ASME Journal of Mechanical Design - T3 prism optimization manuscript

[Copilot]

Issue #75 recovers from agent failures on PR #20 by establishing a clean branch for the ASME Journal of Mechanical Design (JMD) manuscript and addressing the outstanding peer-review feedback.

This branch now merges all commits from PR #20's copilot/create-manuscript-template, bringing in the full manuscript/ (body, SI, build infrastructure), figures, and Edison scripts. ISSUE_75_CONTEXT.md remains as a consolidated working reference for the Issue #19 / PR #20 history.

Round-2 review feedback addressed (comment 4687197892)

• Scope: Title/abstract/intro now consistently frame a planetary-lander/payload energy absorber; the crutch-tip appears only as a future-work item in the Discussion; the abstract uses FDM and omits the crutch-tip motivation.
• Table 1 ↔ parameterization: Deferred to the authoritative T3-prism BO code (bo/t3_prism_sobol_batch.py, PR Add T3-prism (3-strut tensegrity) parametric CAD with Bambu PETG .gcode.3mf slice + re-importable project .3mf (H2D-only, supports enabled, scale 1.5× / cable_d 4.5 mm) + PLA-cables and PLA-struts/TPU-cables MM variants (with modeled-in PLA scaffo... #35) — a 5-variable continuous search space (R, H, twist, a single strut diameter, a single cable diameter) with no categorical variables. Removed the "12→4 orbit axes (1 strut + 3 cable)" claim; Table 1 now matches the code.
• Tendon diameter: Made continuous (3.0–5.5 mm) throughout; removed the categorical {1.2,1.8,2.4,3.0,4.5} mm set.
• BO method: Specified SAASBO (justified for better UQ/predictive accuracy even at ~5 variables), Matérn-5/2 ARD kernel, model-inferred noise, n=9 Sobol initialization followed by T=10 batches × q=5 prints (59 specimens total), fixed-seed policy, and a Zenodo DOI placeholder.
• Novelty: Added a comparison table vs Pajunen 2019 / Intrigila 2022 / Mo 2023 (architecture / fabrication / optimization / ground-truth).
• Language: Softened "ensure cyclic interface durability" pending pull-out/fatigue data; standardized FFF → FDM throughout.

Metal-analog validation plan

Added a Methods subsection plus an SI section describing a validation campaign using hollow aluminum rods and stainless-steel threaded cables. Predicted worst-, mediocre-, and best-performing designs (not only the top performers) will be built and compared against their PLA/TPU equivalents to test rank-order preservation, with a placeholder results table, a rank-correlation figure, and image callouts for the assembled/printed structures (true placeholders for now).

Edison round-3 mock review

Submitted the revised manuscript + SI to Edison ANALYSIS for another round of mock reviewer + editor feedback (task d17a2155, committed under edison-trajectories/mock-jmd-review-3/). Decision: Major Revision, explicitly improved over round 2, with all round-2 items acknowledged resolved; the remaining gate is the intentional placeholder Results/Discussion. Also fixed a budget inconsistency flagged by the reviewers (now n=9 + T=10×q=5 = 59 specimens).

Round-3 review feedback addressed (comment 4699376594)

Implemented the actionable round-3 items (those not requiring real campaign data):

• Citations now real (no longer TODO promises): Added and wired in the primary SAASBO (Eriksson & Jankowiak 2021) and TuRBO (Eriksson et al. 2019) papers, the canonical energy-absorber-metric references (Gibson & Ashby 1997; Avalle, Belingardi & Montanini 2001; Tan et al. 2005; Michailidis et al. 2011), and the SAE J211/1 impact-instrumentation standard for CFC-180 filtering; removed the matching "cite once added to bib" notes.
• BO formulation pre-committed: The primary reported campaign is now stated as a constrained multi-objective problem (maximize SEA and compaction efficiency subject to a peak-force bound fixed from the rigid control), acquisition = qNEHVI, with the hypervolume reference point anchored at the rigid-control point; LogEI single-objective is kept only as a baseline, and the robust/evolution-guided variants are demoted to a contingency.
• SAASBO justified empirically by benchmarking against a standard single-task GP baseline with the same Matérn-5/2 ARD kernel.
• Scope discipline: The Introduction now explicitly places off-axis/combined loading, multi-hit/cyclic durability, and landing-attitude variability out of scope (future work), and scopes the novelty/generality claims to the single-cell prototype space.
• Joint diameter: Added the rationale for fixing d_j at 7.0 mm.
• As-built resolution: New paragraph noting the nominally continuous d_s/d_t are discretized by nozzle/line-width/support, with measured diameters reported and dimensional spread folded into the inferred noise.
• Metal-analog test: Pre-specified the rank-preservation metric as Spearman ρ_s on SEA (peak force secondary) and reframed it as a stringent exploratory transfer test.

Data-dependent items (Results/Discussion, Table 3 print settings, Zenodo DOI) remain honest placeholders.

Edison round-4 mock review

Submitted the further-revised manuscript + SI to Edison ANALYSIS for a fourth round of mock reviewer + editor feedback (task a81649dc, committed with its notebook artifact under edison-trajectories/mock-jmd-review-4/). Decision: Major Revision, "closer to publishable form than the prior round-3 Major Revision." The editor explicitly confirms all four round-3 citation gaps are closed (SAASBO, TuRBO, SEA/densification metrics, SAE J211/1) and that the constrained multi-objective formulation, empirical SAASBO framing, consistent budget, justified joint diameter, acknowledged diameter discretization, and pre-specified metal-analog rank criterion are resolved. The remaining gate is the inherent placeholder Results/Discussion; the only new reference ask is to integrate the already-flagged tensegrity-AM works (Bauer 2021, Pajunen 2021 EML, Santos 2023, Sabouni-Zawadzka 2024) once verified.

Round-4 review feedback addressed (comment 4700329518)

Integrated the already-flagged tensegrity additive-manufacturing literature — the only non-data reference ask remaining from round 4. Each DOI was verified against Crossref before citing, and the prior \todo{} placeholder note was replaced with measured prose positioning this work against the printed-tensegrity literature in the multi-material / tensegrity-architecture background. References added to manuscript/references.bib and wired into manuscript-body.tex:

• Bauer et al. 2021 (Adv. Mater. 33(10):2005647, 10.1002/adma.202005647)
• Pajunen et al. 2021 (Extreme Mech. Lett. 44:101236, 10.1016/j.eml.2021.101236)
• Sabouni-Zawadzka et al. 2024 (Arch. Civ. Eng. 70(2):343–357, 10.24425/ace.2024.150987)
• Almeida et al. 2025 (Int. J. Solids Struct. 322:113590, 10.1016/j.ijsolstr.2025.113590)
• Davami et al. 2025 (Int. J. Impact Eng. 198:105208, 10.1016/j.ijimpeng.2024.105208)
• Wang et al. 2026 (Addit. Manuf. 118:105107, 10.1016/j.addma.2026.105107)

The three "verify-then-cite" extras (Almeida, Davami, Wang) all verified, so they were folded in as the closest dynamic/impact and integrated-fabrication tensegrity-AM works. Santos 2023 (10.1002/adma.202300639) was already cited from an earlier round.

Edison round-5 mock review

Submitted the revised manuscript + SI to Edison ANALYSIS for a fifth round of mock reviewer + editor feedback (task e4c536b4, committed with its notebook artifact under edison-trajectories/mock-jmd-review-5/). Decision: Major Revision, "a meaningful improvement over the round-4 submission … closer to acceptance." The Associate Editor explicitly states the round-4 tensegrity-AM reference ask is now resolved and that all prior bibliographic gaps are closed (SAASBO, TuRBO, SEA/densification metrics, SAE J211/1, plus this tensegrity-AM set), and Reviewer #3 confirms the new references are used appropriately (architecture-class evidence, not proof of the specific PLA/TPU process or internal-anchor joint). The remaining gate is the inherent placeholder Results/Discussion, synthetic example figures, and TBD process/test parameters; the only non-data suggestions are optional/strengthening (justify the homoscedastic inferred-noise choice, rename the novelty table, optionally one more transmitted-force→absorber-design citation).

Build

Rebuilt all PDFs (manuscript, supplementary, todos, and a latexdiff diff against the pre-session baseline) and recompiled the fabrication-workflow figure. Direct download links for co-author review were posted in the PR comment reply.

[sgbaird]

@me-madsen could you make another review of the latest manuscript?

[sgbaird]

@claude run an extensive overhaul of the manuscript to align with #84 #102 and every other recent addition or modification to this repository. See #99, too. Ensure that you are also overhauling supporting information.

Include #33 too.

Download the PPT so you can get a better sense of the most recent key messages.

Once done with your extensive edits, send to Edison to rubber duck it, focusing on adversarial dialogue and Socratic method. Run five iterations of "send one query to Edison, manually correct, ..."

In terms of analysis, at each stage, ensure that you're taking screenshots of each page and using your vision language reasoning. Also do vision language reasoning on all figures.

[claude]

Extensive manuscript overhaul + Edison rubber-duck loop

• Downloaded the shared deck (idetc-2026.pptx, 64 slides, modified 2026-08-21) and extracted all key messages + speaker notes
• Gathered context: IDETC presentation prep: Doumont template and video notes #84 (IDETC deck thread), Add T-3_01 Sobol batch print key (ID-to-spec mapping + as-printed .3mf) #102 (print key + live BO campaign), Where are we at on this project? #99 (project status), Add runnable tensegrity simulation demos (MuJoCo, PyBullet, PyChrono, Newton, DiffPD, PolyFEM+IPC) + 3D animated renders + Edison survey + regime-aware sweeps + PLA/TPU 85A printable-design model + BO integration bridge + PR #35 Sobol T3-prism sweep ac... #33 (simulation ladder), Better understanding the drop tower analysis #94/Energy-absorption measurability review + drop-tower metrics primer #97 (metrics honesty), Defining the Search Space for T3 Optimization Campaign (Parameters/Constraints) #85/Add drop-test protocol, Edison synthesis, and first-data analysis #86/T-3_01 Prints #98/How many "drops" have been run on the drop tower in the context of this repository? #101 (search space, tower, prints, drop counts)
• Fetched the never-collected Edison adversarial BO-objectives review (task 3e398131, submitted from Add T-3_01 Sobol batch print key (ID-to-spec mapping + as-printed .3mf) #102) and committed it (5fdcf87) — headline: drop e_rebound as an objective, use article-level noise, print replicates
• Overhauled manuscript-body.tex (commit ee71a09): pivoted from the stale planned-methods SEA/qNEHVI framing to the executed campaign — drop-tower objectives t180 + rebound energy, real seed-round results table (8 articles, 101 drops each), real Pareto / feature-importance / LOOCV figures (regenerated with consistent axis labels), round-2 batch status, constant-mass projection + printability screens, corrected J211 filter provenance, simulation ladder with honest scorecard, metal-analog metric switched to t180, Edison review folded into the Discussion/round-3 plan
• Overhauled supplementary.tex: print key, drop-tower protocol + rig characterization, printed-mass model, simulation fidelity ladder, support strategy as-printed
• Rebuilt all PDFs (manuscript 13 pp, SI 5 pp, todos, latexdiff) — zero missing citations
• Vision review: inspected every page of both PDFs and all campaign figures; fixed table overflow, doubled periods, tofu glyphs in figure labels, stale captions
• Edison rubber-duck iteration 1 (Socratic: methods + objectives) → manual corrections
• Edison rubber-duck iteration 2 (adversarial: results + figures cross-check) → corrections
• Edison rubber-duck iteration 3 (framing/novelty/scope) → corrections
• Edison rubber-duck iteration 4 (statistics at n=8) → corrections
• Edison rubber-duck iteration 5 (full-referee dialogue) → corrections
• Final commit, download links

View job run

[sgbaird]

@claude continue with where you left off in #76 (comment), note that if you go past an hour, you'll need to use your GitHub token instead of the app token that expires in approximately an hour. Similarly, make sure that you're committing your work frequently

[claude]

Rubber-duck loop complete: all five Edison iterations fetched and applied

Continued from the previous session and finished the five-iteration "send one query to Edison, manually correct" loop. Every task was submitted, fetched, applied, rebuilt, and committed; all artifacts are in edison-trajectories/rubberduck-1/ through rubberduck-5/.

• Iteration 1 (methods/objectives, task ce467b50): applied in the prior session (0a99f29)
• Iteration 2 (results/figures cross-check, task 018be975, fetched 6766a71, applied 139553a): Table 5 value fix (9hhbkp 7.0 to 6.9 mJ, confirmed by recomputation), rows strictly ordered by t180, valid-capture counting stated (101 per article, 103 for autv5r), Pareto set explicitly evaluated over the seven complete-objective articles, removed the unsupported "model-predicted front selects the same three" claim, LOOCV softened with rebound MAPE 37.8% reported and the archived fold-level CSV referenced
• Iteration 3 (framing/novelty/scope, task 96a394eb, fetched 17ff1f0, applied 7c27ed8): title changed to "Experiment-Driven Bayesian Optimization of the Impact Response of Multi-Material 3D-Printed Tensegrity-Inspired Structures" (no measured energy-absorption claim), abstract rewritten with real seed numbers and completed-versus-pending accounting, no-pretension caveat moved into the up-front definition, novelty claim bounded to the reviewed literature and the completed recommendation step, novelty table expanded (Wang 2026, Almeida/Davami 2025, new response-optimized column), scope/durability/generality wording tightened
• Iteration 4 (statistics at n=8, task f2c5dea8, fetched ddd39ca, applied 2caf861): mass-confound paragraph rewritten around non-identifiability at n=7, r=0.83 qualified (95% CI 0.20 to 0.97; r=0.19 without 6lhxfy), attenuation made article-specific everywhere, 0.72% CV demoted to a provisional five-print estimate, "within-session per-drop CV" terminology adopted, feature importances relabeled prior-sensitive diagnostics, LOOCV framed descriptive-only, Tier-C rho reframed as exploratory in-sample association
• Iteration 5 (full JMD referee panel, task 618d67c9, fetched 2a46fe8, applied 1669178) resolved all 12 MUST-FIX-NOW items that were fixable without new data:
  • Round-2 provenance (a FAILS finding): Fig. 7's orange diamonds were plotting the regenerated constant-printed-mass set, not the batch on the printer. Both sets are now archived with unambiguous names (round2-as-printed-solid-mass-projection.csv, round3-candidate-constant-printed-mass.csv) and the text states exactly which set the figure shows
  • Tier-C rank statistic corrected: rho_s = -0.929 with exact two-sided permutation p = 0.0028 (the prior "p about 0.0067" was inconsistent with the exact enumeration)
  • Synthetic mechanistic figure removed; fab-workflow figure corrected ("Pretensioning" and "Static Testing" claims gone) and recompiled
  • Table 3 print settings recovered from the archived as-printed Bambu Studio project (nozzle temps 220/220 C, bed profile 55/35 C, 0.30 mm layers, 0.62 mm line width, filaments, Bambu Studio 2.7.1), with the mid-batch TPU 0.4 to 0.6 mm high-flow nozzle change footnoted
  • Citation integrity: AlphaGo-BO now cites the verified Chen et al. 2018 arXiv paper; the Caminero interface miscitation and unknown-journal Ruwais citation removed; the wang2022bayesian/lee2023bayesian stubs deleted after their DOIs resolved to unrelated or nonexistent works; four structural BibTeX fixes. (The "Johans/Daraoio/Rancy" corruption the referee saw was a PDF text-extraction artifact; the source and rendered bibliography are correct, as is the LOOCV figure's minus sign)
  • SI Fig. S1 placeholder replaced with the real five-variant joint montage renders recovered from the joint-design branch; new SI table of operational signal-processing parameters; metal-analog reframed as a planned exploratory comparison with its missing protocol details enumerated; joint-durability and simulation claims narrowed

Direct downloads (commit 1669178) for @Jeffrayhill1 and @me-madsen:

• 📄 Manuscript (13 pp): manuscript.pdf
• 📎 Supplementary Information (6 pp): supplementary.pdf
• 📝 Review copy with margin TODOs: manuscript-todos.pdf
• 🔍 Latexdiff vs. the pre-rubber-duck baseline (ee71a09): manuscript-diff.pdf

Every page of the rebuilt manuscript and SI was rendered and inspected visually (title/abstract, novelty table, print-parameter table, Table 5, Pareto and LOOCV figures, SI joint montage); zero missing citations and zero overfull boxes beyond a 1.6 pt residue on Table 3.

What remains (data-gated, per the iteration-5 Associate Editor): round-2 predicted-versus-measured, budget-matched baseline, SAASBO-versus-GP calibration, replicate articles, rebound video validation, quasi-static Instron metrics, metal-analog build, dimensional metrology, and pull-out/fatigue testing. Referee polish items still open: labeling Fig. 6 by spec ID with a scale bar and regenerating the Pareto/importance figure axis labels (both need the campaign plotting pipeline with a NUTS refit), reworking the proposal-style Fig. 1, and the version-tagged code/data archival release.

Note: the app git token expired mid-session as anticipated; recovery used the action's own OIDC token-exchange path, and all commits were pushed (nothing stranded locally).

View job run

[sgbaird]

@claude these edits are really bad. It should still read based on the intended final scope, with placeholder data in certain places. Assume that we have the data from the second batch (come up with some dummy data, but clearly mark it as such).

[claude]

Claude finished @sgbaird's task in 20m 39s —— View job

---

Manuscript restored to intended final scope, with clearly-marked dummy round-2 data

• Read current manuscript/SI and identified the status-report framing introduced by the rubber-duck loop
• Rewrote the manuscript at the intended final scope (abstract, intro, results, discussion, conclusions in final-paper voice)
• Generated dummy round-2 batch data, clearly marked as synthetic everywhere
• Replaced the "Later-Round Placeholders" stub with a full Round-2 Results subsection
• Updated the Supplementary Information to match (round-2 print key, draft-note convention)
• Rebuilt all four PDFs, vision-checked every page, fixed a line-number rendering bug
• Committed and pushed (938dbb4, a50b472, 827301d)

Direct downloads (commit 827301d) for @Jeffrayhill1 and @me-madsen:

• 📄 Manuscript (15 pp): manuscript.pdf
• 📎 Supplementary Information (6 pp): supplementary.pdf
• 📝 Review copy with margin TODOs: manuscript-todos.pdf
• 🔍 Latexdiff vs. the pre-session baseline (1669178): manuscript-diff.pdf

How the dummy data is marked

Every invented number is typeset in violet, and a violet draft-note box on page 1 of both the manuscript and the SI states the convention: violet = synthetic placeholder pending the physical round-2 drop sessions, black = real measurement. The dummy figures additionally carry a diagonal "SYNTHETIC PLACEHOLDER DATA" watermark, and the dataset lives at round2-measured-DUMMY.csv, generated by make_round2_dummy_data.py so it can be regenerated or swapped for real pipeline output. The real seed-round measurements are untouched.

What the paper now says (round-2 dummy values anchored to the real archived predictions for trials 10 to 18)

• New Round-2 Results subsection: a full results table (masses, t180 ± sd, rebound score, f_n, prediction column), predicted-versus-measured comparison (MAPE 1.9%, all nine inside the two-sd band), updated Pareto front (four of five front members are round-2 designs; the seed best attenuator is now dominated), hypervolume growth of 79% versus 19% for a budget-matched Sobol baseline, and a SAASBO-versus-standard-GP calibration audit (94% versus 81% interval coverage). All violet.
• Abstract, introduction, discussion, and conclusions now read as the final paper: the loop closes a full recommend-fabricate-measure-update cycle, with a one-line parenthetical noting the round-2 values are marked placeholders. The best dummy design deepens attenuation to t180 = 0.858 and eight of nine recommended designs measure below unity.
• Kept as honest placeholders (as you specified "placeholder data in certain places"): metal-analog table/figure, quasi-static campaign, replicate-article study, seed specs 03/06/07 rows, Zenodo DOI.
• SI additions: a violet round-2 print key (Table S2) and the same draft-note convention box.

Build quality

Vision-checked every page of both PDFs at each build: zero missing citations, violet marking legible in print, watermarks visible. One real bug found and fixed along the way: a bare \color declaration inside the round-2 table float leaked into LaTeX's output routine and displaced the lineno margin numbers into the column gutter on pages 9 to 11; switching to per-cell coloring resolved it (827301d). Also repositioned a clipped annotation in the hypervolume figure.

Not done this round (not requested): no new Edison submission. If you want a round-6 mock review of the final-scope draft, say the word.