This post provides a journey through the entire experiment, including sample preparation, experimental design and data evaluation.

Coral sample preparation: 200 micron thick embedded coral slices

1) Sample labeling
→ every sample was assigned with numbers: 500 - 505
→ every sample side: a, b, c, etc.
→ p = Pocilopora
→ s = Stylophora

1a) Samples measured (highlighted in yellow) with XRD, XRF, absorption –> RADIATION DAMAGE (KATREIN):

1b) Samples measured with XRD, XRF, absorption –> FLOW / NO FLOW (ISABELA):

2) Raw sample cutting
→ Untreated corals were cut into 1-1.5 mm thick slices:
1. Embed end of sample in thin layer of pmma, which then can be stuck to the transparent rectangle that fits in the suction plate of the bandsaw, to better control quality and thickness of slices of raw coral
→ Bandsaw (Name, company,location):
EXAKT dia-plus Walter Messner GmbH, Barsüttlerweg 6, 22113 Oststeinbeck, Germany

3) Embedding
Each sample was potted in methyl-methacrylate (Technovit 4071, Kulzer GmbH, Germany). Firmly secured at the potted ends, samples were then sectioned cross-sectionally into ca. mm-thick sections. Each section was embedded individually (Technovit 4071, Kulzer GmbH, Germany), so as to infiltrate otherwise closed internal pores.

→ Embed these slices in pmma, filling the mold to the top.
→ Side A = bottom of embedding mold = side of puck with sample near surface
→ Side B = top of embedding mold = far from sample
→ End up with a puck, where thin slice of sample is at one end, and the rest is pmma.

4a) Sample polishing short for paper
Embedded pucks containing the sample section were then ground to expose the coral skeleton material and polished (EXAKT 400 CS, EXAKT Advanced Technologies GmbH, Germany) on both sides, to produce 200-400 µm-thick highly polished plane-parallel slices. Specifically, blocks were first roughly ground down to ca. 500 um thick (800 grit), making sure that the coral skeleton was exposed on both sides of the puck. Then, each side was polished using the following protocol: 1. 1 min at 1000 grit with water 2. 1 min at 1200 grit with water 3. 3 minutes at 2500 grit with water 4. 3 minutes at 4000 grit with Na2CO3 All polishing steps were done with xx g weight. The final step at 4000 grit was done with Na2CO3 to prevent surface ACC dissolution (YUT Gong et al., PNAS 2012). Samples were then wiped (Kimtech wipe with Na2CO3), dried (pressurized air), and stored in a clean membrane box.

4b) Sample polishing in detail: Polish side A
→ Can work in batches of ~6 samples.
→ Polish side A (removes 0.1 mm):
1. Manually sand side B with 800 grit paper, just to make sure surface is clean and smooth and will stick well with tape. Wipe dust off with wet tissue and dry surface with compressed air duster.
2. Stick samples (side B stuck, side A exposed) onto transparent rectangle
3. Polishing standard procedure (Removes 0.1mm total):
- 1000 grit, 1 small weight, ~2 minutes (or more if needed) to expose surface
- 1 min @ 1000 grit, 1x small weight
- 1 min @ 1200 grit, 1x small weight
- 3 min @ 2500 grit, 1x small weight
- 3 min @ 4000 grit, 1x small weight

4c) Polish side B
→removes 0.1 mm, Plastic rectangle thickness + 1 layer of tape = 2.2 mm → target thickness = 2.2 + 0.3 = 2.5mm
→ Use bandsaw to cut off excess pmma from side B, leaving pucks of ~1.5mm thick (with the coral slice inside).
→ Grind side B (800 grit, 2x small weitht + large weight) until sample is 0.3 mm thick (0.3 + 2.2 = 2.5 sample plastic tape unit). In polisher machine, can use the meter knob to set thickness at which polishing will stop. Make sure to zero without sample.
→ Stick samples (side A stuck, side B exposed) onto transparent rectangle: To allow eventual detachment of sample without damaging delicate slice, stick it with thin slivers of tape only on two sides of the puck where there is just pmma.
→ This will be slow, goes faster if use little water. Can start with 320 grit and move to 800 once approaching target thickness.
→ Then do standard polishing as above
→ Remove samples from plastic rectangle. Use fine dentistry tools to slowly lift tape off of plastic rectangle.
→ Wipe slice with kimwipe and solution of filtered 22g/L Na2CO3 (in fridge in front of the door of the room where Keyence is, in glass bottle with blue cap, labelled…you will see it).

Note: Not further polished with diamond/silica/alumina paste because in test sample this standard polishing was enough to reach < 1um roughness on side B (last polished surface).

In the end, the polishing machine is not that precise that I cut the samples with the band saw as thin as possible. If I chose to cut the sample too thin, the band saw makes funny things and the sample just breaks. After cutting I polished with 800 grit polishing paper and polishing machine till a thickness of approximately < 1 mmm (determined with blank eyes). Then increasing stepwise the grit of the polishing paper (see polish side A) till I am happy with the surface including thickness. At the end I measured the thickness precisely and noted the size in the table above.

5) Before beamtime measurements:

Samples were measured with light microscopy

6) At the beamtime:

Participants: Katrein Sauer, Paul Zaslansky, Isabela Vitienes, Shreya Ray

Samples were measured within a diaphrame samdwiched within two yellow Kapton films / polyimide films (Kapton-Folie / Polyimid-Folie, Imid-group: -CO-NH-CO- –> electric isolator, thermal stable and chemical- and radiation resistant).

Energy: 17 keV
beamsize: 50 microns

Plan:

1. Mapping the entire samples with a stepsize of 100 x 100 µm
2. choose two ROIs with a stepsize of 50 x 50 points (=highest possible resolution defined by beamsize) with 1s or 2s exposure time
3. Irradiate several choosen spots over and over again, and collect XRD patterns (Debye rings) over time

Close the Hutch:

• press green button on the wall
• close door
• rotate key right beside the door and take it with your
• put key into beamline lights which shows green light if everything works well (MySpot (NOT BAMline!)) and rotate key 1/4 to the right
• press leverage (Hebel) up and release. It will beep and every diode in that line should light up green now

Open the Hutch:

• rotate key from 0–>1 and take it with you to the pace right beside the door
• enter key and bring it to position 1
• press green button
• door will make a noise, you can open it

**Helpful commands:**    -   beamstop_out    - PAUSE/STOP: \
P [=pause] \
r [=resume]\
Strg + C [=der totale Abbruch]
- curs [= to go anywhere within ascan with motor] \
 m [= move motor to that position]
 q [= quit]
- wm kox [= where motor (position) kox]
- wm mz [= where motor (postition) mz]

7) Additional measurements after beamtime:

1. Sample s504d for XRF to look into Magnesium (PTB beamline (Adrian))
2. Leica light microscopy
3. SEM-BEI
4. Laminography (Isabela)

8) Evaluation

Transmission / Absorption (diode1):

### How to read the Spec file:

• AS-IC = current from ionization chamber, during the measurement and has therefore good statistics.

• ionch1 = ionchamber, measured short, statistics not good, but in units of photons per seconds (ph/s) on the ionization chamber before the sample. Although this ionchamber makes more sense to use in order to estimate intensity, the diode1 is calibrated from PTB.

• diode1 = measured short, statistics not good, but in units of photons per seconds (ph/s), on the ionization chamber at the diode behind the sample. Calibrated by PTB and with the energies we used this is the better option to estimate intensity provided there is nothing in the beam.

Wenn ich das Spec in Gnumeric lade, die Werte mit kox beginnen, dann sind die Werte, die in der Counter-Spalte sind (8, Counter, 9), die eigentlichen ionch1-Werte.

• diode1 = absolute absorption, good calibration, gives photons / s
• cyber = transmission (not as good calibrated as beam + has to go to through air and through the sample –> absortion of both. Therefore: transmission = air / sample)

X-ray Absorption Images

Transmission images from Spec-files (BESSY, found wihtin one of the last columns)

Transmission (T) transformed into Absorption (A):
A = 1-T
–> T was determined with Fiji, looking for the highest intensity value within histogram and this is defined then as “100% transmission = 1 in formula”:
a) 100% = 593751.44
As -A = T - 1 and T = our image:
with Fiji:

→ click on transmission image → process → math → substract 593751.44 → afterwards multiply with (-1)

XRF FLUORESCENCE:

Measured elements as part of coral samples:

Measured elements as part of background / beamline setup / contamination:

The arsen (K_alpha) and lead (L-line) energy are both included in one peack as this peak is broad enough to carry both. Therefore, it is not clear which element it really is exactly but most likely LEAD!

From measurement set68 till set74: Here is a mistake in naming: Instead of sample p501c, it actually is the sample s503a and must therefore be set68_s503a,…,set74_s503a, and also set76_s503a,…,set89_s503a!!! The same is true for XRD!

XRD X-Ray diffraction (WAXS):

Energy: 17 keV
beamsize: 50 microns
SSD:
Detector: Eiger 9M
Diaphrame size:
mz = 0 - 25 (window inner size = 24 mm)
koi = -20 -0 - +25 (window inner size = 36 mm)
–> Richtung -20: fährt man zur Wand

XRD Calibration with 2 Standards (Al2O3 = Corundum)

Corundums were placed on left and right side of the sample during BESSY measurement.

For all samples Corundum on both sides of the samples were calibrated and an average of the calibrated left and right Corundum was created in order to do azimuthal integration of the entire sample.

# CALIBRATING sample s504d s504d_Corund_1

Energy: 16.9506007keV
Lamda: 0.731444 Angstroem
Pixel size x, y: 75 x 75 microns²
SDD: 35.2452 cm
Center X: 1619.92 pixels
Center Y: 1695.28 pixels
tilt a: -0.39506460 degrees
tilt b: -13.292978 degrees

s504d_Corund_2

Energy: 16.951478keV
Lamda: 0.731406 Angstroem
Pixel size x, y: 75 x 75 microns²
SDD: 35.1977 cm
Center X: 1619.87 pixels
Center Y: 1695.34 pixels
tilt a: -0.39132528 degrees
tilt b: -13.171041 degrees

AVERAGE s504d Corund 1 and 2
Energy: 16.95103935
SSD: 35.22145
lamda: 0.731425
Center x: 1619.9
Center y: 1695.3
tilt a: -0.393
tilt b: -13.25\

Mask off:
Valid pixels
< 2000
apply mask

Calibrated SDD for s504d damage:

set03: kox = 3.5, SDD = 35.21159
set04: kox = -3.5, SDD = 35.2278097
set05: kox = 3.2, SDD = 35.212053
set06: kox = -2.2, SSD = 35.225029260768295
set07: kox = 5.4, SDD = 35.20718782223171
set08: kox = -3.6, SDD = 35.2280414517683
set09: kox = -3.7, SDD = 35.228273158768296
set10: kox = -3.5, SDD = 35.227809744768294
set11: kox = 4.3, SDD = 35.20973659923171
set12: kox = 3.5, SDD = 35.21159025523171
set13: kox = 2.2, SDD = 35.21460244623171
set14: kox = 5.3, SDD = 35.20718782223171
set15: kox = -4.4, SDD = 35.229895061426895
set16: kox = -4.3,SDD = 35.229663400768295
set17: kox = -4.5, SDD = 35.2301268147683
set18: kox = -4.1, SDD = 35.22919998676829
set19: kox = -3.8, SDD = 35.22873652642689
set20: kox = -4.4, SDD = 35.229895061426895
set21: kox = 2.6, SDD = 35.21367557189031
set22: = 2D mesh
set23: kox = -0.3,SDD = 35.22039512097683
set24: kox = 0.8, SDD = 35.21784634404634
set25: kox = 0.3,SDD = 35.219004879023174
set26: kox = -3.5,SDD = 35.2280414517683
set27: kox = -3.4, SDD = 35.2275779914269
set28: kox = -4.0, SDD = 35.22919998676829
set29: kox = -4.4, SDD = 35.229895061426895
set30: kox = -4.6, SDD = 35.230358521768295

CALIBRATING sample p501c

p501c_Corund_1

Energy: 16.951594 keV
Lamda: 0.731401 Angstroem
Pixel size x, y: 75 x 75 microns²
SDD: 35.2343 cm
Center X: 1619.90 pixels
Center Y: 1695.39 pixels
tilt a: -0.39111405 degrees
tilt b: -14.216970 degrees

p501c_Corund_2

Energy: 16.951797 keV
Lamda: 0.731393 Angstroem
Pixel size x, y: 75 x 75 microns²
SDD: 35.2291 cm
Center X: 1619.85 pixels
Center Y: 1695.37 pixels
tilt a: -0.39320343 degrees
tilt b: -13.538319 degrees

AVERAGE p501c Corund 1 and 2

Energy: 16.9516955 keV
Lamda: 0.731397 Angstroem
Pixel size x, y: 75 x 75 microns²
SDD: 35.2317 xxx FILL IN VALUE BELOW xxx cm
Center X: 1619.88 pixels
Center Y: 1695.38 pixels
tilt a: -0.39215874 degrees
tilt b: -13.8776445 degrees

Calibrated SDD for p501c damage:

set 42: kox = 0.81 SDD = 35.231580000008
set 43: kox = 0.91 SDD = 35.231500000012005
set 44: kox = 0.99 SDD = 35.231500000012005
set 45: kox = 1.12 SDD = 35.23142
set 46: kox = 1.12 SDD = 35.23142
set 47: kox = 1.23 SDD = 35.23142
set 48: kox = 1.41 SDD = 35.23134
set 49: 2d map
set 50: kox = 1.44 SDD = 35.23134
set 51: kox = 1.46 SDD = 35.231300000000005
set 52: kox = 1.62 SDD = 35.231259992000005
set 53: kox = 1.59 SDD = 35.231259992000005
set 54: kox = 1.79 SDD = 35.23118
set 55: kox = 1.90 SDD = 35.23114 CALCITE!!!!
set 56: kox = 2.42 SDD = 35.23090000004
set 57: kox = 1.08 SDD = 35.231459992000005
set 58: kox = 1.30 SDD = 35.23138
set 59: kox = 0.20 SDD = 35.23182000000401
set 60: kox = -2.01 SDD = 35.23273999996
set 61: kox = 2.24 SDD = 35.230980000040006

CALIBRATING sample s503a

s503a_Corund_1

Energy: 16.947503 keV
Lamda: 0.731578 Angstroem
Pixel size x, y: 75 x 75 microns²
SDD: 35.2114 cm
Center X: 1619.63 pixels
Center Y: 1695.34 pixels
tilt a: -0.39548308 degrees
tilt b: -14.412529 degrees

s503a_Corund_2

Energy: 16.946407 keV
Lamda: 0.731625 Angstroem
Pixel size x, y: 75 x 75 microns²
SDD: 35.1929 cm
Center X: 1619.64 pixels
Center Y: 1695.36 pixels
tilt a: -0.39399418 degrees
tilt b: -14.420963 degrees

AVERAGE s503a Corund 1 and 2

Energy: 16.946955 keV
Lamda: 0.7316015 Angstroem
Pixel size x, y: 75 x 75 microns²
SDD: 35.20215 xxx FILL IN VALUE BELOW xxx cm
Center X: 1619.64 pixels
Center Y: 1695.35 pixels
tilt a: -0.39473863 degrees
tilt b: -14.416746 degrees

Calibrated SDD for s503a damage:

set 68: kox = -4.15 SDD = 35.20556097540976
set 69: kox = -3.54 SDD = 35.20465853640976 \ not a real pattern set 70: kox = -3.23 SDD = 35.20420731690976
set 71: kox = -2.82 SDD = 35.20420731690976
set 72: kox = -2.84 SDD = 35.20420731690976
set 73: kox = -1.65 SDD = 35.202853658500004
set 74: kox = -2.12 SDD = 35.20330487790976
set 75: 2D map set 76: kox = -2.04 SDD = 35.20330487790976
set 77: kox = -0.54 SDD = 35.20195121949098
set 78: kox = -0.01 SDD = 35.2015
set 79: kox = 0.57 SDD = 35.201048780509026
set 80: kox = 0.96 SDD = 35.200597561027074
set 81: kox = 0.54 SDD = 35.201048780509026
set 82: kox = 1.35 SDD = 35.2001463415
set 83: kox = 4.07 SDD = 35.197890244090246
set 84: kox = 3.35 SDD = 35.198341463590246
set 85: kox = 2.51 SDD = 35.19924390259025
set 86: kox = 1.77 SDD = 35.19969512209025
set 87: kox = 0.85 SDD = 35.200597561027074
set 88: kox = 0.02 SDD = 35.2015
set 89: kox = -3.76 SDD = 35.20420731690976

CALIBRATING sample p501a

p501a_Corund_1

Energy: 16.947001keV
Lamda: 0.731600 Angstroem
Pixel size x, y: 75 x 75 microns²
SDD: 35.2519 cm
Center X: 1619.59 pixels
Center Y: 1695.34pixels
tilt a: -0.39379773degrees
tilt b: -13.929300 degrees

p501a_Corund_2

Energy: 16.948256 keV
Lamda: 0.731545 Angstroem
Pixel size x, y: 75 x 75 microns²
SDD: 35.1998 cm
Center X: 1619.60 pixels
Center Y: 1695.29 ixels
tilt a: -0.39588908 degrees
tilt b: -14.346396 degrees

AVERAGE p501a Corund 1 and 2

Energy: 16.9476285 keV
Lamda: 0.731572 Angstroem
Pixel size x, y: 75 x 75 microns²
SDD: 35.222585 xxx FILL IN VALUE BELOW xxx cm
Center X: 1619.60 pixels
Center Y: 1695.315 pixels
tilt a: -0.394843405 degrees
tilt b: -14.137848 degrees

Calibrated SDD for p501a damage:

set 98: kox = 2.46 SDD = 35.217445720248094
set 99: kox = 2.03 SDD = 35.21843810024809
set 100: kox = 1.97 SDD = 35.21843810024809
set 101: kox = 1.41 SDD = 35.21992667
set 102: kox = 0.49 SDD = 35.22240762002481
set 103: kox = 0.47 SDD = 35.22240762002481
set 104: kox = 0.96 SDD = 35.22091905007443 CALCITE!!!
set 105: 2D map
set 106: kox = -0.90 SDD = 35.223896189975186 no pattern/beside the sample?!
set 107: kox = -1.25 SDD = 35.22637714 Calcite very little
set 108: kox = -1.89 SDD = 35.227865709999996
set 109: kox = -2.88 SDD = 35.2303466597519
set 110: kox = -3.57 SDD = 35.2323314197519 kein pattern
set 111: kox = -3.27 SDD = 35.2313390397519
set 112: kox = -2.53 SDD = 35.2298504697519
set 113: kox = -0.80 SDD = 35.22538475995038 Calcite!!! BIG PEAK
set 114: kox = -2.34 SDD = 35.229354230132905
set 115: kox = -3.72 SDD = 35.2328276097519
set 116: kox = -1.32 SDD = 35.226873280381
set 117: kox = -2.94 SDD = 35.2308428497519
set 118: kox = -4.25 SDD = 35.233944037499995
set 119: kox = -2.88 SDD = 35.2303466597519

CALIBRATING sample s505d

s505d_Corund_1

Energy: 16.946088 keV
Lamda: 0.731639 Angstroem
Pixel size x, y: 75 x 75 microns²
SDD: 35.2679 cm
Center X: 1619.47 pixels
Center Y: 1695.33 pixels
tilt a: -0.39129060 degrees
tilt b: -14.342627 degrees

s505d_Corund_2

Energy: 16.942555 keV
Lamda: 0.731791 Angstroem
Pixel size x, y: 75 x 75 microns²
SDD: 35.2433 cm
Center X: 1619.50 pixels
Center Y: 1695.27 pixels
tilt a: -0.39803146 degrees
tilt b: -14.675397 degrees

AVERAGE s505d Corund 1 and 2

Energy: 16.9443215 keV
Lamda: 0.731715 Angstroem
Pixel size x, y: 75 x 75 microns²
SDD: 35.2556 cm
Center X: 1619.49 pixels
Center Y: 1695.30 pixels
tilt a: -0.39466103 degrees
tilt b: -14.509012 degrees

Calibrated SDD for s505d damage:

set 125: kox = -3.67 SDD = 35.25675644493705
set 126: kox = -3.67 SDD = 35.25675644493705
set 127: kox = -3.96 SDD = 35.25689385187385
set 128: kox = -4.30 SDD = 35.25752462187384
set 129: kox = -3.94 SDD = 35.2584
set 130: kox = -4.32 SDD = 35.25752462187384
set 131: kox = -4.90 SDD = 35.25815539187384
set 132: 2D map set 133: kox = -3.15 SDD = 35.25611439676945
set 134: kox = -3.19 SDD = 35.25611439676945
set 135: kox = -3.47 SDD = 35.25626308187385
set 136: kox = -3.96 SDD = 35.257184460228245
set 137: kox = -2.68 SDD = 35.25568638147824
set 138: kox = -2.36 SDD = 35.25504433331064
set 139: kox = -2.42 SDD = 35.25525836618704
set 140: kox = 2.20 SDD = 35.24932461212615 creating calcite?
set 141: kox = 1.06 SDD = 35.250764130063196
set 142: kox = -0.75 SDD = 35.25310923197477
set 143: kox = -0.39 SDD = 35.25689385187385
set 144: kox = 0.68 SDD = 35.25121692202523
set 145: kox = -0.64 SDD = 35.25290423172477
set 146: kox = 0.86 SDD = 35.251192145379626

ISA Samples

For all samples Corundum on both sides of the samples were calibrated and an average of the calibrated left and right Corundum was created in order to do azimuthal integration of the entire sample.

CALIBRATING sample pg31b2

CORUNDUMS low
ascans at mz position 27, 28, 29, 30

Corundum top
ascan at mz position: 7.16

Only Corundum top measurements: setIsa06 actually have corundum in it!!!

Corundum TOP average:

Energy: 16.953209 keV
Lamda: 0.731332 Angstroem
Pixel size x, y: 75 x 75 microns²
SDD: 35.2419 cm
Center X: 1619.53 pixels
Center Y: 1695.36 pixels
tilt a: -0.39902648 degrees
tilt b: -13.935506 degrees

setIsa07: relative to all other peaks, the (012) peak is changing dramatically!!! And also some others at the end of the diffraction pattern. –> crazy texture???

setIsa08 shows Calcite at the very beginning of the measurement / sample.

CALIBRATING sample pg11t2

setIsa16 - setIsa21

CORUNDUM 1

Energy: 16.943586 keV
Lamda: 0.731747 Angstroem
Pixel size x, y: 75 x 75 microns²
SDD: 35.2451 cm
Center X: 1619.45 pixels
Center Y: 1695.38 pixels
tilt a: -0.39448358 degrees
tilt b: -14.164142 degrees

CORUNDUM 2

Energy: 16.943612 keV
Lamda: 0.731746 Angstroem
Pixel size x, y: 75 x 75 microns²
SDD: 35.1849 cm
Center X: 1619.45 pixels
Center Y: 1695.35 pixels
tilt a: -0.39514888 degrees
tilt b: -14.367813 degrees

AVERAGE setIsa14 Corund 1 and 2

Energy: 16.943599 keV
Lamda: 0.731715 Angstroem
Pixel size x, y: 75 x 75 microns²
SDD: 35.215 cm
Center X: 1619.45 pixels
Center Y: 1695.37 pixels
tilt a: -0.39466103 degrees
tilt b: -14.209012 degrees

CALIBRATING sample pg31t2

CORUNDUM 1

Energy: 16.949191 keV
Lamda: 0.731505 Angstroem
Pixel size x, y: 75 x 75 microns²
SDD: 35.2709 cm\ (It seems to be high (er) than usual, but still okay) Center X: 1619.34 pixels
Center Y: 1695.33 pixels
tilt a: -0.39427547 degrees
tilt b: -14.447052 degrees

CORUNDUM 2

Energy: 16.945334 keV
Lamda: 0.731671 Angstroem
Pixel size x, y: 75 x 75 microns²
SDD: 35.1922 cm
Center X: 1619.36 pixels
Center Y: 1695.36 pixels
tilt a: -0.39342386 degrees
tilt b: -14.660060 degrees

Average sample pg31t2 CORUNDUM 1 und 2

Energy: 16.9472625 keV
Lamda: 0.731588 Angstroem
Pixel size x, y: 75 x 75 microns²
SDD: 35.23155 cm
Center X: 1619.35 pixels
Center Y: 1695.35 pixels
tilt a: -0.393849665 degrees
tilt b: -14.553826 degrees

CALIBRATING sample pg11t2

setIsa32

CORUNDUM 1

Energy: 16.949503 keV
Lamda: 0.731492 Angstroem
Pixel size x, y: 75 x 75 microns²
SDD: 35.2649 cm
Center X: 1619.44 pixels
Center Y: 1695.35 pixels
tilt a: -0.39416315 degrees
tilt b: -15.159632 degrees

CORUNDUM 2

Energy: 16.938442 keV
Lamda: 0.731969 Angstroem
Pixel size x, y: 75 x 75 microns²
SDD: 35.1842 cm
Center X: 1619.42 pixels
Center Y: 1695.33 pixels
tilt a: -0.39663311 degrees
tilt b: -14.551802 degrees

Average sample pg11t2 CORUNDUM 1 und 2

Energy: 16.9439725 keV
Lamda: 0.7317305 Angstroem
Pixel size x, y: 75 x 75 microns²
SDD: 35.22455 cm
Center X: 1619.43 pixels
Center Y: 1695.34 pixels
tilt a: -0.39539813 degrees
tilt b: -14.855717 degrees

All .h5-files were transformed to .tiff for further evaluation using Fiji.

From measurement set68 till set74: Here is a mistake in naming: Instead of sample p501c, it actually is the sample s503a and must therefore be set68_s503a,…,set74_s503a and also set76_s503a,…,set89_s503a!!! The same is true for XRF! No damage visible in aragonite, i.e., no calcite was created.

XRD Data Evaluation

Damage-experiment samples

2D XRD mapping of entire sample

To identify:

a) Aragonite (111)
b) Calcite (104)

### Showing texture (specific orientation) of mineral crystals

By choosing one sample of each Species

a) Pocillopora Verrucosa
b) Stylophora Pistillata

and within these samples, one ‘zoom-in’ area each sample (50 x 50 µm) was chosen to 2D map all kinds of peaks which are related to certain Miller Indices and therefore to a certain orientation of the crystal.

### Quantifification of mineral versus amorphous content

a) weighting (with RUFF database) individual diffraction peaks within the entire XRD pattern –> (111) = 100 %
b) Compare entire mineral content (adding all weighted mineral parts from a) ) to transmission / absorption image: Subtract one another?

set02: 2D XRD-Mapping - s504d

calcite-channels

k

aragonite channels

set03: Mapping DAMAGE Intensity changes of single spots over time

Fluctuation of XRD intensities within single spots relate rather to beam fluctuation than to actual damage created by the beam.

set 39, 40, 41, 49 2D mapping of sample (overview) p501c

aragonite channels

set552D mapping of damage point in sample p501c

channels

set104, set107 2D mapping of damage point in sample p501a

THE INTENSITY DOES NOT CHANGE!

set65 2D mapping of sample (overview) s503a

aragonite channels

set95 2D mapping of sample (overview) p501a

aragonite channels

set96 2D mapping of sample (overview high resolution) p501a

aragonite and calcite channels

set97 2D mapping of sample (zoom-inhigh resolution) p501a

aragonite channels

set113 2D mapping of damage point in sample p501a

channels

set104, set107 2D mapping of damage point in sample p501a

THE INTENSITY DOES NOT CHANGE!

set122 2D mapping of sample (zoom-in lr resolution) s505d

aragonite channels

set123 2D mapping of sample (overview high resolution) s505d

channels

Looking into all CALCITE peaks (200-300 measurements at the same position), if the intensity over time changes:

sample p501c:
set 55

sample p501a
set104
set107
set113

sample s505d
set140

Isa-samples

2D XRD mapping of entire samples:

Pocillopora grandis

To identify:

a) Aragonite (111)
b) Calcite (104)

Showing texture (specific orientation) of mineral crystals

For every Pocillopora grandis sample:

All peaks were 2D mapped which are related to certain Miller Indices and therefore to a certain orientation of the crystal.

2D mapping of sample pg11t2

setIsa16

aragonite channels

### setIsa17 ### setIsa18 ### setIsa19 ### setIsa20 ### setIsa21 ### setIsa32

Aragonite channels: The same channels related to Miller indices were used as in setIsa16.

In order to have appropriate 2D images of each of those peaks, the background was subtracted. 2D images of the same peak width of the respective peaks were chosen.

**9) XRD Integration from Ivo**

Ivo only took one corundum for all the samples: NEEDS TO TAKE ALL CORUNDUMS LEFT AND RIGHT OF THE Samples

INTEGRATED “CALCITE” IMAGES ACTUALLY BELONG TO AN ARAGONITE PEAK!!!

We see already huge and very few single calcite peaks (~ 1µm-range?!)

Interpretation of data

Looking into single damaging points

set03: SUM,MED, and MAX of 120 images at the beginning compared to 120 images at the end does not give any phase changes, nor creating a phase such as Calcite. Only when zooming in, there is a tiny peak where calcite is supposed to be expected. However, peak intensity does not change at all in terms of creating calcite!!!

However, it might be the case that the intensity of the aragonite increases, as a result of radiation damage? Could it be possible, that the calcite is eradicated as a result of radiation damage? NO: SO FAR: The Intensity of aragonite as well as calcite increases over time, and then slightly seems to diminish and decreases.

set55 sample p501c: Here is calcite!!! Does it grow or disappear over time and radiation????

setIsa07: relative to all other peaks, the (012) peak is changing dramatically!!!

setIsa08: shows calcite at the very beginning of the measurement / top of the sample.