scholarly journals Simulated Annealing of Two Electron Density Solution Systems

10.5772/5574 ◽  
2008 ◽  
Author(s):  
Mario de Oliveira Neto ◽  
Ronaldo Luiz ◽  
Fabio Lima ◽  
Osvaldo N. Oliveira Jr ◽  
Igor Polikarpov ◽  
...  
Keyword(s):  
Simulated Annealing ◽  
Electron Density

Reconstruction of the vertical electron density profile based on vertical TEC using the simulated annealing algorithm

2016 ◽  
Vol 57 (10) ◽  
pp. 2167-2176 ◽  
Author(s):  
Chunhua Jiang ◽  
Guobin Yang ◽  
Peng Zhu ◽  
Michi Nishioka ◽  
Tatsuhiro Yokoyama ◽  
...  
Keyword(s):  
Simulated Annealing ◽  
Electron Density ◽  
Density Profile ◽  
Simulated Annealing Algorithm ◽  
Electron Density Profile ◽  
Annealing Algorithm

Solution of organic crystal structures from powder diffraction by combining simulated annealing and direct methods

2003 ◽  
Vol 36 (2) ◽  
pp. 230-238 ◽  
Author(s):  
Angela Altomare ◽  
Rocco Caliandro ◽  
Carmelo Giacovazzo ◽  
Anna Grazia Giuseppina Moliterni ◽  
Rosanna Rizzi
Keyword(s):  
Monte Carlo ◽  
Simulated Annealing ◽  
Electron Density ◽  
Powder Diffraction ◽  
Direct Methods ◽  
Molecular Geometry ◽  
Molecular Structures ◽  
Chemical Information ◽  
Density Map ◽  
Electron Density Map

Theab initiocrystal structure solution from powder diffraction data can be attemptedviadirect methods. If heavy atoms are present, they are usually correctly located; then some crystal chemical information can be exploited to complete the partial structure model. Organic structures are more resistant to direct methods; as an alternative, their molecular geometry is used as prior information for Monte Carlo methods. In this paper, a new procedure is described which combines the information contained in the electron density map provided by direct methods with a Monte Carlo method which uses simulated annealing as a minimization algorithm. A figure of merit has been designed based on the agreement between the experimental and calculated profiles, and on the positions of the peaks in the electron density map. The procedure is completely automatic and has been included inEXPO; its performance has been validated and tested for a set of known molecular structures.

scholarly journals A new inversion algorithm for backscatter ionogram and its experimental validation

2014 ◽  
Vol 32 (4) ◽  
pp. 465-472 ◽  
Author(s):  
J. J. Zhao ◽  
C. Zhou ◽  
G. B. Yang ◽  
C. H. Jiang ◽  
S. S. Chang ◽  
...  
Keyword(s):  
Simulated Annealing ◽  
Time Delay ◽  
Electron Density ◽  
High Frequency ◽  
Experimental Validation ◽  
Leading Edge ◽  
Inversion Algorithm ◽  
Sweep Frequency ◽  
Ionospheric Electron Density ◽  
Annealing Method

Abstract. Oblique backscatter sounding is a powerful tool for detecting and monitoring the ionosphere continuously at a remote distance. High-frequency (HF) backscatter ionograms provide the amplitudes of backscatter signals with respect to group path or time delay against operating frequency. Application of inversion algorithm to a backscatter ionogram can extract useful information regarding the ionospheric electron density along the propagation paths. The present study proposes a new inversion algorithm on basis of simulated annealing method to acquire the leading edge of sweep-frequency ionogram, which is subsequently validated by ionospheric vertical sounding data. Quantitative comparisons between the vertical sounding measurements and the inversion results obtained from oblique backscatter sounding indicate that the new algorithm enables us to overcome the instability issue that traditional inversion algorithm faces and output reliable information of ionospheric inversion with satisfactory efficiency, thus providing a robust alternative for ionospheric detection based on oblique backscatter ionograms especially when the ionosphere is calm with slow changes.

Charge flipping and VLD (vive la difference)

2013 ◽  
Author(s):  
Carmelo Giacovazzo
Keyword(s):  
Simulated Annealing ◽  
Electron Density ◽  
Simulated Annealing Algorithm ◽  
Fourier Transforms ◽  
Direct Methods ◽  
Efficient Charge ◽  
Density Map ◽  
Annealing Algorithm ◽  
The Fourier Transform ◽  
Electron Density Map

Direct methods procedures (see Chapter 6) or Patterson techniques (see Chapter 10), primarily the former, have been methods of choice for crystal structure solution of small- to medium-sized molecules from diffraction data. Over the last 30 years, several new phasing algorithms have been proposed, not requiring the use of triplet and quartet invariants, but based only on the properties of Fourier transforms. These were not competitive with direct methods and have never became popular, but they contain a nucleus for further advances. Among these we mention: (i) Bhat (1990) proposed a Metropolis technique (Metropolis et al., 1953; Kirkpatrick et al., 1983; Press et al., 1992), also known as simulated annealing (the reader is referred to Section 12.9 for details on the algorithm). From a random set of phases, an electron density map is calculated, modified, and inverted. The corresponding phases are altered according to the simulated annealing algorithm, and then used to calculate a new electron density map. The procedure is cyclic. (ii) A strictly related simulated annealing procedure has been proposed by Su (1995). The objective function to minimize was . . . R = ∑h (S|Fh|calc − |Fh|obs)2, . . . where S is the scale factor. The scheme is as follows: random atomic positions are generated and in succession shifted; the simulated annealing algorithm is applied to accept or reject atomic shifts. At the end, a new atomic structure is generated, whose positions are shifted in succession, and so on in a cyclic way. (iii) The forced coalescence method (FCP) was proposed by Drendel et al. (1995). Hybrid electron density maps (see Section 7.3.4) were actively used with different values of τ and ω. Even if never popular, the above algorithms opened the way to two other methods which are much more efficient, charge flipping and VLD (vive la difference), to which this chapter is dedicated. Both are based on the properties of the Fourier transform; they do not require the explicit use of structure invariants and seminvariants, or a deep knowledge of their properties. The reader should not, however, conclude that the invariance and seminvariance concepts are not necessary in the handling of these approaches, on the contrary, understanding these basic concepts is essential to the appreciation of these new methods.

White-Light Coronal Structures: Streamers and CMEs

1994 ◽  
Vol 144 ◽  
pp. 82
Author(s):  
E. Hildner
Keyword(s):  
Emission Line ◽  
Electron Density ◽  
White Light ◽  
Coronal Mass Ejections ◽  
X Rays ◽  
Solar Cycles ◽  
Temperature Function ◽  
X Ray ◽  
Eclipse Observations ◽  
Coronal Structures

AbstractOver the last twenty years, orbiting coronagraphs have vastly increased the amount of observational material for the whitelight corona. Spanning almost two solar cycles, and augmented by ground-based K-coronameter, emission-line, and eclipse observations, these data allow us to assess,inter alia: the typical and atypical behavior of the corona; how the corona evolves on time scales from minutes to a decade; and (in some respects) the relation between photospheric, coronal, and interplanetary features. This talk will review recent results on these three topics. A remark or two will attempt to relate the whitelight corona between 1.5 and 6 R⊙to the corona seen at lower altitudes in soft X-rays (e.g., with Yohkoh). The whitelight emission depends only on integrated electron density independent of temperature, whereas the soft X-ray emission depends upon the integral of electron density squared times a temperature function. The properties of coronal mass ejections (CMEs) will be reviewed briefly and their relationships to other solar and interplanetary phenomena will be noted.

Glycogen in guinea pig neutrophils: Ultrastructural study of neutrophils at the intradermal site of BCG injection

1983 ◽  
Vol 41 ◽  
pp. 726-727
Author(s):  
Corazon D. Bucana
Keyword(s):  
Bone Marrow ◽  
Guinea Pig ◽  
Electron Density ◽  
Peritoneal Cavity ◽  
Ultrastructural Study ◽  
Guinea Pigs ◽  
Random Distribution ◽  
Glycogen Content ◽  
Polymorphonuclear Neutrophils ◽  
Ultrastructural Studies

In the circulating blood of man and guinea pigs, glycogen occurs primarily in polymorphonuclear neutrophils and platelets. The amount of glycogen in neutrophils increases with time after the cells leave the bone marrow, and the distribution of glycogen in neutrophils changes from an apparently random distribution to large clumps when these cells move out of the circulation to the site of inflammation in the peritoneal cavity. The objective of this study was to further investigate changes in glycogen content and distribution in neutrophils. I chose an intradermal site because it allows study of neutrophils at various stages of extravasation.Initially, osmium ferrocyanide and osmium ferricyanide were used to fix glycogen in the neutrophils for ultrastructural studies. My findings confirmed previous reports that showed that glycogen is well preserved by both these fixatives and that osmium ferricyanide protects glycogen from solubilization by uranyl acetate.I found that osmium ferrocyanide similarly protected glycogen. My studies showed, however, that the electron density of mitochondria and other cytoplasmic organelles was lower in samples fixed with osmium ferrocyanide than in samples fixed with osmium ferricyanide.

Application of ruthenium red/osmium tetroxide to bacteria, plant and animal tissue

1986 ◽  
Vol 44 ◽  
pp. 54-55
Author(s):  
R. L. Grayson ◽  
N. A. Rechcigl
Keyword(s):  
Electron Microscopy ◽  
Electron Density ◽  
Osmium Tetroxide ◽  
Biological Materials ◽  
Ruthenium Red ◽  
Animal Tissue

Ruthenium red (RR), an inorganic dye was found to be useful in electron microscopy where it can combine with osmium tetroxide (OsO4) to form a complex with attraction toward anionic substances. Although Martinez-Palomo et al. (1969) were one of the first investigators to use RR together with OsO4, our computor search has shown few applications of this combination in the intervening years. The purpose of this paper is to report the results of our investigations utilizing the RR/OsO4 combination to add electron density to various biological materials. The possible mechanisms by which this may come about has been well reviewed by previous investigators (1,3a,3b,4).

A study on α-RuCl3 crystal structure by scanning tunneling microscopy

1989 ◽  
Vol 47 ◽  
pp. 30-31
Author(s):  
H.-J. Cantow ◽  
H. Hillebrecht ◽  
S. Magonov ◽  
H. W. Rotter ◽  
G. Thiele
Keyword(s):  
Crystal Structure ◽  
Density Distribution ◽  
Scanning Tunneling Microscopy ◽  
Electron Density ◽  
Structure Determination ◽  
Electron Density Distribution ◽  
Scanning Tunneling ◽  
Monoclinic Space Group ◽  
Tunneling Microscopy ◽  
X Ray

From X-ray analysis, the conclusions are drawn from averaged molecular informations. Thus, limitations are caused when analyzing systems whose symmetry is reduced due to interatomic interactions. In contrast, scanning tunneling microscopy (STM) directly images atomic scale surface electron density distribution, with a resolution up to fractions of Angstrom units. The crucial point is the correlation between the electron density distribution and the localization of individual atoms, which is reasonable in many cases. Thus, the use of STM images for crystal structure determination may be permitted. We tried to apply RuCl3 - a layered material with semiconductive properties - for such STM studies. From the X-ray analysis it has been assumed that α-form of this compound crystallizes in the monoclinic space group C2/m (AICI3 type). The chlorine atoms form an almost undistorted cubic closed package while Ru occupies 2/3 of the octahedral holes in every second layer building up a plane hexagon net (graphite net). Idealizing the arrangement of the chlorines a hexagonal symmetry would be expected. X-ray structure determination of isotypic compounds e.g. IrBr3 leads only to averaged positions of the metal atoms as there exist extended stacking faults of the metal layers.

Improved immunolabelling of ultrathin cryosections using antibody conjugated with 1nm gold particles

1990 ◽  
Vol 48 (3) ◽  
pp. 928-929
Author(s):  
Morten H. Nielsen ◽  
Lone Bastholm
Keyword(s):  
Pituitary Gland ◽  
Liquid Nitrogen ◽  
Electron Density ◽  
Small Diameter ◽  
Cytochemical Staining ◽  
Gold Particles ◽  
Labelling Density ◽  
Ultrathin Cryosections ◽  
Mouse Pituitary ◽  
Electron Microscopical

During the last 5 years the diameter of the gold probes used for immuno-cytochemical staining at the electron microscopical (EM) level has been decreased. The advantage of small diameter gold probes is an overall increased labelling density. The disadvantage is a lower detectability due to the low electron density of smaller gold particles consequently an inconvenient high primary magnification needed for EM examination. Since 1 nm gold particles are barely visible by conventional EM examination the need for enlargement by silverenhancement of the gold particles has increased.In the present study of ultrathin cryosectioned material the results of immunostaining using 5 nm gold conjugated antibody and 1 nm gold conjugated antibodies are compared after silverenhancement of the 1 nm gold particles.Slices of freshly isolated mouse pituitary gland were immersion fixed for 20 min in 2 % glutaraldehyde /2 % paraformaldehyde. Blocks cryoprotected with 2.3 M sucrose were frozen in liquid nitrogen and ultra-cryosectioned on a RMC cryoultra-microtome.

Electron microscope study of the secretory activity of epithelial cells in embryonic thymus

1990 ◽  
Vol 48 (3) ◽  
pp. 382-383
Author(s):  
H. Alasam
Keyword(s):  
Cell Differentiation ◽  
T Cell ◽  
Epithelial Cells ◽  
Electron Density ◽  
Secretory Activity ◽  
T Cell Differentiation ◽  
High Electron ◽  
Transmission Electron ◽  
Medullary Epithelial Cells ◽  
Thymic Factor

The possibility that intrathymic T-cell differentiation involves stem cell-lymphoid interactions in embryos led us to study the ultrastructure of epithelial cell in normal embryonic thymus. Studies in adult thymus showed that it produces several peptides that induce T-cell differentiation. Several of them have been chemically characterized, such as thymosin α 1, thymopoietin, thymic humoral factor or the serum thymic factor. It was suggested that most of these factors are secreted by populations of A and B-epithelial cells.Embryonic materials were obtained from inbred matings of Swiss Albino mice. Thymuses were disected from embryos 17 days old and prepared for transmission electron microscopy. Our studies showed that embryonic thymus at this stage contains undifferentiated and differentiated epithelial cells, large lymphoblasts, medium and few small lymphocytes (Fig. 5). No differences were found between cortical and medullary epithelial cells, in contrast to the findings of Van Vliet et al,. Epithelial cells were mostly of the A-type with low electron density in both cytoplasm and nucleus. However few B-type with high electron density were also found (Fig. 7).

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