1. 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

2. 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

3. 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

4. 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 mechanisms There are two ways to produce synchrotron radiation: Quantum mechanism: transitions of electrons from outer to inner empty energy levels  Emission lines  Characteristic radiation KK KK

5. Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy X-ray ray tubes 0.020.040.060.080.10 Wavelength (nm) Intensity (a. u.) KK KK min Characteristic radiation Bremsstrahlung radiation The spectrum from an X-ray tube has discrete fluorescent lines superimposed on the continuous bremsstrahlung radiation Anode Vacuum tube Cathode Electrons HV Filament supply X-rays

6. 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 I V Z I I RX 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

7. Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy Charged particles moving in circular motion radiate Larmor Formula P = Electromagnetic power q = charge a = centripetal acceleration S = Pointing vector v << c The radiation angular distribution of non-relativistic electrons has the shape of a tire orbiting at the same velocity of the electron bunch v << c The radiation angular distribution of non-relativistic electrons has the shape of a tire orbiting at the same velocity of the electron bunch

8. 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 Synchrotron light Beamline Three types of magnetic systemsAnimation

9. 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-v 2 /c 2 ) -1/2  10000 at ESRF) Synchrotron radiation angular distribution Electron orbit Acceleration v << c v  c Electron orbit Acceleration e-e- e-e-   m 0 c 2 /E = 1/  rad m 0 = electron mass v = electron velocity E = electron energy c = velocity of light v v Top view

10. Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy Properties of synchrotron radiation High collimation   1/  rad Polarization E Temporal structure t I High flux Brillance I Wide spectrum Bending magnets Wigglers Bending Magnets Wigglers Undulators BM ID ?

11. 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.

12. 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

13. 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 m 30 m From the magnetic device to the experimental station 5 m

14. 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)

15. 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

16. Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy Detector Sample X-rays Small angle scattering angle I X-rays Detector Sample I angle Diffraction Inelastic scattering Detector X-rays Energy shift

17. Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy Detector Sample X-rays Absorption X-rays Sample I wavelength Fluorescence Imaging Detector X-rays Elemental analysis 8800 0.0 88009000920094009600980010000 1.0 2.0 E (eV) 9000920094009600980010000 Energy  Detector

18. 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

19. 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

20. 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

21. 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

22. 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

23. 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

24. Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy Diffusion spots Diffuse scattering in crystalline materials Unexpected diffusion peaks appear in a diffraction pattern of a non perfect crystalline structures. Diffraction spots Synchrotron light - Springer Verlag

25. Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy The structure factors for pure silica gel samples treated at different temperatures starting from the as-prepared to 1200 o C. Diffuse scattering in amorphous materials WAXS measurements can be carried out in short time at various conditions of temperature and pressure.

26. 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

27. Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy Coronary Angiography

28. Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy The brilliance versus time

29. 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

30. 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

31. Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy Emission from an x-ray tube

32. Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy Charged particles in accelerated motion radiate Storage ring

33. 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

34. Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy Angular divergence   m 0 c 2 /E = 1/  rad e-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 source the 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

35. Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy Wiggler e-e- N S NN S K/  S N S N S N NS 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

36. Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy Undulator NNSNSNS SNSNSNS N S N S N S S N S N S N NS N S N S Top view Side view Radiation from an undulator: typically N = 50 Storage ring Properties Collimation, Why?

37. 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

38. Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy Flux of synchrotron light. 10 -1 10 0 10 1 10 2 10 3 10 4 10 5 E (eV) InfraredVisibleUltravioletSoft X-rayHard X-rays 10 12 10 13 10 14 10 15 c 10 5 10 4 Photon flux (Photons / s ·m rad (0.1% band pass))  Å) 10 2 10 1 10 0 10 -1 10 3 ECEC

39. Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy Spectral distribution of synchrotron light. 10 -1 10 0 10 1 10 2 10 3 10 4 10 5 E (eV) InfraredVisibleUltravioletSoft X-rayHard X-rays 10 12 10 13 10 14 10 15 c 10 5 10 4 Photon flux  Å) 10 2 10 1 10 0 10 -1 10 3 ECEC Spectra ?

40. Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy Spectral distribution curves from bending magnets of some synchrotron light facilities ESRF is the European facility located in Grenoble, ELETTRA, the Italian facility is located in Trieste. Critical energy Properties

41. Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy Definition of Brilliance 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  Image N (Photons/sec) Source A (mm 2 ) e-e- Focusing device Mirror Spectra

42. Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy Bending magnet Wiggler Undulator E (h ) Photon energy Photon flux Spectral radiation distribution Properties

43. 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

44. 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 vxvx The world as seen from the moving reference frame... u v Moving observer v

45. 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 magnetsWigglers Undulators

46. Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy    R t t+  t tt  Fourier relationship  t  Why a so wide emission spectrum?  19  sec  A cosinusoidal wave train modulated by a Gaussian envelope along with its gaussian transform E(t) t    tt  t    sec  ? Low wavelengths

47. 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/n Magnetic pole periodicity L ’ 0 = L/n  0 /  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

48. Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy E = 1.5 GeV I = 100 mA 10 13 10 12 10 11 1010 2 10 3 10 4 10 5 Wiggler 1.85 T Bending magnet Wiggler 6 T Photon energy (eV) Photon Flux N S e-e- 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

49. Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy NS N SN S NS N SN S e-e- tt

50. 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:

51. Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy E e (GeV) = 1.5 2.5 4 10 9 10 1 10 10 8 10 11 10 2 10 3 10 4 10 5 Photon Energy (eV) Photon Flux Dependence of the critical photon energy on the electron energy ECEC ECEC ECEC

52. 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

53. Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy Time structure t I 1s1s 100  ps e-e- e-e- e-e- e-e- Time pulsed emission is interesting for studying rapid reactions Properties Light pulses

54. 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.

55. 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

56. Crystallography workshop, Ismailia, Egypt, 2-7 February 2002 - Giuseppe Dalba - University of Trento - Italy Principle of operation of a bending magnet Synchrotron light, ESRF