หลักการของXRD

Small/Wide Angle X-ray Scattering (SAXS/WAXS) Station Manual
()
SAXS/WAXS Station 2013

SAXS/WAXS Station Manual
Version 1.1 : 2556

supagorn@slri.or.th
http://www.slri.or.th/th/beamlines/saxs
( )

http://www.slri.or.th
Tel: 044217040
Fax: 044217047
1TU
U1T
Small/Wide Angle X-ray Scattering (SAXS/WAXS)

..................................................................................................................................................................... 9
1
1 SAXS WAXS ................................................................................... 11

1.1
.................................................................................................... 11
1.2
................................................................ 11
1.3
....................................................................................................... 12
1.4
.............................................................................................................................................. 12
1.5
.................................................................................................................................... 12
1.6
............................................................................................................................................ 12
1.7
................................................................................................................................... 13
1.8
................................................................................................... 13
2 SAXS........................................................................................................... 15
2.1
SAXS .............................................................................................................................. 15
2.2
SAXS .................................................................. 17
2.3
x-ray ..................................................................................................... 21
2.4
................................................................................................ 22
2.5
Guinier approximation........................................................................................... 24
2.6
x-ray interaction .......................................................... 26
2.7
Correlation function Pair Distance Distribution Function ......................................................... 27
2.8
.......................................................... 29
2.9
x-ray (periodic structure) .................................................. 30
3 ..................................................................................................................... 32
1
3.1
Detector .............................................................................................................................................. 33
3.2
sample-detector .......................................................................................................... 34
4 .............................................................................................................................. 36
1
4.1
....................................................................................................................................................... 36
4.2
.............................................................................................................................................. 37
4.3
.................................................................................................................................................... 37
4.4
................................................................................................................................................. 37
4.5
............................................................................................................................... 37
4.6
.......................................................................................................... 39
4.7
.................................................................................................... 39
5 ......................................................................................................... 40
1
5.1
ionization chamber photodiode ..................................................................... 40
5.2
detector........................................................................................................... 41
6 pattern alignment sample-detector ...... 43

7 ................................................................................................................................................. 47
1
7.1
CCD detector ................................................................................................................... 47
7.2
Image Plate detector ........................................................................................................ 52
8 SAXSIT ........................................................................................... 57
6
8.1
SAXSIT ............................................................................................................. 57
8.2
SAXSIT ...................................................................................................... 58
8.3
parameter input SAXSIT ...................................................................... 59
8.4
pattern alignment sample-detector ......................................................... 62
8.5
input .............................................................................................................................. 64
8.6
background .......................................................................... 65
8.7
(Scattering profile) circular averaging ............. 67

1
9 ................................................................................................................................ 69
1
9.1
peak period ( d-spacing) ...................................................................... 70
9.2
Guinier approximation ............................................................. 71
9.3
........................................................................ 74
9.4
........................................ 85
9.5
fitting structure model..................................................................................................... 89
9.6
fitting peak ...................................................................................................................... 93
9.7
modeling ...................................................................................... 94
10
SAXS/WAXS ............................................................................................................ 95
10.1 ............................................................................................................................................... 95
1
10.2 SAXS/WAXS ................................................................................................ 95

1
"One of the advantages of being disorganized is that one is always having

surprising discoveries"
A.A. Milne, Winnie the Pooh

(Small / Wide Angle X-ray Scattering: SAXS/WAXS)
SAXS/WAXS

SAXS/WAXS

SAXS/WAXS
10
1 SAXS WAXS
SAXS WAXS
1.1
x-ray
SAXS
(size distribution)
disperse
SAXS Dynamic Light Scattering
(DLS) SAXS x-ray
x-ray
SAXS
( disperse)
1.2
soft matter

( lamellar structure) x-ray
x-ray peak
( X-ray Diffraction)
peak
( 4 ) SAXS
SAXS ,
block co-polymer, (liquid crystal), ( ),
11
SAXS

dynamic

1.3
detector SAXS detector ( area detector) CCD detector
x-ray

orientation factor

( stress-strain )
1.4
(micelles)
x-ray
polymer chain modeling SAXS
1.5
(micro-emulsion) bi-continuous system
quasi-peirodic modeling SAXS (
domain size) correlation function
1.6
(liquid crystal) ( )
d-spacing SAXS
(X-ray Diffraction)
12
SAXS ( cubic hexagonal

lamellar), d-spacing
1.7
SAXS (
) (morphology) modeling
SAXS

interaction

Protein Crystallography
1.8
Wide Angle X-ray Scattering (WAXS) X-ray
Diffraction (XRD) SAXS/WAXS 2 60
d-spacing 1.6
WAXS Bragg peak
() x-ray
( amorphous) (crystallinity)
Bragg peak
crystallinity
crystallinity stress-strain

13
SAXS/WAXS

real time
14
2 SAXS
2.1
SAXS
SAXS WAXS
2 CCD Image Plate

(scattering pattern)

x-ray
(sample)
2.1 SAXS/WAXS
x-ray (pixel) CCD
4,194,304 ( matrix 2048x2048)
79.59 x-ray xray
4,194,304

15
2.2
x
L
x-ray
sample
primary beam
X-ray
2.2
x
= tan1 ( )
2.1
L ( sample-detector)
detector detector x-ray ( primary beam)
2 X-ray Diffraction
azimuth ( )
random
( =0
2.2) x-ray
azimuth
SAXS (scattering vector)

16
x-ray
sin
2.2
x-ray
x-ray
x-ray

x-ray

x-ray
2.2 SAXS
x-ray
() x-ray
( 2.2)
() = 0
()
0 x-ray (incident flux)

x-ray
x-ray (transmission)
detector (detector efficiency)
(solid angle) detector x-ray
17
2.3
() differential cross-section x-ray detector
x-ray (number of photons per second per unit

radiated volume per unit solid angle per unit incident flux)
() (absolute intensity) x-ray
detector absolute intensity
SAXS
(
absolute intensity molecular mass specific surface area)
differential cross-section ()
x-ray SAXS ()
(arbitrary unit)
( x-ray )

2.3
18
(wave function)
(Schrodinger equation)
,
x-ray
wave function plane wave

i0 r
0 (incident wave number) (
ikr k (scattering wave number)
detector (scattering wave function) wave
function detector wave function
scattering wave function detector (
i 0 r +
e ikr
2.4
interaction
scattering vector incident wave number scattering

wave number
0
k
= k
2.5
( )
k = k0 = scattering vector

= k
k0 = 2 sin = sin
scattering vector 2.2
19
2.6
(scattering amplitude)
differential cross-section differential crosssection (squared modulus) scattering amplitude ()
() = ()() = |()|2
2.7
() = ()
2.8
scattering amplitude interaction scattering wave function
interaction ( ) scattering
wave function Schrodinger equation
interaction Small
Angle Scattering scattering wave function plane wave
scattering amplitude Fourier transform interaction
() = ()
2.9
(Born Approximation)

1 2 scattering amplitude
=
1 2
1 + 2
() =
22
()
2.10
reduced mass (Plancks constant) 2
x-ray x-ray
interaction interaction
scattering amplitude
() = ()
20
2.11
classical electron radius ()
(electron density distribution)
electron density distribution

Debye formula
r
iq
=
sin (qr )
2.12
qr
scattering amplitude
() = 4 ()
differential cross-section
sin ( ) 2

2.13
() squared modulus scattering amplitude
2.3 x-ray
differential cross-section
() x-ray

() 3.7
() = () () = |()|2
2.14
() scattering amplitude electron density distribution
() = 4 0 ()
sin ( ) 2

2.15
() electron density distribution
() Form factor x-ray
0 0 electron density
distribution
21
() =
0 ,
0, >
2.16
2.15 form factor

() = 40 3
()
sin ( ) cos ()
2.17
()3
() = |()|2 = (4)2 02 3
sin ( ) cos ( ) 2
( )3
2.4
5 nm
10 nm
2.18
20 nm
1.E+00
Intensity (arbitray unit)
1.E-02
1.E-04
1.E-06
1.E-08
1.E-10
0
0.4
0.8
1.2
q(nm-1)
2.4
2.4
x-ray
(size distribution) (, , )
22
location parameter width parameter
() = |(, )|2 (, , )
2.19
Log normal
(, , ) =
exp
ln ( )
2 2
2.20
parameter Log normal distribution

(standard deviation)
2
= exp( )
2.21
= ( 1)
2.22
= exp( 2 )
Gaussian
(, , ) =
exp
( )2
2 2
2.23
parameter Gaussian distribution (standard

deviation)
=
2.24
2.25
2.5 20
Gaussian standard deviation size distribution smear
23
1.E+10
Monodisperse
1.E+09
sigma=0.5 nm
Intensity (arbitrary unit)
1.E+08
sigma=1.5 nm
1.E+07
1.E+06
1.E+05
1.E+04
1.E+03
1.E+02
1.E+01
1.E+00
0.0
0.2
0.4
0.6
q (nm-1)
0.8
1.0
1.2
2.5 20
Gaussian standard deviation (sigma)
2.5 Guinier approximation

power series
Guinier approximation
() =
2 2
2.26
(radius of gyration)
2.27
=
5
24
2.28
Guinier approximation 2.26
logarithm
ln () =
2
3
2 + ln
2.29
2
ln ()
2
3
radius of gyration = 3 (
) Guinier approximation

< 1
2.30

ln () =
2 + ln
2.31
(cross-sectional radius of gyration)

2.32
2
ln ()
crossectional radius of gyration = 2 (

2 2
ln 2 ( ) =
+ ln
25
2.33
(thickness radius of gyration)
12
2.34
2
ln 2 () 2
thickness radius of gyration = ( )
< 1
2.6 x-ray interaction

2.14

( form factor
() = |()|2 =
=1| ()|
2.35
|()|2 form factor
interaction xray form factor
Structure factor interaction

|()|2
[()
()|2
( ) = |()|2 1 + |
1]
2.36
() Structure factor |()|2 form factor

form factor |()|2

26
|()|2 = |()|2
() = |()|2 ()
2.37
Structure factor () interaction x-ray
analytical form SAXS
2.7 Correlation function Pair Distance Distribution Function

(density
contrast)
2.14
(
1 )
2
() = () () = ()
()
1
2
1
2
2.38
2 () = ()
(1 )1
1
2.39
() = 2 ()
2.40
Auto-correlation ( Patterson function)
=
1 2

() = 4 0 2 ()
sin ( ) 2

2.41

density contrast
() = () 0
2.42
27
0 auto-correlation
2.39 02 auto-correlation density contrast
2 () = 2 () 02
2.43
02 x-ray
density contrast 2
2.41 2 x-ray
auto-correlation Correlation function ()
auto-correlation density contrast

1
() = 2 ()
2.44
3.41
() = 4 0 ()
sin ( ) 2

2.45
Correlation function () density contrast
2.45 Correlation function inverse Fourier transform

() =
2 2
0 ()
sin ( )
2.46
SAXS Pair Distance Distribution

Function () Correlation function
() = 2 ()
2.47
Correlation function Pair Distance Distribution Function xray SAXS

28
inverse Fourier transform 2.46

2.46 = 0
2 =
(0) =
2 2
0 ()2
2.48
density contrast

2.48 Invariance
= 0 ()2
2.49
SAXS (volume
fraction)
2.8
x-ray
Fractals
Fractals (cluster)
cluster (power law)
cluster
=
2.50
, , cluster
mass fractal dimension
x-ray
reciprocal space power law
29
() =
2.51
1 () 2 ()
1 = 1 = 2
2 3
3
() =
2.52
fractal dimension = 2
2 3 x-ray 3
() =
2.53
(Porods law)

-4

-4 -3
2.9 x-ray (periodic structure)

x-ray x-ray
peak period peak xray X-ray Diffraction (XRD)

x-ray
=
sin
2.54
30
Bragg
2 sin =
2.55
2.56
d-spacing peak
()
SAXS
peak peak XRD
d-spacing
fitting Form factor Structure factor
2.36 2.37
31
x-ray
(Be
window)
beam shutter - x-ray SAXS/WAXS
computer beam shutter x-ray
SAXS/WAXS
3
4
7
5
3.1
32

1
2
3
4
5
Beam shutter
Ionization chamber
High voltage power supply
Current amplifier

Photodiode beamstop
Current amplifier
Detector
Sample holder
- x-ray
x-ray
high voltage 500 V ionization chamber
ionization chamber
x-ray
x-ray x-ray
(primary beam)
detector
photo diode
x-ray (
beam shutter)
3.1 Detector
SAXS/WAXS detector
- Mar SX165 detector detector CCD (Charge Couple Device)
sensor 165 79.59 2048x2048
x-ray 0-65,000 .mccd
Tiff file resolution 16 bit CCD detector
2.5
- Mar345 IP detector detector (Image Plate) sensor
345 150 2300x2300
x-ray 0-130,000 .mar2300
33
process Tiff file resolution 16 bit

Image Plate detector 2
detector
sensor
()
output
Mar SX165 CCD

CCD
79.59
2048x2048
Tiff file 16
.mccd
65,000
Mar345 Image Plate

Phosphore
150
2300x2300

.mar2300 (
Tiff file 16 )
130,000
2.5
3.2 sample-detector
SAXS sample-detector
( 5 3.1) detector
500, 1000, 1500, 2000, 2500 3000 WAXS
detector sample-detector 150
sample-detector ( ) scattering vector ( )
sample-detector sampledetector SAXS/WAXS x-ray

1.55 Angstrom ( 8 keV) sample-detector
34
sample-detector (..)
150
150
500
1000
1500
2000
2500
3000
()
2.5 60
2.70 28.81
0.81 9.36
0.40 4.71
0.27 3.14
0.20 2.36
0.16 1.89
0.13 1.57
q (nm-1)
2 - 40
1.91 20.17
0.57 6.62
0.28 3.33
0.19 2.22
0.14 1.67
0.11 1.33
0.09 1.11
35
Image Plate detector

CCD detector
CCD detector
CCD detector
CCD detector
CCD detector
CCD detector
CCD detector
SAXS/WAXS
(sample holder)
sample holder 4.1
liquid cell
4.1 sample holder
4.1
( ) kapton tape
frame sample holder
36
Kapton tape
4.2 2x2.5 ..2 kapton tape
4.2
( kapton tape)
sample holder
4.3
frame
sample holder
4.4
frame
sample holder
4.5
(liquid cell) liquid
cell sample holder liquid cell 4.3
37
Liquid cell 0.5 1.5

.. 5 .. window
kapton tape, mica
30
window
4.3 Liquid cell
38
Liquid cell
4.4 Liquid cell sample holder
4.6

SAXS/WAXS (tensile
stage) SAXS/WAXS tensile stage

20
70 1-1000 26
2 7 tensile stage SAXS/WAXS
stress-strain curve
4.7
SAXS/WAXS
250
39
5

- sample-detector
- detector
- detector align x-ray primary beam beamstop

- High Voltage power supply ionization chamber set 500 V
- gain current amplifier ionization chamber photo diode set
1x107 1x105 V/A
set
setup sample-detector
setup

5.1 ionization chamber photodiode

ionization chamber photodiode
ionization chamber photodiode 1
x-ray (beam shutter ) background 5.1

ionization chamber photodiode ionization
40
chamber 2350 2400 photodiode 2050 2100

5.1 ionization chamber ( ) photodiode (

) background beam shutter
5.2 detector
CCD detector CCD detector
marccd CCD - detector - beam
shutter start CCD beam shutter
start detector
CCD 5.2
detector
Temperature: -80 C , Pressure: 0.1 Torr, Status: OK
41
5.2 CCD detector detector
42
6 pattern alignment
sample-detector

detector primary beam
( X 2.2) primary beam detector beamstop
detector primary beam primary beam
primary beam
primary beam
SAXS silver behenate (AgBh) WAXS 4-Bromobenzoic acid
kapton tape
4.1 primary beam X
primary beam
SAXSIT
primary beam
setup align primary beam

pattern alignment
sample-detector ( L 2.2) d-spacing

peak Bragg
2.1 L
=
6.1
tan
peak Bragg
43
2 sin =
= sin1
d d-spacing peak
2d
6.2
6.3
silver behenate 6.1
peak x-ray periodic d-spacing

5.838
6.1 silver behenate Bragg peak order

1 () order 2 ()
4-Bromobenzoic acid 6.2
44
0.472
0.374
0.331
6.2 4-Bromobenzoic acid peak 3 peak dspacing peak
0.374
2.E-07
1.E-07
0.331
0.472
1.E-07
1.E-07
8.E-08
6.E-08
4.E-08
2.E-08
0.E+00
10
15
20
25
30
35
40
45
(deg)
6.3 4-Bromobenzoic acid peak 3 peak d-spacing

peak ( : Bragg 2 X-ray
Diffraction)
45
SAXS 3 silver behenate

pattern alignment detector
SEBS block co-polymer periodic
d-spacing 32.7778

pattern alignment sample-
detector SAXSIT ( 8.4)
46
7.1 CCD detector

CCD detector
e
d
b
c
7.1 CCD detector

a.
Root Filename
Next Frame Number
Root Filename 20130128_F3t40C.####.mccd Next Frame Number 14
20130128_F3t40C.0014.mccd
47
Next Frame Number 15

20130128_F3t40C.0015.mccd
- 1 Next Frame Number Root Filename
( .. 2 2013
20130102 .####.mccd
2 2013 Root Filename
20130102Collagen.####.mccd
-
run
- Next Frame Number ( 20130102Collagen)

ionization chamber photoiode ( 7.2)
ionization chamber photoiode x-ray
integrate
48
7.2 ionization chamber photodiode

b. Directory
Disk Directory /home/marccd/data directory
49
c. save
Auto Save

d. (exposure time)
Collection Parameters Time detector
beam shutter x-ray exposure time
- exposure time x-ray x-ray
exposure time 3
x-ray
Max
CCD detector ( 7.3) exposure time
10,000 50,000 60,000 (CCD
65,000) exposure time
50
7.3 detector
- MultiRead
detector
- Acquire Background detector background dark

current
51
e. start
start beam shutter detector

exposure time beam shutter

7.2
Image Plate detector

Image Plate detector CCD detector Image
Plate detector mar345 Image Plate detector
7.4 Image Plate detector

Single Set Single Data Set detector
52
7.5 Image Plate detector

a. Directory:

/home/mar345/data
53
b. Image root:
( ..
7 2013 20130307)
collagen 20130307_Collagen
( f. )
c. Scan mode:
2300*2300: 345 mm @ 0.15
2300*2300 150
d. Output format:
mar345 .mar345
e. Collect mode:
Time exposure time
f. First image no.:

1 _001

Image root:
20130307_Collagen
20130307_Collagen_001.mar345
20130307_Collagen_002.mar345
g. Exp. Time (sec):
exposure time ( beam shutter ) exposure time
x-ray x-ray
exposure time 3
x-ray
Max Int.: ( )
54
exposure time 100,000 (Image Plate

detector 130,000) exposure time
h.

i. Go Go / Erase first
beam shutter beam shutter
Go Go / Erase first detector
Image Plate detector Go / Erase first ( Image Plate
detector x-ray
CCD
detector ) Go
detector

Image Plate detector (
.mar2300) SAXSIT SAXSIT
Tiff 16 bit .tiff16 marcvt out tiff16
samplefile.mar2300 ( samplefile.mar2300 ) Tiff 16
bit samplefile.tiff16 SAXSIT
beamstop
primary beam detector detector
55
7.6
56
8 SAXSIT
scattering pattern SAXS WAXS

SAXSIT SAXS/WAXS
SAXS/WAXS
scattering vector (scattering profile)
8.1 SAXSIT
SAXSIT download SAXS/WAXS
( http://www.slri.or.th ) SAXSIT Matlab
executable file ( .exe) Windows
Matlab run MCRInstaller.exe run
SAXSIT SAXSIT version 3.63
SAXSIT
a. copy MCRInstaller.exe ( Windows)
b. copy SAXSIT download SAXSIT

SAXS/WAXS
zip file unzip folder SAXSIT
c. saxsit3p63.exe shortcut desktop

d. Double click MCRInstaller.exe ( library Matlab)
57
8.2
SAXSIT
SAXSIT
a. double click shortcut saxsit3p63.exe (MAIN

MENU) 8.1
b. folder
c. pathname folder Set working directory MAIN
MENU
d. Copy Excel folder SAXSIT MeasPara.xlsx folder
e. Copy parameter Ionization chamber
Photodiode ( 8.3) folder
8.1 MAIN MENU SAXSIT

58
8.3 parameter input SAXSIT
input SAXSIT MeasPara.xlsx

,
ionization chamber photoiode ,
parameter pattern alignment, detector parameter

(scattering profile)
MeasPara.xlsx
a. Experimental condition
x-ray
b. Dark current
dark current CCD detector
c. Reference
( .txt) ionization chamber photodiode
reference liquid cell (
x-ray )
.txt ionization chamber photodiode
d. Sample

- tiff resolution
16 ( .mccd CCD detector .tiff16 Image Plate detector)
59
- ( .txt) ionization chamber photodiode

- median masking ( Y )
median masking CCD detector
exposure time CCD detector

exposure time median masking

e. Background
d background (
) background ( )
( )
f. Parameters obtained from standard sample
pattern alignment
sample-detector distance Center Offset X, Center Offset Y Sample distance
pattern alignment sample-detector distance ( 8.4 8.5)
g. Detector parameter
pixel ( 0.07959 . CCD detector 0.15 . Image Plate
detector) detector ( 82.5 . CCD detector 172.5 .
Image Plate detector)
h. Profile calculation parameter
(scattering profile) parameter
circular averaging
- Normalize beam current
60
Y x-ray (integrated
beam intensity) ionization chamber
x-ray
- Normalize exposure time
Y exposure time
( N) Normalize
beam current integrated beam intensity normalize exposure time

- Subtract dark current pattern
dark current pattern
( N)
- Normalize transmission
Y transmission (
background) x-ray ( background)
- Sample concentration
x-ray background
background 1-c ( c sample concentration)
background
0
- Direction to calculate profile, Averaging range Step size parameter circular
averaging ( 8.6)
MeasPara.xlsx Parameters obtained from
standard sample pattern alignment
61
8.4 pattern alignment sample-detector
primary beam

primary beam pattern alignment primary beam

pattern alignment ()
a. Analyze standard MAIN MENU SAXSIT
8.2
8.2 Analyze standard SAXSIT

b. 1.Load image Browse (
AgBh) Imax
62
c. 2.Approximate center ( 1
AgBh) 3 beamstop
( 8.3)
8.3 Analyze standard SAXSIT

d. 3.Experimental parameters Pixel size detector, X-ray
energy, Peak order d-spacing ( )
e. 4.Search center and SDD Calibration Run
fit peak
c. (
sample-detector distance (SDD)
63
8.4)
8.4 Analyze standard SAXSIT Run

Sample-detector distance (SDD)
f. Run ( )
g. Save output alignstandard.txt
h. (Offset X, Offset Y SDD) MeasPara.xlsx SAXSIT (
8.3 g.)
8.5 input
MAIN MENU SAXSIT Read measurement parameters
input ( Measpara.xlsx)
( 8.5)
Save parameters
64
8.5 MeasPara.xlsx
8.6 background
MAIN MENU SAXSIT Load pattern / BG subtraction
8.6
input MeasPara.xlsx ( 8.3
h.)

- Load sample pattern
MeasPara.xlsx ( 8.3 d.)
- Load background pattern background
MeasPara.xlsx ( 8.3 e.)
65
- Subtract background
background scale background

(1-Sample concentration)
background Load sample pattern
8.6 Load pattern / BG subtraction
66
8.7 (Scattering profile) circular averaging

detector detector (
primary beam)
primary beam

azimuth
( )
(Circular averaging) x-ray

( 1 .) ( 0.2 .)
x-ray ( smearing)
smearing circular averaging
90 () 270 () circular averaging
10 beamstop 8.7 circular averaging 270
10 (step size) 0.25
parameter circular averaging MeasPara.xlsx
Calculate scattering profile
67
8.7 Calculate scattering profile

output Excel
_SP_ azimuth
Sample.mccd 270 output Sample.mccd_SP_270deg.xlsx
output worksheet
68
SAXS WAXS
period
peak
modeling fitting form factor structure factor
Fourier transform Pair Distance Distribution Fuction
SAXSIT scattering profile
peak, fitting
form factor structure factor
SAXS
download
- SASfit Joachim Kohlbrecher Paul Scherer Institute (PSI)
fitting Small Angle Scattering
form factor structure factor size distribution function
download
http://kur.web.psi.ch/sans1/SANSSoft/sasfit.html
9.1 SASfit
69
- ATSAS D.I. Svergun European Molecular Biology Laboratory

(EMBL)
modeling Fourier
transform Small Angle Scattering Pair Distance Distribution Fuction

download http://www.embl-hamburg.de/biosaxs/software.html
9.1 peak period ( d-spacing)

peak peak fitting
Gaussian function Lorentzian function
SAXSIT Line profile analyses ( 9.2) peak,
smoothing, baseline fitting peak peak
peak period peak 2.56
70
9.1
9.2 Line profile analyses

( lamella structure)
d-spacing peak
d-spacing
(liquid crystal)
crystallography
lamella d-spacing
fitting d-spacing
SASfit fitting ( 9.5)
9.2 Guinier approximation

SAXS Guinier approximation
qR<1 Guinier approximation (
71
2.5) SAXSIT Fitting Guinier and Porod fit

a. Guinier and Porod fit ( Fitting MAIN MENU)
b. scattering profile Excel Read new profile from excel
q I ( output Calculate scattering
profile)
c. ( ) Plot profile
2 () Ln-ln
d. Choose valid data range
e. fit
f. Choose data range for fitting fit
g. Fitting Radius of gyration () Fit

fit radius of gyration ( ) Massage
radius of gyration
5
=
3
72
9.3 Guinier and Porod fit

Guinier and Porod fit fit radius of gyration
2.5 Plot profile Fit
straight line to plot
SASfit Guinier
approximation fit Guinier approximation 2.26 ( form
factor Guinier)
73
9.3
SASfit form factor size distribution

fitting size distribution SAXS/WAXS
(BL2.2)
(gold nano particles) liquid cell

background () x-ray
SAXSIT
= (1 )
9.2
transmission (sample) (background)

=
, / ,
, /
, / ,
, / ,
(concentration)
, integrated intensity x-ray ionization chamber
74
, integrated intensity x-ray photodiode beamstop
,
,
integrated intensity x-ray ionization chamber

integrated intensity x-ray photodiode beamstop
, integrated intensity x-ray ionization chamber cell

, integrated intensity x-ray photodiode beamstop
cell
SAXS
- liquid cell reference pattern
- liquid cell background pattern
- liquid cell ( ) sample pattern
- SAXSIT scattering profile ( background, normalize
beam current normalize transmission ) 8.
SASfit
a. Excel output Calculate scattering profile SAXSIT
worksheet Averaged I(q) Save as Text (Tab delimited)
( SASfit text file)
b. SASfit File -> Single Data Set -> Browse ( 9.4)
text file a.
75
9.4 SASfit
c. Options ( 9.5) Input format: xy (
error bar), lines to skip: 1 ( ), File extension:
txt ( ) OK 9.6
76
9.5 set
9.6
77
d. File -> Single Data Set

Merge Files
Skip first n points Skip last points (
9.7) ( Apply ) OK
9.7
e. File -> Calc -> Single Data Set -> fit fitting ( 9.8)
size distrib. and formfactor size distribution
form factor
78
9.8 fitting
f. size distribution LogNorm
Log Normal size distribution
g. form factor Sphere Apply
model form factor size distribution
h. fitting parameter form factor size
distribution fit fit chisquare minimization
parameter model fit
fitting parameter form factor R ( ) eta (
density contrast) distr. parameter distribution
R
79
size distribution parameter N (normalization factor), s (width parameter

log normal), p (shape parameter log normal) mu (location parameter log
normal)
fit model eta form
factor mu s size distribution ( 9.9) eta amplitude
, mu oscillation s
oscillation
9.9 parameter fit

model fit
parameter
eta scaling factor
relative
N
80
normalization factor scaling factor fit eta N

fit eta
s log normal distribution fit s
parameter eta
mu model
i. mu eta fit parameter Run fit
fit parameter model (
9.10)
9.10 fit
81
j. s Run fit ( fit eta, mu s ) model

( 9.11)
9.11
model fit

background
fitting background
fit SASfit background form factor
background c 0+c 1q+c 4q-alpha
background q power law
1 background
82
k. fit contribution: fit

contribution: 1 Add contribution: 2
contribution Previous Next
l. contribution: 2 size distribution monodisperse form
factor background ( 9.12)
9.12 contribution background

m. background c_1=0, alpha=3 (q-3
)
c_0 c_4 model ()
( background
)
n. c_0 c_4 fit parameter Run fit
83
o. c_0 c_4 alpha Run fit

9.13 parameter log normal distribution fit
mu s Log normal distribution
standard deviation ( 2.4)
2
= exp( )
9.3
= ( 1)
9.4
= exp( 2 ) mu s
9.13
parameter tab SASfit
model fit ()
Export Data ascii text
84
Graph
linear
9.4

Global fit Guinier
approximation Power law Beaucage [G. Beaucage, Jounal of Applied Crystallography
28(1995)717-728] SASfit form factor Global fit BeaucageExpPowLaw
non-particular structures form factor ( 9.14) fitting fit
size distribution 9.3 model
9.14 Beaucage unified exponential-power law form factor SASfit

85
unified exponential-power law () Beaucage
erf
2 2
2
6
( ) = exp(
) + exp
3
3
+ exp(
2 2
3
) +
erf
9.5
contribution
plot ln-ln scale q exponential
power law P q power law
P s
q
q

q ln() ln() q
-4 ( 2.8)
(primary particles)
( )
-4 -3 ( ) -3 -2 ( )
Beaucage

() = exp(
2 2
3
) +
86
erf
9.6
fit SASfit set G s=Bs=Rsub=0

parameter fit Beaucage parameter Log normal
distribution [G. Beaucage, H. K. Kammler, S. E. Platsinis, Journal of Applied Crystallography,

37 (2004), 523535] Log normal distribution
=
=
52
9.7
3 exp (14 2 )
4
ln 1.62
9.8
12
standard deviation
2
= exp( )
9.9
= exp( 2 )
= ( 1)
9.10
9.15 fit SASfit form factor Global fit Beaucage

9.16 SAXS Global fit SASfit
model fit exponential power law model
87
9.15 fitting SASfit Beaucage
9.16 SAXS FePt () Fe3O4 ()

Global fit Beaucage () contribution exponential
() power law () [S. Rugmai et al., Materials and Technology 46(2012)369]
88
9.5 fitting structure model
(lamellar
structure) structure factor fitting model

lamella
cluster
SAXS peak
(diffuse peaks)
Model lamellar paracrystalline theory model
thermal disorder Modified
Caille theory lamella [G. Pabst et al., Journal of Applied Crystallography
36(2003)1378] [T. Fruhwirth et al., Journal of Applied Crystallography 37(2004)703]
SASfit fitting lamella form factor
form factor ( )
form factor planar obj. > homogeneousXS size distribution
Gaussian Log normal distribution ( L) ( 9.17)
form factor Guassian Bilayer planar obj. > BiLayerGauss ( membrane
stacks)
89
9.17 form factor Gaussian distribution

structure factor lamellar structure SASfit
ThermalDisorder, Paracrystalline ModifiedCaille Multi Lamellar Structures ( 9.18)
90
9.18 structure factor Modified Caille Theory lamellar structure

fitting fit ( 9.3)
parameter ( SASfit)
model contribution background
model fit
fitting
SAXSIT fitting Paracrystalline theory ( 9.19)
lamella
() = 1 |()|2 () +
9.11
() form factor crystalline lamella model
form factor
91
( ) =
sin (
)
2
9.12
/2
structure factor Paracrystalline theory [R. Hosemann and S.N. Bagchi, Direct analysis of
diffraction by matter, Noth-Holland 1962] [B.K. Vainshtein, Diffraction of x-ray by chain molecules, Elsavier
1966]
() =
1|( )|2
12|()| cos ( )+|()|2
9.13
() Fourier transform distribution function crystalline
lamellae lamella distribution function Gaussian
function standard deviation
( ) =
() Fourier transform ( )
exp(
(+)2
2 2
9.14
Background
lamella power law

= +
model least square fit parameter , , , , ,
9.15
model source
code Matlab
92
9.19 fitting paracystalline model lamellar structure
9.6 fitting peak

WAXS fitting peak
Gaussian, Lorentzian Pseudo Voigt Pearson VII
SASfit peak function Peaks form factor
peak (Area Functions) peak parameter fit
peak (Amplitude function) peak parameter fit
fit peak contribution peak ( Add
contribution) parameter contribution peak
fit
93
9.20 peak function Pearson VII (Area) SASfit
9.7 modeling
SAXS
SAXS ( 9.3)
modeling SAXS profile
fitting SAXS profile
ATSAS D.I. Svergun European Molecular Biology
Laboratory (EMBL) modeling fitting
SAXS profile download
http://www.embl-hamburg.de/biosaxs/software.html
94
10 SAXS/WAXS
10.1
- Small Angle X-ray Scattering, O. Glatter and O. Kratky, Academic Press, 1982

SAXS
PDF download University of Graz

http://physchem.kfunigraz.ac.at/sm/
- Structure Analysis by Small Angle X-ray and Neutron Scattering, L.A. Feigin and D.I. Svergun,
Plenum Press, 1987
- Small Angle Scattering of X-ray, A. Guinier and G. Founet, John Wiley and Sons, 1955
10.2 SAXS/WAXS
- http://www.embl-hamburg.de/biosaxs/software.html
ATSAS modeling Small Angle Scattering
Fourier transform Pair Distance Distribution Fuction
- http://kur.web.psi.ch/sans1/SANSSoft/sasfit.html
SASfit Joachim Kohlbrecher Paul Scherer Institute (PSI)
fitting Small Angle Scattering
form factor structure factor size distribution function
- http://www.esrf.eu/computing/scientific/FIT2D/
image processing European Synchrotron Radiation Facility (ESRF)
0
- http://henke.lbl.gov/optical_constants/
95
Center for X-ray Optics (CXRO) Lawrence Berkley Lab

x-ray Atomic scattering factors, X-ray properties of elements,
Index of refraction, Attenuation length, X-ray transmission X-ray reflectivity
- http://www.ncnr.nist.gov/resources/
Scattering Length Density
x-ray scattering form factor National Institute
of Standard and Technology (NIST)
- http://webmineral.com/MySQL/xray.php?ed1=3.51&minmax=2
x-ray diffraction
- http://scattering.tripod.com/#SAXS
Weblink Small Angle Scattering
SAXS SAXS beamline
SAXS/WAXS
( http://www.slri.or.th/th/SAXS )
96
97

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Small/Wide Angle X-ray Scattering (SAXS/WAXS) Station Manual

SAXS/WAXS Station 2013

SAXS/WAXS Station 2013

Version 1.1 : 2556

SAXS/WAXS Station 2013

SAXS/WAXS Station 2013

Small/Wide Angle X-ray Scattering (SAXS/WAXS)

1 SAXS WAXS ................................................................................... 11

x-ray interaction .......................................................... 26

Correlation function Pair Distance Distribution Function ......................................................... 27

SAXS/WAXS Station 2013

x-ray (periodic structure) .................................................. 30

ionization chamber photodiode ..................................................................... 40

6 pattern alignment sample-detector ...... 43

CCD detector ................................................................................................................... 47

Image Plate detector ........................................................................................................ 52

SAXS/WAXS Station 2013

parameter input SAXSIT ...................................................................... 59

pattern alignment sample-detector ......................................................... 62

(Scattering profile) circular averaging ............. 67

peak period ( d-spacing) ...................................................................... 70

Guinier approximation ............................................................. 71

fitting structure model..................................................................................................... 89

fitting peak ...................................................................................................................... 93

10.2 SAXS/WAXS ................................................................................................ 95

SAXS/WAXS Station 2013

"One of the advantages of being disorganized is that one is always having

SAXS/WAXS Station 2013

SAXS/WAXS Station 2013

SAXS/WAXS Station 2013

SAXS/WAXS Station 2013

SAXS/WAXS Station 2013

SAXS ( cubic hexagonal

SAXS/WAXS Station 2013

SAXS/WAXS Station 2013

2 CCD Image Plate

SAXS/WAXS Station 2013

SAXS/WAXS Station 2013

0 x-ray (incident flux)

detector (detector efficiency)

(solid angle) detector x-ray

SAXS/WAXS Station 2013

() differential cross-section x-ray detector

x-ray (number of photons per second per unit

() (absolute intensity) x-ray

detector absolute intensity

SAXS/WAXS Station 2013

wave function plane wave

ikr k (scattering wave number)

detector (scattering wave function) wave

function detector wave function

scattering wave function detector (

scattering vector incident wave number scattering

scattering vector 2.2

SAXS/WAXS Station 2013

differential cross-section differential crosssection (squared modulus) scattering amplitude ()

scattering amplitude interaction scattering wave function

reduced mass (Plancks constant) 2

SAXS/WAXS Station 2013

classical electron radius ()

(electron density distribution)

electron density distribution

() squared modulus scattering amplitude

() scattering amplitude electron density distribution