XPS-optimized oxygenated amorphous carbon - Revision history

Tigany Zarrouk: /* Motivation for structural inference */

2024-06-19T10:26:09Z

Motivation for structural inference

2024-06-19T10:25:47Z

Motivation for structural inference

2024-06-19T10:25:33Z

2024-06-19T10:24:26Z

Motivation for structural inference

2024-06-19T09:01:37Z

Experimental Observable Optimization

2024-06-19T08:59:34Z

(Grand-Canonical) Monte-Carlo

2024-06-19T08:57:57Z

Experimental Observable prediction/optimization

2024-06-19T08:22:52Z

SOAP (many-body) descriptor

2024-06-18T19:44:54Z

Motivation for structural inference

2024-06-18T19:43:11Z

Deconvolution analysis

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 [[File:deconvolution_comparison_fill_-3_new.png | 400px]]
 We will do simulations similar to the above, which is from our JACS paper ([[#citeproc_bib_item_11|Zarrouk et al. 2024]]).
 <span id="theory-and-methods"></span>

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 [[File:deconvolution_comparison_fill_-3_new.png | 400px]]
-We will do simulations similar to the above, is from our JACS paper ([[#citeproc_bib_item_11|Zarrouk et al. 2024]]).
+We will do simulations similar to the above, which is from our JACS paper ([[#citeproc_bib_item_11|Zarrouk et al. 2024]]).
 <span id="theory-and-methods"></span>

@@ Line 32: / Line 32: @@
 [[File:deconvolution_comparison_fill_-3_new.png | 400px]]
-We will do simulations similar to the above, is from our JACS paper.
+We will do simulations similar to the above, is from our JACS paper ([[#citeproc_bib_item_11|Zarrouk et al. 2024]]).
 <span id="theory-and-methods"></span>

@@ Line 32: / Line 32: @@
 [[File:deconvolution_comparison_fill_-3_new.png | 400px]]
+We will do simulations similar to the above, is from our JACS paper.
 <span id="theory-and-methods"></span>

← Older revision		Revision as of 09:01, 19 June 2024
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	[[File:xps_optimization_gcmc.png \| 800px]]		[[File:xps_optimization_gcmc.png \| 800px]]
		+
		+	We can observe the significant effect of the energy scale here. The experimental energy decreases quickly, with a concurrent increase in the energy per atom. After spectral agreement, the system is allowed to relax.

	<span id="multiple-observables"></span>		<span id="multiple-observables"></span>

← Older revision		Revision as of 08:59, 19 June 2024
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	[[File:standard_gcmc.png \| 800px]]		[[File:standard_gcmc.png \| 800px]]
		+
		+	We see there is a large amount of oxygen inserted due to the large chemical potential for this simulation. This shifts the xps to large binding core electron binding energies, and there is no agreement the final structure with the experimental XPS.

	<span id="experimental-observable-optimization"></span>		<span id="experimental-observable-optimization"></span>

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 ↑ Experimental XPS deconvolution ([[#citeproc_bib_item_9|Santini et al. 2015]])
+We see in the experimental deconvolution analysis that sp3 motifs compose the primary XPS peak. The generation of a-COx here was done by physical vapor deposition of graphitic carbon in an oxygen environment. They see a reduction in the number of sp2 bonds. They also claim there is a complete transformation of sp2 to sp3 that is reversible with a short annealing at 500C.
 [[File:deconvolution_comparison_fill_-3_new.png| 400px]]
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 ↑ Our XPS deconvolution ([[#citeproc_bib_item_9|Santini et al. 2015]])
 [[File:xps_shifts_miguel_first.png| 400px]]
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 [[File:xps_shifts_miguel_last.png| 400px]]
-We see with oxygen content that sp2 motifs are shifted significantly, even past the sp3 reference. This is why the experimental deconvolution did not give what we expect: sp2 carbon that composes the primary XPS peak.
+We see with oxygen content that sp2 motifs are shifted significantly, even past the sp3 reference. Due to the presence of oxygen, there is a shift of sp2 motifs which are not accounted for by the experimental deconvolution references, as these are fixed. This is why the experimental deconvolution did not give what we expect: sp2 carbon that composes the primary XPS peak.
 <span id="summary"></span>

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 * For specifics of SOAP turbo, refer to Miguel's paper ([[#citeproc_bib_item_3|Caro 2019]])
-← SOAP expansion.
+<span id="how-do-we-model-xps"></span>
 == How do we model XPS? ==

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 Need efficient structure search to find '''agreement''' with '''experimental''' data ''and'' '''ab-inito''' data.
-# With <u>CO GAP + Core electron binding energy SOAP</u> model we will perform '''modified (Grand-canonical) Monte-Carlo''' to produce ''experimentally consistent, low energy structures'' of oxygenated amorphous carbon.
+With <u>CO GAP + Core electron binding energy SOAP</u> model we will perform '''modified (Grand-canonical) Monte-Carlo''' to produce ''experimentally consistent, low energy structures'' of oxygenated amorphous carbon.
-# I will further show preliminary work on *“Molecular Augmented Dynamics”*: generate forces from experimental deviation, to match experimental spectra via MD.
 [[File:deconvolution_comparison_fill_-3_new.png | 400px]]

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-[[File:exp_xps_with_background_high.png]]
+[[File:exp_xps_with_background_high.png | 400px]]
 ↑ Experimental XPS deconvolution ([[#citeproc_bib_item_9|Santini et al. 2015]])
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-[[File:deconvolution_comparison_fill_-3_new.png]]
+[[File:deconvolution_comparison_fill_-3_new.png| 400px]]
 ↑ Our XPS deconvolution ([[#citeproc_bib_item_9|Santini et al. 2015]])
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-[[File:xps_shifts_miguel_first.png]]
+[[File:xps_shifts_miguel_first.png| 400px]]
-[[File:xps_shifts_miguel_last.png]]
+[[File:xps_shifts_miguel_last.png| 400px]]
 We see with oxygen content that sp2 motifs are shifted significantly, even past the sp3 reference. This is why the experimental deconvolution did not give what we expect: sp2 carbon that composes the primary XPS peak.