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  1. Background: The unique ability of carbon to form a wide variety of allotropic modificationshas ushered in a new era in material science. Tuning the properties of these materials by functionalizationis a must-have tool for their design customized for a specific practical use. The exponentiallygrowing computational power available to researchers allows for the prediction and thoroughunderstanding of the underlying physicochemical processes responsible for the practical propertiesof pristine and modified carbons using the methods of quantum chemistry. Method: This review focuses on the computational assessment of the influence of functionalizationon the properties of carbons and enabling desired practical properties of the new materials. The firstsection of each part of this review focuses on graphene with nearly planar units built from sp2-carbons. The second section discusses patterns of sp2-carbons rolled up into curved 3D structures in avariety of ways (fullerenes). The overview of other types of carbonaceous materials, including thosewith a high abundance of sp3-carbons, including nanodiamonds, can be found in the third section ofeach manuscript’s part. Conclusion: The computational methods are especially critical for predicting electronic properties ofmaterials such as the bandgap, conductivity, optical and photoelectronic properties, solubility, adsorptivity,the potential for catalysis, sensing, imaging, and biomedical applications. We expect thatintroduction of defectsmore »to carbonaceous materials as a type of their functionalization will be a pointof growth in this area of computational research.« less
    Free, publicly-accessible full text available July 1, 2023
  2. The quantity of grass-root exudates varies by season, suggesting temporal shifts in soil microbial community composition and activity across a growing season. We hypothesized that bacterial community and nitrogen cycle-associated prokaryotic gene expressions shift across three phases of the growing season. To test this hypothesis, we quantified gene and transcript copy number of nitrogen fixation (nifH), ammonia oxidation (amoA, hao, nxrB), denitrification (narG, napA, nirK, nirS, norB, nosZ), dissimilatory nitrate reduction to ammonia (nrfA), and anaerobic ammonium oxidation (hzs, hdh) using the pre-optimized Nitrogen Cycle Evaluation (NiCE) chip. Bacterial community composition was characterized using V3-V4 of the 16S rRNA gene, and PICRUSt2 was used to draw out functional inferences. Surprisingly, the nitrogen cycle genes and transcript quantities were largely stable and unresponsive to seasonal changes. We found that genes and transcripts related to ammonia oxidation and denitrification were different for only one or two time points across the seasons (p < 0.05). However, overall, the nitrogen cycling genes did not show drastic variations. Similarly, the bacterial community also did not vary across the seasons. In contrast, the predicted functional potential was slightly low for May and remained constant for other months. Moreover, soil chemical properties showed a seasonal pattern onlymore »for nitrate and ammonium concentrations, while ammonia oxidation and denitrification transcripts were strongly correlated with each other. Hence, the results refuted our assumptions, showing stability in N cycling and bacterial community across growing seasons in a natural grassland.« less
    Free, publicly-accessible full text available May 1, 2023
  3. Free, publicly-accessible full text available May 1, 2023
  4. Free, publicly-accessible full text available May 1, 2023
  5. Free, publicly-accessible full text available April 1, 2023
  6. Particulate methane monooxygenase (pMMO), a membrane-bound enzyme having three subunits (α, β, and γ) and copper-containing centers, is found in most of the methanotrophs that selectively catalyze the oxidation of methane into methanol. Active sites in the pMMO of Methylosinus trichosporium OB3b were determined by docking the modeled structure with ethylbenzene, toluene, 1,3-dibutadiene, and trichloroethylene. The docking energy between the modeled pMMO structure and ethylbenzene, toluene, 1,3-dibutadiene, and trichloroethylene was −5.2, −5.7, −4.2, and −3.8 kcal/mol, respectively, suggesting the existence of more than one active site within the monomeric subunits due to the presence of multiple binding sites within the pMMO monomer. The evaluation of tunnels and cavities of the active sites and the docking results showed that each active site is specific to the radius of the substrate. To increase the catalysis rates of methane in the pMMO of M. trichosporium OB3b, selected amino acid residues interacting at the binding site of ethylbenzene, toluene, 1,3-dibutadiene, and trichloroethylene were mutated. Based on screening the strain energy, docking energy, and physiochemical properties, five mutants were downselected, B:Leu31Ser, B:Phe96Gly, B:Phe92Thr, B:Trp106Ala, and B:Tyr110Phe, which showed the docking energy of −6.3, −6.7, −6.3, −6.5, and −6.5 kcal/mol, respectively, as compared to the wildmore »type (−5.2 kcal/mol) with ethylbenzene. These results suggest that these five mutants would likely increase methane oxidation rates compared to wild-type pMMO.« less
    Free, publicly-accessible full text available April 1, 2023
  7. Free, publicly-accessible full text available March 29, 2023
  8. The gut microbiome incorporates the ecological niche specific to the totality of the microorganisms in the human gut. Unique to every individual, the blueprint of the microbiome sets up at birth and functions as a human organ and plays a significant role in digestion, detoxification, fighting pathogens, modulating the immune system, and improving health. The gut microbiota and associated health implications are influenced by factors such as birth and age, diseases, use of antibiotics and food components (e.g., complex carbohydrates and dietary fibers, plant proteins, unsaturated fatty acids, and functional compounds of natural origin such as flavones, flavonoids, polyphenols, and antioxidants). Toward this end, diet and the gut microbiome interact and govern each other’s fate. Herein, gut dysbiosis, the alteration of natural state and composition of the gut microbiome, and the gut microflora diversity modulated by food constituents and associated health effects have been discussed. The gut microbiota composition and related metabolites are influenced by the diet which in turn modulates human health. The outcome is deemed to aid in developing personalized diet recommendations (based on the unique gut microbiome) toward improving human health. Keywords: gut microbiome, gut microbiota, gut dysbiosis, short-chain fatty acids, metabolites, health modulation