Development and application of a parallel two-dimensional particle-in-cell code based on an existing three-dimensional parallel PIC code

2003 ◽  
Author(s):  
J.J. Watrous ◽  
G.E. Sasser ◽  
J.W. Luginsland ◽  
S.C. Collela
Keyword(s):  
Three Dimensional ◽  
Two Dimensional ◽  
Particle In Cell ◽  
Pic Code

scholarly journals Electric Propulsion Plume Simulations Using Parallel Computer

2007 ◽  
Vol 15 (2) ◽  
pp. 83-94 ◽  
Author(s):  
Joseph Wang ◽  
Yong Cao ◽  
Raed Kafafy ◽  
Viktor Decyk
Keyword(s):  
Electric Propulsion ◽  
Large Scale ◽  
Three Dimensional ◽  
Particle Simulation ◽  
Parallel Computer ◽  
Solar Array ◽  
Electron Mass ◽  
Ion Thruster ◽  
Particle In Cell ◽  
Pic Code

A parallel, three-dimensional electrostatic PIC code is developed for large-scale electric propulsion simulations using parallel supercomputers. This code uses a newly developed immersed-finite-element particle-in-cell (IFE-PIC) algorithm designed to handle complex boundary conditions accurately while maintaining the computational speed of the standard PIC code. Domain decomposition is used in both field solve and particle push to divide the computation among processors. Two simulations studies are presented to demonstrate the capability of the code. The first is a full particle simulation of near-thruster plume using real ion to electron mass ratio. The second is a high-resolution simulation of multiple ion thruster plume interactions for a realistic spacecraft using a domain enclosing the entire solar array panel. Performance benchmarks show that the IFE-PIC achieves a high parallel efficiency of ≥ 90%

Three-dimensional electromagnetic relativistic particle-in-cell code VLPL (Virtual Laser Plasma Lab)

1999 ◽  
Vol 61 (3) ◽  
pp. 425-433 ◽  
Author(s):  
A. PUKHOV
Keyword(s):  
Laser Plasma ◽  
Inertial Confinement Fusion ◽  
Three Dimensional ◽  
Inertial Confinement ◽  
Particle In Cell ◽  
Laser Plasma Interactions ◽  
Electromagnetic Simulations ◽  
Self Focusing ◽  
Confinement Fusion ◽  
Pic Code

The three-dimensional particle-in-cell (PIC) code VLPL (Virtual Laser Plasma Lab) allows, for the first time, direct fully electromagnetic simulations of relativistic laser–plasma interactions. Physical results on relativistic self-focusing in under-dense plasma are presented. It is shown that background plasma electrons are accelerated to multi-MeV energies and 104 T magnetic fields are generated in the process of self-focusing at high laser intensities. This physics is crucial for the fast ignitor concept in inertial confinement fusion. Advances in the numerical PIC algorithm used in the code VLPL are reviewed here.

scholarly journals Algorithms of motion in the particle-in-cell method

2021 ◽  
pp. 281-293
Author(s):  
Е.С. Воропаева ◽  
К.В. Вшивков ◽  
Л.В. Вшивкова ◽  
Г.И. Дудникова ◽  
А.А. Ефимова
Keyword(s):  
Differential Equation ◽  
Exact Solution ◽  
Charged Particle ◽  
Equations Of Motion ◽  
Three Dimensional ◽  
Charged Particles ◽  
Two Dimensional ◽  
Time Step ◽  
Particle In Cell ◽  
Particles In Electromagnetic Fields

В настоящей работе представлен новый метод решения уравнений движения заряженных частиц в электромагнитных полях и проведено его сравнение с различными известными модификациями метода Бориса. Созданные двумерный и трехмерный алгоритмы основаны на использовании точного решения дифференциального уравнения для скорости заряженной частицы на шаге по времени. Сравнительный анализ метода Бориса и его модификаций проводился как по точности методов, так и по времени их работы. Новая модификация метода Бориса позволяет точнее вычислять траекторию и скорость заряженной частицы без значительного увеличения сложности расчетов. Показано, что при выборе модификации метода Бориса для решения задачи в первую очередь следует обращать внимание на точность решения, так как более простая и быстрая схема может не дать выигрыша по времени. The article proposes a new method for solving the equations of motion of charged particles in electromagnetic fields and compares this method with various known modifications of the Boris method. The created two-dimensional and three-dimensional algorithms are based on the use of an exact solution of the differential equation for the velocity of a charged particle at a time step. A comparative analysis of the Boris method and its modifications was carried out both in terms of the accuracy of the methods and the time of their operation. A new modification of the Boris method allows more accurate calculations of the trajectory and velocity of a charged particle without a significant increase in the complexity of calculations. It is shown that, when choosing a modification of the Boris method to solve a problem, one should pay attention first of all to the accuracy of the solution, since a simpler and faster scheme may not give a gain in time.

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.

Two-Dimensional Crystallization of Tetanus Toxin

1985 ◽  
Vol 43 ◽  
pp. 528-529
Author(s):  
Jeffry A. Reidler ◽  
John P. Robinson
Keyword(s):  
Electron Microscopy ◽  
Tetanus Toxin ◽  
Structural Information ◽  
Three Dimensional ◽  
Two Dimensional ◽  
Membrane Interface ◽  
3D Reconstructions ◽  
Cellular Receptors ◽  
Computer Reconstruction ◽  
2D Crystals

We have prepared two-dimensional (2D) crystals of tetanus toxin using procedures developed by Uzgiris and Kornberg for the directed production of 2D crystals of monoclonal antibodies at an antigen-phospholipid monolayer interface. The tetanus toxin crystals were formed using a small mole fraction of the natural receptor, GT1, incorporated into phosphatidyl choline monolayers. The crystals formed at low concentration overnight. Two dimensional crystals of this type are particularly useful for structure determination using electron microscopy and computer image refinement. Three dimensional (3D) structural information can be derived from these crystals by computer reconstruction of photographs of toxin crystals taken at different tilt angles. Such 3D reconstructions may help elucidate the mechanism of entry of the enzymatic subunit of toxins into cells, particularly since these crystals form directly on a membrane interface at similar concentrations of ganglioside GT1 to the natural cellular receptors.

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