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Preparation of CeNiO 3 in order to elucidate the actual crystal structure with the aim of establishing a structure–property relationship. Three different structural models were proposed accompanied by detailed structural analysis.
ABSTRACT Microbes have adapted to greatly variable environments in order to survive both short-term perturbations and permanent changes. A classical and yet still actively studied example of adaptation to dynamic environments is the diauxic shift of Escherichia coli , in which cells grow on glucose until its exhaustion and then transition to using previously secreted acetate. Here we tested different hypotheses concerning the nature of this transition by using dynamic metabolic modeling. To reach this goal, we developed an open source modeling framework integrating dynamic models (ordinary differential equation systems) with structural models (metabolic networks) which can take into account the behavior of multiple subpopulations and smooth flux transitions between time points. We used this framework to model the diauxic shift, first with a single E. coli model whose metabolic state represents the overall population average and then with a community of two subpopulations, each growing exclusively on one carbon source (glucose or acetate). After introduction of an environment-dependent transition function that determined the balance between subpopulations, our model generated predictions that are in strong agreement with published data. Our results thus support recent experimental evidence that diauxie, rather than a coordinated metabolic shift, would be the emergent pattern of individual cells differentiating for optimal growth on different substrates. This work offers a new perspective on the use of dynamic metabolic modeling to investigate population heterogeneity dynamics. The proposed approach can easily be applied to other biological systems composed of metabolically distinct, interconverting subpopulations and could be extended to include single-cell-level stochasticity. IMPORTANCE Escherichia coli diauxie is a fundamental example of metabolic adaptation, a phenomenon that is not yet completely understood. Further insight into this process can be achieved by integrating experimental and computational modeling methods. We present a dynamic metabolic modeling approach that captures diauxie as an emergent property of subpopulation dynamics in E. coli monocultures. Without fine-tuning the parameters of the E. coli core metabolic model, we achieved good agreement with published data. Our results suggest that single-organism metabolic models can only approximate the average metabolic state of a population, therefore offering a new perspective on the use of such modeling approaches. The open source modeling framework that we provide can be applied to model general subpopulation systems in more-complex environments and can be extended to include single-cell-level stochasticity.
The software is code for analyzing, debugging, and solving optimization models. The code implements several algorithms and provides convenient APIs to apply these algorithms to optimization models. The algorithms are primarily based on graph theory. They compute well-known partitions of graphs, and use these partitions to provide the user information about their optimization model, including diagnosing certain types of structural modeling errors. Some algorithms may be used as a subroutine to solve an optimization problem, and may call an optimization solver to facilitate this. Well-known linear algebra routines are called to provide further diagnostics. The software contains no data and no models other than toy models used for testing.
Zapadnoe Uranium Mill Tailings Site, Pridneprovsky Chemical Plant Ukraine: Two exposure scenarios were utilized to develop performance assessment models in GoldSim and NORMALYSA. The first scenario is an onsite worker exposed to radioactivity through external ground irradiation as well as radon and radioactive dust inhalation. The second being an offsite Resident 300 years after institutional control exposed through the ingestion of garden vegetables irrigated by contaminated ground water, ingestion of fish from Konoplyanka River, and agricultural activities in contaminated garden. NORMALYSA utilizes a modular interface to connect extensive pre-created modules to develop contaminant transport and risk assessment models for safety assessments and performance assessments at NORM and legacy sites. Developed by Facilia AB, the program was tested with the creation of the Zapadnoe model under the International Atomic Energy Agency MODARIA Il Working Group 1 (WG1). Default values are provided for input parameters where site specific data and distributions lack. Probabilistic simulations and inputs are limited to parameters with assigned Gaussian probability functions. Similar results for transient worker inhalation dose were found in comparison with the Zapadnoe GoldSim model. However, the NORMALYSA model has results larger by an order of magnitude for external radiation in the transient worker and for aquatic food ingestion, inhalation, and garden food ingestion to the resident. Performance Assessment Modeling: Radiological performance models promote good management and support in remediation and environmental decision making by optimizing radioactive waste disposal site performance. a performance assessment model of the Zapadnoe uranium mill tailings site and a model for calculating authorized limits at Los Alamos National Laboratory are created to demonstrate and highlight the respective capabilities of three modeling platforms: GoldSim, NORMALYSA, and RESRAD-Onsite. GoldSim is a general-purpose modeling platform with the ability to simulate site-specific FT radionuclide transport and risk assessment using a graphical interface to create and link elements that act as indivisible building blocks of the model. The Zapadnoe performance assessment model created in GoldSim is composed of input parameters collected from site specific parameters from WG1 as well as standard assumptions seen in the Generic PA Model from Neptune and Company. The multivariate Zapadnoe simulation contains both deterministic and probabilistic simulation capabilities with the ability to quantitatively represent the uncertainty and associated risks of the site via the Monte Carlo simulation method. Model parameters, documentation, and assumptions are built directly into the model creating a transparent, reproducible, and more purposeful site specific model. To demonstrate this, an ingestion of water pathway was included in addition to the exposure pathways included in the NORMALYSA model. GoldSim offers a wide variety of probability distributions to choose from as well as many tools to visualize the uncertainty of the models and explore which pathways and radionuclides dominate dose. In contrast to the NORMALYSA model, the GoldSim model uses dynamic simulation to calculate tritium concentrations. Authorized limits support the evaluation of radiological health effects from radionuclides present in bulk contaminated soil in order to assist in the process of clearing land for release under different uses. Calculations of authorized limits in RESRAD-Onsite and GoldSim models support the evaluation for 15 radionuclides using a residential exposure scenario, indoor and outdoor inhalation of dust and vapor phase radionuclides (tritium), incidental soil ingestion, and ingestion grown fruits and Vegetables. RESRAD-Onsite, developed by Argonne National Laboratory is a dedicated computer code for calculating radiation doses and cancer risks to an individual located on top of radioactively contaminated soils. It can also be used to provide guidelines for deriving radionuclide soil levels corresponding to a specific dose criterion. The menu driven user interface facilitates selection of radionuclides and soil concentrations, as well as defines parameter values related to materials, environmental factors, and exposure pathways. The program contains radionuclide-specific data such as dose conversion factors and risk coefficients, as well as soil-water partition coefficients and transfer factors for biotic media. The GoldSim model successfully emulates the RESRAD-Onsite code using identical radiological decay and ingrowth factors, radiation dose conversion factors, and other input parameters. DE EEDE ETS Each model supports dynamic modeling of radionuclide ingrowth and decay over time, and integrate this capability with the transport of radionuclides in the environment via processes such as advection and/or diffusion in fluids, or within porous solid media, The applicability of each program is heavily dependent on project context. In the context of developing Authorized Limits, RESRAD-Onsite may be a more desirable option as it was developed for this particular application. For simple disposal or legacy sites or sites that do not need site-specific model structure, NORMALYSA may be a desirable modeling platform, GoldSim can be used to model any problem for which RESRAD or NORMALYSA is applicable, but its strength lies in its flexibility, analytical, and probabilistic capabilities.
A software for calibrating an X-ray diffractometer with area detector has been developed. It is proposed to search for detector and goniometer calibration models whose parameters are reproduced in a series of measurements on a reference crystal. Reference (standard) crystals are prepared during the investigation; they should provide the agreement of structural models in repeated analyses. The technique developed has been used to calibrate Xcalibur Sapphire and Eos, Gemini Ruby (Agilent) and Apex x8 and Apex Duo (Bruker) diffractometers. The main conclusions are as follows: the calibration maps are stable for several years and can be used to improve structural results, verified CCD detectors exhibit significant inhomogeneity of the efficiency (response) function, and a Bruker goniometer introduces smaller distortions than an Agilent goniometer.
Highlights: • Crystal structure of the C-terminal (CT) domain of Swt1 was determined at 2.3 Å. • Structure of the CT domain was identified as HEPN domain superfamily member. • Low-resolution envelope of Swt1 full-length in solution was analyzed by SAXS. • The middle and CT domains gave good fit to SAXS structural model. - Abstract: Swt1 is an RNA endonuclease that plays an important role in quality control of nuclear messenger ribonucleoprotein particles (mRNPs) in eukaryotes; however, its structural details remain to be elucidated. Here, we report the crystal structure of the C-terminal (CT) domain of Swt1 from Saccharomyces cerevisiae, which shares common characteristics of higher eukaryotes and prokaryotes nucleotide binding (HEPN) domain superfamily. To study in detail the full-length protein structure, we analyzed the low-resolution architecture of Swt1 in solution using small angle X-ray scattering (SAXS) method. Both the CT domain and middle domain exhibited a good fit upon superimposing onto the molecular envelope of Swt1. Our study provides the necessary structural information for detailed analysis of the functional role of Swt1, and its importance in the process of nuclear mRNP surveillance.
The Reduced Order Modeling Unlimited Localized Interface Simulator (ROMULIS) is a set of toolbox scripts in MATLAB designed to perform nonlinear transient integration on a system of reduced order structural models that interact with each other at localized interfaces. ROMULIS is meant to provide a user-friendly interface for applying the latest developments in numerical techniques and modeling in structural dynamics analysis while also giving the freedom to implement new technologies from forthcoming research. This report documents how to use and interpret the toolbox scripts. The theory behind the code is given, followed by a manual for interacting with the scripts to perform simulations. Lastly, a high-level introduction that explains how the scripts interact with each other is given for aspiring developers.
Slab models are simple and useful structural descriptions which have long been used to describe lyotropic lamellar phases, such as lipid bilayers. Typically, slab models assume a midline symmetry and break a bilayer structure into three pieces, a central solvent-free core and two symmetric outer layers composed of the soluble portion of the amphiphile and associated solvent. This breakdown matches reasonably well to the distribution of neutron scattering length density and therefore is a convenient and common approach for the treatment of small-angle scattering data. Here, an implementation of this model within the SasView software suite is reported. The implementation is intended to provide physical consistency through the area per amphiphile molecule and number of solvent molecules included within the solvent-exposed outer layer. The proper use of this model requires knowledge of (or good estimates for) the amphiphile and solvent molecule volume and atomic composition, ultimately providing a self-consistent data treatment with only two free parameters: the lateral area per amphiphile molecule and the number of solvent molecules included in the outer region per amphiphile molecule. Here, the use of this code is demonstrated in the fitting of standard lipid bilayer data sets, obtaining structural parameters consistent with prior literature and illustrating the typical and ideal cases of fitting for neutron scattering data obtained using single or multiple contrast conditions. While demonstrated here for lipid bilayers, this model is intended for general application to block copolymers, surfactants, and other lyotropic lamellar phase structures for which a slab model is able to reasonably estimate the neutron scattering length density/electron-density profile of inner and outer layers of the lamellae.
By considering the scattering distributed throughout space, there is an intensity enhancement at the Bragg angle even when the Bragg condition is not satisfied. This leads to an alternative explanation for the diffraction from powders and small crystals. This article proposes a new theory of X-ray scattering that has particular relevance to powder diffraction. The underlying concept of this theory is that the scattering from a crystal or crystallite is distributed throughout space: this leads to the effect that enhanced scatter can be observed at the ‘Bragg position’ even if the ‘Bragg condition’ is not satisfied. The scatter from a single crystal or crystallite, in any fixed orientation, has the fascinating property of contributing simultaneously to many ‘Bragg positions’. It also explains why diffraction peaks are obtained from samples with very few crystallites, which cannot be explained with the conventional theory. The intensity ratios for an Si powder sample are predicted with greater accuracy and the temperature factors are more realistic. Another consequence is that this new theory predicts a reliability in the intensity measurements which agrees much more closely with experimental observations compared to conventional theory that is based on ‘Bragg-type’ scatter. The role of dynamical effects (extinction etc.) is discussed and how they are suppressed with diffuse scattering. An alternative explanation for the Lorentz factor is presented that is more general and based on the capture volume in diffraction space. This theory, when applied to the scattering from powders, will evaluate the full scattering profile, including peak widths and the ‘background’. The theory should provide an increased understanding of the reliability of powder diffraction measurements, and may also have wider implications for the analysis of powder diffraction data, by increasing the accuracy of intensities predicted from structural models.
We report here a detailed study of the system La{sub 1−x}Sr{sub x}FeO{sub 3−x}F{sub x}, by neutron powder diffraction- and magnetic-measurements. All the compounds are robust antiferromagnetics with ordering temperatures well above room temperature. Magnetic moments are shown to align parallel to the c-axis. FC-ZFC measurements indicate a small canting of the magnetic moments, resulting in a ferromagnetic component with a maximum for La{sub 0.5}Sr{sub 0.5}FeO{sub 2.5}F{sub 0.5}. We show that the system exhibits a composition-driven transition from a phase, for low fluorination levels (x≤0.5), with Pnma symmetry and the usual system of octahedral tiltings, to a phase with space group Imma for higher fluorine contents, where a correlated distortion of the oxygen octahedra plays a significant role. The consistency of the structural models, with respect to the expected continuity of the amplitudes of the different distortion modes and the invariance of their internal form, was monitored through the symmetry mode decomposition of the structures. - Graphical abstract: The crystal and magnetic structure of La{sub 0.5}Sr{sub 0.5}FeO{sub 2.5}F{sub 0.5}. Display Omitted - Highlights: • The compounds La{sub 1−x}Sr{sub x}FeO{sub 3−x}F{sub x} (x=1, 0.8, 0.5, 0.2) were studied by neutron diffraction. • A mode analysis shows lower symmetry for Sr rich compounds than previously reported. • SrFeO{sub 2}F crystallizes in the orthorhombic space group Imma. • Magnetic moments resulting from canting depend on metric distortion. • The magnetic structure was determined for La{sub 0.5}Sr{sub 0.5}FeO{sub 2.5}F{sub 0.5}.
This report describes the potential of a novel class of materials—α-ZrW 2 O 8 , Zr 2 WP 2 O 12 , and related compounds that contract upon amorphization as possible radionuclide waste-forms. The proposed ceramic waste-forms would consist of zoned grains, or sintered ceramics with center- loaded radionuclides and barren shells. Radiation-induced amorphization would result in core shrinkage but would not fracture the shells or overgrowths, maintaining isolation of the radionuclide. In this report, we have described synthesis techniques to produce phase-pure forms of the materials, and how to fully densify those materials. Structural models for the materials were developed and validated using DFPT approaches, and radionuclide substitution was evaluated; U(IV), Pu(IV), Tc(IV) and Tc(VII) all readily substitute into the material structures. MD modeling indicated that strain associated with radiation-induced amorphization would not affect the integrity of surrounding crystalline materials, and these results were validated via ion beam experimental studies. Finally, we have evaluated the leach rates of the barren materials, as determined by batch and flow-through reactor experiments. ZrW 2 O 8 leaches rapidly, releasing tungstate while Zr is retained as a solid oxide or hydroxide. Tungsten release rates remain elevated over time and are highly sensitive to contact times, suggesting that this material will not be an effective waste-form. Conversely, tungsten releases rates from Zr 2 WP 2 O 12 rapidly drop, show little dependence on short-term changes in fluid contact time, and in over time, become tied to P release rates. The results presented here suggest that this material may be a viable waste-form for some hard-to-handle radionuclides such as Pu and Tc.
Prey wrapping spider silk's unique mechanical properties are investigated confirming the silk's high degree of extensibility and superior toughness compared to other types of spider silk. For the first time, the pre-spinning dope phase is studied in isotope-enriched intact aciniform (AC) silk glands using solution NMR that reveals a combination of α-helical domains linked by disordered random coil chains consistent with previously proposed “beads-on-a-string” models. The model is further refined through the AlphaFold2 protein structure prediction tool. Finally, extensive magic angle spinning (MAS) solid-state (SS) NMR data for isotopically-enriched fibers is used to refine the structural model for AC silk from two species, A. aurantia and A. argentata. The SSNMR data shows that the AC silk fibers are highly α-helical, coiled-coil in structure but, also exhibit significant β-sheet components that can be traced back to the Gly-rich disordered linker regions in the pre-spinning dope phase that are converted to β-sheet structures during fiber formation. This combination of mechanical and structural characterization enhances the understanding of AC silk's liquid-to-solid transition and structure-mechanics relationship. In conclusion, these prey wrap silk results and models will provide the basis for the design of biomimetic materials inspired by the AC spider silk system.
Nucleon removal reactions have been shown to be an effective tool for studying the single particle structure of nuclei. This work continues efforts to experimentally probe and benchmark the reaction and structure models used to calculate the removal reaction cross sections when using microscopic nuclear structure inputs. Here, three different single nucleon removal reactions were performed, from p -shell nuclei with masses A = 7, 9, and 10. The residual nuclei from the reactions were detected in coincidence with γ rays to determine partial cross sections to individual final states. The eikonal direct-reaction model is combined with overlap functions and residual nucleus densities from microscopic, variational Monte Carlo calculations to provide consistent nuclear structure input to the partial cross section calculations. Comparisons of measured and calculated cross sections, including for mirror reactions, are presented. The analysis of the partial cross sections leading to the ground states shows a similar behavior to the one observed from analyses of inclusive cross sections using shell model nuclear structure input: the theoretical description of the removal process is in better agreement with the data when removing weakly bound nucleons, than when removing well-bound ones. The two mirror reaction pairs presented here show consistent results between the respective members of the pairs. The results obtained for the population of the excited states, however, show a systematically different trend that appears connected to the structure part of the calculation. Additional cases are needed to better understand the respective roles of structure and dynamical effects in the deviations.
Highlights: • The modifying effects of nanosilica on pore structure of cement-based composites are investigated. • Dual beam SEM/FIB is implemented to create the 3D pore structure model and calculate porosity and pore size distribution. • The porosity and pore diameter are found to decrease with the inclusion of nanosilica. - Abstract: Pozzolanic materials, micro- and nano-, have been found to improve the durability properties of cement-based materials by refining their pore structure. As a relatively newer material, the modifying effects of nanosilica on pore structure are still inconclusive in the literature. In this study, this was characterized by implementing dual beam SEM/FIB, which can generate 3D models of porous materials for quantitative analysis. The sample is milled by focused ion beam layer-by-layer, and each surface layer is 2D imaged via scanning electron microscopy. Three types of pores – large capillary pore, medium capillary pore and gel pore – can be observed. A 3D pore structure model is then reconstructed from 1000 of these 2D images, from which porosity and pore size distribution can be calculated. Cement pastes incorporating nanosilica and silica fume were compared. The porosity and pore diameter were found to decrease with the inclusion of nanosilica. Furthermore, reduction in capillary pores and subsequent increase in gel pores were also observed.
Nominal compositions Bi{sub 2}Cr{sub x}Al{sub 4−x}O{sub 9} with 0.0≤x≤2.0 (Δx=0.2) were prepared using appropriate amounts of nitrates dissolved in glycerine and heated at 800 °C for 24 h as we previously used for the preparation of solid solution series Bi{sub 2}M{sub x}/M′{sub 4−x}O{sub 9} (M/M′=Fe/Al, Ga/Al and Fe/Ga). The samples were characterized using XRD, FTIR and optical microscopic techniques. Analyses of XRD data show mullite type single phase can be prepared up to x=1.2. The lattice parameters (a, b and c) increases with increasing Cr content. Further increase in x (i.e., x≥1.4) show the presence of some additional phases indicating a limiting value for Cr doping is in the range of 1.2≤x<1.4. The effect of Cr incorporation could also be observed in the infrared absorption spectra via systematic hard mode shifts of certain lattice modes, e.g. the Bi–O related vibration changes from 96 cm{sup −1} to 93 cm{sup −1} with increasing x up to 1.2 and certain intensity changes together with shift in peak positions. Interestingly, the absence of any splitting and shift of the high energy IR absorption peak at 821 cm{sup −1} as assigned to the characteristic tetrahedral type dimer, Al{sub 2}O{sub 7}, indicate that the Cr thus partially substitutes only the octahedrally coordinated Al. This is confirmed by Rietveld structure refinements, too. - Graphical abstract: Structural model of Cr doped bismuth aluminate, Bi{sub 2}Cr{sub x}Al{sub 4−x}O{sub 9}. - Highlights: • Chromium doped bismuth aluminate, Bi{sub 2}Cr{sub x}Al{sub 4−x}O{sub 9} with mullite type structure are synthesized. • The samples are characterized by XRD and FTIR techniques. • Cr can replace only certain amount of octahedrally coordinated Al in Bi{sub 2}Al{sub 4}O{sub 9} under present experimental conditions.
The structural models of the fibrils formed by the 40-residue amyloid-β (Aβ40) peptide in Alzheimer’s disease typically consist of linear polypeptide segments, oriented approximately perpendicular to the long axis of the fibril, and joined together as parallel in-register β-sheets to form filaments. However, various models differ in the number of filaments that run the length of a fibril, and in the topological arrangement of these filaments. In addition to questions about the structure of Aβ40 monomers in fibrils, there are important unanswered questions about their structure in prefibrillar intermediates, which are of interest because they may represent the most neurotoxic form of Aβ40. To assess different models of fibril structure and to gain insight into the structure of prefibrillar intermediates, the relative solvent accessibility of amino acid residue side chains in fibrillar and prefibrillar Aβ40 preparations was characterized in solution by hydroxyl radical footprinting and structural mass spectrometry. A key to the application of this technology was the development of hydroxyl radical reactivity measures for individual side chains of Aβ40. When we combined mass-per-length measurements performed by dark-field electron microscopy, we determined that the results of our study were consistent with the core filament structure represented by two- and three-filament solid state nuclear magnetic resonance-based models of the Aβ40 fibril (such as 2LMN, 2LMO, 2LMP, and 2LMQ), with minor refinements, but they are inconsistent with the more recently proposed 2M4J model. Our results also demonstrate that individual Aβ40 fibrils exhibit structural heterogeneity or polymorphism, where regions of two-filament structure alternate with regions of three-filament structure. The footprinting approach utilized in this study will be valuable for characterizing various fibrillar and nonfibrillar forms of the Aβ peptide.
Abstract Lithium phosphorus oxynitride (LiPON) is an amorphous solid‐state lithium ion conductor displaying exemplary cyclability against lithium metal anodes. There is no definitive explanation for this stability due to the limited understanding of the structure of LiPON. Herein, we provide a structural model of RF‐sputtered LiPON. Information about the short‐range structure results from 1D and 2D solid‐state NMR experiments. These results are compared with first principles chemical shielding calculations of Li‐P‐O/N crystals and ab initio molecular dynamics‐generated amorphous LiPON models to unequivocally identify the glassy structure as primarily isolated phosphate monomers with N incorporated in both apical and as bridging sites in phosphate dimers. Structural results suggest LiPON′s stability is a result of its glassy character. Free‐standing LiPON films are produced that exhibit a high degree of flexibility, highlighting the unique mechanical properties of glassy materials.