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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 433 records · Page 24
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Effective biomass fractionation and lignin stabilization using a diol DES system

A sustainable and renewable biorefinery will increase the economic viability of lignocellulose-derived products. In this study, a diol-based deep eutectic solvent (DES) was developed to reduce the recalcitrance of bamboo, facilitate saccharification and valorize the lignin fraction. The DES pretreatment dramatically enhanced glucan digestibility by the effective removal of lignin (as high as 85.45%) and xylan (91.12%). Notably, the recovered lignin from DES pretreatment was protected during the fractionation, showing well-preserved β-O-4 structures (31.82%–59.06%). The mechanism of lignin protection was analyzed to be accomplished by incorporating the diol hydroxyl functional groups into the α position of the lignin β-O-4 structure via etherification. This work highlighted that diol DES is a promising pretreatment solvent to valorize both cellulose and lignin fractions with high enzymatic hydrolysis yield and high-quality lignin co-product.

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

Zng1 is a GTP-dependent zinc transferase needed for activation of methionine aminopeptidase

The evolution of zinc (Zn) as a protein cofactor altered the functional landscape of biology, but dependency on Zn also created an Achilles' heel, necessitating adaptive mechanisms to ensure Zn availability to proteins. A debated strategy is whether metallochaperones exist to prioritize essential Zn-dependent proteins. Here, we present evidence for a conserved family of putative metal transferases in human and fungi, which interact with Zn-dependent methionine aminopeptidase type I (MetAP1/Map1p/Fma1). Deletion of the putative metal transferase in Saccharomyces cerevisiae (ZNG1; formerly YNR029c) leads to defective Map1p function and a Zn-deficiency growth defect. In vitro, Zng1p can transfer Zn 2+ or Co 2+ to apo-Map1p, but unlike characterized copper chaperones, transfer is dependent on GTP hydrolysis. Proteomics reveal mis-regulation of the Zap1p transcription factor regulon due to loss of ZNG1 and Map1p activity, suggesting that Zng1p is required to avoid a compounding effect of Map1p dysfunction on survival during Zn limitation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Iron-activated persulfate oxidation degrades aqueous Perfluorooctanoic acid (PFOA) at ambient temperature

Perfluorooctanoic acid (PFOA, C 8 HF 15 O 2 ) is an industrial surfactant that is highly resistant to natural breakdown processes such as those mediated by heat, hydrolysis, photolysis, and biodegradation. Many efforts have been developed to breakdown PFOA to less harmful species due to its widespread human exposure and potential toxicity. However, these methods require high temperature or specialized equipment with serious disadvantages of high energy cost for long-term use. For this paper, we investigated the effectiveness of PFOA degradation by ferrous iron-activated persulfate oxidation (IAPO) under various aqueous geochemical conditions. Approximately 64% of PFOA (initial concentration = 1.64 μmol L –1 ) was degraded after 4 h under illuminated anoxic conditions at ambient temperature. This degradation rate and magnitude support the potential use of IAPO as a novel inexpensive and environmentally friendly method to remediate PFOA in soil and groundwater.

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

Biotechnological advances in algae-based foods: applications in nutrition and microbiome health

Algae are a sustainable, nutrient-rich resource with growing potential in food biotechnology. Their ability to thrive in diverse environments makes them a promising alternative to conventional crops. Rich in proteins, essential fatty acids, and bioactive compounds, algae support the development of functional foods, including plant-based meat and seafood alternatives. Advances in synthetic biology and fermentation have enhanced algal nutrient profiles and enabled novel applications. Algae-derived polysaccharides, such as alginate, fucoidan, laminarin, and porphyran, exhibit prebiotic effects by modulating the gut microbiota and promoting SCFA production. Enzymatic hydrolysis efficiently produces bioactive oligosaccharides, while engineered microbial systems support scalable production. Algae also enable synbiotic food development by serving as both prebiotic substrates and probiotic carriers.

Yu, Sora↗
DOE OSTI2022

EstG is a novel esterase required for cell envelope integrity in Caulobacter

Proper regulation of the bacterial cell envelope is critical for cell survival. Identification and characterization of enzymes that maintain cell envelope homeostasis is crucial, as they can be targets for effective antibiotics. In this study, we have identified a novel enzyme, called EstG, whose activity protects cells from a variety of lethal assaults in the α-proteobacterium Caulobacter crescentus. Despite homology to transpeptidase family cell wall enzymes and an ability to protect against cell-wall-targeting antibiotics, EstG does not demonstrate biochemical activity toward cell wall substrates. Instead, EstG is genetically connected to the periplasmic enzymes OpgH and BglX, responsible for synthesis and hydrolysis of osmoregulated periplasmic glucans (OPGs), respectively. The crystal structure of EstG revealed similarities to esterases and transesterases, and we demonstrated esterase activity of EstG in vitro. Using biochemical fractionation, we identified a cyclic hexamer of glucose as a likely substrate of EstG. Further, this molecule is the first OPG described in Caulobacter and establishes a novel class of OPGs, the regulation and modification of which are important for stress survival and adaptation to fluctuating environments. Our data indicate that EstG, BglX, and OpgH comprise a previously unknown OPG pathway in Caulobacter. Ultimately, we propose that EstG is a novel enzyme that instead of acting on the cell wall, acts on cyclic OPGs to provide resistance to a variety of cellular stresses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Dual carbonate clumped isotopes (Δ 47 -Δ 48 ) constrains kinetic effects and timescales in peridotite-associated springs at the Cedars, Northern California

The Cedars is an area in Northern California with a chain of highly alkaline springs resulting from CO 2 -charged meteorological water interacting with a peridotite body. Serpentinization resulting from this interaction at depth leads to the sequestration of various carbonate minerals into veins accompanied by a release of Ca 2+ and OH – enriched water to the surface, creating an environment which promotes rapid precipitation of CaCO 3 at surface springs. This environment enables us to apply the recently developed Δ 47 -Δ 48 dual clumped isotope analysis to probe kinetic isotope effects (KIEs) and timescales of CO 2 transformation in a region with the potential for geological CO 2 sequestration. Here, we analyzed CaCO 3 recovered from various localities and identified significant kinetic fractionations associated with CO 2 absorption in a majority of samples, characterized by enrichment in Δ 47 values and depletion in Δ 48 values relative to equilibrium. Surface floes exhibited the largest KIEs (ΔΔ 47 : 0.163‰, ΔΔ 48 : -0.761‰). Surface floe samples begin to precipitate out of solution within the first hour of CO 2 absorption, and the dissolved inorganic carbon (DIC) pool requires a residence time of >100 h to achieve isotopic equilibria. The Δ 48 /Δ 47 slope of samples from the Cedars (-3.223 ± 0.519) is within the range of published theoretical values designed to constrain CO 2 hydrolysis-related kinetic fractionation (-1.724 to -8.330). The Δ 47 /δ 18 O slope (-0.009 ± 0.001) and Δ 47 /δ 13 C slope (-0.009 ± 0.001) are roughly consistent with literature values reported from a peridotite in Oman of -0.006 ± 0.002 and -0.005 ± 0.002, respectively. The consistency of slopes in the multi-isotope space suggests the Δ 47 -Δ 48 dual carbonate clumped isotope framework can be applied to study CO 2 -absorption processes in applied systems, including sites of interest for geological sequestration.

58 GEOSCIENCES↗
DOE OSTI2020

A Physically-Based Model for Thermo-Oxidative and Hydrolytic Aging of Elastomers

A computationally efficient model is proposed to capture the loss of mechanical performance due to chemical aging that are formed as the competition of chain scission and cross-link formation/dissolution, such as thermo-oxidative aging or hydrolytic aging. The model should be considered an extension of our recent models [1, 2, 3] which further simplifies the matrix behavior based on the assumption of independence of environmental and mechanical damage. The model uses this assumption to reduce the necessary material parameters needed to model constitutive and inelastic behavior of elastomers during aging. To this end, the model can provide accurate predictions of the material performance with the significantly fewer number of fitting parameters. The model is relevant for all decay mechanisms formed by the occurrence of two simultaneous micro-mechanisms; (i) formation/reduction of the cross-links, and (ii) chain scission, both of which are present in thermo-oxidation and hydrolytic aging. Assuming the alteration of the chain density along the aging trajectory is identical to the peroxide cross-link density for thermo-oxidation, and the change of the average molecular weight for hydrolysis, the strain energy of polymer matrix can be rewritten as a function of deformation, deformation history, storage time and aging temperature. Next, the modified network alteration model is formulated for implementation into Finite Element (FE) simulations. The model is built on the presumption of homogeneous and consistent oxygen/water absorption and thus is mainly relevant for relatively thin samples exposed to environmental loads for a long time. The proposed model includes only six physically inspired material parameters. Therefore, while it is computationally efficient, it shows good agreement with own experimental data, which performed on various range of accelerated aging temperatures and times. With respect to its computational efficiency, simplicity, accuracy, and interpret-ability, the model is the right choice for advanced implementations in FE programs.

42 ENGINEERING↗
DOE OSTI2021

Ionic liquid-water mixtures enhance pretreatment and anaerobic digestion of agave bagasse

Agave bagasse (AB), a byproduct of tequila production, is a waste generated in large quantities and an emerging alternative for biofuels production. Nevertheless, the use of lignocellulosic biomass for this purpose requires a pretreatment that maximizes its degradation and utilization. Although there are several pretreatment types, using ionic liquids (IL) has become attractive due to its ability to dissolve the lignocellulosic biomass under mild conditions of time and temperature. As a drawback are the high cost of IL's and their high viscosity; thus mixing them with water is a way to overcome these hindrances. This work aimed to evaluate the effect of pretreatment with three diluted ILs on the A. tequilana bagasse structure and sugars production, as well as the potential of the enzymatic hydrolysate to produce methane in batch mode. The evaluated ILs were: 1-ethyl-3-methylimidazolium acetate [Emim][OAc], choline lysinate [Ch][Lys] and ethanolamine acetate [EOA][OAc]. The results showed that the IL with the best performance was [Ch][Lys], which not only offered the highest yields of sugar production (0.57 ± 0.03 g total sugars / g bagasse) but also, it is possible to use it at 30 % in a mix with water obtaining similar yields as with pure IL. Enzymatic hydrolysis of IL pretreated AB achieved 50.7 kg sugars and 49.3 kg of sugars for 90 %-[Ch][Lys] and 30 %-[Ch][Lys], respectively per 100 kg of untreated biomass. The enzymatic hydrolysate from the 30 %-[Ch][Lys] pretreated AB was able to achieve 0.28 L CH4/g CODfed, demonstrating that both sugar and methane yields are maintained when pure or 30 %-[Ch][Lys] are used for pretreatment, representing a step forward towards process feasibility.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Stepwise allomorphic transformations by alkaline and ethylenediamine treatments on bamboo crystalline cellulose for enhanced enzymatic digestibility

Efficient modification and decrystallization of cellulose Iβ in lignocellulosic biomass are potential ways to overcome biomass recalcitrance and facilitates enzymatic degradation. Herein, we have treated moso bamboo and microcrystalline cellulose separately by either alkali or ethylenediamine (EDA) treatments, as well as using both in succession. The pretreatments successfully transformed the initial cellulose Iβ allomorph into cellulose II, III I , and cellulose III II . Crystal structures and crystallinities were determined by Rietveld X-ray diffraction and CP/MAS 13 C NMR. Comparatively, the samples that were sequentially treated by EDA and NaOH had low crystallinity (~50%), larger d-spacings of ~4.4 Å for the hydrophobic (110) planes, and less condensed microfibrillar aggregation. The factors simultaneously contributed to as high enzymatic hydrolysis yield as 89.5% and 91.7% respectively, followed by the yields of mercerized cellulose II and cellulose III II allomorph. Here, the stepwise allomorphic transformations may provide new strategies on improving efficiency of saccharification process and biomass utilization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

cis-p -Coumarates acylate the lignin sidechain in grasses and other plants

In this study, we present evidence that the lignins of grasses and other plants undergo partial acylation by cis-p-coumarate. Unlike the more widely observed trans-p-coumarates, cis-p -coumarates represent a novel acylation pattern on the lignin sidechains. The finding was substantiated by detailed NMR analyses (HSQC, HSQC-TOCSY, HMBC) and alkaline hydrolysis of the lignin isolated from abacá, a plant that exhibits substantial amounts of cis-p -coumarate. The presence of cis-p -coumarates broadens the range of groups known to acylate lignin sidechains and suggests that subtle variations in the acylation pattern can modulate the final structure and properties of the lignin. A broad survey of lignins from diverse plant species revealed that all lignins incorporating trans-p-coumarates also incorporated cis-p-coumarates, albeit in varying proportions. The cis-p-coumarate content ranged from 2 % to 12 % of the total p-coumarate units, depending on the plant species. As cis-p -coumarate is formed through the isomerization of trans-p-coumarate triggered by UV light, this transformation may occur at various stages, including at the free p-coumaric acid level, at the monolignol p-coumarate level, or directly within the lignin polymer. The potential pathways through which cis-p -coumaric acid becomes incorporated into the lignin are discussed.

NMR↗
DOE OSTI2021

The exo-β- N -acetylmuramidase NamZ from Bacillus subtilis is the founding member of a family of exo-lytic peptidoglycan hexosaminidases

Endo-β-N-acetylmuramidases, commonly known as lysozymes, are well-characterized antimicrobial enzymes that catalyze an endo-lytic cleavage of peptidoglycan; i.e., they hydrolyze the β-1,4-glycosidic bonds connecting N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc). In contrast, little is known about exo-β-N-acetylmuramidases, which catalyze an exo-lytic cleavage of β-1,4-MurNAc entities from the non-reducing ends of peptidoglycan chains. Such an enzyme was identified earlier in the bacterium Bacillus subtilis, but the corresponding gene has remained unknown so far. We now report that ybbC of B. subtilis, renamed namZ, encodes the reported exo-β-N-acetylmuramidase. A ΔnamZ mutant accumulated specific cell wall fragments and showed growth defects under starvation conditions, indicating a role of NamZ in cell wall turnover and recycling. Recombinant NamZ protein specifically hydrolyzed the artificial substrate para-nitrophenyl β-MurNAc and the peptidoglycan-derived disaccharide MurNAc-β-1,4-GlcNAc. Together with the exo-β-N-acetylglucosaminidase NagZ and the exo-muramoyl-L-alanine amidase AmiE, NamZ degraded intact peptidoglycan by sequential hydrolysis from the non-reducing ends. A structure model of NamZ, built on the basis of two crystal structures of putative orthologs from Bacteroides fragilis, revealed a two-domain structure including a Rossmann-fold-like domain that constitutes a unique glycosidase fold. Thus, NamZ, a member of the DUF1343 protein family of unknown function, is now classified as the founding member of a new family of glycosidases (CAZy GH171). NamZ-like peptidoglycan hexosaminidases are mainly present in the phylum Bacteroidetes and less frequently found in individual genomes within Firmicutes (Bacilli, Clostridia), Actinobacteria, and γ-proteobacteria.

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

Fission yeast Duf89 and Duf8901 are cobalt/nickel-dependent phosphatase–pyrophosphatases that act via a covalent aspartyl–phosphate intermediate

Domain of Unknown Function 89 (DUF89) proteins are metal-dependent phosphohydrolases. Exemplary DUF89 enzymes differ in their metal and phosphosubstrate preferences. Here, we interrogated the activities and structures of two DUF89 paralogs from fission yeast—Duf89 and Duf8901. We find that Duf89 and Duf8901 are cobalt/nickel-dependent phosphohydrolases adept at hydrolyzing p-nitrophenylphosphate and PP i . Crystal structures of metal-free Duf89 and Co 2+ -bound Duf8901 disclosed two enzyme conformations that differed with respect to the position of a three-helix module, which is either oriented away from the active site in Duf89 or forms a lid over the active site in Duf8901. Lid closure results in a 16 Å movement of Duf8901 Asp195, vis-à-vis Asp199 in Duf89, that brings Asp195 into contact with an octahedrally coordinated cobalt. Reaction of Duf8901 with BeCl 2 and NaF in the presence of divalent cations Co 2+ , Ni 2+ , or Zn 2+ generated covalent Duf8901-(Asp248)–beryllium trifluoride (BeF 3 )•Co 2+ , Duf8901-(Asp248)–BeF 3 •Ni 2+ , or Duf8901-(Asp248)–BeF 3 •Zn 2+ adducts, the structures of which suggest a two-step catalytic mechanism via formation and hydrolysis of an enzyme-(aspartyl)–phosphate intermediate. Alanine mutations of Duf8901 Asp248, Asn249, Lys401, Asp286, and Asp195 that interact with BeF 3 •Co 2+ squelched p-nitrophenylphosphatase activity. A 1.8 Å structure of a Duf8901-(Asp248)–AlF 4 –OH 2 •Co 2+ transition-state mimetic suggests an associative mechanism in which Asp195 and Asp363 orient and activate the water nucleophile. Whereas deletion of the duf89 gene elicited a phenotype in which expression of phosphate homeostasis gene pho1 was derepressed, deleting duf8901 did not, thereby hinting that the DUF89 paralogs have distinct functional repertoires in vivo.

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

Revealing the mechanism of action of a first-in-class covalent inhibitor of $\mathrm{KRASG12C}$ $\mathrm{(ON)}$ and other functional properties of oncogenic $\text{KRAS}$ by 31 P $\mathrm{NMR}$

Individual oncogenic KRAS mutants confer distinct differences in biochemical properties and signaling for reasons that are not well understood. KRAS activity is closely coupled to protein dynamics and is regulated through two interconverting conformations: state 1 (inactive, effector binding deficient) and state 2 (active, effector binding enabled). Here, we use 31 P NMR to delineate the differences in state 1 and state 2 populations present in WT and common KRAS oncogenic mutants (G12C, G12D, G12V, G13D, and Q61L) bound to its natural substrate GTP or a commonly used nonhydrolyzable analog GppNHp (guanosine-5'-[(β,γ)-imido] triphosphate). Our results show that GppNHp-bound proteins exhibit significant state 1 population, whereas GTP-bound KRAS is primarily (90% or more) in state 2 conformation. This observation suggests that the predominance of state 1 shown here and in other studies is related to GppNHp and is most likely nonexistent in cells. We characterize the impact of this differential conformational equilibrium of oncogenic KRAS on RAF1 kinase effector RAS-binding domain and intrinsic hydrolysis. Through a KRAS G12C drug discovery, we have identified a novel small-molecule inhibitor, BBO-8956, which is effective against both GDP- and GTP-bound KRAS G12C. We show that binding of this inhibitor significantly perturbs state 1–state 2 equilibrium and induces an inactive state 1 conformation in GTP-bound KRAS G12C. In the presence of BBO-8956, RAF1–RAS-binding domain is unable to induce a signaling competent state 2 conformation within the ternary complex, demonstrating the mechanism of action for this novel and active-conformation inhibitor.

31P NMR↗
DOE OSTI2024

Characterization of alternate encounter assemblies of SARS-CoV-2 main protease

The assembly of two monomeric constructs spanning segments 1-199 (MPro 1-199 ) and 10-306 (MPro 10-306 ) of SARS-CoV-2 main protease (MPro) was examined to assess the existence of a transient heterodimer intermediate in the N-terminal autoprocessing pathway of MPro model precursor. Together, they form a heterodimer population accompanied by a 13-fold increase in catalytic activity. Addition of inhibitor GC373 to the proteins increases the activity further by ~7-fold with a 1:1 complex and higher order assemblies approaching 1:2 and 2:2 molecules of MPro 1-199 and MPro 10-306 detectable by analytical ultracentrifugation and native mass estimation by light scattering. Assemblies larger than a heterodimer (1:1) are discussed in terms of alternate pathways of domain III association, either through switching the location of helix 201 to 214 onto a second helical domain of MPro 10-306 and vice versa or direct interdomain III contacts like that of the native dimer, based on known structures and AlphaFold 3 prediction, respectively. At a constant concentration of MPro 1-199 with molar excess of GC373, the rate of substrate hydrolysis displays first order dependency on the MPro 10-306 concentration and vice versa. An equimolar composition of the two proteins with excess GC373 exhibits half-maximal activity at ~6 μM MPro 1-199 . Catalytic activity arises primarily from MPro 1-199 and is dependent on the interface interactions involving the N-finger residues 1 to 9 of MPro 1-199 and E290 of MPro 10-306 . Importantly, our results confirm that a single N-finger region with its associated intersubunit contacts is sufficient to form a heterodimeric MPro intermediate with enhanced catalytic activity.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Antibacterial ADP-ribosyl cyclase toxins inhibit bacterial growth by rapidly depleting NAD(P) +

In metazoans, enzymes belonging to the bifunctional ADP-ribosyl cyclase/cyclic ADP-ribose (cADPr) hydrolase family regulate diverse cellular processes by synthesizing and hydrolyzing the intracellular second messenger cADPr, derived from the electron carrier NAD+. However, bacterial enzymes belonging to this family have not been characterized. Here, we identify a bacterial ADP-ribosyl cyclase that is associated with the type VII secretion system and functions as an antibacterial toxin. This enzyme, which we name Tac1, inhibits bacterial growth by rapidly hydrolyzing NAD+ and NADP+. We determine the X-ray crystal structure of Tac1 to a resolution of 1.4 Å, which reveals that this protein adopts the core catalytic fold of metazoan ADP-ribosyl cyclase enzymes such as CD38. Using a combination of biochemical and mutagenesis approaches, we identify catalytic residues within the active site of Tac1, which are responsible for the formation of a cADPr catalytic intermediate and subsequent hydrolysis of this intermediate into linear ADP-ribose. A bioinformatic analysis reveals that Tac1 is the founding member of a widespread family of bacterial ADP-ribosyl cyclase enzymes, many of which are associated with interbacterial conflict systems. We also identify enzymes in this family that are not associated with biological conflict systems and demonstrate that they produce cADPr as their major product rather than linear ADP-ribose, suggesting that these enzymes serve a biological function distinct from interbacterial antagonism. Together, these findings demonstrate that ADP-ribosyl cyclase/cADPr hydrolase enzymes function as toxins in diverse bacterial conflict systems and suggest that cADPr may play a previously overlooked role in bacterial physiology.

Colautti, Jake↗
DOE OSTI2020

A new approach of reduction of carbon dioxide emission and optimal use of carbon and hydrogen content for the desired syngas production from coal

We report this research is designed to make progress in overcoming the challenges through the development of a two-stage coal processing. Specifically, a two-stage process was used to maximize the use of the carbon in coal or increase the carbon monoxide yield or lower carbon dioxide and methane yields. Carbon dioxide-char gasification in the absence of water can generate carbon monoxide with near-zero methane, which is desired to produce high-carbon and low-hydrogen chemicals such as oxalic acid through catalytic carbon monoxide coupling and hydrolysis. The technology is applicable to any coal, although Power River Basin (PRB) coal is used as an example feedstock in this research Also, the sodium-iron catalyst can accelerate not only the reaction kinetics in both stages but also increase the hydrogen/carbon monoxide ratio in the syngas produced in the second stage. In other words, the catalyst is a multifunctional agent, which can not only intensify the overall coal process efficiency but also improve the qualities of the desired syngas products and reduce carbon dioxide emission. Thus, In the 1st stage, the catalysts can significantly reduce the CO 2 -char gasification by as high as 75.00%. In the 2nd stage, the H 2 /CO ratio of ideal syngas is ~2:1 with near-0 CH 4 generation and the CH4 production can be reduced as high as 61.29% for the CO 2 –H 2 O-Char coal gasification. The activation energy for the 2nd stage is reduced by as high as 35.43% than that of raw coal without use Na–Fe catalyst. The overall carbon footprint reduction for the study is reduced by 87.33% in the 1st stage and 96.77% compared to the direct coal combustion.

01 COAL, LIGNITE, AND PEAT↗