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At least 109 records · Page 6

Understanding nucleic acid structural changes by comparing wide-angle x-ray scattering (WAXS) experiments to molecular dynamics simulations

Wide-angle x-ray scattering (WAXS) is emerging as a powerful tool for increasing the resolution of solution structure measurements of biomolecules. Compared to its better known complement, small angle x-ray scattering (SAXS), WAXS targets higher scattering angles and can enhance structural studies of molecules by accessing finer details of solution structures. Although the extension from SAXS to WAXS is easy to implement experimentally, the computational tools required to fully harness the power of WAXS are still under development. Currently, WAXS is employed to study structural changes and ligand binding in proteins; however, the methods are not as fully developed for nucleic acids. Here, we show how WAXS can qualitatively characterize nucleic acid structures as well as the small but significant structural changes driven by the addition of multivalent ions. We show the potential of WAXS to test all-atom molecular dynamics (MD) simulations and to provide insight into understanding how the trivalent ion cobalt(III) hexammine (CoHex) affects the structure of RNA and DNA helices. We find that MD simulations capture the RNA structural change that occurs due to addition of CoHex.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Effects of Al:Si and (Al+Na):Si Ratios on the Properties of the International Simple Glass, Part II: Structure

High-alumina containing high-level waste (HLW) will be vitrified at the Waste Treatment Plant at the Hanford Site. The resulting glasses, high in alumina, will have distinct composition-structure-property (C-S-P) relationships compared to previously studied HLW glasses. These C-S-P relationships determine the processability and product durability of glasses and therefore must be understood. The main purpose of this study is to understand the detailed structural changes caused by Al:Si and (Al+Na):Si substitutions in a simplified nuclear waste model glass (ISG, International Simple Glass) by combining experimental structural characterizations and molecular dynamics (MD) simulations. The structures of these two series of glasses were characterized by neutron total scattering and 27Al, 23Na, 29Si, and 11B solid-state nuclear magnetic resonance (NMR) spectroscopy. Additionally, MD simulations were used to generate atomistic structural models of the borosilicate glasses and simulation results were validated by the experimental structural data. Short-range (e.g., bond distance, coordination number, etc.) and medium-range (e.g., oxygen speciation, network connectivity, polyhedral linkages) structural features of the borosilicate glasses were systematically investigated as a function of the degree of substitution. The results show that bond distance and coordination number of the cation-oxygen pairs are relatively insensitive to Al:Si and (Al+Na):Si substitutions with the exception of the B-O pair. Additionally, the Al:Si substitution results in an increase of tri-bridging oxygen species, while (Al+Na):Si substitution creates non-bridging oxygen species. Charge compensator preferences were found for Si-[NBO] (Na+), [3]B-[NBO] (Na+), [4]B (mostly Ca2+), [4]Al (nearly equally split Na+ and Ca2+), and [6]Zr (mostly Ca2+). The network former-BO-network former linkages preferences were also tabulated; Si-O-Al and Al-O-Al were preferred at the expense of lower Si-O-[3]B and [3]B-O-[3]B linkages. These results provide insights on the structural origins of property changes such as glass transition temperature caused by the substitutions, providing a basis for future improvements of theoretical and computer simulation models.

Lu, Xiaonan↗

Enumeration as a Tool for Structure Solution: A Materials Genomic Approach to Solving the Cation-Ordered Structure of Na 3 V 2 (PO 4 ) 2 F 3

While powder diffraction methods are routinely utilized to optimize structural models for compounds whose crystal structures are known, the determination of unknown structures is far more challenging. When the unknown structure is large, structure solution can become a virtually intractable problem using standard structure solution methodologies, especially when the space group cannot be unambiguously resolved. One such system is the promising Na-ion battery cathode material Na 3 V 2 (PO 4 ) 2 F 3 whose high temperature and room temperature structures were previously solved, but whose more complex low-temperature structure could not be determined. Here, a novel materials genomic approach is demonstrated for the solution of the unknown 100 K structure of Na 3 V 2 (PO 4 ) 2 F 3 in which enumeration methods are first used to generate a large number (~3,000) of trial structures based on plausible orderings of Na ions and then automated Rietveld refinements are carried out to optimize each of these trial structures. Based on both the analysis of the ensemble of optimized trial structures and the density functional theory energy minimization of selected trial structures, the 100 K structure of Na 3 V 2 (PO 4 ) 2 F 3 is best described as belonging to the space group A2 1 am with unit cell dimensions of a = 9.01928(4), b = 27.1379(1), c = 10.73307(5). The 100 K unit cell has a large volume of 2627.07(2) Å 3 with Z = 12 and 33 independent crystallographic sites (9 Na, 3 V, 3 P, 12 O, and 6 F) that is 3x and 6x larger than the room- and high-temperature polymorphs of this phase, respectively. Finally, the novel methods described here will be generally applicable for the solution of the complex cation-ordered structures that commonly occur for battery materials.

36 MATERIALS SCIENCE↗

Advanced composites structural concepts and materials technologies for primary aircraft structures. Structural response and failure analysis: ISPAN modules users manual

The ISPAN Program (Interactive Stiffened Panel Analysis) is an interactive design tool that is intended to provide a means of performing simple and self contained preliminary analysis of aircraft primary structures made of composite materials. The program combines a series of modules with the finite element code DIAL as its backbone. Four ISPAN Modules were developed and are documented. These include: (1) flat stiffened panel; (2) curved stiffened panel; (3) flat tubular panel; and (4) curved geodesic panel. Users are instructed to input geometric and material properties, load information and types of analysis (linear, bifurcation buckling, or post-buckling) interactively. The program utilizing this information will generate finite element mesh and perform analysis. The output in the form of summary tables of stress or margins of safety, contour plots of loads or stress, and deflected shape plots may be generalized and used to evaluate specific design.

Hairr, John W.↗

Structural and Machine Design Using Piezoceramic Materials: A Guide for Structural Design Engineers

Using piezoceramic materials is one way the design engineer can create structures which have an ability to both sense and respond to their environment. Piezoceramic materials can be used to create structural sensors and structural actuators. Because piezoceramic materials have transduction as a material property, their sensing or actuation functions are a result of what happens to the material. This is different than discrete devices we might attach to the structure. For example, attaching an accelerometer to a structure will yield an electrical signal proportional to the acceleration at the attachment point on the structure. Using a electromagnetic shaker as an actuator will create an applied force at the attachment point. Active material elements in a structural design are not easily modeled as providing transduction at a point, but rather they change the physics of the structure in the areas where they are used. Hence, a designer must not think of adding discrete devices to a structure to obtain an effect, but rather must design a structural system which accounts for the physical principles of all the elements in the structure. The purpose of this manual is to provide practicing engineers the information necessary to incorporate piezoelectric materials in structural design and machine design. First, we will review the solid-state physics of piezoelectric materials. Then we will discuss the physical characteristics of the electrical-active material-structural system. We will present the elements of this system which must be considered as part of the design task for a structural engineer. We will cover simple modeling techniques and review the features and capabilities of commercial design tools that are available. We will then cover practical how-to elements of working with piezoceramic materials. We will review sources of piezoceramic materials and built-up devices, and their characteristics. Finally, we will provide two design examples using piezoceramic materials, first as discrete actuators for vibration isolation, and second as structurally-distributed sensor/actuators for active acoustic control.

Inman, Daniel J.↗

Quantitative Structure–Property Relationship (QSPR) Analysis of ZrO 2 -Containing Soda-Lime Borosilicate Glasses

Quantitative structure–property relationship (QSPR) analysis is a promising approach to correlate structural features with properties of glass materials that lack long-range order and usually have complex structures. By using carefully chosen descriptors based on structural models generated from molecular dynamics (MD) simulations, correlations with properties and insights on glass behaviors can be obtained. Zirconia can significantly alter glass properties including chemical durability, even in a small amount, and hence plays an important role in vitrification of nuclear waste where long-term chemical durability is desired. In this study, borosilicate glasses with the composition of xZrO 2 –(61 – x)SiO 2 –17B 2 O 3 –18Na 2 O–4CaO with x = 0, 1, 2, 4, 6, and 8 were simulated using classical MD simulations with the recently developed composition-dependent potentials. Short-range (e.g., bond distance and coordination numbers) and medium-range (e.g., Qn distribution, network connectivity, and ring-size distribution) structural features altered by ZrO 2 were obtained and analyzed. The use of a descriptor (Fnet descriptor) that combines short-range structural characteristics, from MD simulations, and the cation-oxygen single bond strength was found to provide excellent linear correlations with the density and initial dissolution rate of these glasses. Furthermore, the results show that by combining MD simulations and QSPR analysis the composition and structural effect on the properties of complex multicomponent glasses can be elucidated, thus suggesting that this is a promising approach for future glass research and new composition design.

36 MATERIALS SCIENCE↗

Unveiling the Structural Evolution of Ag 1.2 Mn 8 O 16 under Coulombically Controlled (De)Lithiation

MnO 2 materials are considered promising cathode materials for rechargeable lithium, sodium, and magnesium batteries due to their earth abundance and environmental friendliness. One polymorph of MnO 2 , α-MnO 2 , has 2 × 2 tunnels (4.6 Å × 4.6 Å) in its structural framework, which provide facile diffusion pathways for guest ions. In this work, a silver-ion-containing α-MnO 2 (Ag 1.2 Mn 8 O 16 ) is examined as a candidate cathode material for Li based batteries. Electrochemical stability of Ag 1.2 Mn 8 O 16 is investigated through Coulombically controlled reduction under 2 or 4 molar electron equivalents (e.e.). Terminal discharge voltage remains almost constant under 2 e.e. of cycling, whereas it continuously decreases under repetitive reduction by 4 e.e. Thus, detailed structural analyses were utilized to investigate the structural evolution upon lithiation. Significant increases in lattice a (17.7%) and atomic distances (~4.8%) are observed when x in Li x Ag 1.2 Mn 8 O 16 is >4. Ag metal forms at this level of lithiation concomitant with a large structural distortion to the Mn–O framework. In contrast, lattice a only expands by 2.2% and Mn–O/Mn-Mn distances show minor changes (~1.4%) at x < 2. The structural deformation (tunnel breakage) at x > 4 inhibits the recovery of the original structure, leading to poor cycle stability at high lithiation levels. This report establishes the correlation among local structure changes, amorphization processes, formation of Ag 0 , and long-term cycle stability for this silver-containing α-MnO 2 type material at both low and high lithiation levels.

36 MATERIALS SCIENCE↗

Structures of the Mycobacterium tuberculosis GlpX protein (class II fructose-1,6-bisphosphatase): implications for the active oligomeric state, catalytic mechanism and citrate inhibition

The crystal structures of native class II fructose-1,6-bisphosphatase (FBPaseII) from Mycobacterium tuberculosis at 2.6 Å resolution and two active-site protein variants are presented. The variants were complexed with the reaction product fructose 6-phosphate (F6P). The Thr84Ala mutant is inactive, while the Thr84Ser mutant has a lower catalytic activity. The structures reveal the presence of a 222 tetramer, similar to those described for fructose-1,6/sedoheptulose-1,7-bisphosphatase from Synechocystis (strain 6803) as well as the equivalent enzyme from Thermosynechococcus elongatus . This homotetramer corresponds to a homologous oligomer that is present but not described in the crystal structure of FBPaseII from Escherichia coli and is probably conserved in all FBPaseIIs. The constellation of amino-acid residues in the active site of FBPaseII from M. tuberculosis ( Mt FBPaseII) is conserved and is analogous to that described previously for the E. coli enzyme. Moreover, the structure of the active site of the partially active (Thr84Ser) variant and the analysis of the kinetics are consistent with the previously proposed catalytic mechanism. The presence of metabolites in the crystallization medium (for example citrate and malonate) and in the corresponding crystal structures of Mt FBPaseII, combined with their observed inhibitory effect, could suggest the existence of an uncharacterized inhibition of this class of enzymes besides the allosteric inhibition by adenosine monophosphate observed for the Synechocystis enzyme. The structural and functional insights derived from the structure of Mt FBPaseII will provide critical information for the design of lead inhibitors, which will be used to validate this target for future chemical intervention.

Wolf, Nina M.↗

The Sudbury Structure (Ontario, Canada) and Vredefort Structure (South Africa): A comparison

Both the Sudbury Structure (SS) and the Witwatersrand Basin surrounding the Vredefort Structure (VS) host some of the most important base and precious metal deposits on earth. In both structures Precambrian igneous, sedimentary and volcanic rocks were affected by the structure forming process, either meteorite impact or endogenic explosion, or as some VS workers propose, by high strain tectonics. Besides these general features there are some geological and geophysical characteristics that are strikingly similar in both structures. There are, however, some obvious differences. Directly related to the structure forming processes are breccias in the footwall rocks of both structures. Pseudotachylite breccias occurring in both structures display great similarities. Chemical and physical characteristics of the pseudotachylites are similar in both structures. Both structures are characterized by overturned collar rocks, not evident everywhere around the SS. The VS is rimmed by an up or overturned collar of sediments and volcanics of the Witwatersrand, Ventersdorp and Transvaal Supergroups. Drilling information proved that the strata of the Witwatersrand Supergroup in the south of the VS are lying horizontally. Shockmetamorphic features such as planar microdeformations in rock forming minerals and shatter cones are present in both structures in the footwall rocks and in the SS also in the breccias of the OF. Both structures have large geophysical anomalies associated with them. In both structures the anomalies were interpreted as being caused by mafic-ultramafic complexes underlying the structures.

Dressler, B. O.↗

Nondestructive Structural Damage Detection in Flexible Space Structures Using Vibration Characterization

Spacecraft are susceptible to structural damage over their operating life from impact, environmental loads, and fatigue. Structural damage that is not detected and not corrected may potentially cause more damage and eventually catastrophic structural failure. NASA's current fleet of reusable spacecraft, namely the Space Shuttle, has been flown on several missions. In addition, configurations of future NASA space structures, e.g. Space Station Freedom, are larger and more complex than current structures, making them more susceptible to damage as well as being more difficult to inspect. Consequently, a reliable structural damage detection capability is essential to maintain the flight safety of these structures. Visual inspections alone can not locate impending material failure (fatigue cracks, yielding); it can only observe post-failure situations. An alternative approach is to develop an inspection and monitoring system based on vibration characterization that assesses the integrity of structural and mechanical components. A methodology for detecting structural damage is presented. This methodology is based on utilizing modal test data in conjunction with a correlated analytical model of the structure to: (1) identify the structural dynamic characteristics (resonant frequencies and mode shapes) from measurements of ambient motions and/or force excitation; (2) calculate modal residual force vectors to identify the location of structural damage; and (3) conduct a weighted sensitivity analysis in order to assess the extent of mass and stiffness variations, where structural damage is characterized by stiffness reductions. The approach is unique from other existing approaches in that varying system mass and stiffness, mass center locations, the perturbation of both the natural frequencies and mode shapes, and statistical confidence factors for structural parameters and experimental instrumentation are all accounted for directly.

Ricles, James M.↗

An expert system for integrated structural analysis and design optimization for aerospace structures

The results of a research study on the development of an expert system for integrated structural analysis and design optimization is presented. An Object Representation Language (ORL) was developed first in conjunction with a rule-based system. This ORL/AI shell was then used to develop expert systems to provide assistance with a variety of structural analysis and design optimization tasks, in conjunction with procedural modules for finite element structural analysis and design optimization. The main goal of the research study was to provide expertise, judgment, and reasoning capabilities in the aerospace structural design process. This will allow engineers performing structural analysis and design, even without extensive experience in the field, to develop error-free, efficient and reliable structural designs very rapidly and cost-effectively. This would not only improve the productivity of design engineers and analysts, but also significantly reduce time to completion of structural design. An extensive literature survey in the field of structural analysis, design optimization, artificial intelligence, and database management systems and their application to the structural design process was first performed. A feasibility study was then performed, and the architecture and the conceptual design for the integrated 'intelligent' structural analysis and design optimization software was then developed. An Object Representation Language (ORL), in conjunction with a rule-based system, was then developed using C++. Such an approach would improve the expressiveness for knowledge representation (especially for structural analysis and design applications), provide ability to build very large and practical expert systems, and provide an efficient way for storing knowledge. Functional specifications for the expert systems were then developed. The ORL/AI shell was then used to develop a variety of modules of expert systems for a variety of modeling, finite element analysis, and design optimization tasks in the integrated aerospace structural design process. These expert systems were developed to work in conjunction with procedural finite element structural analysis and design optimization modules (developed in-house at SAT, Inc.). The complete software, AutoDesign, so developed, can be used for integrated 'intelligent' structural analysis and design optimization. The software was beta-tested at a variety of companies, used by a range of engineers with different levels of background and expertise. Based on the feedback obtained by such users, conclusions were developed and are provided.

Source record↗

Structural Loads Analysis for Wave Energy Converters: Preprint

This study explores and verifies the generalized body-modes method for evaluating the structural loads on a wave energy converter (WEC). Historically, WEC design methodologies have focused primarily on accurately evaluating hydrodynamic loads, while methodologies for evaluating structural loads have yet to be fully considered and incorporated into the WEC design process. As wave energy technologies continue to advance, however, it has become increasingly evident that an accurate evaluation of the structural loads will enable an optimized structural design, as well as the potential utilization of composites and flexible materials, and hence reduce WEC costs. Although there are many computational fluid dynamics, structural analyses and fluid-structure-interaction (FSI) codes available, the application of these codes is typically too computationally intensive to be practical in the early stages of the WEC design process. The generalized body-modes method, however, is a reduced order, linearized, frequency-domain FSI approach, performed in conjunction with the linear hydrodynamic analysis, with computation times that could realistically be incorporated into the WEC design process. The objective of this study is to verify the generalized body-modes approach in comparison to high-fidelity FSI simulations to accurately predict structural deflections and stress loads in a WEC. Two verification cases are considered, a free-floating barge and a fixed-bottom column. Details for both the generalized body-modes models and FSI models are first provided. Results for each of the models are then compared and discussed. Finally, based on the verification results obtained, future plans for incorporating the generalized body-modes method into the WEC simulation tool, WEC-Sim, and the overall WEC design process are discussed.

17 WIND ENERGY↗