Fundamentals of X-Ray Interaction With Matter - Son (Cleaned)

Fundamentals of X-ray interaction
with matter
Sang-Kil Son
CFEL-DESY Theory Division
Center for Free-Electron Laser Science, DESY, Hamburg, Germany
———————————————————————————————
DESY Summer Student Lectures ‘Photon Science’
August 2 and 3, 2021
Center for Free-Electron Laser Science

CFEL is a scientific cooperation of the three organizations:
DESY – Max Planck Society – University of Hamburg

Outline
> First day (August 2, 2021)
§ Introduction
§ Theory of X-ray–matter interaction
§ X-ray absorption
§ X-ray atomic physics on computer: XATOM
> Second day (August 3, 2021)

§ X-ray fluorescence
§ Auger-Meitner decay
§ X-ray scattering
§ Computer simulations with XATOM
Sang-Kil Son | Fundamentals of X-ray interaction with matter | August 2 and 3, 2021 | 2 / 65

What is X-ray?
X-ray is…
> discovered by Wilhelm Röntgen in 1895
> photon energy: 100 eV ~ 100 keV
> wavelength: 0.01 nm to 10 nm
> penetrability
> element selectivity

X-ray absorption
+ e–
Radiography: see inside due to

X-ray absorption contrast
Hand with rings: Röntgen’s first medical X-ray in 1895

(Nobel prize in 1901)
X-ray fluorescence
Different chemical
compositions identified
by X-ray fluorescence
Chemical analysis of elements: First qualitative

X-ray chemical analysis by Henry Moseley, Phil.
Mag. 26, 1024 (1913).
X-ray scattering / diffraction
Elastic X-ray scatterings

from a crystal make a
diffraction pattern.
Zinc blend: First published diffraction

pattern of a crystal by Max von Laue in 1912
X-ray crystallography
Photosystem I: 3D Visualization of
diffraction patterns using serial
femtosecond crystallography (left) and
electron density map obtained from
these diffraction data (top)
Chapman et al., Nature 470, 73 (2011).

Image courtesy: Thomas White, CFEL

High X-ray intensity
Xe@4.5 keV
> Here we will discuss only one-photon absorption limit.

> Later you will see more interesting physics with intense x-ray pulses.

Main references
http://xdb.lbl.gov R. Santra, J. Phys. B 42, 023001 (2010).
How to treat interaction between
X-ray and matter?
 
Total Hamiltonian
Ĥ = Ĥmol + ĤEM + Ĥint
Atomic units used:
> X-rays interact with the electrons only

me = 1
> Non-relativistic quantum electrodynamics |e| = 1
> Principle of Minimal Coupling ~=1
> Time-dependent perturbation theory 1/4⇡✏0 = 1
(c = 1/↵, a0 = 1)

Hamiltonian for free electromagnetic field
Hamiltonian for the free electromagnetic field (harmonic oscillator)

X
ĤEM = !k â†k, âk, , !k = |k|/↵
k,
Field operator: annihilates or creates a photon in the mode (k,λ).

p
âk, |nk, i = nk, |nk, 1i
p
â†k, |nk, i = nk, + 1|nk, + 1i
Commutator relations for

photon mode operators
[âk, , âk0 , 0 ] = 0
[âk, , â†k0 , 0 ] = k,k0 , 0
[a, b] = ab ba
[â†k, , â†k0 , 0 ] = 0
Molecular Hamiltonian
Molecular Hamiltonian Ĥmol = T̂N + V̂NN + Ĥel
X r2 X Z a Z a0
a V̂NN =
T̂N =
2Ma |Ra Ra0 |
a a<a0
Electronic Hamiltonian using the second quantization
Z ( )
r 2 X Za
Ĥel = 3
d x ˆ† (x) ˆ(x)
2 a
|x Ra |
Z Z
1 1
+ 3
d x d x ˆ† (x) ˆ† (x0 )
3 0 ˆ(x0 ) ˆ(x)
2 |x x0 |
Anticommutator relations
for electron field operators { ˆ (x), ˆ 0 (x0 )} = 0,
{ ˆ (x), ˆ† 0 (x0 )} = , 0
(3)
(x x0 ),
{a, b} = ab + ba
{ ˆ† (x), ˆ† 0 (x0 )} = 0.
Interaction Hamiltonian
Interaction between electrons and photons

(minimal coupling, Coulomb gauge)
p•A and A2
Z  2 Z
r ↵
Ĥint = ↵ d3 x ˆ† (x) Â(x) · ˆ(x) + d3 x ˆ† (x)Â2 (x) ˆ(x)
i 2
r
Mode expansion of
X 2⇡ n ik·x † ⇤ ik·x
o
Â(x) = 2
â k, ✏ k, e + â k, k, e
✏
vector potential V !k ↵
k,
k · ✏k, = 0, ✏⇤k,1 · ✏k,2 = 0
p•A: one-photon absorption in first order; one-photon scattering in second order

A2: one-photon scattering in first order
 

Time-dependent perturbation theory
Full Hamiltonian and unperturbed part Ĥ = Ĥmol + ĤEM +Ĥint

| {z }
Ĥ0
Nel
Initial state: |Ii = | 0 i|NEM i
Interaction-picture state vector to second order in perturbation

Z t
0 iĤ0 t0 ✏|t0 | iĤ0 t0
| , tiint =|Ii i dt e Ĥint e e |Ii
1
Z t Z t0
0
✏|t0 | iĤ0 t0 00
✏|t00 | iĤ0 t00
dt0 eiĤ0 t Ĥint e e dt00 eiĤ0 t Ĥint e e |Ii + · · ·
1 1
Transition rate to second order in perturbation

2
X hF |Ĥint |M ihM |Ĥint |Ii
FI = 2⇡ (EF EI ) hF |Ĥint |Ii + + ···
EI EM i✏
M
X-ray absorption
X-ray absorption
Nel
Nel
Final state: |F i = | F i|NEM 1i
2
Absorption rate: FI = 2⇡ (EF EI ) hF |Ĥint |Ii
X-ray absorption cross section
X-ray 4⇡ 2 NEM ⇣ Nel ⌘

FI = EF E0Nel !in
absorption rate !in V
Z 2
3 ˆ† rˆ
⇥ h N F
el
| d x (x)e ikin ·x
✏kin , in
· (x)| Nel
0 i
i
1 NEM
X-ray photon flux JEM =
↵ V
X-ray absorption cross section = F I /JEM
4⇡ 2 ⇣ Nel Nel
⌘
F (kin , in ) = ↵ EF E0 !in
!in
Z 2
rˆ
⇥ h NF |
el
d3 x ˆ† (x)eikin ·x ✏kin , in
· (x)| Nel
0 i
i
how to treat many-electron systems?
Electronic many-body problem
Introducing a set of orthonormal spin orbitals {'p (x)}

which are eigenstates of an one-body Hamiltonian F̂ |'p i = "p |'p i
X
An electronic one-body Hamiltonian F̂ = "p ĉ†p ĉp
p
Creation and annihilation
operators for | φp⟩: c†p̂ and cp̂ Connecting with the field operators
X
{ĉp , ĉq } = 0, ˆ(x) = 'p (x)ĉp ,
p
ĉp , ĉ†q = p,q , X
ˆ† (x) = '†p (x)ĉ†p
ĉ†p , ĉ†q = 0.
p
Mean-field model
Independent-electron model Ĥel ⇡ F̂
Mean-field ground state in terms of a single Slater determinant

Nel
Y
| Nel
0 i ⇡| Nel
0 i ⌘ ĉ†i |vacuumi
i=1
Nel
X
Mean-field ground-state energy E0Nel ⇡ h Nel
0 |F̂ |
Nel
0 i = "i
i=1
Nel Nel
Hartree-Fock (HF) method: minimizing h 0 |Ĥel | 0 i
the best choice among the mean-field models

Koopmans’ theorem
Nel 1 Nel
One-hole state | i i ⌘ ĉi | 0 i
8 9
<XNel =
Energy of
one-hole state
EiNel 1
⇡h Nel 1
i |F̂ | Nel 1
i i = "j "i
: ;
j=1
Ionization potential Ii ⌘ EiNel 1

E0Nel ⇡ "i
Koopmans’ theorem: valid for HF orbitals For Neon,

Nel 1 Nel 1 Koopmans EXP
Ii =h i | Ĥ el | i i
"2p = 23.1 eV 21.6 eV
h N0
el
| Ĥ el | Nel
0 i= "i "2s = 52.5 eV 48.5 eV
"1s = 892 eV 870 eV
Note: Koopmans received a Nobel prize in Economics
in 1975, of course, not for this theorem.
X-ray absorption within mean-field model
Nel 1 Nel
Particle-hole state | a
ii ⌘ ĉ†a | i i = ĉ†a ĉi | 0 i
Nel
Initial state |Ii = | 0 i|NEM i
Nel
Final state |F i = ĉ†a ĉi | 0 i|NEM 1i
Cross section for particle-hole transition
2 2
4⇡ r
a
i (kin , in ) = ↵ ("a + Ii !in ) h'a |eikin ·x ✏kin , in
· |'i i
!in i
Energy of excited electron "a = !in Ii > 0 “Photoelectric effect”
Note: Einstein received a Nobel prize in 1921 for
the photoelectric effect, not for theory of relativity.
Subshell x-ray absorption X
a
cross section i (kin , in ) = i (kin , in )
a
K-shell photoionization: a simple model
> After employing the dipole approximation and atomic orbitals

li+1 2
∞
4 2 l>
∑ ∫
σP(i, ω) = απ ωNi unili(r)uεlj(r)rdr
3 2li + 1 0
lj=|li−1|
> Simple model of an atomic species of atomic number Z

§ 1s orbital ~ H-like 1s orbital of Z, u1s(r) ∼ Z 3/2re −Zr, I1s = Z 2 /2
§ photoelectron wave function ~ plane wave (assuming ωin ≫ I1s)
> At fixed photon energy ω, σP ∼ Z5

Compare σC (Z=6) and σCa (Z=20): (20/6)5 ~ 400 times
> At fixed Z, σP ∼ ωin−7/2

For a given atom, the x-ray absorption cross section above the 1s
threshold decreases with increasing photon energy.
 
 
 

 
Photoionization cross section calculation
102 10-2
10-3
101
C Ca
10-4
0 10-5
Cross section (Mb)
Cross section (Mb)

10
10-6
10-1 C 10-7
10-8
10-2
10-9
10-10
10-3
At 60 keV 10-11
10-4 10-12
1 10 100 1000 10000 0 10 20 30 40 50 60
Photon energy (eV) Z
> PCS changes by varying ω and Z; edge structures
Table of photoionization cross sections
or
running
XATOM
Applications of X-ray absorption
> X-ray photoelectron spectroscopy (XPS): measuring photoelectron
energy
§ PES: Photo-Electron Spectroscopy or Photo-Emission Spectroscopy
§ ESCA: Electron Spectroscopy for Chemical Analysis
> X-ray absorption spectroscopy (XAS): measuring absorption cross

section as a function of photon energy
§ XANES: X-ray Absorption Near-Edge Structure
NEXAFS: Near Edge X-Ray Absorption Fine Structure
§ EXAFS: Extended X-ray Absorption Fine Structure

XPS: X-ray Photoelectron Spectroscopy
PES: Photo-Emission
(or Photo-Electron)
Spectroscopy
fixed
measured
ESCA: Electron Spectroscopy for Chemical Analysis
fixed
measured
ESCA molecule:
first molecule used for
ESCA by Kai Siegbahn
 
XAS: X-ray Absorption Spectroscopy
varied
solid target:
transmission
gas phase or very

dilute target:
fluorescence
NE: depends on local coordination E: depends on nearest-neighbor

environment and oxidation state geometry

EXAFS: Extended X-ray Absorption Fine Structure
EXAFS reflects nearest-neighbor geometry and

it is highly sensitive to changes in bond lengths.
XANES: X-ray Absorption Near-Edge Structure
Also called NEXAFS: Near-Edge

X-ray Absorption Fine Structure
different
coordination
environments
different
oxidation
states
Summary
> X-rays can probe atomic structure and electronic structure of matter.
> X-rays interact with the electrons only.
> Hamiltonians for EM, molecule, and interaction between them
Ĥ = Ĥmol + ĤEM + Ĥint

> The mean-field theory for electronic many-body problem
> Transition rate calculated within the time-dependent perturbation theory
2
FI = 2⇡ (EF EI ) hF |Ĥint |Ii
> The theoretical framework applied for calculating a photoabsorption
cross section
> X-ray absorption applications: XPS, ESCA, XAS, XANES, EXAFS, …
 
 

 
X-ray atomic physics on computer:
XATOM
XATOM: all about x-ray atomic physics
> Computer program suite to

describe dynamical behaviors
of atoms interacting with
XFEL pulses SO
P
> Uses the Hartree-Fock-Slater

S RS P
model
> Calculates all cross sections A
F
and rates of x-ray-induced
processes for any given
element
Son, Young & Santra,
Phys. Rev. A 83, 033402 (2011).
Jurek, Son, Ziaja & Santra,

J. Appl. Cryst. 49, 1048–1056 (2016). https://www.desy.de/~xraypac/

Dynamical behavior of atom in XFEL pulses
1.0
Fe0+
Fe5+
0.8
Fe10+
Fe15+
Population
0.6
Fe20+
0.4
0.2 Fe at 8 keV
5×1012 ph/µm2
10 fs (FWHM)
0.0
-20 -10 0 10 20
Time (fs)
Son, Chapman & Santra, Phys. Rev. Lett. 107, 218102 (2011).

Photoionization cross section calculation

101
L-edge
Ne
100
K-edge
Cross section (Mb)
10-1
10-2
0 500 1000 1500 2000 2500 3000
Photon energy (eV)
calculated using XATOM
Outline
> First day (August 2, 2021)
§ Introduction
§ Theory of X-ray–matter interaction
§ X-ray absorption
§ X-ray atomic physics on computer: XATOM
> Second day (August 3, 2021)

§ X-ray fluorescence
§ Auger-Meitner decay
§ X-ray scattering
§ Computer simulations with XATOM

Relaxation processes
Decay of inner-shell-excited systems
+319 eV
C0+ C1+✱ C2+ C1+✱
(1s–1: SCH)
P A
C1+
+40 eV
+13 eV
+0 eV C2+
C0+ C1+
 
X-ray fluorescence within mean-field model
Nel
Initial state: |Ii = ĉi | 0 i|0i
Nel †
Final state: |F i = ĉi0 | 0 iâkF , F
|0i
2
Fluorescence rate: FI = 2⇡ (EF EI ) hF |Ĥint |Ii
X-ray fluorescence rate and energy
Partial X-ray fluorescence rate

2
FI = 2⇡ (EF EI ) hF |Ĥint |Ii
2
4⇡ 2 ikF ·x ⇤ r
= (Ii0 + !F Ii ) h'i |e ✏kF , · |'i0 i
V !F F
i
X X Z Z 1
V
i,i0 = FI = d⌦F dkF kF2 FI
(2⇡)3 0
kF , F F
X-ray fluorescence energy !F = I i Ii0
X-ray fluorescence transition lines
Characteristic transition energies

➔ fingerprint of elements
...

X-ray fluorescence transition lines (cont.)
XRF: X-Ray Fluorescence
25.3 keV Transition lines
Sn Kα1 : K1 – L3, 1s – 2p3/2
Kα2 : K1 – L2, 1s – 2p1/2
Kβ1 : K1 – M2, 1s – 3p1/2
Kβ2 : K1 – N2,3, 1s – 4p1/2,3/2
Kβ3 : K1 – M3, 1s – 3p3/2
29.1 keV
position: transition energy
intensity: transition rate

Kα fluorescence: a simple model

> Simple model of an atomic species of atomic number Z
§ 1s orbital ~ H-like 1s orbital of Z
§ 2p orbital ~ H-like 2p orbital of Z
> Kα photon energy: ωKα ∼ Z 2
> Kα fluorescence rate: ΓKα ∼ Z 4
Moseley’s law
ω∝Z
Phil. Mag. 27, 702 (1914).

Auger-Meitner within mean-field model

A renaming proposal to Auger-Meitner: Physics Today 72, 10 (2019).
Nel
Initial state: |Ii = ĉi | 0 i
Nel
Final state: |F i = ĉ†a ĉj ĉj 0 | 0 i, j, j 0 6= i
2
Auger rate: FI = 2⇡ (EF EI ) hF |Ĥint |Ii
Auger-Meitner rate and energy
1X XX
Perturbation theory Ĥ0 = F̂ , Ĥint = vpqrs ĉ†p ĉ†q ĉs ĉr {vpiqi vpiiq } ĉ†p ĉq
2 pqrs pq i
Coulomb matrix element
Partial Auger-Meitner rate
Auger-Meitner electron energy "a = I i Ij Ij 0
KLL Auger-Meitner decay: a simple model
> Simple model of an atomic species
of atomic number Z
§ 1s orbital ~ H-like 1s orbital of Z
§ 2p orbital ~ H-like 2p orbital of Z
§ Auger electron wave function ~
plane wave
> Focus on the channel with two 2p

holes in the final state
> KLL Auger electron E: εKLL ∼ Z 2
> KLL Auger decay rate: ΓKLL ∼ Z 0

AES: Auger-Meitner Electron Spectrum

2s2 2p4 (1D)
"a = I i Ij Ij 0
Auger-Meitner channels
1s – 2s 2s : 2s02p6 1S
2s1 2p5 2s1 2p5 2s2 2p4
2s0 2p6 (1S) (1P) (3P) (1S) 1s – 2s 2p : 2s12p5 1P
3P
1s – 2p 2p : 2s22p4 1S
3P
1D
position: AM energy
intensity: AM rate

X-ray scattering
Elastic X-ray scattering
Nel
Nel †
Final state: |F i = | 0 iâkF , F
|NEM 1i
2
Scattering rate: FI = 2⇡ (EF EI ) hF |Ĥint |Ii
Elastic X-ray scattering form factor
Transition rate
Scattering vector
(or momentum transfer)
Z
Scattering (or form) factor f 0 (Q) = d3 x ⇢(el) (x)eiQ·x
Electron density
 
Elastic x-ray scattering cross section
Differential cross section

X FI V XZ 1
FI
3
d = = ↵ d⌦ d!F !F2
JEM (2⇡)3 0 JEM
kF , F F
✓ ◆
d (Q) 2X 2 d 2
= ↵4 f 0 (Q) ✏⇤kF , · ✏kin , in
= f 0 (Q)
d⌦ F
d⌦ T
F
Total form factor

decomposed in terms of
atomic contributions
Atomic form factor
40
Kr (Z=36)
35
Ar (Z=18)
30 Ne (Z=10)
25
20
f0
15
10
0
0 5 10 15 20
-1
Q (a.u. )
Absorption vs. scattering
Carbon C@10 keV

σabsorption=41 barn
σel. scattering=3.2 barn
σinel. scattering=2.7 barn
el. sc 1
⇠
abs 13
XCOM, NIST: https://dx.doi.org/10.18434/T48G6X

Dispersive correction to elastic X-ray scattering
> Resonant elastic x-ray scattering:

When the photon energy approaches to the ionization potential, the
second order of p•A becomes important.
Elastic X-ray scattering tensor: second-order correction with p•A
 
Dispersive correction to elastic X-ray scattering
Elastic X-ray scattering in the forward direction
Scalar scattering factor
Total number of electrons
Relationship between imaginary

part of scattering factor and
absorption cross section
Kramers-Kronig relation

Dispersive correction (anomalous scattering)
X-ray scattering
elastic vs. inelastic without M vs. with M

| el
Ii =| el
Fi | el
Ii 6= | el
Fi
(A2) (p•A)
> Elastic X-ray scattering

§ Non-resonant elastic X-ray scattering via A2
§ Resonant elastic X-ray scattering via p•A (Dispersion correction)
> Inelastic X-ray scattering

§ Non-resonant inelastic X-ray scattering via A2 (Compton scattering)
§ Resonant inelastic X-ray scattering via p•A (RIXS or resonant X-ray Raman)

X-ray crystallography
Protein crystal X-ray diffraction pattern Molecular structure

2 of a protein
I ⇠ f 0 (Q)
IFT
0
f (Q) ⇢(el) (x)
FT
Summary
Photoionization /
photoabsorption
SO
P Double core hole
formation
Scattering S RS P
high X-ray intensity

A
F
Auger-Meitner decay
Fluorescence
> Theoretical aspects of X-ray-induced processes

> Many-electron system: mean-field approach
> σ and Γ calculated within the same framework (QED and TDPT)
⬇︎

References
> D. Attwood, Soft x-rays and extreme ultraviolet radiation (Cambridge University Press).
> J. Als-Nielsen and D. McMorrow, Elements of Modern X-Ray Physics (Wiley).
> S. Bare, EXAFS Data Collection and Analysis Workshop, July 14-17, 2003, National
Synchrotron Light Source, Brookhaven National Laboratory
http://cars9.uchicago.edu/xafs/NSLS_EDCA/July2003/.
> J. M. Hollas, Modern Spectroscopy (Wiley).
> F. Reinert and S. Huefner, Photoemission spectroscopy—from early days to recent
applications, New Journal of Physics 7, 97 (2005).
> R. Santra, Concepts in x-ray physics, Journal of Physics B 42, 023001 (2009).
> R. Santra et al., Strong-field control of x-ray processes, Advances in Atomic, Molecular,
and Optical Physics 56, 219 (2008).
> J. Stoehr, NEXAFS Spectroscopy (Springer).
> A. C. Thompson and D. Vaughan, X-ray data booklet, Center for X-Ray Optics and
Advanced Light Source, Lawrence Berkeley National Laboratory
http://xdb.lbl.gov/.
> Z. Jurek, S.-K. Son, et al., XMDYN and XATOM, J. Appl. Cryst. 49, 1048 (2016).

 
 

Computer simulations with XATOM
Let’s go with neon!
> Let’s calculate electronic structure of Ne
> Let’s calculate photoionization cross section of Ne at 2 keV
A0+ A1+ A2+

SCH DCH
P P
A
> Lifetime of single-core-hole? F
> Lifetime of double-core-hole?

> How would you prepare
a double-core-hole state?
 

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Fundamentals of X-ray interaction

Center for Free-Electron Laser Science

> Second day (August 3, 2021)

Radiography: see inside due to

Hand with rings: Röntgen’s first medical X-ray in 1895

Chemical analysis of elements: First qualitative

Elastic X-ray scatterings

Zinc blend: First published diffraction

Chapman et al., Nature 470, 73 (2011).

High X-ray intensity

> Here we will discuss only one-photon absorption limit.

Ĥ = Ĥmol + ĤEM + Ĥint

Atomic units used:

> X-rays interact with the electrons only

Hamiltonian for free electromagnetic field

Hamiltonian for the free electromagnetic field (harmonic oscillator)

Field operator: annihilates or creates a photon in the mode (k,λ).

Commutator relations for

Interaction between electrons and photons

k · ✏k, = 0, ✏⇤k,1 · ✏k,2 = 0

p•A: one-photon absorption in first order; one-photon scattering in second order

Time-dependent perturbation theory

Full Hamiltonian and unperturbed part Ĥ = Ĥmol + ĤEM +Ĥint

Interaction-picture state vector to second order in perturbation

Transition rate to second order in perturbation

X-ray 4⇡ 2 NEM ⇣ Nel ⌘

X-ray absorption cross section = F I /JEM

Introducing a set of orthonormal spin orbitals {'p (x)}

Independent-electron model Ĥel ⇡ F̂

Mean-field ground state in terms of a single Slater determinant

Ionization potential Ii ⌘ EiNel 1

Koopmans’ theorem: valid for HF orbitals For Neon,

> After employing the dipole approximation and atomic orbitals

> Simple model of an atomic species of atomic number Z

> At fixed photon energy ω, σP ∼ Z5

> At fixed Z, σP ∼ ωin−7/2

Cross section (Mb)

> PCS changes by varying ω and Z; edge structures

> X-ray absorption spectroscopy (XAS): measuring absorption cross

XPS: X-ray Photoelectron Spectroscopy

gas phase or very

NE: depends on local coordination E: depends on nearest-neighbor

EXAFS: Extended X-ray Absorption Fine Structure

EXAFS reflects nearest-neighbor geometry and

Also called NEXAFS: Near-Edge

Ĥ = Ĥmol + ĤEM + Ĥint

> Computer program suite to

> Uses the Hartree-Fock-Slater

Jurek, Son, Ziaja & Santra,

Dynamical behavior of atom in XFEL pulses

Photoionization cross section calculation

> Second day (August 3, 2021)

Partial X-ray fluorescence rate

X-ray fluorescence energy !F = I i Ii0

Characteristic transition energies

X-ray fluorescence transition lines (cont.)

Kα fluorescence: a simple model

> Kα photon energy: ωKα ∼ Z 2

> Kα fluorescence rate: ΓKα ∼ Z 4

Auger-Meitner within mean-field model

Coulomb matrix element

Partial Auger-Meitner rate