Simulations of Structure and Vibrational Spectra of Deoxyoctanucleotides
Bibliographic record
Abstract
Combined molecular dynamics and ab initio computations were applied for analysis of infrared absorption and vibrational circular dichroism spectra of deoxyoctanucleotides. Unlike for previous idealized models, molecular geometries of these shorter DNA fragments in solutions were obtained as dynamic averages from simulations in a periodic water box. Vibrational spectra for the whole octamers including hydrogen-bonded solvent molecules were simulated on the basis of density-functional calculations on small fragments and subsequent transfer of molecular property tensors. Explicit and continuum solvent models were compared. Apparently, the DNA segments retain an approximate B-conformation in the aqueous solutions, but the terminal base pairs significantly deviate from the planar arrangement and the vibrational circular dichroism spectrum for (CG)(2) nucleotide indicates a larger average helical twist. Sodium counterions moved freely around the molecule during the simulation and do not influence spectral intensities. Simulated absorption spectra faithfully reproduced the experimental signal of principal functional groups, while only qualitative agreement was obtained for the dependence on the basis sequence.
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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 | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| 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".