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

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**PowerPoint File available:**http://bl831.als.lbl.gov/ ~jamesh/powerpoint/ BNL_2011.ppt**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.**The optimum wavelength for macromolecular crystallography**Higher? or Lower?**~1 cm at 1 MeV**dose Johns, H. & Cunningham, J. (1974). The physics of radiology. Thomas Springfield, Illinois. Charged Particle Equilibrium (CPE) fNH**X-ray**e- Assume a spherical crystal… collimator crystal satisfies CPE violates CPE**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)**Secondary ionization**+ e- e-**e-**Excitation**Excitation**e-**e-**Excitation**non-ionizing interactions**ionizing interactions + e- Violating CPE: two kinds of “dose”? ICRU report 36 “Microdosimetry” (1984)**Charged Particle Equilibrium (CPE)**skin not burned Johns, H. & Cunningham, J. (1974). The physics of radiology. Thomas Springfield, Illinois.**X-ray**particle transport simulationusing MCNP collimator crystal**Transmitted (98%)**Where do photons go? Protein 1A x-rays beamstop**elastic scattering (6%)**Where do photons go? Protein 1A x-rays Transmitted (98%) beamstop**Inelastic scattering**e- +**Where do photons go?**Protein 1A x-rays elastic scattering (6%) Transmitted (98%) beamstop**Where do photons go?**Protein 1A x-rays elastic scattering (6%) Transmitted (98%) beamstop inelastic scattering (7%)**Where do photons go?**Protein 1A x-rays elastic scattering (6%) Transmitted (98%) beamstop inelastic scattering (7%) Re-emitted (99%) Absorbed (~0%)**Where do photons go?**Protein 1A x-rays elastic scattering (6%) Transmitted (98%) beamstop inelastic scattering (7%) Re-emitted (99%) Absorbed (~0%)**Where do photons go?**Protein 1A x-rays elastic scattering (6%) Transmitted (98%) beamstop inelastic scattering (7%) Photoelectric (87%) Re-emitted (99%) Absorbed (~0%)**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%)**Fluorescence**e- +**Auger emission**e- ++**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)**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.**X-ray**particle transport simulationusing MCNP collimator crystal**1 keV e- pathlength**dose reduction with 1 Å radiation fNH Dose capture fraction ←???→ Crystal diameter (µm)**100 μm crystal vs energy**fNH Dose capture fraction 1 keV 10 keV 100 keV 1 MeV Photon Energy**dose reduction vs energy**Dose capture fraction 1 keV 10 keV 100 keV 1 MeV Photon Energy**2 variables**Dose capture fraction**Critical escape diameter**Crystal diameter (µm) Photon Energy (eV)**Critical escape diameter**Crystal diameter (µm) Photon Energy (eV)**Critical escape diameter**Crystal diameter (µm) 1 keV 10 keV 100 keV 1 MeV 10 MeV Photon Energy**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.**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.**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.**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)**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)**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**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.

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