PowerPoint File available:

1. PowerPoint File available: http://bl831.als.lbl.gov/ ~jamesh/powerpoint/ BNL_2011.ppt

2. Acknowledgements Ken Frankel Rick Donahue Howard Padmore Alastair MacDowell 8.3.1 creator: Tom Alber 8.3.1 PRT head: Jamie Cate Center for Structure of Membrane Proteins (PSI) Membrane Protein Expression Center II Center for HIV Accessory and Regulatory Complexes W. M. Keck Foundation Plexxikon, Inc. M D Anderson CRC University of California Berkeley University of California San Francisco National Science Foundation University of California Campus-Laboratory Collaboration Grant Henry Wheeler The Advanced Light Source is supported by the Director, Office of Science, Office of Basic Energy Sciences, Materials Sciences Division, of the US Department of Energy under contract No. DE-AC02-05CH11231 at Lawrence Berkeley National Laboratory.

3. The optimum wavelength for macromolecular crystallography Higher? or Lower?

4. ~1 cm at 1 MeV dose Johns, H. & Cunningham, J. (1974). The physics of radiology. Thomas Springfield, Illinois. Charged Particle Equilibrium (CPE) fNH

5. X-ray e- Assume a spherical crystal… collimator crystal satisfies CPE violates CPE

6. is there a “problem” with violating CPE? for air: W ~ 30 eV/ion-pair yet, final ions are thermalized (<0.1 eV each) Where does 99% of the energy go? Answer: non-ionizing excitations ICRU report 31 “Average Energy Required to Produce an Ion Pair” (1979)

7. Secondary ionization e-

8. Secondary ionization + e- e-

9. e- Excitation

10. Excitation e-

11. e- Excitation

12. Excitation

13. non-ionizing interactions ionizing interactions + e- Violating CPE: two kinds of “dose”? ICRU report 36 “Microdosimetry” (1984)

14. Charged Particle Equilibrium (CPE) skin not burned Johns, H. & Cunningham, J. (1974). The physics of radiology. Thomas Springfield, Illinois.

15. Ionization track

16. X-ray particle transport simulationusing MCNP collimator crystal

17. Transmitted (98%) Where do photons go? Protein 1A x-rays beamstop

18. elastic scattering (6%) Where do photons go? Protein 1A x-rays Transmitted (98%) beamstop

19. Elastic scattering

20. Elastic scattering

21. Inelastic scattering e- +

22. Where do photons go? Protein 1A x-rays elastic scattering (6%) Transmitted (98%) beamstop

23. Where do photons go? Protein 1A x-rays elastic scattering (6%) Transmitted (98%) beamstop inelastic scattering (7%)

24. Where do photons go? Protein 1A x-rays elastic scattering (6%) Transmitted (98%) beamstop inelastic scattering (7%) Re-emitted (99%) Absorbed (~0%)

25. Photoelectric absorption

26. Photoelectric absorption e- +

27. Where do photons go? Protein 1A x-rays elastic scattering (6%) Transmitted (98%) beamstop inelastic scattering (7%) Re-emitted (99%) Absorbed (~0%)

28. Where do photons go? Protein 1A x-rays elastic scattering (6%) Transmitted (98%) beamstop inelastic scattering (7%) Photoelectric (87%) Re-emitted (99%) Absorbed (~0%)

29. Where do photons go? Protein 1A x-rays elastic scattering (6%) Transmitted (98%) beamstop inelastic scattering (7%) Photoelectric (87%) Re-emitted (99%) Absorbed (~0%) Re-emitted (~0%) Absorbed (99%)

30. Fluorescence +

31. Fluorescence e- +

32. Auger emission +

33. Auger emission e- ++

34. MCNP cuts off at 1 keV 1 MeV 100 GJ/mol Medical radiation therapy 100 keV 10 GJ/mol Medical imaging 10 keV 1 GJ/mol X-ray crystallography 1 keV 100 MJ/mol S and P K-edges 100 eV 10 MJ/mol “water window” 10 eV 1 MJ/mol C≡C bond 1 eV 100 kJ/mol C-C bond, visible light 100 meV 10 kJ/mol hydrogen bond 10 meV 1 kJ/mol heat (~300 K)

35. MCNP model bonding affects absorption Almkvist, et al. (2010)."K-edge XANES analysis of sulfur compounds: an investigation of the relative intensities using internal calibration", J. Sync. Rad.17, 683-688.

36. X-ray particle transport simulationusing MCNP collimator crystal

37. 1 keV e- pathlength dose reduction with 1 Å radiation fNH Dose capture fraction ←???→ Crystal diameter (µm)

38. 100 μm crystal vs energy fNH Dose capture fraction 1 keV 10 keV 100 keV 1 MeV Photon Energy

39. dose reduction vs energy Dose capture fraction 1 keV 10 keV 100 keV 1 MeV Photon Energy

40. 2 variables Dose capture fraction

41. Critical escape diameter Crystal diameter (µm) Photon Energy (eV)

42. Critical escape diameter Crystal diameter (µm) Photon Energy (eV)

43. Critical escape diameter Crystal diameter (µm) 1 keV 10 keV 100 keV 1 MeV 10 MeV Photon Energy

44. Vxtal λ3 L Vcell ωVcell Darwin’s Formula I(hkl) = Ibeam re2 P A | F(hkl) |2 I(hkl) - photons/spot (fully-recorded) Ibeam - incident (photons/s/m2 ) re - classical electron radius (2.818x10-15 m) Vxtal - volume of crystal (in m3) Vcell - volume of unit cell (in m3) λ - x-ray wavelength (in meters!) ω - rotation speed (radians/s) L - Lorentz factor (speed/speed) P - polarization factor (1+cos2(2θ) -Pfac∙cos(2Φ)sin2(2θ))/2 A - absorption factor exp(-μxtal∙lpath) F(hkl) - structure amplitude (electrons) Darwin, C. G. (1914)."The theory of X-ray reflexion. Part I", Philos. Mag.27, 315-333.

45. Vxtal λ3L Vcell ωVcell Darwin’s Formula I(hkl) = Ibeam re2 P A | F(hkl) |2 I(hkl) - photons/spot (fully-recorded) Ibeam - incident (photons/s/m2 ) re - classical electron radius (2.818x10-15 m) Vxtal - volume of crystal (in m3) Vcell - volume of unit cell (in m3) λ - x-ray wavelength (in meters!) ω - rotation speed (radians/s) L - Lorentz factor (speed/speed) P - polarization factor (1+cos2(2θ) -Pfac∙cos(2Φ)sin2(2θ))/2 A - absorption factor exp(-μxtal∙lpath) F(hkl) - structure amplitude (electrons) Darwin, C. G. (1914)."The theory of X-ray reflexion. Part I", Philos. Mag.27, 315-333.

46. Vxtal λ3 L Vcell ωVcell Darwin’s Formula I(hkl) = Ibeam re2 P A | F(hkl) |2 I(hkl) - photons/spot (fully-recorded) Ibeam - incident (photons/s/m2 ) re - classical electron radius (2.818x10-15 m) Vxtal - volume of crystal (in m3) Vcell - volume of unit cell (in m3) λ - x-ray wavelength (in meters!) ω - rotation speed (radians/s) L - Lorentz factor (speed/speed) P - polarization factor (1+cos2(2θ) -Pfac∙cos(2Φ)sin2(2θ))/2 A - absorption factor exp(-μxtal∙lpath) F(hkl) - structure amplitude (electrons) Darwin, C. G. (1914)."The theory of X-ray reflexion. Part I", Philos. Mag.27, 315-333.

47. λ2 2000 Dose Formula dose ≈ Ibeam ·texp dose - absorbed energy (Gy) Ibeam - incident (photons/s/μm2 ) texp - exposure time (s) λ - x-ray wavelength (in Å)

48. λ2 Dmax ≈ Ibeam ·tdataset 2000 Dose Formula Dmax - maximum dose (Gy) Ibeam - incident (photons/s/μm2 ) tdataset - accumulated exposure time (s) λ - x-ray wavelength (in Å)

49. 3qeEph 4R Dose Formula Dmax = Ibeam ·tdataset (1-Ten) Dmax - maximum dose (Gy) Ibeam - incident (photons/s/μm2 ) tdataset - accumulated exposure time (s) R - radius of crystal Ten - transmission of a sphere ~ exp(-μen·2R)  - density of crystal Eph - photon energy qe - electron charge

50. Vxtal λ3 L Vcell ωVcell Darwin’s Formula I(hkl) = Ibeam re2 P A | F(hkl) |2 I(hkl) - photons/spot (fully-recorded) Ibeam - incident (photons/s/m2 ) re - classical electron radius (2.818x10-15 m) Vxtal - volume of crystal (in m3) Vcell - volume of unit cell (in m3) λ - x-ray wavelength (in meters!) ω - rotation speed (radians/s) L - Lorentz factor (speed/speed) P - polarization factor (1+cos2(2θ) -Pfac∙cos(2Φ)sin2(2θ))/2 A - absorption factor exp(-μxtal∙lpath) F(hkl) - structure amplitude (electrons) Darwin, C. G. (1914)."The theory of X-ray reflexion. Part I", Philos. Mag.27, 315-333.