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Engineering quantum optical responses of microtubules through tryptophan-network simulations and ultraviolet spectroscopy

Lea Gassab; Travis J. A. Craddock · 2026

AI-verified citationSRC-GASSAB-2026A
identifier / locator
arxiv:2604.18604
url
https://arxiv.org/html/2604.18604
verification note
text retrieved and shown to the drafter on 2026-09-11 (run 2026-09-11-draft-orch-or-115454); passages checked by the verify verb
reliability notes
  • Preprint (arXiv:2604.18604v1, 9 Apr 2026); read as arXiv HTML, which carries no page numbers, so locators name sections.
  • Steady-state microplate absorbance and fluorescence; microtubule absorbance contains a large wavelength-dependent scattering term, so microtubule quantum yields are reported by the authors as bounds rather than single values.
  • Partly independent of the Babcock/Kurian line but shares the Craddock modelling lineage.

Evidence drawn from this source

Supports· moderateORCH-E056

Cross-lab: polymerization raises tubulin quantum yield at 280 nm in porcine tubulin

what the source states
Measuring porcine tubulin dimers against taxol-stabilized microtubules in UV-transparent microplates, the authors report that "polymerization enhances microtubule quantum yield at 280 nm" and that "the polymerization percent change is positive for both bounds" of the absorbance treatment, with the difference statistically significant on both branches.
what we infer
The direction of the quantum-yield trend now has partial cross-lab support in a different preparation, which firms up the collective-optics observation rung — as condensed-matter physics of an ordered aromatic lattice, which is what the adopted assessment already says.
limitations
  • Preprint; steady-state microplate geometry.
  • Shares the Craddock modelling lineage with the superradiance literature it tests, so independence is partial.
  • 280 nm excitation is not tryptophan-selective.
  • Second reader (claude-sonnet-5, 2026-09-11, run 2026-09-11-verify-orch-or-120610, verify-v6) found the passage bears in different directions on the claims the record named; this record carries "supports" toward ORCH-C021, the rest went to a record of its own at intake: The quotes are accurate and correctly located, and the paper does report a robust 280 nm polymerization-induced QY increase consistent with the superradiance model's small predicted enhancement, so it supports ORCH-C021. However, the paper explicitly cautions (in 'Local photophysics versus cooperative emission') that such steady-state polymerization increases can arise from conventional, non-collective photophysical mechanisms, so this single observation does not itself establish nontrivial collective electrodynamics distinct from a passive-scaffold account; it is at best contextual for ORCH-C013, not supporting evidence. The record's blanket 'supports' direction for both claims therefore overstates what the passage establishes for C013.
Lea Gassab (2026)AI-verified citationORCH-C021
Context· moderateORCH-E074

Cross-lab: polymerization raises tubulin quantum yield at 280 nm in porcine tubulin — toward ORCH-C013

what the source states
Measuring porcine tubulin dimers against taxol-stabilized microtubules in UV-transparent microplates, the authors report that "polymerization enhances microtubule quantum yield at 280 nm" and that "the polymerization percent change is positive for both bounds" of the absorbance treatment, with the difference statistically significant on both branches.
what we infer
The direction of the quantum-yield trend now has partial cross-lab support in a different preparation, which firms up the collective-optics observation rung — as condensed-matter physics of an ordered aromatic lattice, which is what the adopted assessment already says.
limitations
  • Preprint; steady-state microplate geometry.
  • Shares the Craddock modelling lineage with the superradiance literature it tests, so independence is partial.
  • 280 nm excitation is not tryptophan-selective.
  • Second reader (claude-sonnet-5, 2026-09-11, run 2026-09-11-verify-orch-or-120610, verify-v6) found the passage bears in different directions on the claims the record named; this record carries "context" toward ORCH-C013, the rest went to a record of its own at intake: The quotes are accurate and correctly located, and the paper does report a robust 280 nm polymerization-induced QY increase consistent with the superradiance model's small predicted enhancement, so it supports ORCH-C021. However, the paper explicitly cautions (in 'Local photophysics versus cooperative emission') that such steady-state polymerization increases can arise from conventional, non-collective photophysical mechanisms, so this single observation does not itself establish nontrivial collective electrodynamics distinct from a passive-scaffold account; it is at best contextual for ORCH-C013, not supporting evidence. The record's blanket 'supports' direction for both claims therefore overstates what the passage establishes for C013.
Lea Gassab (2026)AI-verified citationORCH-C013
Qualifies· moderateORCH-E075

The magnitude of the polymerization effect spans nearly an order of magnitude on the scattering correction — part 1

what the source states
At 280 nm excitation in the no-Trp condition, the polymerization percent change is positive for both bounds, "ranging from approximately + 6.1 % +6.1\% using Q ​ Y raw" to approximately +46.8% using the scattering-corrected branch (QY_bgA).
what we infer
My inference: the observable is not yet metrologically stable. Running an anesthetic potency series against it (ORCH-R002, ORCH-R009) before the scattering correction is closed risks measuring the correction rather than the physics.
limitations
  • The bounds arise from an analysis choice, not from replicate scatter.
  • Preprint.
Lea Gassab (2026)AI-verified citationORCH-C021
Qualifies· moderateORCH-E076

At tryptophan-selective excitation the polymerization effect reverses sign between treatments — part 1

what the source states
At 295 nm excitation in the no-Trp condition, the two polymerization percent-change bounds differ substantially and reverse sign: "the two bounds differ substantially and reverse sign".
what we infer
My inference: 295 nm is where excitation is most selective for tryptophan and therefore where comparison with a tryptophan-only excitonic model is most meaningful — and it is exactly there that the measurement cannot yet fix a sign. This is a metrological, not a biological, obstacle, and it is fixable.
limitations
  • A single dataset in one geometry.
  • Preprint.
Lea Gassab (2026)AI-verified citationORCH-C021
Qualifies· moderateORCH-E077

At tryptophan-selective excitation the polymerization effect reverses sign between treatments — part 2

what the source states
The uncorrected absorbance branch gives an apparent polymerization decrease at 295 nm, "an apparent decrease of about" −58.6% using QY_raw.
what we infer
My inference: 295 nm is where excitation is most selective for tryptophan and therefore where comparison with a tryptophan-only excitonic model is most meaningful — and it is exactly there that the measurement cannot yet fix a sign. This is a metrological, not a biological, obstacle, and it is fixable.
limitations
  • A single dataset in one geometry.
  • Preprint.
Lea Gassab (2026)AI-verified citationORCH-C021
Qualifies· moderateORCH-E078

At tryptophan-selective excitation the polymerization effect reverses sign between treatments — part 3

what the source states
The background-corrected absorbance branch gives an apparent polymerization increase at 295 nm, "an apparent increase of about" +12.7% using QY_bgA.
what we infer
My inference: 295 nm is where excitation is most selective for tryptophan and therefore where comparison with a tryptophan-only excitonic model is most meaningful — and it is exactly there that the measurement cannot yet fix a sign. This is a metrological, not a biological, obstacle, and it is fixable.
limitations
  • A single dataset in one geometry.
  • Preprint.
Lea Gassab (2026)AI-verified citationORCH-C021
Qualifies· moderateORCH-E079

At tryptophan-selective excitation the polymerization effect reverses sign between treatments — part 4

what the source states
Because the sign reverses across plausible absorbance treatments, no single effect size is assigned at 295 nm; "the polymerization comparison remains bounded in this dataset".
what we infer
My inference: 295 nm is where excitation is most selective for tryptophan and therefore where comparison with a tryptophan-only excitonic model is most meaningful — and it is exactly there that the measurement cannot yet fix a sign. This is a metrological, not a biological, obstacle, and it is fixable.
limitations
  • A single dataset in one geometry.
  • Preprint.
Lea Gassab (2026)AI-verified citationORCH-C021
Context· moderateORCH-E080

Structural variability suppresses the superradiant enhancement the collective reading relies on — part 2

what the source states
Despite the reduced maximal enhancement, the molecular-dynamics-derived ensembles "maintained quantum yields above 0.14 over the lengths examined".
what we infer
Two things come apart here: a modest quantum-yield trend that survives disorder, and the large cooperative radiative-rate gain that does not. Only the latter is what the scale-bridging argument needs.
limitations
  • Computational; disorder is MD-sampled, not measured in vivo.
  • Preprint.
  • Direction set to "context" (from "supports") by the second reader (claude-sonnet-5, 2026-09-11, run 2026-09-11-verify-orch-or-120610, verify-v6) at intake: The quote is accurately taken from the 'Structural variability suppresses superradiance' section and is atomic, but it reports that quantum yield stayed above 0.14 despite the enhancement drop, not the magnitude or nature of the enhancement reduction itself (that claim is made in the preceding sentence). Since ORCH-C063 concerns the degree of superradiant enhancement suppression relative to the ordered 1JFF lattice, this QY-stability statement only presupposes that reduction rather than evidencing it, so it functions as context rather than direct support.
Lea Gassab (2026)AI-verified citationORCH-C063