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This presentation offers an analysis of infrastructure science with goals to provide third-party independent science based input into complex problems of national concern and to use scientific analysis to "turn down the noise" around complex problems.
We report a projection-based reduced order model (pROM) methodology has been developed for transient heat transfer problems involving coupled conduction and enclosure radiation. The approach was demonstrated on two test problems of varying complexity. The reduced order models demonstrated substantial speedups (up to 185×) relative to the full order model with good accuracy (less than 3% L ∞ error). An attractive feature of pROMs is that there is a natural error indicator for the ROM solution: the final residual norm at each time-step of the converged ROM solution. Using example test cases, we discuss how to interpret this error indicator to assess the accuracy of the ROM solution. The approach shows promise for many-query applications, such as uncertainty quantification and optimization. The reduced computational cost of the ROM relative to the full-order model (FOM) can enable the analysis of larger and more complex systems as well as the exploration of larger parameter spaces.
Euryarchaeal lineages have been believed to have a methanogenic last common ancestor. However, members of euryarchaeal Archaeoglobi have long been considered nonmethanogenic and their evolutionary history remains elusive. Here, three high-quality metagenomic-assembled genomes (MAGs) retrieved from high-temperature oil reservoir and hot springs, together with three newly assembled Archaeoglobi MAGs from previously reported hot spring metagenomes, are demonstrated to represent a novel genus of Archaeoglobaceae, “Candidatus Methanomixophus.” All “Ca. Methanomixophus” MAGs encode an M methyltransferase (MTR) complex and a traditional type of methyl-coenzyme M reductase (MCR) complex, which is different from the divergent MCR complexes found in “Ca. Polytropus marinifundus.” In addition, “Ca. Methanomixophus dualitatem” MAGs preserve the genomic capacity for dissimilatory sulfate reduction. Comparative phylogenetic analysis supports a laterally transferred origin for an MCR complex and vertical heritage of the MTR complex in this lineage. Metatranscriptomic analysis revealed concomitant in situ activity of hydrogen-dependent methylotrophic methanogenesis and heterotrophic fermentation within populations of “Ca. Methanomixophus hydrogenotrophicum” in a high-temperature oil reservoir.
To more fully understand the molecular mechanisms responsible for variations in binding affinity with antibody maturation, we explored the use of site specific fluorine labeling and {sup 19}F nuclear magnetic resonance (NMR). Several single-chain (scFv) antibodies, derived from an affinity-matured series of anti-hen egg white lysozyme (HEL) mouse IgG1, were constructed with either complete or individual replacement of tryptophan residues with 5-fluorotryptophan ({sup 5F}W). An array of biophysical techniques was used to gain insight into the impact of fluorine substitution on the overall protein structure and antigen binding. SPR measurements indicated that {sup 5F}W incorporation lowered binding affinity for the HEL antigen. The degree of analogue impact was residue-dependent, and the greatest decrease in affinity was observed when {sup 5F}W was substituted for residues near the binding interface. In contrast, corresponding crystal structures in complex with HEL were essentially indistinguishable from the unsubstituted antibody. {sup 19}F NMR analysis showed severe overlap of signals in the free fluorinated protein that was resolved upon binding to antigen, suggesting very distinct chemical environments for each {sup 5F}W in the complex. Preliminary relaxation analysis suggested the presence of chemical exchange in the antibody-antigen complex that could not be observed by X-ray crystallography. These data demonstrate that fluorine NMR can be an extremely useful tool for discerning structural changes in scFv antibody-antigen complexes with altered function that may not be discernible by other biophysical techniques.
Disclosed is a method for analyzing the organismic complexity of a sample through analysis of the nucleic acid in the sample. In the disclosed method, through a series of steps, including digestion with a type II restriction enzyme, ligation of capture adapters and linkers and digestion with a type IIS restriction enzyme, genome signature tags are produced. The sequences of a statistically significant number of the signature tags are determined and the sequences are used to identify and quantify the organisms in the sample. Various embodiments of the invention described herein include methods for using single point genome signature tags to analyze the related families present in a sample, methods for analyzing sequences associated with hyper- and hypo-methylated CpG islands, methods for visualizing organismic complexity change in a sampling location over time and methods for generating the genome signature tag profile of a sample of fragmented DNA.
The SAGUARO (Scalable Algorithms for Groundwater Uncertainty Analysis and Robust Optimization) Project focused on the development of scalable numerical algorithms for large-scale Bayesian inversion in complex systems that capitalize on advances in large-scale simulation-based optimization and inversion methods. The project was a collaborative effort among MIT, the University of Texas at Austin, Georgia Institute of Technology, and Sandia National Laboratories. The research was directed in three complementary areas: efficient approximations of the Hessian operator, reductions in complexity of forward simulations via stochastic spectral approximations and model reduction, and employing large-scale optimization concepts to accelerate sampling. The MIT₋Sandia component of the SAGUARO Project addressed the intractability of conventional sampling methods for large-scale statistical inverse problems by devising reduced-order models that are faithful to the full-order model over a wide range of parameter values; sampling then employs the reduced model rather than the full model, resulting in very large computational savings. Results indicate little effect on the computed posterior distribution. On the other hand, in the Texas₋Georgia Tech component of the project, we retain the full-order model, but exploit inverse problem structure (adjoint-based gradients and partial Hessian information of the parameter-to-observation map) to implicitly extract lower dimensional information on the posterior distribution; this greatly speeds up sampling methods, so that fewer sampling points are needed. We can think of these two approaches as "reduce then sample" and "sample then reduce." In fact, these two approaches are complementary, and can be used in conjunction with each other. Moreover, they both exploit deterministic inverse problem structure, in the form of adjoint-based gradient and Hessian information of the underlying parameter-to-observation map, to achieve their speedups.
Mg batteries are an attractive alternative to Li-based energy storage due to the possibility of higher volumetric capacities with the added advantage of using sustainable materials. A promising emerging electrolyte for Mg batteries is the magnesium aluminum chloride complex (MACC) which shows high Mg electrodeposition and stripping efficiencies and relatively high anodic stabilities. As prepared, MACC is inactive with respect to Mg deposition; however, efficient Mg electrodeposition can be achieved following an electrolytic conditioning process. Through the use of Raman spectroscopy, surface enhanced Raman spectroscopy, 27Al and 35Cl nuclear magnetic resonance spectroscopy, and pair distribution function analysis, we explore the active vs inactive complexes in the MACC electrolyte and demonstrate the codependence of Al and Mg speciation. These techniques report on significant changes occurring in the bulk speciation of the conditioned electrolyte relative to the as-prepared solution. Analysis shows that the active Mg complex in conditioned MACC is very likely the [Mg2(μ–Cl)3·6THF]+ complex that is observed in the solid state structure. Additionally, conditioning creates free Cl– in the electrolyte solution, and we suggest the free Cl– adsorbs at the electrode surface to enhance Mg electrodeposition.
In this report, we conduct a bottom-up analysis of the installed costs for FPV systems deployed on artificial water bodies under average site conditions (wind load of about 40 m/s, snow load of 20 psf, water depth of 50 m, water level variation of 10 m, and swell height of 1 m). We estimate an installed system cost premium of $\$0.26$/WDC (25%) for 10-MWDC fixed-tilt FPV systems, compared with ground-mounted, fixed-tilt PV installed over bare ground. Higher structural costs related to the floats and anchoring system are the largest contributors to this premium. Currently, site investigation costs are also higher for FPV because of the additional effort needed to plan and design these more complex installations. Our preliminary sensitivity analysis shows that the installed cost of FPV systems is most sensitive to float costs, wind and snow loading, and module efficiency. FPV deployment is in an early stage, and additional experience, best practice development, and new configurations and technologies could help reduce the costs of FPV systems over time.
An azadithiolate bridged CN — bound pentacarbonyl bis-iron complex, mimicking the active site of [Fe–Fe] H 2 ase is synthesized. The geometric and electronic structure of this complex is elucidated using a combination of EXAFS analysis, infrared and Mössbauer spectroscopy and DFT calculations. The electrochemical investigations show that complex 1 effectively reduces H + to H 2 between pH 0–3 at diffusion-controlled rates (10 11 M —1 s —1 ) i.e. 10 8 s —1 at pH 3 with an overpotential of 140 mV. Electrochemical analysis and DFT calculations suggests that a CN— ligand increases the p K a of the cluster enabling hydrogen production from its Fe(I)–Fe(0) state at pHs much higher and overpotential much lower than its precursor bis-iron hexacarbonyl model which is active in its Fe(0)–Fe(0) state. The formation of a terminal Fe–H species, evidenced by spectroelectrochemistry in organic solvent, via a rate determining proton coupled electron transfer step and protonation of the adjacent azadithiolate, lowers the kinetic barrier leading to diffusion controlled rates of H 2 evolution. The stereo-electronic factors enhance its catalytic rate by 3 order of magnitude relative to a bis-iron hexacarbonyl precursor at the same pH and potential.
Virulence of Candida is linked with its ability to form biofilms. Once established, biofilm infections are nearly impossible to eradicate. Biofilm cells live immersed in a self-produced matrix, a blend of extracellular biopolymers, many of which are uncharacterized. In this study, we provide a comprehensive analysis of the matrix manufactured by Candida albicans both in vitro and in a clinical niche animal model. We further explore the function of matrix components, including the impact on drug resistance. We uncovered components from each of the macromolecular classes (55% protein, 25% carbohydrate, 15% lipid, and 5% nucleic acid) in the C. albicans biofilm matrix. Three individual polysaccharides were identified and were suggested to interact physically. Surprisingly, a previously identified polysaccharide of functional importance, β-1,3-glucan, comprised only a small portion of the total matrix carbohydrate. Newly described, more abundant polysaccharides included β-1,2 branched β-1,6-mannans (87%) associated with unbranched β-1,6-glucans (13%) in an apparent mannan-glucan complex (MGCx). Functional matrix proteomic analysis revealed 458 distinct activities. The matrix lipids consisted of neutral glycerolipids (89.1%), polar glycerolipids (10.4%), and sphingolipids (0.5%). Examination of matrix nucleic acid identified DNA, primarily noncoding sequences. Several of the in vitro matrix components, including proteins and each of the polysaccharides, were also present in the matrix of a clinically relevant in vivo biofilm. Nuclear magnetic resonance (NMR) analysis demonstrated interaction of aggregate matrix with the antifungal fluconazole, consistent with a role in drug impedance and contribution of multiple matrix components.
Recent studies involving several viral systems have highlighted the importance of cellular intrinsic defense mechanisms through nuclear antiviral proteins that restrict viral propagation. These factors include among others components of PML nuclear bodies, the nuclear DNA sensor IFI16, and a potential restriction factor PHF13/SPOC1. For several nuclear replicating DNA viruses, it was shown that these factors sense and target viral genomes immediately upon nuclear import. In contrast to the anticipated view, we recently found that incoming adenoviral genomes are not targeted by PML nuclear bodies. Here we further explored cellular responses against adenoviral infection by focusing on specific conditions as well as additional nuclear antiviral factors. In line with our previous findings, we show that neither interferon treatment nor the use of specific isoforms of PML nuclear body components results in co-localization between incoming adenoviral genomes and the subnuclear domains. Furthermore, our imaging analyses indicated that neither IFI16 nor PHF13/SPOC1 are likely to target incoming adenoviral genomes. Thus our findings suggest that incoming adenoviral genomes may be able to escape from a large repertoire of nuclear antiviral mechanisms, providing a rationale for the efficient initiation of lytic replication cycle. - Highlights: • Host nuclear antiviral factors were analyzed upon adenovirus genome delivery. • Interferon treatments fail to permit PML nuclear bodies to target adenoviral genomes. • Neither Sp100A nor B targets adenoviral genomes despite potentially opposite roles. • The nuclear DNA sensor IFI16 does not target incoming adenoviral genomes. • PHF13/SPOC1 targets neither incoming adenoviral genomes nor genome-bound protein VII.
The current impetus towards a sustainable bio-based economy has accelerated research to better understand the mechanisms through which filamentous fungi convert plant biomass, a valuable feedstock for biotechnological applications. Several transcription factors have been reported to control the polysaccharide degradation and metabolism of the resulting sugars in fungi. However, little is known about their individual contributions, interactions and crosstalk. D-galactose is a hexose sugar present mainly in hemicellulose and pectin in plant biomass. Here, we study D-galactose conversion by Aspergillus niger and describe the involvement of the arabinanolytic and xylanolytic activators AraR and XlnR, in addition to the D-galactose-responsive regulator GalX. Our results deepen the understanding of the complexity of the filamentous fungal regulatory network for plant biomass degradation and sugar catabolism, and facilitate the generation of more efficient plant biomass-degrading strains for biotechnological applications.
Three Cu{sup II} coordination polymers, ([Cu{sub 2}(CH{sub 3}O-ip){sub 2}(bmib)]){sub n} (1), ([Cu{sub 2}(CH{sub 3}O-ip){sub 2}(bmib){sub 2}]){sub n} (2) and ([Cu(CH{sub 3}O-ip)(bbip)]∙2H{sub 2}O){sub n} (3) (CH{sub 3}O-H{sub 2}ip is 5-methoxyisophthalic acid, bmib is 1,4-bis(2-methylimidazol-1-yl)butane and bbip is 1,3-bis(1H-benzimidazolyl)propane), have been synthesized by hydrothermal methods. Complexes 1–3 were structurally characterized by elemental analysis, infrared (IR) spectra and X-ray single-crystal diffraction. Complex 1 shows a 3D six-connected self-penetrating network based on paddlewheel secondary building units. Complex 2 has a 3-fold interpenetrating 3D diamond framework. Complex 3 possesses a 1D tube-like chain. Thermo-gravimetric and magnetic properties of 1–3 were also investigated. - Graphical abstract: Structures and magnetic properties of copper(II) coordination polymers constructed from 5-methoxyisophthalate linker and two flexible N-donor ancillary ligands. Three copper(II) coordination polymers with 5-methoxyisophthalate and two related flexible N-donor ancillary ligands have been synthesized and structurally characterized. Moreover, thermal behaviors and magnetic properties of these complexes have also been investigated. - Highlights: • Three Cu(II) coordination polymers were synthesized. • The conformations of N-donor ligands and pH value have an effect on the final structures. • The magnetic properties of 1–3 have been investigated.
Three Ln 2+ 18-crown-6 complexes of the formula Ln(18-crown-6)I 2 (Ln = Sm, Eu, Yb) were isolated from the explicit synthesis of the corresponding LnI 2 salts with 18-crown-6 and tetrabutylammonium tetraphenylborate in organic media under air-free conditions. Each metal complex forms a distorted hexagonal bipyramidal geometry and crystallizes in the monoclinic space group P2 1 /n. Comparatively, crystallization of Ln(benzo-18-crown-6)I 2 (Ln = Sm, Eu, Yb) from the reaction of LnI2 with tetrabutylammonium tetraphenylborate and benzo-18-crown-6 in THF/ethanol under similarly air-free conditions yields two polymorphs. The first form, α, crystallizes in the monoclinic space group P2 1 /c (or the nonstandard setting P2 1 /n for α-Yb); whereas the second polymorph, β, crystallizes in P$\bar{1}$. While the geometries of the molecules only vary slightly, the molecular packing and intramolecular contacts are quite different. In the structure of β, π–π interactions between the benzo- moieties of adjacent molecules are observed, whereas these interactions are absent in α. Despite the similarities in these classically 4f n+1 lanthanide systems, the complexes display distinct spectroscopic features in their respective absorption and photoluminescence spectra. Broadband 5d → 4f photoluminescence was observed for the Sm and Eu compounds in the NIR region and UV–visible region, respectively. None of the three Yb compounds exhibit photoluminescence UV–visible-NIR region; however, a unique photooxidation event was observed resulting in characteristic Yb(III) 4f → 4f transitions in the NIR region of the absorption spectra of these compounds. Finally, these findings are discussed along with structural comparisons of the 18-crown-6 and benzo-18-crown-6 compounds as well as other reported Ln(II) crown complexes in the literature.
Natural transition orbitals (NTOs) are in widespread use for visualizing and analyzing electronic transitions. Here, the present work introduces the analysis of formally spin-forbidden transitions with the help of complex-valued spin-orbit (SO) NTOs. The analysis specifically focuses on the components in such transitions that cause their intensity to be non-zero because of SO coupling. Transition properties such as transition dipole moments are partitioned into SO-NTO hole-particle pairs, such that contributions to the intensity from specific occupied and unoccupied orbitals are obtained. The method has been implemented within the restricted active space (RAS) self-consistent field wave function theory framework, with SO coupling treated by RAS state interaction. SO-NTOs have a broad range of potential applications, which is illustrated by the T 2 -S 1 state mixing in pyrazine, spin-forbidden vs. spin-allowed 4f–5d transitions in the Tb 3+ ion, and the phosphorescence of tris(2-phenylpyridine) iridium [Ir(ppy) 3 ].
As data grows in size and complexity, finding frameworks which aid in interpretation and analysis has become critical. This is particularly true when data comes from complex systems where extensive structure is available, but must be drawn from peripheral sources. In this paper we argue that in such situations, sheaves can provide a natural framework to analyze how well a statistical model fits at the local level (that is, on subsets of related datapoints) vs the global level (on all the data). The sheaf-based approach that we propose is suitably general enough to be useful in a range of applications, from analyzing sensor networks to understanding the feature space of a deep learning model.
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