Three-Dimensional Structural Model of Chicken Liver Sulfite Oxidase in its Activated Form

2010 ◽  
Vol 1 (23) ◽  
pp. 2159-2164 ◽  
Author(s):  
Tillmann Utesch ◽  
Maria Andrea Mroginski
Keyword(s):  
Structural Model ◽  
Three Dimensional ◽  
Sulfite Oxidase ◽  
Chicken Liver

scholarly journals Na3Co2(As0.52P0.48)O4(As0.95P0.05)2O7

2013 ◽  
Vol 69 (12) ◽  
pp. i85-i86 ◽  
Author(s):  
Youssef Ben Smida ◽  
Abderrahmen Guesmi ◽  
Mohamed Faouzi Zid ◽  
Ahmed Driss
Keyword(s):  
Solid State ◽  
Solid State Reaction ◽  
Title Compound ◽  
General Position ◽  
Structural Model ◽  
Three Dimensional ◽  
The Other ◽  
Coordination Polyhedra ◽  
Bond Valence Sum ◽  
Full Occupancy

The title compound, trisodium dicobalt(II) (arsenate/phosphate) (diarsenate/diphosphate), was prepared by a solid-state reaction. It is isostructural with Na3Co2AsO4As2O7. The framework shows the presence of CoX22O12(X2 is statistically disordered with As0.95P0.05) units formed by sharing corners between Co1O6octahedra andX22O7groups. These units form layers perpendicular to [010]. Co2O6octahedra andX1O4(X1 = As0.54P0.46) tetrahedra form Co2X1O8chains parallel to [001]. Cohesion between layers and chains is ensured by theX22O7groups, giving rise to a three-dimensional framework with broad tunnels, running along thea- andc-axis directions, in which the Na+ions reside. The two Co2+cations, theX1 site and three of the seven O atoms lie on special positions, with site symmetries 2 andmfor the Co,mfor theX1, and 2 andm(× 2) for the O sites. One of two Na atoms is disordered over three special positions [occupancy ratios 0.877 (10):0.110 (13):0.066 (9)] and the other is in a general position with full occupancy. A comparison between structures such as K2CdP2O7, α-NaTiP2O7and K2MoO2P2O7is made. The proposed structural model is supported by charge-distribution (CHARDI) analysis and bond-valence-sum (BVS) calculations. The distortion of the coordination polyhedra is analyzed by means of the effective coordination number.

scholarly journals Reorganization of chromosome architecture in replicative cellular senescence

2016 ◽  
Vol 2 (2) ◽  
pp. e1500882 ◽  
Author(s):  
Steven W. Criscione ◽  
Marco De Cecco ◽  
Benjamin Siranosian ◽  
Yue Zhang ◽  
Jill A. Kreiling ◽  
...  
Keyword(s):  
Cellular Senescence ◽  
Structural Model ◽  
Three Dimensional ◽  
Chromatin Accessibility ◽  
Genome Chromosome ◽  
Chromosome Conformation ◽  
Topologically Associated Domains ◽  
Chromosomal Architecture ◽  
Fundamental Biological Process ◽  
3D Architecture

Replicative cellular senescence is a fundamental biological process characterized by an irreversible arrest of proliferation. Senescent cells accumulate a variety of epigenetic changes, but the three-dimensional (3D) organization of their chromatin is not known. We applied a combination of whole-genome chromosome conformation capture (Hi-C), fluorescence in situ hybridization, and in silico modeling methods to characterize the 3D architecture of interphase chromosomes in proliferating, quiescent, and senescent cells. Although the overall organization of the chromatin into active (A) and repressive (B) compartments and topologically associated domains (TADs) is conserved between the three conditions, a subset of TADs switches between compartments. On a global level, the Hi-C interaction matrices of senescent cells are characterized by a relative loss of long-range and gain of short-range interactions within chromosomes. Direct measurements of distances between genetic loci, chromosome volumes, and chromatin accessibility suggest that the Hi-C interaction changes are caused by a significant reduction of the volumes occupied by individual chromosome arms. In contrast, centromeres oppose this overall compaction trend and increase in volume. The structural model arising from our study provides a unique high-resolution view of the complex chromosomal architecture in senescent cells.

Wave propagation simulation on a 3D model of the Ruhr district for locations of seismic monitoring.

2021 ◽  
Author(s):  
Gabriela de los Angeles Gonzalez de Lucio ◽  
Claudia Finger ◽  
Erik Saenger
Keyword(s):  
Wave Propagation ◽  
Seismic Risk ◽  
Structural Model ◽  
Three Dimensional ◽  
Seismic Source ◽  
Industrial Area ◽  
Structural Features ◽  
Maximum Energy ◽  
Seismic Events ◽  
Ruhr District

<p>The Ruhr district meets the necessary elements to carry out geothermal projects due to its geothermal potential and demand, as it is a densely populated industrial area. Currently, there are projects for direct use, whereas projects for electricity generation are planned. The latter, due to greater depths, reservoir enhancement techniques are required in some cases. This may increase the associated seismic risk which should be elaborated in detail.</p><p>With available data, a three-dimensional geological and structural model was created. The shallower parts have been widely studied and documented by mining activity in the Ruhr region during the last century.  Below a depth of 1 km, data are scarce, and uncertainties increase. The full elastic wavefield emitted by a realistic seismic source has been simulated using a finite differences scheme and the derived geological model. The elastic properties were estimated with well data. The source has common characteristics of real seismic events in the area.</p><p>The wave propagation simulations let us analyze the seismic response with different sources and velocities models. Three cases are considered, two seismic events with distinct depths based on real events. The third case is based on the proposed location of a deep geothermal project.</p><p>Especially for the case with the deeper source, the areas with relatively high amplitudes of displacement correlated with structural features of the model. Applying the imaging condition of maximum energy density allows us to define zones with a potentially increased seismic risk that should be monitored more closely.</p>

A Scalable Time-Parallel Solution of Periodic Rotor Dynamics in X3D

2021 ◽  
Author(s):  
Mrinalgouda Patil ◽  
Anubhav Datta
Keyword(s):  
Harmonic Balance ◽  
Large Scale ◽  
Structural Model ◽  
Three Dimensional ◽  
Harmonic Balance Method ◽  
Flight Test ◽  
Solution Procedure ◽  
Balance Method ◽  
Computational Time ◽  
Near Resonance

A time-parallel algorithm is developed for large-scale three-dimensional rotor dynamic analysis. A modified harmonic balance method with a scalable skyline solver forms the kernel of this algorithm. The algorithm is equipped with a solution procedure suitable for large-scale structures that have lightly damped modes near resonance. The algorithm is integrated in X3D, implemented on a hybrid shared and distributed memory architecture, and demonstrated on a three-dimensional structural model of a UH-60A-like fully articulated rotor. Flight-test data from UH-60A Airloads Program transition flight C8513 are used for validation. The key conclusion is that the new solver converges to the time marching solution more than 50 times faster and achieves a performance greater than 1 teraFLOPS. The significance of this conclusion is that the principal barrier of computational time for trim solution using high-fidelity three-dimensional structures can be overcome with the scalable harmonic balance method demonstrated in this paper.

scholarly journals An efficient three-dimensional foil structure model for bump-type gas foil bearings considering friction

Friction ◽  
2020 ◽  
Author(s):  
Yongpeng Gu ◽  
Xudong Lan ◽  
Gexue Ren ◽  
Ming Zhou
Keyword(s):  
Structural Model ◽  
Three Dimensional ◽  
Element Model ◽  
Experimental Results ◽  
Synthesis Methods ◽  
Structure Model ◽  
Foil Bearings ◽  
Static Responses ◽  
Bearing Sleeve ◽  
Shell Finite Element

Abstract This paper presents an efficient three-dimensional (3D) structural model for bump-type gas foil bearings (GFBs) developed by considering friction. The foil structures are modeled with a 3D shell finite element model. Using the bump foil mechanical characteristics, the Guyan reduction and component mode synthesis methods are adopted to improve computational efficiency while guaranteeing accurate static responses. A contact model that includes friction and separation behaviors is presented to model the interactions of the bump foil with the top foil and bearing sleeve. The proposed structural model was validated with published analytical and experimental results. The coupled elastohydrodynamics model of GFBs was established by integration of the proposed structural model with data on hydrodynamic films, and it was validated by comparisons with existing experimental results. The performance of a bearing with an angular misalignment was studied numerically, revealing that the reaction torques of the misaligned bearing predicted by GFB models with 2D and 3D foil structure models are quite different. The 3D foil structure model should be used to study GFB misalignment.

The Integrative Establishment of a Three-Dimensional Structure Model of Changling Gas Field in Changling Fault Depression

2014 ◽  
Vol 556-562 ◽  
pp. 3779-3782
Author(s):  
Xiao Yu Yu ◽  
Xue Li ◽  
Xiao Song Li ◽  
Guo Yi Zhang
Keyword(s):  
Structural Model ◽  
High Reliability ◽  
Three Dimensional ◽  
Physical Property ◽  
Modeling Technique ◽  
Dimensional Structure ◽  
Gas Field ◽  
3D Geological Modeling ◽  
Micro Features ◽  
Reservoir Description

The three-dimensional (3D) geological modeling technique which is considered as an important skill of fine reservoir description has been gaining more and more attention. On one hand, it can efficiently promote the transformation of reservoir description from two-dimensional (2D) to 3D, and from qualification to quantification as well. The 3D reservoir geological model can be used as basic geological knowledge in terms of adjusting well patterns and indicating remaining oil distribution, through reflecting the spatial distribution characteristics and the variation of the reservoir physical property. On the other hand, the 3D modeling technique specializes in the representation of local micro features in comparison of regular ways. This article aims at subtly describing the structural modeling of Changling gas field of Changling fault depression. The result of this case study shows that the establishment of structural model is consistent with the understanding of fault development which was proved during the process of producing gas, thus the structural model has high reliability. Therefore, the structural model is of great guiding significance for the design of new well and the well patter optimization.

A Harmonic Balance Approach for Modeling Three-Dimensional Nonlinear Unsteady Aerodynamics and Aeroelasticity

2002 ◽  
Author(s):  
Jeffrey P. Thomas ◽  
Earl H. Dowell ◽  
Kenneth C. Hall
Keyword(s):  
Limit Cycle ◽  
Harmonic Balance ◽  
Structural Model ◽  
Oscillation Amplitude ◽  
Three Dimensional ◽  
Unsteady Aerodynamics ◽  
Finite Amplitude ◽  
Limit Cycle Oscillation ◽  
Unsteady Aerodynamic ◽  
Cycle Oscillation

Presented is a frequency domain harmonic balance (HB) technique for modeling nonlinear unsteady aerodynamics of three-dimensional transonic inviscid flows about wing configurations. The method can be used to model efficiently nonlinear unsteady aerodynamic forces due to finite amplitude motions of a prescribed unsteady oscillation frequency. When combined with a suitable structural model, aeroelastic (fluid-structure), analyses may be performed at a greatly reduced cost relative to time marching methods to determine the limit cycle oscillations (LCO) that may arise. As a demonstration of the method, nonlinear unsteady aerodynamic response and limit cycle oscillation trends are presented for the AGARD 445.6 wing configuration. Computational results based on the inviscid flow model indicate that the AGARD 445.6 wing configuration exhibits only mildly nonlinear unsteady aerodynamic effects for relatively large amplitude motions. Furthermore, and most likely a consequence of the observed mild nonlinear aerodynamic behavior, the aeroelastic limit cycle oscillation amplitude is predicted to increase rapidly for reduced velocities beyond the flutter boundary. This is consistent with results from other time-domain calculations. Although not a configuration that exhibits strong LCO characteristics, the AGARD 445.6 wing nonetheless serves as an excellent example for demonstrating the HB/LCO solution procedure.

VESTA: a three-dimensional visualization system for electronic and structural analysis

2008 ◽  
Vol 41 (3) ◽  
pp. 653-658 ◽  
Author(s):  
Koichi Momma ◽  
Fujio Izumi
Keyword(s):  
Structural Model ◽  
Three Dimensional ◽  
Electronic Energy ◽  
Oxidation States ◽  
Chemical Information ◽  
Volumetric Data ◽  
Visualization System ◽  
Cross Platform ◽  
Diffraction Patterns ◽  
Physical Quantities

A cross-platform program,VESTA, has been developed to visualize both structural and volumetric data in multiple windows with tabs.VESTArepresents crystal structures by ball-and-stick, space-filling, polyhedral, wireframe, stick, dot-surface and thermal-ellipsoid models. A variety of crystal-chemical information is extractable from fractional coordinates, occupancies and oxidation states of sites. Volumetric data such as electron and nuclear densities, Patterson functions, and wavefunctions are displayed as isosurfaces, bird's-eye views and two-dimensional maps. Isosurfaces can be colored according to other physical quantities. Translucent isosurfaces and/or slices can be overlapped with a structural model. Collaboration with external programs enables the user to locate bonds and bond angles in the `graphics area', simulate powder diffraction patterns, and calculate site potentials and Madelung energies. Electron densities determined experimentally are convertible into their Laplacians and electronic energy densities.

Prediction of Residual Stresses and Buckling Distortion in Welding of a Thin Wall Aluminum Butt Joint

2006 ◽  
Author(s):  
Sanaz Yazdanparast ◽  
Mohsen Asle Zaeem ◽  
Iraj Rajabi
Keyword(s):  
Residual Stresses ◽  
Structural Model ◽  
Flow Analysis ◽  
Three Dimensional ◽  
Butt Joint ◽  
Thin Wall ◽  
Global Buckling ◽  
Motion Speed ◽  
Stress And Deformation ◽  
Buckling Distortion

In this paper, global welding buckling distortion of a thin wall aluminum butt joint is investigated. To determine longitudinal residual stresses, a thermo-elastoplastic model is employed; analysis of thermal model and elastic-viscoplastic (Anand) model are decoupled. By using birth and death element method and time dependent model, molten puddle motion (speed of welding) is modeled. Three dimensional nonlinear-transient heat flow analysis has been used to obtain temperature distribution. By applying thermal results and using three dimensional Anand elastic-viscoplastic model, stress and deformation distributions are obtained. Residual stresses are applied on a structural model and by using eigenvalue methods, global buckling instability of butt welded joint is determined. The result of buckling investigation in the numerical model is compared with the result of an experiment.

Fully Three Dimensional Modeling of Fluid-Structure Interaction Problems Using High Order Finite Elements for the Structural Simulation

2004 ◽  
Author(s):  
Dominik Scholz ◽  
Alexander Du¨ster ◽  
Ernst Rank
Keyword(s):  
Structural Model ◽  
Three Dimensional ◽  
High Order ◽  
Polynomial Degree ◽  
Three Dimensional Modeling ◽  
Thin Walled Structures ◽  
Aspect Ratios ◽  
Hexahedral Elements ◽  
Plane Direction ◽  
Three Dimensional Models

Our approach is to use fully three-dimensional models for both the fluid and the structure. For thin-walled structures, which are typically sensitive to loads resulting from the surrounding fluid, it will be shown that the use of high-order hexahedral elements with high aspect ratios is feasible. Furthermore, it will be demonstrated that three-dimensional elements of high order can be used very efficiently by choosing a high polynomial degree in in-plane direction and a low polynomial degree in thickness direction. By varying the polynomial degrees in the local directions of the elements, the choice of an appropriate structural model can be achieved in an adaptive way. This will be demonstrated by means of a numerical example.

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