (C 2 H 5 ) loss, yielding a family of propargyl‑type RSFRs. RRKM calculations reveal that the branching ratios are highly sensitive to the alkene structure. While the methyl loss channel, affording 1‑methylpropargyl, dominates for 2 butenes (80–90%), the predicted hydrogen atom loss channel (≈10%) leading to 1,3 dimethylpropargyl is identified in the experiment by comparison with theoretical energetics. For isobutene, a near‑equal competition is seen, with the reaction producing 3‑methylpropargyl (≈50%) and 1,1‑dimethylpropargyl (≈40%), along with 2‑vinylallyl (≈5%), whose formation is supported by the experimental data. Most notably, the reaction with 1 butene uniquely favors an enthalpically driven hydrogen shift, eventually producing 1 vinylallyl (≈38%), which is assigned based on the excellent agreement between the measured and calculated reaction exothermicity. Rapid entropically favored fragmentation channels yield ≈40% of propargyl type species (propargyl, 1- and 3-ethylpropargyls), slightly outcompeting the allyl type product. Furthermore, these results establish a systematic progression from C 2 H 4 to C 4 H 8 , where the increasing alkyl substitution unlocks new fragmentation channels, providing a versatile gas phase route to alkylated RSFRs—key intermediates in the growth of methylated and ethylated PAHs and aliphatic chains in combustion and cold interstellar environments (molecular clouds).

Alkyls↗
DOE OSTI2025

Ligand Influence on Indium–Sulfide Cluster Formation and Reactivity

An indium–sulfide tetramer ([InMe 2 (SSiMe 3 )] 4 ), which contains reactive silyl and methyl groups, is shown to be an isolable intermediate in cluster synthesis. The reactive groups allow it to act as a synthon in the formation of multinuclear indium–sulfide architectures, evidenced by the crystallization of a coordination polymer ([In 20 S 14 Me 32 (4,4’-bpy) 5 ·5CH 2 Cl 2 ] n ) utilizing In 10 S 7 clusters as nodes. The reaction between trimethylindium (InMe 3 ) and bis­(trimethylsilyl)­sulfide (S­(SiMe 3 ) 2 ) is explored with and without the presence of a ligating bipyridine. In both cases, a sulfide-indium adduct is formed, which slowly converts into a multimetallic complex. Here, the ligand 2,2’-bipyridine (2,2’-bpy) is coordinated to InMe 3 to form the adduct InMe 3 (bpy), which upon addition of sulfide, eliminates tetramethylsilane (TMS) and binds two additional InMe 3 moieties (InMe 2 (bpy)­(μ 3 -SSiMe 3 )­(InMe 3 ) 2 ). When reacted neatly without bipyridine, InMe 3 and S­(SiMe 3 ) 2 form the adduct InMe 3 (S­(SiMe 3 ) 2 ), which subsequently eliminates TMS and intermolecularly associates to yield [InMe 2 (SSiMe 3 )] 4 . Although stable in an inert atmosphere, [InMe 2 (SSiMe 3 )] 4 undergoes facile hydrolysis to yield [InMeS] n when exposed to air. The effect of ligand addition (4,4’-bipyridine (4,4’-bpy)) to [InMe 2 (SSiMe 3 )] 4 is then examined. In every case, it is shown that the presence of the bpy ligand has a profound influence on the resulting structure, as shown by the unexpected formation of a trimer and In 10 S 7 cluster network.

Bell, Colby Seth [Argonne National Laboratory (ANL↗
DOE OSTI2023

Intramolecular 1,2 C-H Addition of o -Methyl Groups to Form Unique Ruthenium Pincer Tuck-in Complexes

New RPN H P ligands containing 2,4-xylyl (4mXPN H P) and mesityl (MesPN H P) groups on the phosphorus atoms were synthesized. 4mXPN H P reacts with [(cymene)RuCl 2 ] 2 followed by PMe 3 to produce κ 3 -4mXPN H PRu(PMe 3 )Cl 2 . MesPN H P reacts with [(cymene)RuCl 2 ] 2 to produce monomeric κ 3 -MesPN H PRuCl 2 that reacts with CO forming κ 3 -MesPN H PRu(CO)Cl 2 . Surprisingly, dehydrohalogenation of these complexes results in the activation of ortho methyl groups of the pincer ligands, rather than formation of κ 3 -RPNPRuLCl complexes. This results from transient κ 3 -RPNPRuLCl formation followed by 1,2-addition of an ortho C-H bond across the Ru-amide bond. The transient amide complex of κ 4 -4mXPN H PRu(PMe 3 )Cl was trapped with CO forming κ 3 -4mXPNPRu(PMe 3 )(CO)Cl. In contrast, κ 4 -MesPNHPRu(CO)Cl does not react with ligands to trap the expected amide complex of reverse C-H addition. Instead, CO and PMe 3 displace the chloride ligand forming cationic complexes. In both cases, hemi-lability of the pincer ligand was observed spectroscopically. In conclusion, the new complexes serve as precursors to moderately active catalysts for the acceptorless dehydrogenative coupling of n-butanol.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Vacuum-ultraviolet absorption cross-sections of functionalized four-carbon species

Absorption cross-sections were measured in the vacuum ultraviolet from 5.17 – 9.92 eV using differential absorption spectroscopy for 33 four-carbon species: n-butane, trans-2-butene, cis-2-butene, butanal, butyric acid, ethyloxirane, trans-2,3-dimethyloxirane, cis-2,3-dimethyloxirane, 2-methyloxetane, 2,2'-bioxirane, vinyl oxirane, 3,4-epoxybutan-2-one, diacetyl, diethyl ether, ethyl vinyl ether, vinyl acetate, acetic anhydride, 1-butanol, 3-buten-1-ol, 1–hydroxy-butan-2-one, 1–hydroxy-butan-3-one, 2,3-epoxybutan-1-ol, 3,4-epoxybutan-1-ol, 2-oxetanemethanol, butanone, methyl vinyl ketone, 4H-1,3-dioxine, allyl formate, 2-oxobutanal, 4-hydroxybutanal, 2-methyloxetan-3-one, cis–but-2-en-1-ol, and trans-2–but-enal. Uncertainties were quantified in all cases by accounting for errors in gas-phase concentration, experimental repeatability, and signal-to-noise ratio as a function of photon energy. With the exception of 2-oxobutanal, which is reported with an uncertainty of 10%, convolving the sources of error using the root-sum-square method led to an upper limit of 5% uncertainty above the detection limit, which is largely attributable to chemical purity. Here, the primary objective of the present work is to provide absolute cross-sections along with quantified uncertainty limits. The majority of the absorption spectra, which reflect electronic transitions such as σ → σ* and n → σ*, are reported for the first time and provide insight into fundamental chemical physics, such as vibrational band structure and Rydberg transitions. The quantitative spectra in the present work facilitates the discovery of chemical intermediates that support improvement in the accuracy of computational models for low-temperature combustion and atmospheric chemistry.

biofuels↗
DOE OSTI2022

In Situ Tracking of Nonthermal Plasma Etching of ZIF-8 Films

Surface characterization is critical for understanding the processes used for preparing catalysts, sorbents, and membranes. Nonthermal plasma (NTP) is a process that achieves high reactivity at low temperatures and is used to tailor the surface properties of materials. In this work, we combine the capabilities of infrared reflection absorption spectroscopy (IRRAS) with NTP for the in situ interrogation of zeolitic imidazolate framework-8 (ZIF-8) thin films to probe modifications in the material induced by oxygen and nitrogen plasmas. The IRRAS measurements in oxygen plasma reveal etching of organic ligands with sequential removal of the methyl group and imidazole ring and with the formation of carbonyl moieties (C═O). In contrast, nitrogen plasma induces mild etching and grafting of nitrile groups (−C≡N). Scanning electron microscopy imaging shows that oxygen plasma, at prolonged times, significantly degrades the ZIF-8 film at the grain boundaries. Treatment of ZIF-8 membranes using mild plasma conditions yields a fivefold enhancement for H 2 /N 2 and CO 2 /CH 4 ideal selectivities and an eightfold enhancement for CO 2 /N 2 ideal selectivity. Additionally, the new tools described here can be used for spectroscopic in situ tracking of plasma-induced chemistry on thin films in general.

IRRAS↗
DOE OSTI2020

Resolving the Atomic Structure of Sequential Infiltration Synthesis Derived Inorganic Clusters

Sequential infiltration synthesis (SIS) is a route to the precision deposition of inorganic solids in analogy to atomic layer deposition but occurs within (vs upon) a soft material template. SIS has enabled exquisite nanoscale morphological complexity in various oxides through selective nucleation in block copolymers templates. However, the earliest stages of SIS growth remain unresolved, including the atomic structure of nuclei and the evolution of local coordination environments, before and after polymer template removal. We employed In K-edge extended X-ray absorption fine structure and atomic pair distribution function analysis of high-energy X-ray scattering to unravel (1) the structural evolution of InO x H y clusters inside a poly(methyl methacrylate) (PMMA) host matrix and (2) the formation of porous In 2 O 3 solids (obtained after annealing) as a function of SIS cycle number. Early SIS cycles result in InO x H y cluster growth with high aspect ratio, followed by the formation of a three-dimensional network with additional SIS cycles. That the atomic structures of the InO x H y clusters can be modeled as multinuclear clusters with bonding patterns related to those in In 2 O 3 and In(OH) 3 crystal structures suggests that SIS may be an efficient route to 3D arrays of discrete-atom-number clusters. As a result, annealing the mixed inorganic/polymer films in air removes the PMMA template and consolidates the as-grown clusters into cubic In 2 O 3 nanocrystals with structural details that also depend on SIS cycle number.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

A 100+ RON Gasoline Blendstock for High Efficiency, Low Emission Vehicles Engines - CRADA 493 (Final Report)

This study aimed at demonstrating production of a 100+RON gasoline fraction from a linear olefins feedstock to help improve further the viability and flexibility of the Pacific Northwest National Laboratory/ LanzaTech alcohol-to-jet (ATJ) patented process that converts ethanol from LanzaTech’s syngas fermentation process to low aromatic jet-range iso-paraffins. To achieve a high RON gasoline and ultimately a 100+RON, the technical approach consisted of converting the linear olefins into an iso-olefins rich mixture and then oligomerizing the iso-olefins rich mixture into high RON compounds in a single bed loaded with an acid catalyst that allows conversion at low reaction temperature. Three families of acid catalysts labeled as type A, B and C were investigated for the single-bed conversion of linear olefins into high RON gasoline range compounds. The effects of the nature of the catalyst, acid sites concentration and operating conditions were investigated. Fuel properties measurements and engine testing were conducted for the most promising catalyst. For type A catalysts, we demonstrated that the conversion increases with the increase of the Brönsted acid site concentration and that lower reaction temperature favors the formation of desired highly branched compounds. The highest dRON obtained with type A catalyst was equal to 94 (from NMR and IQT). Type B catalysts appear very effective for producing dimethyl-olefins compounds when operating at low reaction temperature (i.e., < 100°C). The highest dRON obtained with type B catalyst was equal to 92. The results suggest that type B catalysts are less favorable to internal conversion of linear olefins into iso-olefins compared to type A catalysts which leads to the formation of a gasoline blendstock with a lower dRON. A Type C catalyst that is less commonly used for production of gasoline range compounds from linear olefins was investigated due to its ability to favor conversion of linear olefins into iso-olefins. Compared to type A and type B catalyst, type C favors the formation of highly branched compounds (i.e., with 3+ methyl groups) in the gasoline range. Indeed, a gasoline blendstock containing about 33 wt.% of highly branched compounds was produced with type C catalyst while maintaining a high linear olefins conversion (i.e., 70%). A large quantity of this gasoline blendstock was produced and fuel properties measurements including engine testing for Research Octane Number (RON), Motor Octane Number (MON) and octane sensitivity (S) were conducted. A high RON = 97, MON = 82.7, S =14.3, AKI = 90 and HoV = 334.1kJ/kg were measured. While a RON of 100 was not achieved, the fuel properties of the gasoline blendstock are very acceptable as compared to current premium gasoline. Overall, these results highlight the potential for producing a high RON/ premium gasoline blendstock starting from a linear olefins feedstock.

02 PETROLEUM↗
DOE OSTI2024

Enhanced Resistance Pines for Improved Renewable Biofuel and Chemical Production (Technical Report)

We completed phenotyping constitutive and inducible oleoresin flow across two seasons, constitutive resin canal number and density and wood terpene content in our ADEPT2 and CCLONES populations. We completed genetic association between 19 oleoresin phenotypes and a total of 523,192 SNP markers from ADEPT2 and 13,883 SNP markers in CCLONES using four mixed linear models. A total of 293 significant SNPs (FDR = 0.20) were identified. We used the MENTOR tool to mine mechanistic connections from a multiplex network constructed from poplar multi-omic data to construct a conceptual model for a subset of these significant SNPs. Our model contains 6 transcriptional regulators in addition to 3 monoterpene synthases. To generate more lines of evidence for these significant SNPs, we completed a time course RNAseq experiment after inducing vascular zone cells to differentiate into new resin canals with a methyl jasmonate treatment, a single nuclei RNAseq that identified differentiating resin canal epithelial cells and are completing analysis for a QTL study in a hybrid pine population. The time course identified 4634 significantly down and 1890 significantly up regulated transcripts after treatment with methyl jasmonate, an inducer of new resin canal formation in the vascular cambial meristem. To analyze this large set of differentially regulated genes, we created a predictive expression network and analyzed it with random walk restart using 6 seed genes coding for transcription factors regulating xylem differentiation in poplar. Of the top ranked 200 transcripts, 119 transcripts were significant differentially expressed supporting these transcripts as potential candidates regulating resin canal formation. Analysis of single nuclei sequencing of shoot tips that contain differentiating resin canals, identified 10 clusters. One cluster was highly enriched in transcripts coding for 9 of the enzymes in the MEP pathway 3 prenyl synthetases, and 3 monoterpene synthases strongly suggesting that this cluster represents resin canal epithelial cells. We are mining the additional transcripts to create a trajectory analysis. In summary, we have identified > 10 novel genes that are strongly supported candidates for further analysis in breeding lines and for genetic engineering over- and under- expressing lines to increase wood terpene content to improve resistance to insect and fungal pathogens while simultaneously increasing terpene supplies for renewable chemicals and biofuels.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Direct recycling of lithium-ion battery scraps for manufacturing a new anode

An improved method of recycling lithium-ion battery anode scraps is provided. The method involves isolating an anode scrap including a graphite anode film adhered to a current collector foil with a polyvinylidene fluoride binder. The anode scrap is combined with deionized water to form a first mixture. The graphite anode film is delaminated from the current collector foil to form a second mixture comprising a free collector foil and a free graphite anode film. The free graphite anode film is filtered and dried from the second mixture to recover the free graphite anode film. The free graphite anode film is combined with a solvent comprising N-methyl-2-pyrrolidone (NMP) to form an anode formation slurry. The slurry is coated onto a copper current collector to produce a new anode.

Bai, Yaocai↗
DOE OSTI2025

Discovering methylated DNA motifs in bacterial nanopore sequencing data with MIJAMP

Abstract Bacterial DNA methylation is involved in diverse cellular functions, including modulation of gene expression, DNA repair, and restriction–modification systems for defense against viruses and other foreign DNA. Restriction systems hinder efforts to engineer organisms to produce fuels and chemicals from waste and renewable feedstocks by degrading DNA during transformation. Methylome analysis allows identification of motifs within a bacterial chromosome that may be targeted by native restriction enzymes. Further expression of the corresponding methyltransferases in Escherichia coli allows plasmid DNA to be protected from restriction in the target organism, thereby drastically enhancing transformation efficiency. Nanopore sequencing can detect methylated bases, but software is needed to transform modified base coordinates into methylated motifs. Here, we develop MIJAMP (MIJAMP Is Just A MethylBED Parser), a software package that was developed to discover methylated motifs from the output of ONT’s Modkit or other data in the methylBED format. MIJAMP employs a human-driven refinement strategy that empirically validates all motifs against genome-wide methylation data, thus eliminating incorrect motifs. MIJAMP also reports methylation data on specific, user-defined motifs. Using MIJAMP, we determined the methylated motifs both in a control strain (wild-type E. coli) and in Synecococcus sp. strain PCC7002, laying the foundation for improved transformation in this organism. MIJAMP is available at https://code.ornl.gov/alexander-public/mijamp/. One Sentence Summary: Here we describe software written to discover DNA methylation motifs from nanopore sequencing data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

MIJAMP

Here, we develop MIJAMP (MIJAMP Is Just A MethylBED Parser), a software package that was developed to discover methylated motifs from the output of ONT’s Modkit or other data in the methylBED format. MIJAMP employs a human-driven refinement strategy that empirically validates all motifs against genome-wide methylation data, thus eliminating false, under-, or overexplained motifs. MIJAMP can also report methylation data on a specific, user-defined motif.

Alexander, William↗
DOE OSTI2026

Role of Surface Hydroxyls and Lattice Oxygen in Governing Selectivity and Restructuring During Acetic Acid Conversion on Fe 3 O 4 (001)

Understanding the reactivity of carboxylic acids on metal oxide surfaces is critical for elucidating ketonization mechanisms relevant to biomass upgrading. Here, we investigate the adsorption and thermal decomposition of acetic acid (CH 3 COOH) on Fe 3 O 4 (001) using scanning tunneling microscopy (STM), temperature-programmed reaction spectroscopy (TPRS), and X-ray photoelectron spectroscopy (XPS). At room temperature, acetic acid adsorbs dissociatively to form ordered bidentate acetate (CH 3 COO) overlayer that lifts the (√2 × √2)R 45° surface reconstruction. TPRS reveals ketene (CH 2 CO) as the dominant product, along with CO, CO 2 , and H 2 O, the latter evolving via a Mars–van Krevelen (MvK) mechanism. Isotopic labeling shows preferential CO 2 formation from the carboxyl carbon and a more balanced CO/CO 2 ratio from the methyl carbon, suggesting distinct oxidation pathways. STM imaging reveals embedded acetate intermediates filling surface oxygen vacancies created in MvK steps. Upon product formation completion (~700 K), extensive surface etching is observed, with pits elongated along the octahedral Fe rows. Approximately 20% of the surface oxygen is removed, consistent with vacancy formation stoichiometry inferred from product distributions. These findings demonstrate that carboxylate-induced restructuring of Fe 3 O 4 (001) involves both surface healing and reduction processes, offering mechanistic insights relevant to ketonization and broader carboxylic acid chemistry on metal oxides.

acetic acid↗