Prority

  • Readings :
    • review on simulating protein ED
    • review on multislice small molecule
  • Simulation :
    • simulate rotating crystal
    • Background scattering from solvent
    • ion scattering potential
    • mosaicity, thermal vibration, defects on protein and compare with data from Gruene
    • Compare multislice with N-beam Bloch, nearBragg

paper

  • Plot :
  • fig1 : problem setup
  • fig4b : fonts
  • fig5a : fit+ax-A,ax-kV
  • fig5b : fonts
  • figa : add carbone points on sigma
  • fig6b : Born+MS
  • fig7ab : fonts + sum(err(cp)) instead of f2
  • fig7cd : bp and ff at selected
  • fig8a : error with 2,3,4,5 multiple at 2sets of params
  • fig8b : error bp for nscat=1..n ka=30,N=10,kp=1.001
  • fig9a : multiple scattering probabilities
  • fig9b : plot multiple scattering Fi

Secondary

Codes

  • Multislice :
    • compile QSTEM3, PyPrismatic, JMUTLIS
  • Bloch :
    • pyQt
  • nearBragg :
    • angle dependent scattering, multiple scattering
    • compare with Green functions integral within Born approximation

Readings ED

  • Spence Advanced TEM : chap 4
  • Kirkland Advanced Computing EM : chap3-4
  • Zou2011, Electron Crystallo : chap4-5,9-13+apx
  • multislice simus applications : Glaeser&Downing1993
  • web material Bfactor.

Explore

  • Experimental small molecule resolution

Methods :

  • Patterson method
  • Direct method

misc

  • Document theory of scattering : Rutherford, QM perturbative
  • Hartree-Fock
  • microscope program(actually the image)
  • Generalized transfer matrix method for special geometries
  • Read and summarize on spectroscopic techniques
  • review ClabbersAbrahams2018

other

  • multi_2D
    • Bloch
    • BPM/FD with periodic boundary conditions
    • Redo 2-beam Iq at the exact Bragg condition.
    • Redo rocking curves with proper label
    • redo zeta_g, labels h=1,2
  • Multislice :
    • biotin
      • run and compare 100+10, 101
      • TDS get wobble parameters
    • Development
      • Documentation with sphinx
      • embedded C
      • smv format
      • multithread fft, no openMP, no--enable-float
      • solvent scattering
      • defects vacancy, bending, TDS
    • lyzozyme
  • misc
  • 1 thread per simulation flag
    • Implement multithreads access to fftw
    • Force 1 thread on splines?
  • integration/spot broadening
  • flux taking Poisson distribution

  • Detector modelling projected intensity at larger angles

  • XDS + dials processing ireloh

  • rfactor transmission with thickness optimization
  • relative thickness dependent correction
  • yana
  • high absorption in X-ray
  • integration rocking curves
  • fft,clipper,bigFFT

  • solvent not in small molecules

  • relativistic mass nearBragg

  • nearBragg brute force figure,pure N**2 with backward scattering
  • phase shift
  • multislice transmission function cmp to multislice run