Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy Giuseppe Dalba Department of Physics, University of Trento - Italy Workshop on Computer Based Crystallographic Teaching Materials
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Giuseppe Dalba
Department of Physics, University of Trento - Italy
Workshop on
Computer Based Crystallographic Teaching Materials
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Outline
Which are their properties?
How is it produced?
Principles of synchrotron radiation and its main applications
What is it?
… which the main uses?
Synchrotron Radiation:
Synchrotron light, Springer-Verlag Compact Disk 2000.
Teaching material
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
The shorter the wavelength, the greater the resolution for observing small object
Electromagnetic Radiation and Structure of matter
Synchrotron ligh sources
Synchrotron radiation sources span wide regions of the electromagnetic spectrum
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Classical mechanism: acceleration of charged particle (for instance, electrons and positrons)
Bremsstrahlung: deceleration of high energy electrons in a metal
Synchrotron radiation emitted by relativistic charged particles in particle accelerators
Cosmic synchrotron radiation
Radiation production mechanismsThere are two ways to produce synchrotron radiation:
Quantum mechanism: transitions of electrons from outer to inner empty energy levels
Emission lines
Characteristic radiationKK
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
X-ray ray tubes
0.02 0.04 0.06 0.08 0.10Wavelength (nm)
Inte
nsit
y (
a. u
.)
K
K
min
Characteristicradiation
Bremsstrahlungradiation
The spectrum from an X-ray tube has discrete fluorescent lines superimposed on the continuous bremsstrahlung radiation
Anode
Vacuum tube
CathodeElectrons
HV
Filament supply
X-rays
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Radiazione X
Anode
Electron beam e-
The radiation of a tube is emitted in a solid angle of 2
Radiation angular distribution in an X-ray tube
IV
Z
I
IRX
However only a very small fraction of the emitted photons is utilized in a beam requiring an angular divergence of a few squared milli-radian
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Charged particles moving in circular motion radiate
Larmor FormulaP = Electromagnetic powerq = chargea = centripetal acceleration
S = Pointing vector
v << cThe radiation angular distribution of non-relativistic electrons hasthe shape of a tire orbiting at the same velocity of the electron bunch
v << cThe radiation angular distribution of non-relativistic electrons hasthe shape of a tire orbiting at the same velocity of the electron bunch
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Synchrotron light from a storage ring
Undulator
injector
R.F. cavity
1 m
Wiggler
Bending magnet, BM
BM
BM BM
BM
BM
BM
BM
Synchrotron light
Synchrotron light
Beamline
Three types of magnetic systems Animation
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Radiation angular distribution (a) electrons travelling at low speed(b) electrons travelling at relativistic speed (= (1-v2/c2)-1/2 10000 at ESRF)
Synchrotron radiation angular distribution
Electron orbit
Acceleration
v << c
v c
Electron orbit
Acceleratione-
e-
m0c2/E= 1/ radm0 = electron mass
v = electron velocityE = electron energyc = velocity of light
v
v
Top view
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Properties of synchrotron radiation
High collimation 1/ rad
PolarizationE
Temporal structuret
I
High fluxBrillance
I
Wide spectrum
Bending magnetsWigglers
Wigglers
Bending Magnets
Wigglers
Undulators
BM
ID
?
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
wavelength
flux
Spectral distributions of different sources
Intensity and spectral range of synchrotron radiation sources are several order of magnitude greater than those of rare gas discharge lamps.
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
The greatest concentration of laboratories in matter Physics in Europe
ESRF - Grenoble
ESRF
ILL
CNRS
EMBL
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Als-Nielsen Introduction to Modern X-ray Physics
Synchrotron storage ring
Spectrometer
Monochromator Undulator
300 m
Focusing device
10 m
2 m30 m
From the magnetic device to the experimental station
5 m
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
The Grenoble machine
Beamlines
300 m
The European Synchrotron Radiation Facility (ESRF)
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
ESRF beamlines
Each beamline hosts one or more specialized experimental stations
ESRF
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
DetectorSampleX-rays
Small angle scattering
angle
I
X-rays
Detector
Sample
I
angle
Diffraction
Inelastic scattering
Detector
X-rays
Energy shift
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
DetectorSampleX-rays
Absorption
X-rays
Sample
I
wavelength
Fluorescence
Imaging
Detector
X-rays
Elemental analysis
88000.0
8800 9000 9200 9400 9600 9800 10000
1.0
2.0
E (eV)
9000 9200 9400 9600 9800 10000
Energy
Detector
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Laue Diffraction
Synchrotron light: ESRF
High flux beam
Low flux beam
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Laue pattern of a crystal of metabolic enzyme isocitrate deydrogenase
NSLS Brookhaven
Time resolved crystallography: Exposure time: 10 ms
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Biology
The functions of the life molecules, like proteins and nucleic acids, depend on three-dimensional atomic structure. For instance the knowledge of viruses has allowed the preparation of anti-viruses compounds to be prepared
Diffraction is the technique to study the molecular structure of biological
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Film of molecular process
The myoglobine molecule
a CO molecule nteracting with a myoglobine molecule
iron site
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
The collection of precise information on the molecular structure of chromosomes
and their components can improve the knowledge of how the genetic code of DNA
is maintained and reproduced
Reconstruction of the molecular structure of nucleosome with a resolution of .2 nm
The life construction plan reported by the genetic code
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Study o materials under extreme conditions
In laboratory it is possible to reach pressures of some milions of atm (100 Gpa) comparable with those present in the Earth nucleus
High pressures and temperatures
Cella di diamante
Iron is the dominant element present in the nucleus of the Earth. The knowledge of ron properties at high temperature and pressure is fundamental for Earth science. At ESRF a new orthorombic phase of Fe has been discovered at 45 GPa and 2100 K
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Diffusionspots
Diffuse scattering in crystalline materials
Unexpected diffusion peaks appear in a diffraction pattern of a non perfect crystalline structures.
Diffractionspots
Synchrotron light - Springer Verlag
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
0 2 4 6 8 10 12 14 160
1
2 as-prepared
S(k)
[e.
u.]
k [Å-1]
0
1
2 500oC
0
12
3
800oC
0
1
2 950oC
0
1
2
3
1000oC
0
1
2
3
1100oC
0
3
6
1200oC
The structure factors for pure silica gel samples treated at different temperatures starting from the as-prepared to 1200oC.
Diffuse scattering in amorphous materials
WAXS measurements can be carried out in short time at various conditions of temperature and pressure.
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Microtomogram of illiac crest bone from a female patient undergoing haemodialysis. The three images are of biopsies taken at three ages, 24, 27 and 32 years. The severe loss of bone mass is apparent. The ratios of bone volume to total volume fell from 29.6% to 23.7% between the ages of 24 and 32
X-ray ray micro-tomography
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Coronary Angiography
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
The brilliance versus time
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Bibliography
Synchrotron light, Springer-Verlag Compact Disk 2000, ISBN 3540148884.
100 anni di Raggi X, 2001, P. Fornasini, Università dgli Studi di Trento Dipartimento di Fisica, Compact Disk, 2001
http://www.elettra.trieste.it (web site of Italian Synchrotron Light Source, named ELETTRA, Trieste Italy))
http://www. sesame.htm
http://www.esrf.fr (web site of European Synchrotron Radiation Facility, Grenoble, France)
http://www.lbl.gov/MicroWorlds/ALSTool/ (web site of theAdvanced Light Source)
Time Resolved Macromolecular Crystallography, Physics Today, 54 (2001) 33.Mr. Tompkins in paperback by G. Gamow
J Als-Nielsen, Des McMorrow Elements of modern X-ray Physics Wiley
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Sicily
Milan
Cagliari
Venice
Florence
Naples
Italy
Sardinia
Trento
Palermo
Rome
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Emission from an x-ray tube
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Charged particles in accelerated motion radiate
Storage ring
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Bunch of relativistic electrons
Light
Bending magnet
N
S
Storage ring
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Angular divergence
m0c2/E= 1/ rad
e-Electron orbit
v c
1/ rad
The beam collimation is defined as the photon opening angle 1/ rad. For GeV electrons can be smaller than 0.1 m rad. It means that at 100 m from the sourcethe vertical dimension of the beam, h, is 1 cm.
Horizontally the beam opens as a fan. A very thin sheet of light spreads out from the orbit on the orbital plane.
h
Properties
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Wiggler
e-
N S N N S K/
S N S N S N
N S N S N S
1/
Top view
Side view
Radiation from a wiggler: the horizontal opening is higher than the vertical one: K is around 20 for a wiggler Properties
Storage ring
S
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Undulator
NN S N S N S
S N S N S N S
N S N S N S
S N S N S N
N S N S N S
Top view
Side view
n
1
n
1
Radiation from an undulator: typically N = 50
Storage ring
Properties
Collimation, Why?
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
An X-ray beam at the ESRF facility
Are X-rays visible? Properties
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Flux of synchrotron light .
10-1 100 101 102 103 104 105E (eV)
Infrared Visible Ultraviolet Soft X-ray Hard X-rays
1012
1013
1014
1015
c
105 104
Ph
oton
flu
x (P
hoto
ns /
s ·m
rad
(0.
1% b
and
pass
))
Å) 102 101 100 10-1103
EC
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Spectral distribution of synchrotron light .
10-1 100 101 102 103 104 105E (eV)
Infrared Visible Ultraviolet Soft X-ray Hard X-rays
1012
1013
1014
1015
c
105 104
Pho
ton
flux
Å) 102 101 100 10-1103
EC
23
61865
EB
.
E
R.C
Spectra
?
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Spectral distribution curves from bending magnetsof some synchrotron light facilities
ESRF is the European facility located in Grenoble, ELETTRA, the Italian facility is located in Trieste.
Critical energy
Properties
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Definition of Brilliance
ban%.radm.mm
sec/Photons
A
NBrilliance
1022
The brilliance represents the largest number of photons per second in a given band pass that can be focused by a perfect optics onto the unit area at the sample
ImageN (Photons/sec)
SourceA (mm2)
e-
Focusing device
Mirror
Spectra
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Bending magnet
Wiggler
Undulator
E (h)Photon energy
Phot
on f
lux
Spectral radiation distribution
Properties
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Brilliance
Comparison of brilliances between synchrotron and conventional x-ray sources
Properties
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
The relativistic effect on the vertical opening of the light beam
Properties
...and from the laboratory reference frame
Unbelively shortned
u
v’Lab observer vx
The world as seen from the movingreference frame...
u
vMoving observer
v
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Electron bunches, their trajectory and synchrotron radiation in three different magnetic devices: bending magnets, wigglers, undulators
Insertion devices
Storage ring
Bending magnets
Wigglers
Undulators
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
R
t t+t
t
Fourier relationshipt
Why a so wide emission spectrum?
19sec
A cosinusoidal wave train modulated by a Gaussian envelope along with its gaussian transform
E(t)
t
t
tsec
?Low
wavelengths
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
An undulator as seen in the laboratory reference system
0 = L/nMagnetic pole periodicity
L
’0
= L/n0 /
The undulator as seen from the electron
n = number of periods
Spectrum
= L/2n
Further reduction of the light periodicity due to the Doppler effect
Doppler shift
Relativistic contraction
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
E = 1.5 GeV I = 100 mA1013
1012
1011
10 102 103 104 105
Wiggler 1.85 T
Bending magnet
Wiggler 6 T
Photon energy (eV)
Phot
on F
lux
TB
GeVER
N
Se-
S
N
N
S
S
N
N
S
S
N
By decreasing the curvature radius of the electron trajectory the spectrum shifts to higher photon energies
Ec=k/R
ID comparison
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
N S N S N S
N S N S NSe-
t
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Side view
Top view
mrad
Synchrotron light is spread on the orbital plane as a very thin sheet
Angular distribution
Electron orbital plane
Giuseppe Dalba:Giuseppe Dalba:
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Ee (GeV) = 1.5 2.5 4109
101
1010
108
1011
102 103 104 105
Photon Energy (eV)
Phot
on F
lux
Dependence of the critical photon energy on the electron energy
R
hcEC
3
4
3
EC
EC
EC
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
The on-axis synchrotron light is polarized in the orbital plane
The synchrotron light out of the orbital plane has circular components with opposite helicities above and below the horizontal plane.
Polarization is exploited for studying magnetic interactions. The difference in absorption in left and right hand circularly polarised light by a solid can be directly related to the ferromagnetic magnetization density (circular dichroism).
Polarization
Orbital plane
Circularar polarization
Synchrotron light - Springer Verlag
Properties
Synchrotron light - Springer Verlag
Linear polarization
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Time structure
t
I
1s
100ps
e- e-e-e-
Time pulsed emission is interesting for studying rapid reactions
Properties
Light pulses
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Synchrotron-light for Experimental Science and Applications in the Middle East
Eleven countries have so far joined the project. These are: Armenia, Cyprus, Egypt, Greece, Iran, Israel, Jordan, Morocco, Oman, Palestinian Authority, and Turkey.
The SESAME Project aims to establish the Middle East's first major international research center as a cooperative venture by the scientists of the region
The project is being developed under the umbrella of UNESCO and will be located in Allaan, Jordan (30 km from Amman and 30 km from the King Hussein/Allenby Bridge crossing of the Jordan River.
SESAME will have as its centerpiece a
synchrotron radiation source based on a
gift from Germany of the 0.8 GeV BESSY I
storage ring and injector system which
stopped operation at the end of November
1999.
Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy
Principle of operation of a bending bending magnet
Synchrotron light Springer Verlag