scholarly journals The structure and features of the software for geophysical geometrical 3D inversions

2021 ◽  
pp. 35-46
Author(s):  
Denis Vagin ◽  
Keyword(s):  
Inverse Problems ◽  
Software Package ◽  
Three Dimensional ◽  
Main Idea ◽  
Dimensional Structure ◽  
Computational Domain ◽  
Direct And Inverse Problems ◽  
Geophysical Model ◽  
Efficient Calculation ◽  
Direct Problems

The structure and features of a software package for 3D inversion of geophysical data are considered. The presented software package is focused on solving direct and inverse problems of electrical exploration and engineering geophysics. In addition to the parameters that determine physical properties of the medium, the software package allows you to restore the geometry parameters of the geophysical model, namely layer reliefs and boundaries of three-dimensional inclusions. The inclusions can be in the form of arbitrary hexagons or prisms with a polygonal base. The software package consists of four main subsystems: an interface, subsystems for solving direct and inverse problems, and a client-server part for performing calculations on remote computing nodes. The graphical interface consists of geophysicist-oriented pre- and postprocessor modules that allow you to describe the problem and present the results of its solution in user-friendly terms. To solve direct problems, the finite element method and the technology for dividing the field into normal and anomalous components are used. At the same time, special methods of discretization of the computational domain are used, which make it possible to take into account both the complex three-dimensional structure of the environment and the presence of man-made objects (wells) in the computational domain. To increase the efficiency of solving direct problems, nonconforming grids with cells in the form of arbitrary hexahedrons are used. Methods for efficient calculation of derivatives (with respect to these parameters) necessary for solving inverse problems by the Gauss-Newton method are also described for the geometry parameters. The main idea for efficient derivatives computation is to identify the effect of changing the value of the parameter (used to compute the value of the generalized derivative) on the problem. The main actions performed by the subsystem for solving inverse problems and the features associated with the processing of geometry parameters are described.

scholarly journals The Ambiguity Issue in Solving Inverse Problems of Small-Angle Scattering: A Consistent Approach Using an Insulin Receptor-Related Receptor as an Example. Methods for Interpreting SAXS Data

2021 ◽  
Vol 15 (3) ◽  
pp. 270-283
Author(s):  
M. V. Petoukhov ◽  
P. V. Konarev ◽  
V. V. Volkov ◽  
A. A. Mozhaev ◽  
E. V. Shtykova
Keyword(s):  
Inverse Problems ◽  
Insulin Receptor ◽  
Small Angle ◽  
Three Dimensional ◽  
Small Angle Scattering ◽  
Dimensional Structure ◽  
Model Parameters ◽  
Three Dimensional Structure ◽  
Angle Scattering ◽  
Consistent Approach

Abstract The construction of three-dimensional models of protein macromolecules is a serious challenge due to the possible ambiguity of solving the inverse problem of reconstructing a three-dimensional structure from a one-dimensional small-angle scattering profile. The target function of this task can have several local minima, which leads to the dependence of the solution on the initial values of the model parameters and on the method of finding the global minimum. The problem of creating structural models is also complicated by averaging the scattering pattern over all orientations of particles in space and by the size and shape distribution of scattering objects in the case of polydispersity and/or polymorphism. In this study, the issue of ambiguity in solving inverse problems and restoring the three-dimensional structure of a protein is considered using the structure of the ectodomain of an insulin receptor-related receptor (ectoIRR) in solution as an example. The paper presents a consistent approach to solving this problem, starting from the determination of general structural parameters and ab initio reconstruction of shape to modeling by rigid bodies (using molecular tectonics), hybrid methods, and analysis of scattering profiles by singular vector decomposition.

scholarly journals ANALYSIS OF THE CAPABILITIES OF THE LOGOS SOFTWARE PACKAGE FOR CALCULATING THE SEISMIC IMPACT ON A STRUCTURE

2021 ◽  
Vol 83 (2) ◽  
pp. 160-169
Author(s):  
N.S. Dyukina ◽  
V.L. Kotov ◽  
D.Yu. Dyanov ◽  
V.V. Borlyaev
Keyword(s):  
Boundary Conditions ◽  
Gravity Field ◽  
Relative Error ◽  
Software Package ◽  
Three Dimensional ◽  
Dynamic Strength ◽  
Stationary Problem ◽  
Calculation Error ◽  
Computational Domain ◽  
Dynamic Relaxation

The possibilities of the LOGOS software package for calculating seismic vibrations of buried structures, considering the contact interaction with the ground and the gravity field, are investigated and expanded. To reduce computational costs, the LOGOS software package includes a method for modeling non-reflective boundary conditions that was developed earlier and implemented in the “Dynamics-2” software package, which allows reducing the size of the computational domain. The results of numerical simulation in the LOGOS of shear wave propagation in an elastic bounded subdomain of a continuous medium are presented, demonstrating the effectiveness of non-reflecting boundary conditions for a three-dimensional formulation. The dynamic relaxation technique used in the dynamic strength module of the LOGOS software package for calculating the initial static stresses from the action of the gravity field with the subsequent solution of the non-stationary problem is investigated. Numerical estimates of the expected accuracy of the dynamic solution are obtained, depending on the specified accuracy of the static calculation. Thus, the relative error in the change in kinetic energy when using the dynamic relaxation algorithm 10–4 gives a relative error of 10–3 in velocities and 10–2 in stresses, reducing the specified calculation error by 2 orders of magnitude reduces the relative error in calculating velocities by 3 times, stresses – by 5 times. The calculation of the initial stress-strain state of the building-ground system from the action of the gravity field is compared using the dynamic relaxation procedure and using the stationing procedure implemented in the “Dynamics-2” software package. In all problems in the three-dimensional formulation, 8-node hexahedra with one-point integration are used, in the two-dimensional formulation – equivalent 4-node finite elements, for the integration of the defining system of equations, an explicit “cross” scheme is used. Between the subdomains, variants of contact with gluing and contact with friction are implemented. The capabilities of LOGOS for conducting multiprocessor calculations allowed us to make estimates of the convergence of the problem under consideration based on a series of computational experiments.

Conformation of Ribosomes from Escherichia Coli

1974 ◽  
Vol 32 ◽  
pp. 210-211
Author(s):  
M. Boublik ◽  
W. Hellmann ◽  
F. Jenkins
Keyword(s):  
Binding Sites ◽  
Ribosomal Proteins ◽  
Fluorescent Dyes ◽  
Protein Biosynthesis ◽  
Three Dimensional ◽  
Spatial Arrangement ◽  
Dimensional Structure ◽  
Complete Understanding ◽  
And Function

The present knowledge of the three-dimensional structure of ribosomes is far too limited to enable a complete understanding of the various roles which ribosomes play in protein biosynthesis. The spatial arrangement of proteins and ribonuclec acids in ribosomes can be analysed in many ways. Determination of binding sites for individual proteins on ribonuclec acid and locations of the mutual positions of proteins on the ribosome using labeling with fluorescent dyes, cross-linking reagents, neutron-diffraction or antibodies against ribosomal proteins seem to be most successful approaches. Structure and function of ribosomes can be correlated be depleting the complete ribosomes of some proteins to the functionally inactive core and by subsequent partial reconstitution in order to regain active ribosomal particles.

Three-Dimensional Reconstruction Using Stereo Pairs from Serial Thick Sections

1977 ◽  
Vol 35 ◽  
pp. 562-563
Author(s):  
Robert Glaeser ◽  
Thomas Bauer ◽  
David Grano
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
Serial Sections ◽  
Thin Sections ◽  
3 Dimensional ◽  
Transmission Electron ◽  
Freeze Dried ◽  
Dimensional Reconstruction ◽  
Stereo Imagery ◽  
Whole Mounts

In transmission electron microscopy, the 3-dimensional structure of an object is usually obtained in one of two ways. For objects which can be included in one specimen, as for example with elements included in freeze- dried whole mounts and examined with a high voltage microscope, stereo pairs can be obtained which exhibit the 3-D structure of the element. For objects which can not be included in one specimen, the 3-D shape is obtained by reconstruction from serial sections. However, without stereo imagery, only detail which remains constant within the thickness of the section can be used in the reconstruction; consequently, the choice is between a low resolution reconstruction using a few thick sections and a better resolution reconstruction using many thin sections, generally a tedious chore. This paper describes an approach to 3-D reconstruction which uses stereo images of serial thick sections to reconstruct an object including detail which changes within the depth of an individual thick section.

Electron Microscopy of Cytoplasmic Contractile Proteins

1978 ◽  
Vol 36 (3) ◽  
pp. 606-614 ◽  
Author(s):  
T.D. Pollard ◽  
P. Maupin
Keyword(s):  
Electron Microscopy ◽  
Actin Filaments ◽  
Three Dimensional ◽  
Uranyl Acetate ◽  
Contractile Proteins ◽  
Dimensional Structure ◽  
X Ray Diffraction ◽  
Cytoplasmic Matrix ◽  
Computer Image Processing ◽  
Nonmuscle Cells

In this paper we review some of the contributions that electron microscopy has made to the analysis of actin and myosin from nonmuscle cells. We place particular emphasis upon the limitations of the ultrastructural techniques used to study these cytoplasmic contractile proteins, because it is not widely recognized how difficult it is to preserve these elements of the cytoplasmic matrix for electron microscopy. The structure of actin filaments is well preserved for electron microscope observation by negative staining with uranyl acetate (Figure 1). In fact, to a resolution of about 3nm the three-dimensional structure of actin filaments determined by computer image processing of electron micrographs of negatively stained specimens (Moore et al., 1970) is indistinguishable from the structure revealed by X-ray diffraction of living muscle.

A New 1000kv Electron Microscope

1969 ◽  
Vol 27 ◽  
pp. 100-101
Author(s):  
J.L. Williams ◽  
K. Heathcote ◽  
E.J. Greer
Keyword(s):  
Electron Microscope ◽  
Direct Observation ◽  
High Voltage ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Specimen Thickness ◽  
Voltage Electron ◽  
High Voltage Electron Microscope ◽  
Dynamic Experiments ◽  
Conventional Instrument

High Voltage Electron Microscope already offers exciting experimental possibilities to Biologists and Materials Scientists because the increased specimen thickness allows direct observation of three dimensional structure and dynamic experiments on effectively bulk specimens. This microscope is designed to give maximum accessibility and space in the specimen region for the special stages which are required. At the same time it provides an ease of operation similar to a conventional instrument.

High-voltage electron microscopy of maxillary gland of spirochete-infected brine shrimp: lesion of efferent tubule

1988 ◽  
Vol 46 ◽  
pp. 362-363
Author(s):  
G. E. Tyson ◽  
M. J. Song
Keyword(s):  
Electron Microscopy ◽  
High Voltage ◽  
Brine Shrimp ◽  
Natural Populations ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
High Voltage Electron Microscopy ◽  
Voltage Electron ◽  
High Voltage Electron ◽  
Infected Adult

Natural populations of the brine shrimp, Artemia, may possess spirochete- infected animals in low numbers. The ultrastructure of Artemia's spirochete has been described by conventional transmission electron microscopy. In infected shrimp, spirochetal cells were abundant in the blood and also occurred intra- and extracellularly in the three organs examined, i.e. the maxillary gland (segmental excretory organ), the integument, and certain muscles The efferent-tubule region of the maxillary gland possessed a distinctive lesion comprised of a group of spirochetes, together with numerous small vesicles, situated in a cave-like indentation of the base of the tubule epithelium. in some instances the basal lamina at a lesion site was clearly discontinuous. High-voltage electron microscopy has now been used to study lesions of the efferent tubule, with the aim of understanding better their three-dimensional structure.Tissue from one maxillary gland of an infected, adult, female brine shrimp was used for HVEM study.

Mitochondrial Reconstructions Based on Serial Thick Sections and HVEM

1975 ◽  
Vol 33 ◽  
pp. 286-287
Author(s):  
Jerome J. Paulin
Keyword(s):  
Imaging Techniques ◽  
Three Dimensional ◽  
Posterior Pole ◽  
Dimensional Structure ◽  
Stereo Imaging ◽  
Thin Sections ◽  
Anatomical Features ◽  
The Past ◽  
Cellular Components ◽  
Mitochondrial Reticulum

Within the past decade it has become apparent that HVEM offers the biologist a means to explore the three-dimensional structure of cells and/or organelles. Stereo-imaging of thick sections (e.g. 0.25-10 μm) not only reveals anatomical features of cellular components, but also reduces errors of interpretation associated with overlap of structures seen in thick sections. Concomitant with stereo-imaging techniques conventional serial Sectioning methods developed with thin sections have been adopted to serial thick sections (≥ 0.25 μm). Three-dimensional reconstructions of the chondriome of several species of trypanosomatid flagellates have been made from tracings of mitochondrial profiles on cellulose acetate sheets. The sheets are flooded with acetone, gluing them together, and the model sawed from the composite and redrawn.The extensive mitochondrial reticulum can be seen in consecutive thick sections of (0.25 μm thick) Crithidia fasciculata (Figs. 1-2). Profiles of the mitochondrion are distinguishable from the anterior apex of the cell (small arrow, Fig. 1) to the posterior pole (small arrow, Fig. 2).

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