NANO106 is UCSD Department of NanoEngineering's core course on crystallography of materials taught by Prof Shyue Ping Ong. For more information, visit the course wiki at http://nano106.wikispaces.com.
Crystallography is the experimental science of determining the arrangement of atoms in crystalline solids. Crystallography is a fundamental subject in the fields of materials science and solid-state physics (condensed matter physics). The word crystallography is derived from the Ancient Greek word κρύσταλλος (krústallos; "clear ice, rock-crystal"), with its meaning extending to all solids with some degree of transparency, and γράφειν (gráphein; "to write"). In July 2012, the United Nations recognised the importance of the science of crystallography by proclaiming that 2014 would be the International Year of Crystallography.
NANO106 is UCSD Department of NanoEngineering's core course on crystallography of materials taught by Prof Shyue Ping Ong. For more information, visit the course wiki at http://nano106.wikispaces.com.
Crystallography is the experimental science of determining the arrangement of atoms in crystalline solids. Crystallography is a fundamental subject in the fields of materials science and solid-state physics (condensed matter physics). The word crystallography is derived from the Ancient Greek word κρύσταλλος (krústallos; "clear ice, rock-crystal"), with its meaning extending to all solids with some degree of transparency, and γράφειν (gráphein; "to write"). In July 2012, the United Nations recognised the importance of the science of crystallography by proclaiming that 2014 would be the International Year of Crystallography.
Space lattice, Unit cell, Bravais lattices (3-D), Miller indices, Lattice planes, Hexagonal closed packing (hcp) structure, Characteristics of an hcp cell, Imperfections in crystal: Point defects (Concentration of Frenkel and Schottky defects).
X – ray diffraction : Bragg’s law and Bragg’s spectrometer, Powder method, Rotating crystal method.
Crystallography and X-ray diffraction (XRD) Likhith KLIKHITHK1
Atoms in materials are arranged into crystal structures and microstructures.
Periodic arrangement of atoms depends strongly on external factors such as temperature, pressure, and cooling rate during solidification. Solid elements and their compounds are classified into amorphous, polycrystalline, and single crystalline materials. The amorphous solid materials are isotropic in nature because their atomic arrangements are not regular and possess the same properties in all directions. In contrast, the crystalline materials are anisotropic because their atoms are arranged in regular and repeated pattern, and their properties vary with direction. The polycrystalline materials are combinations of several crystals of varying shapes and sizes. The properties of polycrystalline materials are strongly dependent on distribution of crystals sizes, shapes, and orientations within the individual crystal. Diffraction pattern or intensities of X-ray diffraction techniques are used for characterizing and probing arrangement of atoms in each unit cell, position of atoms, and atomic spacing angles because of comparative wavelength of X-ray to atomic size.The X-ray diffraction, which is a non-destructive technique, has wide range of material analysis including minerals, metals, polymers, ceramics, plastics, semiconductors, and solar cells. The technique also has wide industry application including aerospace, power generation, microelectronics, and several others. The X-ray crystallography remained a complex field of study despite wide industrial applications.
FellowBuddy.com is an innovative platform that brings students together to share notes, exam papers, study guides, project reports and presentation for upcoming exams.
We connect Students who have an understanding of course material with Students who need help.
Benefits:-
# Students can catch up on notes they missed because of an absence.
# Underachievers can find peer developed notes that break down lecture and study material in a way that they can understand
# Students can earn better grades, save time and study effectively
Our Vision & Mission – Simplifying Students Life
Our Belief – “The great breakthrough in your life comes when you realize it, that you can learn anything you need to learn; to accomplish any goal that you have set for yourself. This means there are no limits on what you can be, have or do.”
Like Us - https://www.facebook.com/FellowBuddycom
The study of crystal geometry helps to understand the behaviour of solids and their
mechanical,
electrical,
magnetic
optical and
Metallurgical properties
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
This pdf is about the Schizophrenia.
For more details visit on YouTube; @SELF-EXPLANATORY;
https://www.youtube.com/channel/UCAiarMZDNhe1A3Rnpr_WkzA/videos
Thanks...!
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...University of Maribor
Slides from:
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Track: Artificial Intelligence
https://www.etran.rs/2024/en/home-english/
2. Crystal Structure
A crystal structure is defined as the particular repeating arrangement
of atoms (molecules or ions) throughout a crystal. Structure refers to
the internal arrangement of particles and not the external appearance
of the crystal.
Bravais lattice
The Bravais lattice is the basic building block from which all
crystals can be constructed. Each point would be surrounded by an
identical set of points as any other point, so that all points would be
indistinguishable from each other. Mathematician Auguste Bravais
discovered that there were 14 different collections of the groups of
points, which are known as Bravais lattices. These lattices fall into
seven different "crystal systems”, as differentiated by the
relationship between the angles between sides of the “unit cell” and
the distance between points in the unit cell.
3. Unit Cell
The unit cell is the smallest group of atoms, ions or molecules
that, when repeated at regular intervals in three dimensions,
will produce the lattice of a crystal system. The “lattice
parameter” is the length between two points on the corners of a
unit cell. Each of the various lattice parameters are designated
by the letters a, b, and c. If two sides are equal, such as in a
tetragonal lattice, then the lengths of the two lattice parameters
are designated a and c, with b omitted. The angles are
designated by the Greek letters α, β, and γ, such that an angle
with a specific Greek letter is not subtended by the axis with its
Roman equivalent. For example, α is the included angle
between the band c axis.
4. System Axial lengths and angles Unit cell geometry
cubic a = b = c, α = β = γ= 90°
tetragonal a = b ≠ c, α = β = γ= 90°
orthorhombic a ≠ b ≠ c, α = β = γ= 90°
rhombohedral a = b = c, α = β = γ ≠ 90°
hexagonal
a = b ≠ c, α = β = 90°, γ =
120°
monoclinic a ≠ b ≠ c, α = γ = 90°, β ≠ 90°
triclinic a ≠ b ≠ c, α ≠ β ≠ γ
TABLE 1: Geometrical characteristics of the seven crystal systems.
11. 1 atom/unit cell
(8 x 1/8 = 1)
2 atoms/unit cell
(8 x 1/8 + 1 = 2)
4 atoms/unit cell
(8 x 1/8 + 6 x 1/2 = 4)
12.
13. Atom positions, crystal directions and Miller indices
The structure of a crystal is defined with respect to a unit cell. As the entire crystal consists
of repeating unit cells, this definition is sufficient to represent the entire crystal. Within the
unit cell, the atomic arrangement is expressed using coordinates. For example, consider a
cubic cell of dimension 3.52 Å. Pretend that this cell contains an atom that has the
coordinates (1.5, 2.1, 2.4). That is, the atom is 1.5 Å away from the origin in the x direction
(which coincides with the a cell axis), 2.1 Å in the y (which coincides with the b cell axis) and
2.4 Å in the z (which coincides with the c cell axis). There will be an equivalent atom in the
next unit cell along the x-direction, which will have the coordinates (1.5 + 3.52, 2.1, 2.4) or
(5.02, 2.1, 2.4). This was a rather simple calculation, as the cell has very high symmetry and
so the cell axes, a, b and c, coincide with the Cartesian axes, X, Y and Z. Accordingly, atomic
coordinates are usually expressed in terms of fractional coordinates, (x, y, z). This
coordinate system is coincident with the cell axes (a, b, c) and relates to the position of the
atom in terms of the fraction along each axis. Consider the atom in the cubic cell discussion
above. The atom was 1.5 Å in the a direction away from the origin. As the a axis is 3.52 Å
long, the atom is (1.5/3.52) or 0.43 of the axis away from the origin. Similarly, it is (2.1/3.52) or
0.60 of the b axis and (2.4/3.5) or 0.68 of the c axis. The fractional coordinates of this atom
are, therefore, (0.43, 0.60, 0.68). The coordinates of the equivalent atom in the next cell over
in the a direction, however, are easily calculated as this atom is simply 1 unit cell away in a.
Thus, all one has to do is add 1 to the x coordinate: (1.43, 0.60, 0.68). Such transformations
can be performed regardless of the shape of the unit cell. Fractional coordinates, therefore,
are used to retain and manipulate crystal information.
14. Miller Indices (hkl)
Miller indices are a notation system in crystallography for planes
and directions in crystal (Bravais) lattices.
The orientation of a surface or a crystal plane may be defined by
considering how the plane (or indeed any parallel plane) intersects
the main crystallographic axes of the solid. The application of a set
of rules leads to the assignment of the Miller Indices , (hkl) ; A set
of numbers which quantify the intercepts and thus may be used to
uniquely identify the plane or surface.
The designation of the individual vectors within any given crystal
lattice is indicated by the notation [hkl], where h, k, and l are
reciprocals of the point at which the vector exits the unit cell. The
origination of all vectors is assumed defined as [000]. For example,
the direction along the a-axis according to this scheme would be
[100] because this has a component only in the a-direction and no
component along either the b or c axial direction.
15. Miller Indices are a symbolic vector representation for the orientation of an
atomic plane in a crystal lattice and are defined as the reciprocals of the
fractional intercepts which the plane makes with the crystallographic axes.
A vector diagonally along the face defined by the a and b axis would be
[110], while going from one corner of the unit cell to the opposite
corner would be in the [111] direction.
Figure 2 shows some examples of the various directions in the unit cell.
The crystal direction notation is made up of the lowest combination of
integers and represents unit distances rather than actual distances. A
[222] direction is identical to a [111], so [111] is used. Fractions are not
used. For example, a vector that intercepts the center of the top face of
the unit cell has the coordinates x = 1/2, y = 1/2, z = 1. All have to be
inversed to convert to the lowest combination of integers (whole
numbers); i.e., [221] in Figure 2. Finally, all parallel vectors have the
same crystal direction, e.g., the four vertical edges of the cell shown
in Figure 2 all have the crystal direction [hkl] = [001].
16.
17. Crystal directions may be grouped in families. To avoid confusion
there exists a convention in the choice of brackets surrounding the
three numbers to differentiate a crystal direction from a family of
direction. For a direction, square brackets [hkl] are used to
indicate an individual direction. Angle brackets <hkl> indicate a
family of directions. A family of directions includes any directions
that are equivalent in length and types of atoms encountered. For
example, in a cubic lattice, the [100], [010], and [001] directions
all belong to the <100> family of planes because they are
equivalent. If the cubic lattice were rotated 90°, the a, b,
and c directions would remain indistinguishable, and there would
be no way of telling on which crystallographic positions the atoms
are situated, so the family of directions is the same. In a hexagonal
crystal, however, this is not the case, so the [100] and [010] would
both be <100> directions, but the [001] direction would be
distinct. Finally, negative directions are identified with a bar over
the negative number instead of a minus sign.
19. Planes in a crystal can be specified using a notation called Miller
indices. The Miller index is indicated by the notation [hkl]
where h, k, and l are reciprocals of the plane with the x, y,
and z axes. To obtain the Miller indices of a given plane requires
the following steps:
Step 1. The plane in question is placed on a unit cell.
Step 2. Its intercepts with each of the crystal axes are then
found.
Step 3. The reciprocal of the intercepts are taken.
Step 4. These are multiplied by a scalar to insure that is in the
simple ratio of whole numbers.
For example, the face of a lattice that does not intersect the y or z
axis would be (100), while a plane along the body diagonal would
be the (111) plane. An illustration of this along with the (111) and
(110) planes is given in Figure 3.
Crystal Planes & Miller Indices
21. Description of Crystal Structure
1. The size and shape of the unit cell
2. Positions of the atoms (or ions) within the cell
However, this information is sometimes insufficient to allow for an
understanding of the true structure in three dimensions. Consideration
of several unit cells, the arrangement of the atoms with respect to each
other, the number of other atoms they in contact with, and the
distances to neighboring atoms, often will provide a better
understanding.
Close packed structures: hexagonal close packing and cubic close packing
In geometry, close-packing of spheres is a dense arrangement of equal spheres in
an infinite, regular arrangement (or lattice). The highest average density – that is,
the greatest fraction of space occupied by spheres – that can be achieved by a
regular lattice arrangement is 0.74048. The packing efficiency (volume of space
occupied by the spheres/total volume) is 74.05 % for both cubic and hexagonal
close packing schemes.
22. Within the square packed layer the coordination # of each atom is 4, in the
close packed layer it is 6.
Square Packed Layer Close packed array.
23. FCC and HCP lattices
There are two simple regular lattices that achieve this highest average
density. They are called face-centered cubic (fcc) (also called cubic close
packed) and hexagonal close-packed (hcp), based on their symmetry. Both
are based upon sheets of spheres arranged at the vertices of a triangular tiling;
they differ in how the sheets are stacked upon one another.
A single layer of spheres is closest-packed with HEXAGONAL coordination
of each sphere
24. A second layer of spheres is placed in the indentations left by the first layer
space is trapped between the layers that is not filled by the spheres
TWO different types of HOLES (so-called INTERSTITIAL sites) are left
OCTAHEDRAL (O) holes with 6 nearest sphere neighbours
TETRAHEDRAL (T±) holes with 4 nearest sphere neighbours
25. When a third layer of spheres is placed in the indentations of the second layer
there are TWO choices
The third layer lies in indentations directly in line (eclipsed) with the 1st layer.
Layer ordering may be described as ABA
The third layer lies in the alternative indentations leaving it staggered with
respect to both previous layers. Layer ordering may be described as ABC
26. Figure : Schematic representation of the three close packed layers in a cubic
close packed arrangement: A (dark grey), B (medium grey), and C (light grey).
27. If two close packed layers A and B are placed in contact with each
other so as to maximize the density, then the spheres of layer B will
rest in the hollow (vacancy) between three of the spheres in layer A.
This is demonstrated in Figure. Atoms in the second layer, B (shaded
light gray), may occupy one of two possible positions (Figure a or b)
but not both together or a mixture of each. If a third layer is placed on
top of layer B such that it exactly covers layer A, subsequent
placement of layers will result in the following sequence
...ABABAB.... This is known as hexagonal close packing or hcp.
28. Octahedral and tetrahedral vacancies
As was mentioned above, the packing fraction in both fcc and hcp cells is
74.05%, leaving 25.95% of the volume unfilled. The unfilled lattice sites
(interstices) between the atoms in a cell are called interstitial sites or
vacancies. The shape and relative size of these sites is important in
controlling the position of additional atoms. In both fcc and hcp cells most
of the space within these atoms lies within two different sites known as
octahedral sites and tetrahedral sites. The difference between the two lies in
their “coordination number”, or the number of atoms surrounding each site.
Tetrahedral sites (vacancies) are surrounded by four atoms arranged at the
corners of a tetrahedron. Similarly, octahedral sites are surrounded by six
atoms which make-up the apices of an octahedron. For a given close
packed lattice an octahedral vacancy will be larger than a tetrahedral
vacancy.
Within a face centered cubic lattice, the eight tetrahedral sites are positioned
within the cell, at the general fractional coordinate of (n/4,n/4,n/4) where n = 1 or 3,
e.g., (1/4,1/4,1/4), (1/4,1/4,3/4), etc. The octahedral sites are located at the center of
the unit cell (1/2,1/2,1/2), as well as at each of the edges of the cell, e.g., (1/2,0,0). In
the hexagonal close packed system, the tetrahedral sites are at (0,0,3/8) and
(1/3,2/3,7/8), and the octahedral sites are at (1/3,1/3,1/4) and all symmetry equivalent
positions.
29. Diamond Cubic Structure
The diamond cubic structure consists of two
interpenetrating face-centered cubic lattices,
with one offset 1/4 of a cube along the cube
diagonal. It may also be described as face
centered cubic lattice in which half of the
tetrahedral sites are filled while all the
octahedral sites remain vacant. The diamond
cubic unit cell is shown in Figure . Each of the
atoms (e.g., C) is four coordinate, and the
shortest interatomic distance (C-C) may be
determined from the unit cell parameter (a).
Figure : Unit cell structure of a
diamond cubic lattice showing the
two interpenetrating face-centered
cubic lattices.
30. Zinc blende
As with the diamond lattice, zinc blende
consists of the two
interpenetrating fcc lattices. However, in zinc
blende one lattice consists of one of the types
of atoms (Zn in ZnS), and the other lattice is
of the second type of atom (S in ZnS). It may
also be described as face centered cubic
lattice of S atoms in which half of the
tetrahedral sites are filled with Zn atoms. All
the atoms in a zinc blende structure are 4-
coordinate. The zinc blende unit cell is shown
in Figure. A number of inter-atomic distances
may be calculated for any material with a zinc
blende unit cell using the lattice parameter
(a).
Figure : Unit cell structure of a
zinc blende (ZnS) lattice. Zinc
atoms are shown in green
(small), sulfur atoms shown in
red (large), and the dashed lines
show the unit cell.
31. Rock salt
As its name implies the archetypal rock salt
structure is NaCl (table salt). In common with
the zinc blende structure, rock salt consists of
two interpenetrating face-centered cubic
lattices. However, the second lattice is offset
1/2aalong the unit cell axis. It may also be
described as face centered cubic lattice in
which all of the octahedral sites are filled,
while all the tetrahedral sites remain vacant,
and thus each of the atoms in the rock salt
structure are 6-coordinate. The rock salt unit
cell is shown in Figure. A number of inter-
atomic distances may be calculated for any
material with a rock salt structure using the
lattice parameter (a).
Figure : Unit cell structure of a
rock salt lattice. Sodium ions
are shown in purple (small
spheres) and chloride ions are
shown in red (large spheres).
32. Cesium Chloride
The cesium chloride structure is found
in materials with large cations and
relatively small anions. It has a simple
(primitive) cubic cell (Figure ) with a
chloride ion at the corners of the cube
and the cesium ion at the body center.
The coordination numbers of both
Cs+ and Cl-, with the inner atomic
distances determined from the cell
lattice constant (a).