Vibrational spectroscopy and the structure of solids: The example \nof carbonate minerals
Bibliographic record
Abstract
Studying material structure on the atomic scale in solids can give clues as to how that material was \nformed, aged, or used. Atoms in solids are constantly in motion. A material’s specific composition \nand crystal arrangement results in a unique profile of atomic vibrations. These vibrations, or modes, \ncan be grouped into two main types; internal modes are higher energy vibrations related to atomic \nmotion of single atoms or moieties within the unit cell, whereas external modes are lower in energy \nand correspond to the collective movement of multiple coordinated atoms or moieties. Past investigations \nfocused on the vibrations of solids have explored the effect of crystalline ordering on internal \nmodes both experimentally and computationally. In this thesis, I explore the viability of established \nexperimental and computational methods to examine the influence of structural differences on the \nthe external mode vibrations using calcium carbonate as a case study material. The experimental \nprojects focus on infrared spectroscopy. This tool is sensitive enough to observe subtle differences in \nthe internal modes that are linked to structural differences but has yet to be explored for the external \nmodes. \nWe study calcium carbonate systems using infrared spectroscopic methods to understand the impact \nof structure on vibrational properties. Our initial goal was to correlate novel external mode vibration \ndata trends with the established understanding of internal mode changes and atomic structure \ndata. We found that the broadness of the external modes makes extracting structural information using \nthe previous analysis protocols impractical. The results highlight potential pitfalls for researchers \nwho are new to these spectroscopic techniques. We preach caution when attempting to interpret \nenergy shifts of external modes as structural differences amongst samples without correlating with \nadditional experimental methods. \nFurther experiments focused on photoacoustic infrared spectroscopy, a specialized version of the \ntechnique. Previous works have highlighted but failed to explain how this specialized setup can \nenhance the detection of weak internal modes. We sought to determine the mechanism for this documented \nphenomenon. While we could not identify the cause of the enhancement, our experiments \nand analysis showed that it is intrinsic to the photoacoustic method and eliminated detector saturation, \noften thought to be the cause, as the root mechanism. \nii \nFinally, I used computational molecular dynamics methods to simulate calcium carbonate vibrations. \nUsing previously published parameters, I was able to generate a vibrational density of states \n(VDOS) for the calcium carbonate polymorph aragonite. This work is valuable as alternative computational \nmethods to simulate the external vibrations of calcium carbonates are computationally \nexpensive. The computed VDOS of aragonite shows a reasonable level of qualitative agreement with \nexperimental measurements. This work serves as a proof-of-concept and starting point to observe \ndisorder’s effects on the calculated vibrational density of states.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.001 | 0.002 |
| Science and technology studies | 0.002 | 0.002 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".