crystallography workshop, ismailia, egypt, 2-7 february 2002 - giuseppe dalba - university of trento...

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


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


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


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


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


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


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


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


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


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

?


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.


The greatest concentration of laboratories in matter Physics in Europe

ESRF - Grenoble

ESRF

ILL

CNRS

EMBL


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


The Grenoble machine

Beamlines

300 m

The European Synchrotron Radiation Facility (ESRF)


ESRF beamlines

Each beamline hosts one or more specialized experimental stations

ESRF


DetectorSampleX-rays

Small angle scattering

angle

I

X-rays

Detector

Sample

I

angle

Diffraction

Inelastic scattering

Detector

X-rays

Energy shift


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


Laue Diffraction

Synchrotron light: ESRF

High flux beam

Low flux beam


Laue pattern of a crystal of metabolic enzyme isocitrate deydrogenase

NSLS Brookhaven

Time resolved crystallography: Exposure time: 10 ms


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


Film of molecular process

The myoglobine molecule

a CO molecule nteracting with a myoglobine molecule

iron site


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


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


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


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.


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


Coronary Angiography


The brilliance versus time


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


Sicily

Milan

Cagliari

Venice

Florence

Naples

Italy

Sardinia

Trento

Palermo

Rome


Emission from an x-ray tube


Charged particles in accelerated motion radiate

Storage ring


Bunch of relativistic electrons

Light

Bending magnet

N

S

Storage ring


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


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


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?


An X-ray beam at the ESRF facility

Are X-rays visible? Properties


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


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

?


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


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


Bending magnet

Wiggler

Undulator

E (h)Photon energy

Phot

on f

lux

Spectral radiation distribution

Properties


Brilliance

Comparison of brilliances between synchrotron and conventional x-ray sources

Properties


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


Electron bunches, their trajectory and synchrotron radiation in three different magnetic devices: bending magnets, wigglers, undulators

Insertion devices

Storage ring

Bending magnets

Wigglers

Undulators


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


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


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


N S N S N S

N S N S NSe-

t


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:


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


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


Properties


Linear polarization


Time structure

t

I

1s

100ps

e- e-e-e-

Time pulsed emission is interesting for studying rapid reactions

Properties

Light pulses


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.


Principle of operation of a bending bending magnet

Synchrotron light Springer Verlag


Principle of operation of a bending magnet

Synchrotron light, ESRF

crystallography workshop, ismailia, egypt, 2-7 february 2002 - giuseppe dalba - university of trento...

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