Modeling of Various Optical Spectra in the Presence of Slow Excitation Energy Transfer in Dimers and Trimers with Weak Interpigment Coupling: FMO as an Example
Bibliographic record
Abstract
We present an improved simulation methodology to describe nonphotochemical hole-burned (NPHB) spectra. The model, which includes both frequency-dependent excitation energy transfer (EET) rate distributions and burning following EET, provides reasonable fits of various optical spectra including resonant and nonresonant holes in the case of FMO complex. A qualitative description of the NPHB process in light of a very complex protein energy landscape is briefly discussed. As an example, we show that both resonant and nonresonant HB spectra obtained for the 825 nm band of the trimeric FMO of C. tepidum are consistent with the presence of a relatively slow EET between the lowest energy states of the monomers of the trimer (mostly localized on BChl a 3), with a weak (∼1 cm(-1)) coupling between these states revealed via calculated emission spectra. We argue that the nature of the so-called 825 nm absorption band of the FMO trimer, contrary to the presently accepted consensus, cannot be explained by a single transition.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.001 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.001 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 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 source (direct Gemma or distilled Codex), 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".