scholarly journals Robust 3D modelling reveals spatiosyntenic properties of animal genomes

2021 ◽  
Author(s):  
Tereza Clarence ◽  
Nicolas Robert ◽  
Fatih Sarigol ◽  
Xiao Fu ◽  
Paul Bates ◽  
...  
Keyword(s):  
Genomic Sequence ◽  
Three Dimensional ◽  
3D Modelling ◽  
Gene Content ◽  
Evolutionary Constraints ◽  
Two Dimensional ◽  
Interaction Spheres ◽  
Show Evidence ◽  
Animal Genomes ◽  
Modelling Approach

Abstract Animal genomes are organized into chromosomes that are remarkably conserved in their gene content, forming distinct evolutionary units (macrosynteny). We developed a novel three-dimensional chromosomal modelling approach to show that syntenic signals are reflected in conserved three-dimensional networks, encompassed within interaction spheres. We show evidence for evolutionary constraints that could not be surmised by genomic sequence alone, thereby underlining the importance of three-, rather than just two-, dimensional organization.

An Investigation of the Predicting Capabilities of a Variable Flow Stress Machining Theory

2001 ◽  
Author(s):  
P. Mathew
Keyword(s):  
Flow Stress ◽  
Material Flow ◽  
Three Dimensional ◽  
Experimental Results ◽  
Two Dimensional ◽  
Variable Flow ◽  
Comparative Results ◽  
Intermittent Cutting ◽  
Theoretical Results ◽  
Modelling Approach

Abstract The Oxley Machining Theory, which has been developed over the last 40 years, is presented in this paper. The capability of the model is described with its initial two-dimensional machining approach followed by the extension to the generalised model for three-dimensional machining. The theoretical results from the model are compared with the experimental results to determine the model capability. A brief description of the work associated with the effect of strain hardening at the interface is presented and comparative results are shown. A further extension of the model to intermittent cutting process of reaming is also presented and a comparison with the experimental results indicates the model developed is quite capable of predicting cutting forces for reaming. In explaining the results obtain, the assumptions made are explained and the inputs required. The limitations of the modelling approach are presented. It is pointed out that the Oxley model is a versatile model as long as proper description of the material flow stress properties is presented.

scholarly journals The Effects of Rotation during Star Formation

1981 ◽  
Vol 93 ◽  
pp. 5-26
Author(s):  
Peter Bodenheimer
Keyword(s):  
Star Formation ◽  
Spatial Resolution ◽  
Molecular Clouds ◽  
Three Dimensional ◽  
Pressure Gradients ◽  
Two Dimensional ◽  
Magnetic Effects ◽  
Show Evidence ◽  
Hydrodynamic Calculations ◽  
Effects Of Rotation

Observations of molecular clouds show evidence of rotation and of fragmentation of subregions of the clouds into multiple stellar or protostellar systems. This review concentrates on the effects that rotation and pressure gradients have in a self-gravitating cloud to cause it to undergo the crucial process of fragmentation. Recent two-dimensional and three-dimensional numerical hydrodynamic calculations have made progress in determining these effects. In most cases the calculations are performed with modest spatial resolution and are limited to isothermal clouds with neglect of viscous and magnetic effects. The combined results of several calculations strongly suggest that rotating clouds that are unstable to collapse are also unstable to fragmentation.

An integrated model for the performance of piston ring pack in internal combustion engines

2017 ◽  
Vol 232 (3) ◽  
pp. 371-384 ◽  
Author(s):  
Kamel G Mahmoud ◽  
Oliver Knaus ◽  
Tigran Parikyan ◽  
Guenter Offner ◽  
Stjepan Sklepic
Keyword(s):  
Internal Combustion Engines ◽  
Piston Ring ◽  
Three Dimensional ◽  
Combustion Engines ◽  
Two Dimensional ◽  
Modelling Method ◽  
Ring Dynamics ◽  
Piston Ring Pack ◽  
Ring Pack ◽  
Modelling Approach

Piston rings are important components in internal combustion engines. Their primary function is to seal dynamically the gap between moving piston and cylinder liner surface in order to prevent the combustion gases from penetrating into the crankcase. The rings also control the oil leakage from the crankcase to the combustion chamber. The performance of the piston ring pack impacts the engine efficiency, durability and emissions. The recognition of the impact of the ring-pack performance on the engine design resulted in a sustained effort of research and development aimed at understanding the operation of the piston ring pack. Most of the published models developed in this field are two-dimensional assuming that the ring and liner are perfect circles for the purpose of modelling the axial and radial dynamics. Although this approach has proved to be useful, there exist a number of asymmetrical characteristics of the power cylinder system that can be crucial to the ring-pack performance and therefore it is considered to be appropriate. In this work, an integrated methodology that handles the complex ring-pack mechanism is presented. The physics of the ring-pack mechanism covers the three-dimensional piston ring dynamics of asymmetric engine cylinder due to bore distortion, the mixed lubrication at ring running face as well as the ring flanks and the interring gas dynamics. The modelling method is verified in two steps. In the first step, the dynamic behaviour of the three-dimensional ring model is verified against a commercial finite element software by comparing the eigenmodes up to a frequency of about 1 kHz. In the second step, the ring-pack modelling approach using three-dimensional ring models is also verified against a commercial ring dynamics program, which is based on the two-dimensional modelling. It is shown that the three-dimensional ring dynamics modelling method has advantages over the two-dimensional modelling approach as it facilitates studying the influence of the non-uniform twist along its circumference (ring winding), the effect of bore distortion on blow-by, ring friction, friction power losses and wear.

High Resolution Microscopy of Multi-Layered Biological Crystals

1982 ◽  
Vol 40 ◽  
pp. 80-83
Author(s):  
H.A. Cohen ◽  
T.W. Jeng ◽  
W. Chiu
Keyword(s):  
High Resolution ◽  
Low Dose ◽  
Three Dimensional ◽  
Data Interpretation ◽  
Two Dimensional ◽  
Biological Objects ◽  
Density Maps ◽  
Density Map ◽  
Complex Crystal ◽  
High Resolution Microscopy

This tutorial will discuss the methodology of low dose electron diffraction and imaging of crystalline biological objects, the problems of data interpretation for two-dimensional projected density maps of glucose embedded protein crystals, the factors to be considered in combining tilt data from three-dimensional crystals, and finally, the prospects of achieving a high resolution three-dimensional density map of a biological crystal. This methodology will be illustrated using two proteins under investigation in our laboratory, the T4 DNA helix destabilizing protein gp32*I and the crotoxin complex crystal.

Instrumentation For Quantitative Microscopy

1977 ◽  
Vol 35 ◽  
pp. 206-209
Author(s):  
B. Ralph ◽  
A.R. Jones
Keyword(s):  
Volume Fraction ◽  
Three Dimensional ◽  
Two Dimensional ◽  
Automatic Data ◽  
Phase Volume Fraction ◽  
Statistical Confidence ◽  
Resultant Data ◽  
Automatic Data Collection ◽  
Third Dimension ◽  
Evolution Of Microstructure

In all fields of microscopy there is an increasing interest in the quantification of microstructure. This interest may stem from a desire to establish quality control parameters or may have a more fundamental requirement involving the derivation of parameters which partially or completely define the three dimensional nature of the microstructure. This latter categorey of study may arise from an interest in the evolution of microstructure or from a desire to generate detailed property/microstructure relationships. In the more fundamental studies some convolution of two-dimensional data into the third dimension (stereological analysis) will be necessary.In some cases the two-dimensional data may be acquired relatively easily without recourse to automatic data collection and further, it may prove possible to perform the data reduction and analysis relatively easily. In such cases the only recourse to machines may well be in establishing the statistical confidence of the resultant data. Such relatively straightforward studies tend to result from acquiring data on the whole assemblage of features making up the microstructure. In this field data mode, when parameters such as phase volume fraction, mean size etc. are sought, the main case for resorting to automation is in order to perform repetitive analyses since each analysis is relatively easily performed.

A linearity test for thick specimens imaged by HVEM over a 180° angular range

1991 ◽  
Vol 49 ◽  
pp. 552-553
Author(s):  
Yu Liu
Keyword(s):  
Phase Contrast ◽  
Three Dimensional ◽  
Angular Range ◽  
Two Dimensional ◽  
Back Projection ◽  
Line Integral ◽  
Exponential Law ◽  
Transmission Electron ◽  
Absorption Law ◽  
Linearity Test

The image obtained in a transmission electron microscope is the two-dimensional projection of a three-dimensional (3D) object. The 3D reconstruction of the object can be calculated from a series of projections by back-projection, but this algorithm assumes that the image is linearly related to a line integral of the object function. However, there are two kinds of contrast in electron microscopy, scattering and phase contrast, of which only the latter is linear with the optical density (OD) in the micrograph. Therefore the OD can be used as a measure of the projection only for thin specimens where phase contrast dominates the image. For thick specimens, where scattering contrast predominates, an exponential absorption law holds, and a logarithm of OD must be used. However, for large thicknesses, the simple exponential law might break down due to multiple and inelastic scattering.

An Image Reconstruction System Applied to High Voltage Microscopy

1975 ◽  
Vol 33 ◽  
pp. 292-293
Author(s):  
D. E. Johnson
Keyword(s):  
High Voltage ◽  
Prior Information ◽  
Block Diagram ◽  
Three Dimensional ◽  
Real Space ◽  
Two Dimensional ◽  
Efficient Manner ◽  
Fourier Methods ◽  
Tilt Series ◽  
Methods Of Reconstruction

Increased specimen penetration; the principle advantage of high voltage microscopy, is accompanied by an increased need to utilize information on three dimensional specimen structure available in the form of two dimensional projections (i.e. micrographs). We are engaged in a program to develop methods which allow the maximum use of information contained in a through tilt series of micrographs to determine three dimensional speciman structure.In general, we are dealing with structures lacking in symmetry and with projections available from only a limited span of angles (±60°). For these reasons, we must make maximum use of any prior information available about the specimen. To do this in the most efficient manner, we have concentrated on iterative, real space methods rather than Fourier methods of reconstruction. The particular iterative algorithm we have developed is given in detail in ref. 3. A block diagram of the complete reconstruction system is shown in fig. 1.

Computer Assisted Image Reconstruction of Oligomer Structure

1976 ◽  
Vol 34 ◽  
pp. 472-473
Author(s):  
A.M. Jones ◽  
A. Max Fiskin
Keyword(s):  
Three Dimensional ◽  
Depth Of Field ◽  
Computer Assisted ◽  
Projection Data ◽  
Two Dimensional ◽  
Single Particles ◽  
Dimensional Reconstruction ◽  
Computer Assisted Image ◽  
The Fourier Transform ◽  
Space Approach

If the tilt of a specimen can be varied either by the strategy of observing identical particles orientated randomly or by use of a eucentric goniometer stage, three dimensional reconstruction procedures are available (l). If the specimens, such as small protein aggregates, lack periodicity, direct space methods compete favorably in ease of implementation with reconstruction by the Fourier (transform) space approach (2). Regardless of method, reconstruction is possible because useful specimen thicknesses are always much less than the depth of field in an electron microscope. Thus electron images record the amount of stain in columns of the object normal to the recording plates. For single particles, practical considerations dictate that the specimen be tilted precisely about a single axis. In so doing a reconstructed image is achieved serially from two-dimensional sections which in turn are generated by a series of back-to-front lines of projection data.

Polymorphic phase transition of a membrane protein - analysis of continuous diffuse electron diffraction intensity

1986 ◽  
Vol 44 ◽  
pp. 166-167
Author(s):  
Douglas L. Dorset ◽  
Andrew K. Massalski
Keyword(s):  
Molecular Sieve ◽  
Three Dimensional ◽  
Pore Geometry ◽  
Two Dimensional ◽  
Diffraction Intensity ◽  
Polymorphic Phase Transition ◽  
E Coli ◽  
Crystallographic Study ◽  
Hexagonal Form ◽  
Polymorphic Forms

Matrix porin, the ompF gene product of E. coli, has been the object of a electron crystallographic study of its pore geometry in an attempt to understand its function as a membrane molecular sieve. Three polymorphic forms have been found for two-dimensional crystals reconstituted in phospholipid, two hexagonal forms with different lipid content and an orthorhombic form coexisting with and similar to the hexagonal form found after lipid loss. In projection these have been shown to retain the same three-fold pore triplet geometry and analyses of three-dimensional data reveal that the small hexagonal and orthorhombic polymorphs have similar structure as well as unit cell spacings.

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