Target highlights in CASP14: Analysis of models by structure providers
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Alexander, Leila T.↗
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Structure of the polysaccharide sheath from the B race of the green microalga Botryococcus braunii
The green microalga Botryococcus braunii forms a colony of cells held together by an intricate extracellular matrix. This extracellular matrix also acts as a storage location for liquid hydrocarbons initially produced inside the cells. These hydrocarbons can be used as feedstocks to produce transportation fuels. In the B race of B. braunii, the extracellular matrix is composed of several elements: a cross-linked hydrocarbon network filled with the liquid hydrocarbons, a retaining wall to hold the hydrocarbons in the extracellular matrix, an arabinogalactan polysaccharide fibrillar sheath that extends outward from the retaining wall, and a single protein known as polysaccharide associated protein is found at the base of the polysaccharide fibers where they connect to the retaining wall. During growth, colonies of the B race of B. braunii shed fragments of the retaining wall with polysaccharide fibrils attached into the media. Here we describe the isolation and structural analysis of these polysaccharides using a series of chemical degradations in combination with glycosyl residue composition and linkage analysis, as well as 2-dimensional nuclear magnetic resonance spectroscopy. The results demonstrate that the polysaccharide is highly branched, consisting of a galactan backbone with short branches comprised of Dgalactopyranose, L-arabinofuranose, 4-O-methyl-D-glucopyranuronic acid, and 6-deoxy-D-altropyranose. To our knowledge, this is the first description of 6-deoxyaltrose in algae or plants.
59 BASIC BIOLOGICAL SCIENCES↗
Structural design and analysis. Part 1
Topics in anisotropic elasticity are discussed along with the analysis of truss, beam, frame, and membrane components. Attention is given to failure criteria and failure analysis of composite structural components. Other subjects considered are related to the analysis of plates, the analysis of shells, and questions of wave propagation and impact in composite materials. Individual items are announced in this issue.
Chamis, C. C.↗
Continuous wavelet analysis of coherent structures
We perform an analysis of planar cuts through three dimensional turbulent fields (planar channel flow and mixing layer) using the 2D continuous wavelet transform. We propose two new diagnostics: (1) a measure of intermittency I(r, vector x), which is the ratio of local energy and average energy at a given scale r; and (2) a local Reynolds number, defined on the local velocity contribution at a given scale, computed from the wavelet transform of the three velocity components, the scale of the transform, and molecular viscosity; this gives a representation of the local non-linearity of the flow viewed in both space and scale. We find, for the analyzed flows, strong small-scale intermittency located in the ejection regions for the channel flow and in the vortex core of the mixing layer.
Farge, M.↗
Structure-Based Comparative Analysis and Prediction of N-Linked Glycosylation Sites in Evolutionarily Distant Eukaryotes
Abstract The asparagine-X-serine/threonine (NXS/T) motif, where X is any amino acid except proline, is the consensus motif for N-linked glycosylation. Significant numbers of high-resolution crystal structures of glycosylated proteins allow us to carry out structural analysis of the N-linked glycosylation sites (NGS). Our analysis shows that there is enough structural information from diverse glycoproteins to allow the development of rules which can be used to predict NGS. A Python-based tool was developed to investigate asparagines implicated in N-glycosylation in five species: Homo sapiens, Mus musculus, Drosophila melanogaster, Arabidopsis thaliana and Saccharomyces cerevisiae. Our analysis shows that 78% of all asparagines of NXS/T motif involved in N-glycosylation are localized in the loop/turn conformation in the human proteome. Similar distribution was revealed for all the other species examined. Comparative analysis of the occurrence of NXS/T motifs not known to be glycosylated and their reverse sequence (S/TXN) shows a similar distribution across the secondary structural elements, indicating that the NXS/T motif in itself is not biologically relevant. Based on our analysis, we have defined rules to determine NGS. Using machine learning methods based on these rules we can predict with 93% accuracy if a particular site will be glycosylated. If structural information is not available the tool uses structural prediction results resulting in 74% accuracy. The tool was used to identify glycosylation sites in 108 human proteins with structures and 2247 proteins without structures that have acquired NXS/T site/s due to non-synonymous variation. The tool, Structure Feature Analysis Tool (SFAT), is freely available to the public at http://hive.biochemistry.gwu.edu/tools/sfat.
59 BASIC BIOLOGICAL SCIENCES↗
Simultaneous analysis and design
Optimization techniques are increasingly being used for performing nonlinear structural analysis. The development of element by element (EBE) preconditioned conjugate gradient (CG) techniques is expected to extend this trend to linear analysis. Under these circumstances the structural design problem can be viewed as a nested optimization problem. There are computational benefits to treating this nested problem as a large single optimization problem. The response variables (such as displacements) and the structural parameters are all treated as design variables in a unified formulation which performs simultaneously the design and analysis. Two examples are used for demonstration. A seventy-two bar truss is optimized subject to linear stress constraints and a wing box structure is optimized subject to nonlinear collapse constraints. Both examples show substantial computational savings with the unified approach as compared to the traditional nested approach.
Haftka, R. T.↗
Simultaneous analysis and design
Optimization techniques are increasingly being used for performing nonlinear structural analysis. The development of element by element (EBE) preconditioned conjugate gradient (CG) techniques is expected to extend this trend to linear analysis. Under these circumstances the structural design problem can be viewed as a nested optimization problem. There are computational benefits to treating this nested problem as a large single optimization problem. The response variables (such as displacements) and the structural parameters are all treated as design variables in a unified formulation which performs simultaneously the design and analysis. Two examples are used for demonstration. A seventy-two bar truss is optimized subject to linear stress constraints and a wing box structure is optimized subject to nonlinear collapse constraints. Both examples show substantial computational savings with the unified approach as compared to the traditional nested approach.
Haftka, R. T.↗
Project Report: Design and Analysis for the Deep Space Network BWG Type 2 Antenna Feed Platform
The following report explains in detail the solid modeling design process and structural analysis of the LNA (Low Noise Amplifier) feed platform to be constructed and installed on the new BWG (Beam Wave Guide) Type-2 tracking antenna in Canberra, Australia, as well as all future similar BWG Type-2 antennas builds. The Deep Space Networks new BWG Type-2 antennas use beam waveguides to funnel and 'extract' the desired signals received from spacecraft, and the feed platform supports and houses the LNA(Low Noise Amplifier) feed-cone and cryogenic cooling equipment used in the signal transmission and receiving process. The mandated design and construction of this platform to be installed on the new tracking antenna will be used and incorporated on all future similar antenna builds.
structural analysis software↗
Crystal structure of the Arabidopsis SPIRAL2 C-terminal domain reveals a p80-Katanin-like domain
Epidermal cells of dark-grown plant seedlings reorient their cortical microtubule arrays in response to blue light from a net lateral orientation to a net longitudinal orientation with respect to the long axis of cells. The molecular mechanism underlying this microtubule array reorientation involves katanin, a microtubule severing enzyme, and a plant-specific microtubule associated protein called SPIRAL2. Katanin preferentially severs longitudinal microtubules, generating seeds that amplify the longitudinal array. Upon severing, SPIRAL2 binds nascent microtubule minus ends and limits their dynamics, thereby stabilizing the longitudinal array while the lateral array undergoes net depolymerization. To date, no experimental structural information is available for SPIRAL2 to help inform its mechanism. To gain insight into SPIRAL2 structure and function, we determined a 1.8 Å resolution crystal structure of the Arabidopsis thaliana SPIRAL2 C-terminal domain. The domain is composed of seven core α-helices, arranged in an α-solenoid. Amino-acid sequence conservation maps primarily to one face of the domain involving helices α1, α3, α5, and an extended loop, the α6-α7 loop. The domain fold is similar to, yet structurally distinct from the C-terminal domain of Ge-1 (an mRNA decapping complex factor involved in P-body localization) and, surprisingly, the C-terminal domain of the katanin p80 regulatory subunit. The katanin p80 C-terminal domain heterodimerizes with the MIT domain of the katanin p60 catalytic subunit, and in metazoans, binds the microtubule minus-end factors CAMSAP3 and ASPM. Structural analysis predicts that SPIRAL2 does not engage katanin p60 in a mode homologous to katanin p80. The SPIRAL2 structure highlights an interesting evolutionary convergence of domain architecture and microtubule minus-end localization between SPIRAL2 and katanin complexes, and establishes a foundation upon which structure-function analysis can be conducted to elucidate the role of this domain in the regulation of plant microtubule arrays.
59 BASIC BIOLOGICAL SCIENCES↗
Quantifying charge resonance and multiexciton character in coupled chromophores by charge and spin cumulant analysis
We extend excited-state structural analysis to quantify the charge-resonance and multi-exciton character in wave functions of weakly interacting chromophores such as molecular dimers. The approach employs charge and spin cumulants which describe inter-fragment electronic correlations in molecular complexes. We introduce indexes corresponding to the weights of local, charge resonance, and biexciton (with different spin structure) configurations that can be computed for general wave functions thus allowing one to quantify the character of doubly excited states. The utility of the approach is illustrated by applications to several small dimers, e.g., He-H{sub 2}, (H{sub 2}){sub 2}, and (C{sub 2}H{sub 4}){sub 2}, using full and restricted configuration interaction schemes. In addition, we present calculations for several systems relevant to singlet fission, such as tetracene, 1,6-diphenyl-1,3,5-hexatriene, and 1,3-diphenylisobenzofuran dimers.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
CORSS: Cylinder Optimization of Rings, Skin, and Stringers
Launch vehicle designs typically make extensive use of cylindrical skin stringer construction. Structural analysis methods are well developed for preliminary design of this type of construction. This report describes an automated, iterative method to obtain a minimum weight preliminary design. Structural optimization has been researched extensively, and various programs have been written for this purpose. Their complexity and ease of use depends on their generality, the failure modes considered, the methodology used, and the rigor of the analysis performed. This computer program employs closed-form solutions from a variety of well-known structural analysis references and joins them with a commercially available numerical optimizer called the 'Design Optimization Tool' (DOT). Any ring and stringer stiffened shell structure of isotropic materials that has beam type loading can be analyzed. Plasticity effects are not included. It performs a more limited analysis than programs such as PANDA, but it provides an easy and useful preliminary design tool for a large class of structures. This report briefly describes the optimization theory, outlines the development and use of the program, and describes the analysis techniques that are used. Examples of program input and output, as well as the listing of the analysis routines, are included.
Finckenor, J.↗
Design Oriented Structural Modeling for Airplane Conceptual Design Optimization
The main goal for research conducted with the support of this grant was to develop design oriented structural optimization methods for the conceptual design of airplanes. Traditionally in conceptual design airframe weight is estimated based on statistical equations developed over years of fitting airplane weight data in data bases of similar existing air- planes. Utilization of such regression equations for the design of new airplanes can be justified only if the new air-planes use structural technology similar to the technology on the airplanes in those weight data bases. If any new structural technology is to be pursued or any new unconventional configurations designed the statistical weight equations cannot be used. In such cases any structural weight estimation must be based on rigorous "physics based" structural analysis and optimization of the airframes under consideration. Work under this grant progressed to explore airframe design-oriented structural optimization techniques along two lines of research: methods based on "fast" design oriented finite element technology and methods based on equivalent plate / equivalent shell models of airframes, in which the vehicle is modelled as an assembly of plate and shell components, each simulating a lifting surface or nacelle / fuselage pieces. Since response to changes in geometry are essential in conceptual design of airplanes, as well as the capability to optimize the shape itself, research supported by this grant sought to develop efficient techniques for parametrization of airplane shape and sensitivity analysis with respect to shape design variables. Towards the end of the grant period a prototype automated structural analysis code designed to work with the NASA Aircraft Synthesis conceptual design code ACS= was delivered to NASA Ames.
Livne, Eli↗
Multi-Disciplinary System Reliability Analysis
The objective of this study is to develop a new methodology for estimating the reliability of engineering systems that encompass multiple disciplines. The methodology is formulated in the context of the NESSUS probabilistic structural analysis code developed under the leadership of NASA Lewis Research Center. The NESSUS code has been successfully applied to the reliability estimation of a variety of structural engineering systems. This study examines whether the features of NESSUS could be used to investigate the reliability of systems in other disciplines such as heat transfer, fluid mechanics, electrical circuits etc., without considerable programming effort specific to each discipline. In this study, the mechanical equivalence between system behavior models in different disciplines are investigated to achieve this objective. A new methodology is presented for the analysis of heat transfer, fluid flow, and electrical circuit problems using the structural analysis routines within NESSUS, by utilizing the equivalence between the computational quantities in different disciplines. This technique is integrated with the fast probability integration and system reliability techniques within the NESSUS code, to successfully compute the system reliability of multi-disciplinary systems. Traditional as well as progressive failure analysis methods for system reliability estimation are demonstrated, through a numerical example of a heat exchanger system involving failure modes in structural, heat transfer and fluid flow disciplines.
Mahadevan, Sankaran↗
Multidisciplinary System Reliability Analysis
The objective of this study is to develop a new methodology for estimating the reliability of engineering systems that encompass multiple disciplines. The methodology is formulated in the context of the NESSUS probabilistic structural analysis code, developed under the leadership of NASA Glenn Research Center. The NESSUS code has been successfully applied to the reliability estimation of a variety of structural engineering systems. This study examines whether the features of NESSUS could be used to investigate the reliability of systems in other disciplines such as heat transfer, fluid mechanics, electrical circuits etc., without considerable programming effort specific to each discipline. In this study, the mechanical equivalence between system behavior models in different disciplines are investigated to achieve this objective. A new methodology is presented for the analysis of heat transfer, fluid flow, and electrical circuit problems using the structural analysis routines within NESSUS, by utilizing the equivalence between the computational quantities in different disciplines. This technique is integrated with the fast probability integration and system reliability techniques within the NESSUS code, to successfully compute the system reliability of multidisciplinary systems. Traditional as well as progressive failure analysis methods for system reliability estimation are demonstrated, through a numerical example of a heat exchanger system involving failure modes in structural, heat transfer and fluid flow disciplines.
Mahadevan, Sankaran↗
Parallel Aeroelastic Analysis Using ENSAERO and NASTRAN
A high fidelity parallel static structural analysis capability is created and interfaced to the multidisciplinary analysis package ENSAERO-MPI of Ames Research Center. This new module replaced ENSAERO's lower fidelity simple finite element and modal modules. Full aircraft structures may be more accurately modeled using the new finite element capability. Parallel computation is performed by breaking the full structure into multiple substructures. This approach is conceptually similar to ENSAERO's multi-zonal fluid analysis capability. The new substructure code is used to solve the structural finite element equations for each substructure in parallel. NASTRAN/COSMIC is utilized as a front end for this code. Its full library of elements can be used to create an accurate and realistic aircraft mode. It is used to create the stiffness matrices for each sub-structure. The new parallel code then uses an iterative preconditioned conjugate gradient method to solve the global structural equations for the sub-structure boundary nodes. Results are presented for a wing-body configuration.
Eldred, Lloyd B.↗
Program for Analysis and Resizing of Structures
Program for Analysis and Resizing of Structures (PARS) determines optimum resizing of structures subject to stress, displacement, and flutter constraints. Is an efficient code for sizing large- or small-scale finite-element models in presence of strength, thermal, and aeroelastic constraints with minimum and maximum bounds on structural dimensions. PARS is composed of individual processors that are executed in a logical sequence to perform analysis or synthesis.
Haftka, R. T.↗
Efficient, Multi-Scale Designs Take Flight
Engineers can solve aerospace design problems faster and more efficiently with a versatile software product that performs automated structural analysis and sizing optimization. Collier Research Corporation's HyperSizer Structural Sizing Software is a design, analysis, and documentation tool that increases productivity and standardization for a design team. Based on established aerospace structural methods for strength, stability, and stiffness, HyperSizer can be used all the way from the conceptual design to in service support. The software originated from NASA s efforts to automate its capability to perform aircraft strength analyses, structural sizing, and weight prediction and reduction. With a strategy to combine finite element analysis with an automated design procedure, NASA s Langley Research Center led the development of a software code known as ST-SIZE from 1988 to 1995. Collier Research employees were principal developers of the code along with Langley researchers. The code evolved into one that could analyze the strength and stability of stiffened panels constructed of any material, including light-weight, fiber-reinforced composites.
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