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KETCHUP: Parameterizing of large-scale kinetic models using multiple datasets with different reference states
Large-scale kinetic models provide the computational means to dynamically link metabolic reaction fluxes to metabolite concentrations and enzyme levels while also conforming to substrate level regulation. However, the development of broadly applicable frameworks for efficiently and robustly parameterizing models remains a challenge. Challenges arise due to both the heterogeneity, paucity, and difficulty in obtaining flux and/or concentration data but also due to the computational difficulties of the underlying parameter identification problem. Both the computational demands for parameterization, degeneracy of obtained parameter solutions and interpretability of results has so far limited widespread adoption of large-scale kinetic models despite their potential. Herein, we introduce the Kinetic Estimation Tool Capturing Heterogeneous Datasets Using Pyomo (KETCHUP), a flexible parameter estimation tool that leverages a primal-dual interior-point algorithm to solve a nonlinear programming (NLP) problem that identifies a set of parameters capable of recapitulating the (non)steady-state fluxes and concentrations in wild-type and perturbed metabolic networks. KETCHUP is benchmarked against previously parameterized large-scale kinetic models demonstrating an at least an order of magnitude faster convergence than the tool K-FIT while at the same time attaining better data fits. Finally, this versatile toolbox accepts different kinetic descriptions, metabolic fluxes, enzyme levels and metabolite concentrations, under either steady-state or instationary conditions to enable robust kinetic model construction and parameterization. KETCHUP supports the SBML format and can be accessed at https://github.com/maranasgroup/KETCHUP.
Three-Dimensional Analysis of Materials at Multiple Length Scales.
Abstract not provided.
Multiple-Scale Synchrotron and Lab Source X-Ray Fluorescence 2D Mapping of Gold Mineralization Style
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Quantification of Hydrogen Isotopes Utilizing Raman Spectroscopy Paired with Chemometric Analysis for Application across Multiple Systems
On-line and real-time analysis of a chemical process is a major analytical challenge that can drastically change the way the chemical industry or chemical research operates. With in situ analyses, new and powerful understanding of chemistry can be gained; however, building robust tools for long-term monitoring faces many challenges that include compensating for instrument drift, instrument replacement, and sensor or probe replacement. Accounting for these changes by recollecting calibration data and rebuilding quantification models can be costly and time consuming. Here, in this study, methods to overcome these challenges are demonstrated with an application of Raman spectroscopy to monitoring hydrogen isotopes with varied speciation within dynamic gas streams. Specifically, chemical data science tools such as chemometric modeling are leveraged along with several examples of calibration transfer approaches. Furthermore, the optimization of instrument and sensors cell parameters for targeted gas phase analyses is discussed. While the particular focus on hydrogen is highly beneficial within the nuclear energy sector, mechanisms built and demonstrated here are widely applicable to optical spectroscopy monitoring in numerous other chemical systems that can be leveraged in other hazardous processes.
Optimized Substrates for Analysis of an Individual Atmospheric Particle Across Multiple Microspectroscopy Techniques: Fabrication and Characterization
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Targeting Multiple Binding Sites on Cholera Toxin B with Glycomimetic Polymers Promotes the Formation of Protein-Polymer Aggregates
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Mixed-Valent Copper Chalcogenides: Tuning Structures and Electronic Properties Using Multiple Anions
A series of mixed-anion copper chalcogenides have been prepared using solid-state methods including ACu 4.2 TeS 2 (A = K, Rb, Cs), which adopt the KCu 4 S 3 structure type. The mixedanion motif has an expanded sublattice, relative to KCu 4 S 3 , that can accommodate additional Cu atoms at its interstitial sites that are unoccupied in the parent structure. The variable temperature transport shows that the materials are p-type metals with carrier densities on the order of 10 21 cm -3 and room-temperature electrical conductivity as high as 4000 S cm -1 . Band structures calculated using density functional theory corroborate the experimental data and indicate that the interstitial Cu atoms lower the carrier concentration and increase the Fermi level of the materials. The layered structure has Te and S atoms occupying unique sites within the ACu 4.2 TeS 2 structure, where relatively hard S 2- anions prefer Wyckoff positions where they can form energetically favorable acid-base interactions with hard alkali cations. The phenomenon is observed in the related K 3 Cu 8 Te 2 S 4 system, which also has a fully ordered layered structure. Here, we believe that the report provides new chemical guidelines for targeting ordered multianion structures, as well as a unique method for tuning the electronic properties of metallic chalcogenides.
Titrating Controlled Defects into Si-LTA Zeolite Crystals Using Multiple Organic Structure-Directing Agents
Controlling defects in zeolites is crucial for tuning their adsorption and catalytic properties. In this work, we have performed an integrated zeolite synthesis, spectroscopy, and density functional theory study to test the limit of F– as a charge-balancing agent that mitigates defects in siliceous zeolites. We focused on the synthesis of siliceous zeolite LTA at 150 °C with 1,2-dimethyl-3-(4-methylbenzyl) imidazolium as the primary organic structure-directing agent (OSDA) and tetramethyl ammonium (TMA) as the secondary OSDA. By varying the amount of TMA in the synthesis gel, positive charges were titrated into the resulting as-made Si-LTA. Surprisingly, we found that greater TMA concentration does not induce more F– to enter into the zeolite. 29Si solid-state MAS NMR, Raman spectroscopy, and density functional theory suggest that this system has surpassed its capacity for F– to balance OSDA charge, and additional positive charge is balanced by Si–O– framework defects. The number of defects in the as-made Si-LTA can be precisely titrated by the amount of TMA in the zeolite structures. For the Si-LTA synthesized without TMA, framework defects formed in the early stage of crystal growth were found to heal during later crystallization, leading to defect-free Si-LTA. However, for the Si-LTA synthesized with TMA, the defects formed in early stages do not heal. A DFT thermodynamic analysis explains that crowding of Si-LTA pores by TMA impedes defect healing; this prediction is corroborated by synthesis experiments at an elevated temperature (170 °C). These results indicate that F– can have a limited capacity to balance OSDA charge in zeolite synthesis, opening up a third route to zeolite synthesis intermediate between the fluoride and hydroxide routes.
First-Principles Examination of Multiple Criteria of Organic Solvent Oxidative Stability in Batteries
Oxidative instability of the liquid electrolyte at or near battery cathode oxide surfaces has significant detrimental effects on batteries. Organic solvent molecules are often the fuel and precursors of such degradation processes, releasing electrons and protons that react with cathode oxides and electrolyte anions. These reactions contribute to cathode–electrolyte interphase (CEI) film formation, transition-metal ion dissolution, and phase transformation of the surface regions of the cathode. Here we apply density functional theory calculations to examine four criteria of oxidative stability (oxidation potential, hydrogen removal energies, and initial reactivity on two types of oxide facets) using four different solvent/additive molecules (ethylene carbonate, fluoroethylene carbonate, 1,3-dioxolane, and dimethyl ether). The ranking of molecular stability differs with each criterion. Surprisingly, the all-oxygen-terminated basal planes of layered oxides exhibit lower reaction barriers than spinel surface facets with exposed transition-metal cations, especially for ether solvents; the calculations also suggest basal planes contribute to the dissolution of transition-metal ions. Further, the structure–degradation relation complexity underscores the challenge of understanding the function of the CEI but also offers a guide to future degradation-mitigation strategies including facet engineering. Our predictions and models help establish a framework for future studies relevant to high-voltage conditions.
Mn2(Fe0.8Mo0.2)MoO6: A Double-Perovskite with Multiple Transition Metal Sublattice Magnetic Effects
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Simple Plant and Microbial Exudates Destabilize Mineral-Associated Organic Matter via Multiple Pathways
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Simulated Aquifer Heterogeneity Leads to Enhanced Attenuation and Multiple Retention Processes of Zinc
Alluvial aquifers serve as one of the main water sources for domestic, agricultural, and industrial purposes globally. Groundwater quality, however, can be threatened by naturally occurring and anthropogenic metal contaminants. Differing hydrologic and biogeochemical conditions between predominantly coarse-grained aquifer sediments and embedded layers or lenses of fine-grained materials lead to variation in metal behavior. Here, we examine processes controlling Zn partitioning within a dual-pore domain-reconstructed alluvial aquifer. Natural coarse aquifer sediments from the Wind River-Little Wind River floodplain near Riverton, WY, were used in columns with or without fine-grained lenses to examine biogeochemical controls on Zn concentrations, retention mechanisms, and transport. Furthermore, following the introduction of Zn to the groundwater source, Zn preferentially accumulated in the fine-grained lenses, despite their small volumetric contributions. While the clay fraction dominated Zn retention in the sandy aquifer, the lenses supported additional reaction pathways of retention—the reducing conditions within the lenses resulted in ZnS precipitation, overriding the contribution of organic matter. Zinc concentration in the groundwater controlled the formation of Zn-clays and Zn-layered double hydroxides, whereas the extent of sulfide production controlled precipitation of ZnS. Our findings illustrate how both spatial and compositional heterogeneities govern the extent and mechanisms of Zn retention in intricate groundwater systems, with implications for plume behavior and groundwater quality.
A Critical Review on the Multiple Roles of Manganese in Stabilizing and Destabilizing Soil Organic Matter
Not Available
Multiple Sources of Riparian Wetland Suspended Solids during Episodic Rain Events: Influence on Uranium Transport
Suspended solids can be the primary vector for transporting contaminants in streams. The objective of this study was to determine whether changes in the properties of suspended solids during rain events impacted contaminant transport. Stream water was collected during five episodic events downstream from a U-contaminated wetland located in South Carolina, USA. The suspended particles were initially composed of Fe-flocs (particles formed in situ prior to the rain event) that had significantly greater Fe, Mn, organic-C, and U content than particles collected later during a sampling rain event. XANES and EXAFS revealed that U in the Fe-flocs was U(VI) and that it was not incorporated in a mineral structure but existed as inner- or outer-sphere adsorbed uranyl species associated with organic matter and Fe-oxides. The uranyl had an extraordinarily high affinity for the suspended solids, with solid to liquid U ratios of >72,000 (μg/kg)/(μg/L). After the initial flush of Fe-flocs, a greater fraction of the suspended solids had lower organic-C, Fe, Mn, and amorphous phases and were composed of more quartz, kaolinite, and gibbsite, resulting in lower U concentrations than those in the solids collected earlier in the rain event. This study highlights the importance of understanding suspended solids as transport vectors and their potential dynamic nature during rain events.
Insights into the Solvation Characteristics of Zwitterionic Deep Eutectic Solvents Using Multiple Polarity Scales
Deep eutectic solvents (DESs) formed by mixing zwitterionic hydrogen bond acceptors (HBAs) with diol- and organic acid-based hydrogen bond donors (HBDs) are popular sustainable solvents. In addition to possessing an amphiphilic character, zwitterionic DESs offer unique solvation properties, unlike those composed of halide-containing HBAs. While all other popular classes of DESs have been investigated, no study has attempted to characterize the solvation characteristics of zwitterionic DESs. In this study, the solvation properties of betaine [Bet]-, sulfobetaine-, and l-carnitine [l-Car]-based DESs were thoroughly investigated for the first time using solvatochromic dye methods and inverse gas chromatography (IGC). Herein, the Nile red polarity scale revealed that DESs composed of organic acids were generally more polar than diol-based DESs. Kamlet–Taft solvent parameters revealed that glycerol-based DESs offered exceptionally high hydrogen bond donating ability compared to those composed of 1,4-butane diol and triethylene glycol. The Abraham solvation parameter model revealed hydrogen bond basicity to be the most dominant interaction, and it was generally higher for diol-based HBDs compared to organic acid-based HBDs. Additionally, sulfobetaine HBAs possessing longer alkyl chains generally offered higher dispersive-type interactions and hydrogen bond basicity compared to [Bet] and [l-Car] salts. This is the first study to combine and compare results from solvatochromic dye methods and IGC in an attempt to comprehensively explain and predict the solvation characteristics of zwitterionic DESs.