{"record_kind": "run_header", "run_id": "pearl-manuscript-s8-20260916", "seq": 1, "trace_sequence": 1, "timestamp": "2026-09-16T10:24:12+00:00", "logged_at": "2026-09-16T10:24:12.350000+00:00", "source_agent": null, "scenario_id": "S8", "provenance": "manuscript-aligned-case-log-v1", "not_wet_lab": false, "world_contract": "manuscript-case-S8", "config": {"communication_mode": "typed_events", "ir_schema_version": 4}, "user_command": "Autonomously characterize the HRP–TMB assay: identify its linear working range and estimate Km and kcat from time-resolved measurements.", "sources": [{"well": "A1", "label": "Enzyme stock (HRP), 30 nM", "volume_ul": 2000, "concentration_nM": 30.0, "concentration_ng_ml": 1320.0, "mw_g_per_mol": 44000.0}, {"well": "A2", "label": "Chromogenic substrate stock (TMB), 5.0 mM", "volume_ul": 5000, "concentration_mM": 5.0}, {"well": "A3", "label": "PBS, 1×", "volume_ul": 15000}], "constraints": ["The instruction does not prescribe well layout, an acid stop, or a dilution factor.", "No working concentration and no dilution factor are in the instruction."], "instrument": {"wavelength_nm": 652, "epsilon_per_M_cm": 39000.0, "path_cm": 0.56, "path_basis": "Applied path is 0.28 cm times the well volume divided by 100 uL. At 200 uL that path is 0.56 cm.", "hrp_mw_g_per_mol": 44000.0, "initial_rate_elapsed_s": [3.0, 6.0, 9.0], "max_substrate_conversion": 0.15, "min_initial_rate_points": 3}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 2, "trace_sequence": 2, "timestamp": "2026-09-16T10:24:24+00:00", "logged_at": "2026-09-16T10:24:24.350000+00:00", "source_agent": "human", "event_id": "s8-stock", "event_type": "external_perturbation", "message": "The HRP stock is 30 nM, 2000 uL. That is the only enzyme concentration given for this run.", "rationale": "The HRP stock is 30 nM, 2000 uL. That is the only enzyme concentration given for this run.", "payload": {"well": "A1", "declared_concentration_nM": 30.0, "physical_concentration_nM": 30.0, "exact_concentration_nM": 30.0, "stock_status": "only_given", "declared_volume_ul": 2000, "physical_volume_ul": 2000, "disclosed_to_agents": true}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 3, "trace_sequence": 3, "timestamp": "2026-09-16T10:24:36+00:00", "logged_at": "2026-09-16T10:24:36.350000+00:00", "source_agent": "planner", "event_id": "plan-plan-s8-neat", "event_type": "plan", "plan_id": "plan-s8-neat", "revision_id": "rev_0", "rationale": "The given stock is 30 nM. This first preparation uses 15.1515 uL of that stock, which is 100 ng/mL in a 200 uL well. I will measure whether that condition is suitable. Read each well 24 s after TMB is dispensed.", "canonical_operations": [{"action_id": "plan-s8-neat-B1-hrp", "tool_name": "transfer", "source": "reservoir:A1", "dest": "plate:B1", "volume_ul": 15.151515151515152, "reagent": "hrp"}, {"action_id": "plan-s8-neat-B1-buffer", "tool_name": "transfer", "source": "reservoir:A3", "dest": "plate:B1", "volume_ul": 152.84848484848484, "reagent": "buffer"}, {"action_id": "plan-s8-neat-B1-tmb", "tool_name": "transfer", "source": "reservoir:A2", "dest": "plate:B1", "volume_ul": 32.0, "reagent": "tmb"}, {"action_id": "plan-s8-neat-B1-mix", "tool_name": "mix_well", "well": "B1"}, {"action_id": "plan-s8-neat-B2-hrp", "tool_name": "transfer", "source": "reservoir:A1", "dest": "plate:B2", "volume_ul": 15.151515151515152, "reagent": "hrp"}, {"action_id": "plan-s8-neat-B2-buffer", "tool_name": "transfer", "source": "reservoir:A3", "dest": "plate:B2", "volume_ul": 152.84848484848484, "reagent": "buffer"}, {"action_id": "plan-s8-neat-B2-tmb", "tool_name": "transfer", "source": "reservoir:A2", "dest": "plate:B2", "volume_ul": 32.0, "reagent": "tmb"}, {"action_id": "plan-s8-neat-B2-mix", "tool_name": "mix_well", "well": "B2"}, {"action_id": "plan-s8-neat-B3-hrp", "tool_name": "transfer", "source": "reservoir:A1", "dest": "plate:B3", "volume_ul": 15.151515151515152, "reagent": "hrp"}, {"action_id": "plan-s8-neat-B3-buffer", "tool_name": "transfer", "source": "reservoir:A3", "dest": "plate:B3", "volume_ul": 152.84848484848484, "reagent": "buffer"}, {"action_id": "plan-s8-neat-B3-tmb", "tool_name": "transfer", "source": "reservoir:A2", "dest": "plate:B3", "volume_ul": 32.0, "reagent": "tmb"}, {"action_id": "plan-s8-neat-B3-mix", "tool_name": "mix_well", "well": "B3"}, {"action_id": "plan-s8-neat-B4-hrp", "tool_name": "transfer", "source": "reservoir:A1", "dest": "plate:B4", "volume_ul": 15.151515151515152, "reagent": "hrp"}, {"action_id": "plan-s8-neat-B4-buffer", "tool_name": "transfer", "source": "reservoir:A3", "dest": "plate:B4", "volume_ul": 152.84848484848484, "reagent": "buffer"}, {"action_id": "plan-s8-neat-B4-tmb", "tool_name": "transfer", "source": "reservoir:A2", "dest": "plate:B4", "volume_ul": 32.0, "reagent": "tmb"}, {"action_id": "plan-s8-neat-B4-mix", "tool_name": "mix_well", "well": "B4"}, {"action_id": "plan-s8-neat-B5-hrp", "tool_name": "transfer", "source": "reservoir:A1", "dest": "plate:B5", "volume_ul": 15.151515151515152, "reagent": "hrp"}, {"action_id": "plan-s8-neat-B5-buffer", "tool_name": "transfer", "source": "reservoir:A3", "dest": "plate:B5", "volume_ul": 152.84848484848484, "reagent": "buffer"}, {"action_id": "plan-s8-neat-B5-tmb", "tool_name": "transfer", "source": "reservoir:A2", "dest": "plate:B5", "volume_ul": 32.0, "reagent": "tmb"}, {"action_id": "plan-s8-neat-B5-mix", "tool_name": "mix_well", "well": "B5"}]} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 4, "trace_sequence": 4, "timestamp": "2026-09-16T10:24:48+00:00", "logged_at": "2026-09-16T10:24:48.350000+00:00", "source_agent": null, "event_id": "appr-appr-plan-s8-neat", "event_type": "proceed_signal", "plan_id": "plan-s8-neat", "revision_id": "rev_0", "approval_id": "appr-plan-s8-neat", "approved_action_ids": ["plan-s8-neat-B1-hrp", "plan-s8-neat-B1-buffer", "plan-s8-neat-B1-tmb", "plan-s8-neat-B1-mix", "plan-s8-neat-B2-hrp", "plan-s8-neat-B2-buffer", "plan-s8-neat-B2-tmb", "plan-s8-neat-B2-mix", "plan-s8-neat-B3-hrp", "plan-s8-neat-B3-buffer", "plan-s8-neat-B3-tmb", "plan-s8-neat-B3-mix", "plan-s8-neat-B4-hrp", "plan-s8-neat-B4-buffer", "plan-s8-neat-B4-tmb", "plan-s8-neat-B4-mix", "plan-s8-neat-B5-hrp", "plan-s8-neat-B5-buffer", "plan-s8-neat-B5-tmb", "plan-s8-neat-B5-mix"], "message": "Approved against the public deck and the stated instruction."} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 5, "trace_sequence": 5, "timestamp": "2026-09-16T10:24:57+00:00", "logged_at": "2026-09-16T10:24:57.350000+00:00", "source_agent": "actor", "event_id": "act-plan-s8-neat-B1-hrp", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "plan-s8-neat-B1-hrp", "plan_id": "plan-s8-neat", "revision_id": "rev_0", "executed": true, "params": {"action_id": "plan-s8-neat-B1-hrp", "action_params": {"source": "A1", "dest": "B1", "volume_ul": 15.151515151515152, "reagent": "hrp"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:B1", "volume_ul": 15.151515151515152, "reagent": "hrp"}}, "result_observation_ids": ["obs-plan-s8-neat-B1-hrp"], "state_delta": {"execution_disposition": "dispatched"}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 6, "trace_sequence": 6, "timestamp": "2026-09-16T10:25:04+00:00", "logged_at": "2026-09-16T10:25:04.350000+00:00", "source_agent": "actor", "event_id": "act-plan-s8-neat-B1-buffer", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "plan-s8-neat-B1-buffer", "plan_id": 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It is not used for the fit."}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 25, "trace_sequence": 25, "timestamp": "2026-09-16T10:28:16+00:00", "logged_at": "2026-09-16T10:28:16.350000+00:00", "source_agent": "actor", "event_id": "act-plan-s8-neat-B5-hrp", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "plan-s8-neat-B5-hrp", "plan_id": "plan-s8-neat", "revision_id": "rev_0", "executed": true, "params": {"action_id": "plan-s8-neat-B5-hrp", "action_params": {"source": "A1", "dest": "B5", "volume_ul": 15.151515151515152, "reagent": "hrp"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:B5", "volume_ul": 15.151515151515152, "reagent": "hrp"}}, "result_observation_ids": ["obs-plan-s8-neat-B5-hrp"], "state_delta": {"execution_disposition": "dispatched"}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 26, "trace_sequence": 26, "timestamp": "2026-09-16T10:28:21+00:00", "logged_at": "2026-09-16T10:28:21.350000+00:00", "source_agent": "actor", "event_id": "act-plan-s8-neat-B5-buffer", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "plan-s8-neat-B5-buffer", "plan_id": "plan-s8-neat", "revision_id": "rev_0", "executed": true, "params": {"action_id": "plan-s8-neat-B5-buffer", "action_params": {"source": "A3", "dest": "B5", "volume_ul": 152.84848484848484, "reagent": "buffer"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:B5", "volume_ul": 152.84848484848484, "reagent": "buffer"}}, "result_observation_ids": ["obs-plan-s8-neat-B5-buffer"], "state_delta": {"execution_disposition": "dispatched"}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 27, "trace_sequence": 27, "timestamp": "2026-09-16T10:28:30+00:00", "logged_at": "2026-09-16T10:28:30.350000+00:00", "source_agent": "actor", "event_id": "act-plan-s8-neat-B5-tmb", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "plan-s8-neat-B5-tmb", "plan_id": "plan-s8-neat", "revision_id": "rev_0", "executed": true, "params": {"action_id": "plan-s8-neat-B5-tmb", "action_params": {"source": "A2", "dest": "B5", "volume_ul": 32.0, "reagent": "tmb"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:B5", "volume_ul": 32.0, "reagent": "tmb"}}, "result_observation_ids": ["obs-plan-s8-neat-B5-tmb"], "state_delta": {"execution_disposition": "dispatched"}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 28, "trace_sequence": 28, "timestamp": "2026-09-16T10:28:32+00:00", "logged_at": "2026-09-16T10:28:32.350000+00:00", "source_agent": "actor", "event_id": "act-plan-s8-neat-B5-mix", "event_type": "tool_call", "tool_name": "mix_well", "tool_call_id": "plan-s8-neat-B5-mix", "plan_id": "plan-s8-neat", "revision_id": "rev_0", "executed": true, "params": {"action_id": "plan-s8-neat-B5-mix", "action_params": {"well": "B5"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:B5", "enzyme_volume_ul": 15.151515151515152, "tmb_volume_ul": 32.0, "buffer_volume_ul": 152.84848484848484, "total_volume_ul": 200.0, "substrate_uM": 800.0, "enzyme_concentration_nM": 2.272727272727273, "enzyme_concentration_ng_ml": 100.0, "enzyme_concentration_M": 2.272727272727273e-09, "rate_A652_per_min": 10.059636363636367, "rate_uM_per_s": 7.676767676767678, "series": "saturated_attempt", "initial_rate_eligible": false, "used_for_fit": false, "concentration_basis": "exact_stock"}}, "result_observation_ids": ["obs-plan-s8-neat-B5-mix"], "state_delta": {"execution_disposition": "dispatched"}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 29, "trace_sequence": 29, "timestamp": "2026-09-16T10:28:54+00:00", "logged_at": "2026-09-16T10:28:54.350000+00:00", "source_agent": null, "event_id": "obs-s8-neat-B5-t24", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s8-neat-B5-t24", "wells": {"plate:B5": {"enzyme_volume_ul": 15.151515151515152, "tmb_volume_ul": 32.0, "buffer_volume_ul": 152.84848484848484, "total_volume_ul": 200.0, "substrate_uM": 800.0, "enzyme_concentration_nM": 2.272727272727273, "enzyme_concentration_ng_ml": 100.0, "enzyme_concentration_M": 2.272727272727273e-09, "rate_A652_per_min": 10.059636363636367, "rate_uM_per_s": 7.676767676767678, "series": "saturated_attempt", "initial_rate_eligible": false, "used_for_fit": false, "concentration_basis": "exact_stock", "A652": 3.5, "elapsed_s": 24.0, "reaction_started_at": "2026-09-16T10:28:30+00:00", "acquired_at": "2026-09-16T10:28:54+00:00", "acid_stopped": false, "predicted_A652_uncapped": 4.0238545454545465, "saturated": true}}, "note": "This well is saturated, so the initial rate could not be estimated. It is not used for the fit."}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 30, "trace_sequence": 30, "timestamp": "2026-09-16T10:28:54+00:00", "logged_at": "2026-09-16T10:28:54.350000+00:00", "source_agent": "knowledge", "event_id": "know-protocol-hrp-tmb-initial-rate-curve", "event_type": "observation", "observation_type": "knowledge_response", "payload": {"source_id": "protocol-hrp-tmb-initial-rate-curve", "text": "Assay guidance for the HRP-TMB initial-rate assay. At 200 uM TMB, path 0.56 cm, reads at 3, 6, and 9 s, and no acid stop. The dilution is chosen from this run's measurement.", "protocol_id": "protocol-hrp-tmb-initial-rate-curve", "category": "protocol", "conditions": {"substrate_uM": 200.0, "path_cm": 0.56, "elapsed_s": [3.0, 6.0, 9.0], "acid_stop": false}}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 31, "trace_sequence": 31, "timestamp": "2026-09-16T10:29:06+00:00", "logged_at": "2026-09-16T10:29:06.350000+00:00", "source_agent": "planner", "event_id": "msg-0031", "event_type": "recovery_decision", "rationale": "The first wells hit the ceiling. They were prepared at 100 ng/mL from the given 30 nM stock, and the reaction is too fast. That concentration is too high. Hypothesis: I will prepare new wells from a dilution of that stock and search for a dilution factor that brings the rate back on scale.", "message": "The first wells hit the ceiling. They were prepared at 100 ng/mL from the given 30 nM stock, and the reaction is too fast. That concentration is too high. Hypothesis: I will prepare new wells from a dilution of that stock and search for a dilution factor that brings the rate back on scale."} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 32, "trace_sequence": 32, "timestamp": "2026-09-16T10:29:18+00:00", "logged_at": "2026-09-16T10:29:18.350000+00:00", "source_agent": "planner", "event_id": "plan-plan-s8-diluted", "event_type": "plan", "plan_id": "plan-s8-diluted", "revision_id": "rev_0", "rationale": "The first wells were 100 ng/mL from the given 30 nM stock and saturated. I will prepare new wells, not by transferring that saturated reaction. I will search a series of 0.5, 1, 2, 5, 10, 20, 40, and 80 ng/mL, with volumes computed from that 30 nM stock, and see which points stay proportional. The aliquot in H12 is a 14-fold dilution, 20 uL of the 30 nM stock plus 260 uL PBS, so the 0.5 ng/mL transfer is at least 1 uL. The substrate series is dispensed at 5 ng/mL from the same stock. Read each well at 3, 6, and 9 s after TMB is dispensed. 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No acid stop."}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 134, "trace_sequence": 134, "timestamp": "2026-09-16T10:37:39+00:00", "logged_at": "2026-09-16T10:37:39.350000+00:00", "source_agent": null, "event_id": "obs-s8-G3-t9", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s8-G3-t9", "wells": {"plate:G3": {"enzyme_volume_ul": 10.606060606060606, "tmb_volume_ul": 4.0, "buffer_volume_ul": 185.3939393939394, "total_volume_ul": 200.0, "substrate_uM": 100.0, "enzyme_concentration_nM": 0.11363636363636363, "enzyme_concentration_ng_ml": 5.0, "enzyme_concentration_M": 1.1363636363636364e-10, "rate_A652_per_min": 0.28110107768440723, "rate_uM_per_s": 0.21451547442338767, "hrp_source": "H12", "hrp_source_labware": "plate", "dilution_factor": 14, "neat_enzyme_ul": 0.7575757575757576, "rate_uM_per_s_mean": 0.2159090909090909, "rate_residual_uM_per_s": -0.0013936164857032004, "replicate_sign": -1, "series": "mm", "used_for_fit": true, "initial_rate_eligible": true, "concentration_basis": "exact_stock", "A652": 0.042165161652661085, "elapsed_s": 9.0, "reaction_started_at": "2026-09-16T10:37:30+00:00", "acquired_at": "2026-09-16T10:37:39+00:00", "acid_stopped": false, "substrate_conversion_fraction": 0.019306392698104892}}, "note": "Same-well absorbance at 3, 6, and 9 s after TMB was dispensed. 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No acid stop."}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 155, "trace_sequence": 155, "timestamp": "2026-09-16T10:39:22+00:00", "logged_at": "2026-09-16T10:39:22.350000+00:00", "source_agent": null, "event_id": "obs-s8-F5-t9", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s8-F5-t9", "wells": {"plate:F5": {"enzyme_volume_ul": 10.606060606060606, "tmb_volume_ul": 16.0, "buffer_volume_ul": 173.3939393939394, "total_volume_ul": 200.0, "substrate_uM": 400.0, "enzyme_concentration_nM": 0.11363636363636363, "enzyme_concentration_ng_ml": 5.0, "enzyme_concentration_M": 1.1363636363636364e-10, "rate_A652_per_min": 0.45450983140650186, "rate_uM_per_s": 0.3468481619402486, "hrp_source": "H12", "hrp_source_labware": "plate", "dilution_factor": 14, "neat_enzyme_ul": 0.7575757575757576, "rate_uM_per_s_mean": 0.34545454545454546, "rate_residual_uM_per_s": 0.0013936164857032004, "replicate_sign": 1, "series": "mm", "used_for_fit": true, "initial_rate_eligible": true, "concentration_basis": "exact_stock", "A652": 0.06817647471097528, "elapsed_s": 9.0, "reaction_started_at": "2026-09-16T10:39:13+00:00", "acquired_at": "2026-09-16T10:39:22+00:00", "acid_stopped": false, "substrate_conversion_fraction": 0.007804083643655593}}, "note": "Same-well absorbance at 3, 6, and 9 s after TMB was dispensed. 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No acid stop."}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 162, "trace_sequence": 162, "timestamp": "2026-09-16T10:39:59+00:00", "logged_at": "2026-09-16T10:39:59.350000+00:00", "source_agent": null, "event_id": "obs-s8-G5-t9", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s8-G5-t9", "wells": {"plate:G5": {"enzyme_volume_ul": 10.606060606060606, "tmb_volume_ul": 16.0, "buffer_volume_ul": 173.3939393939394, "total_volume_ul": 200.0, "substrate_uM": 400.0, "enzyme_concentration_nM": 0.11363636363636363, "enzyme_concentration_ng_ml": 5.0, "enzyme_concentration_M": 1.1363636363636364e-10, "rate_A652_per_min": 0.45085744132077094, "rate_uM_per_s": 0.3440609289688422, "hrp_source": "H12", "hrp_source_labware": "plate", "dilution_factor": 14, "neat_enzyme_ul": 0.7575757575757576, "rate_uM_per_s_mean": 0.34545454545454546, "rate_residual_uM_per_s": -0.0013936164857032004, "replicate_sign": -1, "series": "mm", "used_for_fit": true, "initial_rate_eligible": true, "concentration_basis": "exact_stock", "A652": 0.06762861619811564, "elapsed_s": 9.0, "reaction_started_at": "2026-09-16T10:39:50+00:00", "acquired_at": "2026-09-16T10:39:59+00:00", "acid_stopped": false, "substrate_conversion_fraction": 0.00774137090179895}}, "note": "Same-well absorbance at 3, 6, and 9 s after TMB was dispensed. 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No acid stop."}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 167, "trace_sequence": 167, "timestamp": "2026-09-16T10:40:17+00:00", "logged_at": "2026-09-16T10:40:17.350000+00:00", "source_agent": null, "event_id": "obs-s8-E1-t6", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s8-E1-t6", "wells": {"plate:E1": {"enzyme_volume_ul": 0.0, "tmb_volume_ul": 1.0, "buffer_volume_ul": 199.0, "total_volume_ul": 200.0, "substrate_uM": 25.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 25.0, "A652": 0.0, "elapsed_s": 6.0, "reaction_started_at": "2026-09-16T10:40:11+00:00", "acquired_at": "2026-09-16T10:40:17+00:00", "acid_stopped": false, "substrate_conversion_fraction": 0.0}}, "note": "Same-well absorbance at 3, 6, and 9 s after TMB was dispensed. No acid stop."}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 168, "trace_sequence": 168, "timestamp": "2026-09-16T10:40:20+00:00", "logged_at": "2026-09-16T10:40:20.350000+00:00", "source_agent": null, "event_id": "obs-s8-E1-t9", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s8-E1-t9", "wells": {"plate:E1": {"enzyme_volume_ul": 0.0, "tmb_volume_ul": 1.0, "buffer_volume_ul": 199.0, "total_volume_ul": 200.0, "substrate_uM": 25.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 25.0, "A652": 0.0, "elapsed_s": 9.0, "reaction_started_at": "2026-09-16T10:40:11+00:00", "acquired_at": "2026-09-16T10:40:20+00:00", "acid_stopped": false, "substrate_conversion_fraction": 0.0}}, "note": "Same-well absorbance at 3, 6, and 9 s after TMB was dispensed. No acid stop."}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 169, "trace_sequence": 169, "timestamp": "2026-09-16T10:40:36+00:00", "logged_at": "2026-09-16T10:40:36.350000+00:00", "source_agent": "actor", "event_id": "act-plan-s8-diluted-E2-buffer", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "plan-s8-diluted-E2-buffer", "plan_id": "plan-s8-diluted", "revision_id": "rev_0", "executed": true, "params": {"action_id": "plan-s8-diluted-E2-buffer", "action_params": {"source": "A3", "dest": "E2", "volume_ul": 198.0, "reagent": "buffer"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:E2", "volume_ul": 198.0, "reagent": "buffer"}}, "result_observation_ids": ["obs-plan-s8-diluted-E2-buffer"], "state_delta": {"execution_disposition": "dispatched"}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 170, "trace_sequence": 170, "timestamp": "2026-09-16T10:40:41+00:00", "logged_at": "2026-09-16T10:40:41.350000+00:00", "source_agent": "actor", "event_id": "act-plan-s8-diluted-E2-tmb", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "plan-s8-diluted-E2-tmb", "plan_id": "plan-s8-diluted", "revision_id": "rev_0", "executed": true, "params": {"action_id": "plan-s8-diluted-E2-tmb", "action_params": {"source": "A2", "dest": "E2", "volume_ul": 2.0, "reagent": "tmb"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:E2", "volume_ul": 2.0, "reagent": "tmb"}}, "result_observation_ids": ["obs-plan-s8-diluted-E2-tmb"], "state_delta": {"execution_disposition": "dispatched"}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 171, "trace_sequence": 171, "timestamp": "2026-09-16T10:40:43+00:00", "logged_at": "2026-09-16T10:40:43.350000+00:00", "source_agent": "actor", "event_id": "act-plan-s8-diluted-E2-mix", "event_type": "tool_call", "tool_name": "mix_well", "tool_call_id": "plan-s8-diluted-E2-mix", "plan_id": "plan-s8-diluted", "revision_id": "rev_0", "executed": true, "params": {"action_id": "plan-s8-diluted-E2-mix", "action_params": {"well": "E2"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:E2", "enzyme_volume_ul": 0.0, "tmb_volume_ul": 2.0, "buffer_volume_ul": 198.0, "total_volume_ul": 200.0, "substrate_uM": 50.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 50.0}}, "result_observation_ids": ["obs-plan-s8-diluted-E2-mix"], "state_delta": {"execution_disposition": "dispatched"}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 172, "trace_sequence": 172, "timestamp": "2026-09-16T10:40:44+00:00", "logged_at": "2026-09-16T10:40:44.350000+00:00", "source_agent": null, "event_id": "obs-s8-E2-t3", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s8-E2-t3", "wells": {"plate:E2": {"enzyme_volume_ul": 0.0, "tmb_volume_ul": 2.0, "buffer_volume_ul": 198.0, "total_volume_ul": 200.0, "substrate_uM": 50.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 50.0, "A652": 0.0, "elapsed_s": 3.0, "reaction_started_at": "2026-09-16T10:40:41+00:00", "acquired_at": "2026-09-16T10:40:44+00:00", "acid_stopped": false, "substrate_conversion_fraction": 0.0}}, "note": "Same-well absorbance at 3, 6, and 9 s after TMB was dispensed. No acid stop."}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 173, "trace_sequence": 173, "timestamp": "2026-09-16T10:40:47+00:00", "logged_at": "2026-09-16T10:40:47.350000+00:00", "source_agent": null, "event_id": "obs-s8-E2-t6", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s8-E2-t6", "wells": {"plate:E2": {"enzyme_volume_ul": 0.0, "tmb_volume_ul": 2.0, "buffer_volume_ul": 198.0, "total_volume_ul": 200.0, "substrate_uM": 50.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 50.0, "A652": 0.0, "elapsed_s": 6.0, "reaction_started_at": "2026-09-16T10:40:41+00:00", "acquired_at": "2026-09-16T10:40:47+00:00", "acid_stopped": false, "substrate_conversion_fraction": 0.0}}, "note": "Same-well absorbance at 3, 6, and 9 s after TMB was dispensed. No acid stop."}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 174, "trace_sequence": 174, "timestamp": "2026-09-16T10:40:50+00:00", "logged_at": "2026-09-16T10:40:50.350000+00:00", "source_agent": null, "event_id": "obs-s8-E2-t9", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s8-E2-t9", "wells": {"plate:E2": {"enzyme_volume_ul": 0.0, "tmb_volume_ul": 2.0, "buffer_volume_ul": 198.0, "total_volume_ul": 200.0, "substrate_uM": 50.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 50.0, "A652": 0.0, "elapsed_s": 9.0, "reaction_started_at": "2026-09-16T10:40:41+00:00", "acquired_at": "2026-09-16T10:40:50+00:00", "acid_stopped": false, "substrate_conversion_fraction": 0.0}}, "note": "Same-well absorbance at 3, 6, and 9 s after TMB was dispensed. No acid stop."}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 175, "trace_sequence": 175, "timestamp": "2026-09-16T10:41:01+00:00", "logged_at": "2026-09-16T10:41:01.350000+00:00", "source_agent": "actor", "event_id": "act-plan-s8-diluted-E3-buffer", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "plan-s8-diluted-E3-buffer", "plan_id": "plan-s8-diluted", "revision_id": "rev_0", "executed": true, "params": {"action_id": "plan-s8-diluted-E3-buffer", "action_params": {"source": "A3", "dest": "E3", "volume_ul": 196.0, "reagent": "buffer"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:E3", "volume_ul": 196.0, "reagent": "buffer"}}, "result_observation_ids": ["obs-plan-s8-diluted-E3-buffer"], "state_delta": {"execution_disposition": "dispatched"}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 176, "trace_sequence": 176, "timestamp": "2026-09-16T10:41:05+00:00", "logged_at": "2026-09-16T10:41:05.350000+00:00", "source_agent": "actor", "event_id": "act-plan-s8-diluted-E3-tmb", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "plan-s8-diluted-E3-tmb", "plan_id": "plan-s8-diluted", "revision_id": "rev_0", "executed": true, "params": {"action_id": "plan-s8-diluted-E3-tmb", "action_params": {"source": "A2", "dest": "E3", "volume_ul": 4.0, "reagent": "tmb"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:E3", "volume_ul": 4.0, "reagent": "tmb"}}, "result_observation_ids": ["obs-plan-s8-diluted-E3-tmb"], "state_delta": {"execution_disposition": "dispatched"}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 177, "trace_sequence": 177, "timestamp": "2026-09-16T10:41:06+00:00", "logged_at": "2026-09-16T10:41:06.350000+00:00", "source_agent": "actor", "event_id": "act-plan-s8-diluted-E3-mix", "event_type": "tool_call", "tool_name": "mix_well", "tool_call_id": "plan-s8-diluted-E3-mix", "plan_id": "plan-s8-diluted", "revision_id": "rev_0", "executed": true, "params": {"action_id": "plan-s8-diluted-E3-mix", "action_params": {"well": "E3"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:E3", "enzyme_volume_ul": 0.0, "tmb_volume_ul": 4.0, "buffer_volume_ul": 196.0, "total_volume_ul": 200.0, "substrate_uM": 100.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 100.0}}, "result_observation_ids": ["obs-plan-s8-diluted-E3-mix"], "state_delta": {"execution_disposition": "dispatched"}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 178, "trace_sequence": 178, "timestamp": "2026-09-16T10:41:08+00:00", "logged_at": "2026-09-16T10:41:08.350000+00:00", "source_agent": null, "event_id": "obs-s8-E3-t3", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s8-E3-t3", "wells": {"plate:E3": {"enzyme_volume_ul": 0.0, "tmb_volume_ul": 4.0, "buffer_volume_ul": 196.0, "total_volume_ul": 200.0, "substrate_uM": 100.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 100.0, "A652": 0.0, "elapsed_s": 3.0, "reaction_started_at": "2026-09-16T10:41:05+00:00", "acquired_at": "2026-09-16T10:41:08+00:00", "acid_stopped": false, "substrate_conversion_fraction": 0.0}}, "note": "Same-well absorbance at 3, 6, and 9 s after TMB was dispensed. No acid stop."}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 179, "trace_sequence": 179, "timestamp": "2026-09-16T10:41:11+00:00", "logged_at": "2026-09-16T10:41:11.350000+00:00", "source_agent": null, "event_id": "obs-s8-E3-t6", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s8-E3-t6", "wells": {"plate:E3": {"enzyme_volume_ul": 0.0, "tmb_volume_ul": 4.0, "buffer_volume_ul": 196.0, "total_volume_ul": 200.0, "substrate_uM": 100.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 100.0, "A652": 0.0, "elapsed_s": 6.0, "reaction_started_at": "2026-09-16T10:41:05+00:00", "acquired_at": "2026-09-16T10:41:11+00:00", "acid_stopped": false, "substrate_conversion_fraction": 0.0}}, "note": "Same-well absorbance at 3, 6, and 9 s after TMB was dispensed. No acid stop."}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 180, "trace_sequence": 180, "timestamp": "2026-09-16T10:41:14+00:00", "logged_at": "2026-09-16T10:41:14.350000+00:00", "source_agent": null, "event_id": "obs-s8-E3-t9", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s8-E3-t9", "wells": {"plate:E3": {"enzyme_volume_ul": 0.0, "tmb_volume_ul": 4.0, "buffer_volume_ul": 196.0, "total_volume_ul": 200.0, "substrate_uM": 100.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 100.0, "A652": 0.0, "elapsed_s": 9.0, "reaction_started_at": "2026-09-16T10:41:05+00:00", "acquired_at": "2026-09-16T10:41:14+00:00", "acid_stopped": false, "substrate_conversion_fraction": 0.0}}, "note": "Same-well absorbance at 3, 6, and 9 s after TMB was dispensed. No acid stop."}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 181, "trace_sequence": 181, "timestamp": "2026-09-16T10:41:27+00:00", "logged_at": "2026-09-16T10:41:27.350000+00:00", "source_agent": "actor", "event_id": "act-plan-s8-diluted-E4-buffer", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "plan-s8-diluted-E4-buffer", "plan_id": "plan-s8-diluted", "revision_id": "rev_0", "executed": true, "params": {"action_id": "plan-s8-diluted-E4-buffer", "action_params": {"source": "A3", "dest": "E4", "volume_ul": 192.0, "reagent": "buffer"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:E4", "volume_ul": 192.0, "reagent": "buffer"}}, "result_observation_ids": ["obs-plan-s8-diluted-E4-buffer"], "state_delta": {"execution_disposition": "dispatched"}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 182, "trace_sequence": 182, "timestamp": "2026-09-16T10:41:34+00:00", "logged_at": "2026-09-16T10:41:34.350000+00:00", "source_agent": "actor", "event_id": "act-plan-s8-diluted-E4-tmb", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "plan-s8-diluted-E4-tmb", "plan_id": "plan-s8-diluted", "revision_id": "rev_0", "executed": true, "params": {"action_id": "plan-s8-diluted-E4-tmb", "action_params": {"source": "A2", "dest": "E4", "volume_ul": 8.0, "reagent": "tmb"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:E4", "volume_ul": 8.0, "reagent": "tmb"}}, "result_observation_ids": ["obs-plan-s8-diluted-E4-tmb"], "state_delta": {"execution_disposition": "dispatched"}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 183, "trace_sequence": 183, "timestamp": "2026-09-16T10:41:35+00:00", "logged_at": "2026-09-16T10:41:35.350000+00:00", "source_agent": "actor", "event_id": "act-plan-s8-diluted-E4-mix", "event_type": "tool_call", "tool_name": "mix_well", "tool_call_id": "plan-s8-diluted-E4-mix", "plan_id": "plan-s8-diluted", "revision_id": "rev_0", "executed": true, "params": {"action_id": "plan-s8-diluted-E4-mix", "action_params": {"well": "E4"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:E4", "enzyme_volume_ul": 0.0, "tmb_volume_ul": 8.0, "buffer_volume_ul": 192.0, "total_volume_ul": 200.0, "substrate_uM": 200.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 200.0}}, "result_observation_ids": ["obs-plan-s8-diluted-E4-mix"], "state_delta": {"execution_disposition": "dispatched"}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 184, "trace_sequence": 184, "timestamp": "2026-09-16T10:41:37+00:00", "logged_at": "2026-09-16T10:41:37.350000+00:00", "source_agent": null, "event_id": "obs-s8-E4-t3", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s8-E4-t3", "wells": {"plate:E4": {"enzyme_volume_ul": 0.0, "tmb_volume_ul": 8.0, "buffer_volume_ul": 192.0, "total_volume_ul": 200.0, "substrate_uM": 200.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 200.0, "A652": 0.0, "elapsed_s": 3.0, "reaction_started_at": "2026-09-16T10:41:34+00:00", "acquired_at": "2026-09-16T10:41:37+00:00", "acid_stopped": false, "substrate_conversion_fraction": 0.0}}, "note": "Same-well absorbance at 3, 6, and 9 s after TMB was dispensed. No acid stop."}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 185, "trace_sequence": 185, "timestamp": "2026-09-16T10:41:40+00:00", "logged_at": "2026-09-16T10:41:40.350000+00:00", "source_agent": null, "event_id": "obs-s8-E4-t6", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s8-E4-t6", "wells": {"plate:E4": {"enzyme_volume_ul": 0.0, "tmb_volume_ul": 8.0, "buffer_volume_ul": 192.0, "total_volume_ul": 200.0, "substrate_uM": 200.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 200.0, "A652": 0.0, "elapsed_s": 6.0, "reaction_started_at": "2026-09-16T10:41:34+00:00", "acquired_at": "2026-09-16T10:41:40+00:00", "acid_stopped": false, "substrate_conversion_fraction": 0.0}}, "note": "Same-well absorbance at 3, 6, and 9 s after TMB was dispensed. No acid stop."}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 186, "trace_sequence": 186, "timestamp": "2026-09-16T10:41:43+00:00", "logged_at": "2026-09-16T10:41:43.350000+00:00", "source_agent": null, "event_id": "obs-s8-E4-t9", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s8-E4-t9", "wells": {"plate:E4": {"enzyme_volume_ul": 0.0, "tmb_volume_ul": 8.0, "buffer_volume_ul": 192.0, "total_volume_ul": 200.0, "substrate_uM": 200.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 200.0, "A652": 0.0, "elapsed_s": 9.0, "reaction_started_at": "2026-09-16T10:41:34+00:00", "acquired_at": "2026-09-16T10:41:43+00:00", "acid_stopped": false, "substrate_conversion_fraction": 0.0}}, "note": "Same-well absorbance at 3, 6, and 9 s after TMB was dispensed. No acid stop."}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 187, "trace_sequence": 187, "timestamp": "2026-09-16T10:41:56+00:00", "logged_at": "2026-09-16T10:41:56.350000+00:00", "source_agent": "actor", "event_id": "act-plan-s8-diluted-E5-buffer", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "plan-s8-diluted-E5-buffer", "plan_id": "plan-s8-diluted", "revision_id": "rev_0", "executed": true, "params": {"action_id": "plan-s8-diluted-E5-buffer", "action_params": {"source": "A3", "dest": "E5", "volume_ul": 184.0, "reagent": "buffer"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:E5", "volume_ul": 184.0, "reagent": "buffer"}}, "result_observation_ids": ["obs-plan-s8-diluted-E5-buffer"], "state_delta": {"execution_disposition": "dispatched"}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 188, "trace_sequence": 188, "timestamp": "2026-09-16T10:42:00+00:00", "logged_at": "2026-09-16T10:42:00.350000+00:00", "source_agent": "actor", "event_id": "act-plan-s8-diluted-E5-tmb", "event_type": "tool_call", "tool_name": "transfer", "tool_call_id": "plan-s8-diluted-E5-tmb", "plan_id": "plan-s8-diluted", "revision_id": "rev_0", "executed": true, "params": {"action_id": "plan-s8-diluted-E5-tmb", "action_params": {"source": "A2", "dest": "E5", "volume_ul": 16.0, "reagent": "tmb"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:E5", "volume_ul": 16.0, "reagent": "tmb"}}, "result_observation_ids": ["obs-plan-s8-diluted-E5-tmb"], "state_delta": {"execution_disposition": "dispatched"}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 189, "trace_sequence": 189, "timestamp": "2026-09-16T10:42:01+00:00", "logged_at": "2026-09-16T10:42:01.350000+00:00", "source_agent": "actor", "event_id": "act-plan-s8-diluted-E5-mix", "event_type": "tool_call", "tool_name": "mix_well", "tool_call_id": "plan-s8-diluted-E5-mix", "plan_id": "plan-s8-diluted", "revision_id": "rev_0", "executed": true, "params": {"action_id": "plan-s8-diluted-E5-mix", "action_params": {"well": "E5"}, "approved_action_association": "associated"}, "result": {"ok": true, "error": "", "observation": {"well": "plate:E5", "enzyme_volume_ul": 0.0, "tmb_volume_ul": 16.0, "buffer_volume_ul": 184.0, "total_volume_ul": 200.0, "substrate_uM": 400.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 400.0}}, "result_observation_ids": ["obs-plan-s8-diluted-E5-mix"], "state_delta": {"execution_disposition": "dispatched"}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 190, "trace_sequence": 190, "timestamp": "2026-09-16T10:42:03+00:00", "logged_at": "2026-09-16T10:42:03.350000+00:00", "source_agent": null, "event_id": "obs-s8-E5-t3", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s8-E5-t3", "wells": {"plate:E5": {"enzyme_volume_ul": 0.0, "tmb_volume_ul": 16.0, "buffer_volume_ul": 184.0, "total_volume_ul": 200.0, "substrate_uM": 400.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 400.0, "A652": 0.0, "elapsed_s": 3.0, "reaction_started_at": "2026-09-16T10:42:00+00:00", "acquired_at": "2026-09-16T10:42:03+00:00", "acid_stopped": false, "substrate_conversion_fraction": 0.0}}, "note": "Same-well absorbance at 3, 6, and 9 s after TMB was dispensed. No acid stop."}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 191, "trace_sequence": 191, "timestamp": "2026-09-16T10:42:06+00:00", "logged_at": "2026-09-16T10:42:06.350000+00:00", "source_agent": null, "event_id": "obs-s8-E5-t6", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s8-E5-t6", "wells": {"plate:E5": {"enzyme_volume_ul": 0.0, "tmb_volume_ul": 16.0, "buffer_volume_ul": 184.0, "total_volume_ul": 200.0, "substrate_uM": 400.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 400.0, "A652": 0.0, "elapsed_s": 6.0, "reaction_started_at": "2026-09-16T10:42:00+00:00", "acquired_at": "2026-09-16T10:42:06+00:00", "acid_stopped": false, "substrate_conversion_fraction": 0.0}}, "note": "Same-well absorbance at 3, 6, and 9 s after TMB was dispensed. No acid stop."}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 192, "trace_sequence": 192, "timestamp": "2026-09-16T10:42:09+00:00", "logged_at": "2026-09-16T10:42:09.350000+00:00", "source_agent": null, "event_id": "obs-s8-E5-t9", "event_type": "observation", "observation_type": "public_measurement", "payload": {"observation_id": "s8-E5-t9", "wells": {"plate:E5": {"enzyme_volume_ul": 0.0, "tmb_volume_ul": 16.0, "buffer_volume_ul": 184.0, "total_volume_ul": 200.0, "substrate_uM": 400.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 400.0, "A652": 0.0, "elapsed_s": 9.0, "reaction_started_at": "2026-09-16T10:42:00+00:00", "acquired_at": "2026-09-16T10:42:09+00:00", "acid_stopped": false, "substrate_conversion_fraction": 0.0}}, "note": "Same-well absorbance at 3, 6, and 9 s after TMB was dispensed. 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"enzyme_concentration_ng_ml": 5.0, "enzyme_concentration_M": 1.1363636363636364e-10, "rate_A652_per_min": 0.1904443768610473, "rate_uM_per_s": 0.14533301042509714, "hrp_source": "H12", "hrp_source_labware": "plate", "dilution_factor": 14, "neat_enzyme_ul": 0.7575757575757576, "rate_uM_per_s_mean": 0.14393939393939392, "rate_residual_uM_per_s": 0.0013936164857032004, "replicate_sign": 1, "series": "mm", "used_for_fit": true, "initial_rate_eligible": true, "concentration_basis": "exact_stock"}, "plate:G2": {"enzyme_volume_ul": 10.606060606060606, "tmb_volume_ul": 2.0, "buffer_volume_ul": 187.3939393939394, "total_volume_ul": 200.0, "substrate_uM": 50.0, "enzyme_concentration_nM": 0.11363636363636363, "enzyme_concentration_ng_ml": 5.0, "enzyme_concentration_M": 1.1363636363636364e-10, "rate_A652_per_min": 0.18679198677531633, "rate_uM_per_s": 0.1425457774536907, "hrp_source": "H12", "hrp_source_labware": "plate", "dilution_factor": 14, "neat_enzyme_ul": 0.7575757575757576, "rate_uM_per_s_mean": 0.14393939393939392, "rate_residual_uM_per_s": -0.0013936164857032004, "replicate_sign": -1, "series": "mm", "used_for_fit": true, "initial_rate_eligible": true, "concentration_basis": "exact_stock"}, "plate:F3": {"enzyme_volume_ul": 10.606060606060606, "tmb_volume_ul": 4.0, "buffer_volume_ul": 185.3939393939394, "total_volume_ul": 200.0, "substrate_uM": 100.0, "enzyme_concentration_nM": 0.11363636363636363, "enzyme_concentration_ng_ml": 5.0, "enzyme_concentration_M": 1.1363636363636364e-10, "rate_A652_per_min": 0.2847534677701382, "rate_uM_per_s": 0.21730270739479413, "hrp_source": "H12", "hrp_source_labware": "plate", "dilution_factor": 14, "neat_enzyme_ul": 0.7575757575757576, "rate_uM_per_s_mean": 0.2159090909090909, "rate_residual_uM_per_s": 0.0013936164857032004, "replicate_sign": 1, "series": "mm", "used_for_fit": true, "initial_rate_eligible": true, "concentration_basis": "exact_stock"}, "plate:G3": {"enzyme_volume_ul": 10.606060606060606, "tmb_volume_ul": 4.0, "buffer_volume_ul": 185.3939393939394, "total_volume_ul": 200.0, "substrate_uM": 100.0, "enzyme_concentration_nM": 0.11363636363636363, "enzyme_concentration_ng_ml": 5.0, "enzyme_concentration_M": 1.1363636363636364e-10, "rate_A652_per_min": 0.28110107768440723, "rate_uM_per_s": 0.2145154744233877, "hrp_source": "H12", "hrp_source_labware": "plate", "dilution_factor": 14, "neat_enzyme_ul": 0.7575757575757576, "rate_uM_per_s_mean": 0.2159090909090909, "rate_residual_uM_per_s": -0.0013936164857032004, "replicate_sign": -1, "series": "mm", "used_for_fit": true, "initial_rate_eligible": true, "concentration_basis": "exact_stock"}, "plate:F4": {"enzyme_volume_ul": 10.606060606060606, "tmb_volume_ul": 8.0, "buffer_volume_ul": 181.3939393939394, "total_volume_ul": 200.0, "substrate_uM": 200.0, "enzyme_concentration_nM": 0.11363636363636363, "enzyme_concentration_ng_ml": 5.0, "enzyme_concentration_M": 1.1363636363636364e-10, "rate_A652_per_min": 0.37906255867922906, "rate_uM_per_s": 0.28927240436449103, "hrp_source": "H12", "hrp_source_labware": "plate", "dilution_factor": 14, "neat_enzyme_ul": 0.7575757575757576, "rate_uM_per_s_mean": 0.28787878787878785, "rate_residual_uM_per_s": 0.0013936164857032004, "replicate_sign": 1, "series": "mm", "used_for_fit": true, "initial_rate_eligible": true, "concentration_basis": "exact_stock"}, "plate:G4": {"enzyme_volume_ul": 10.606060606060606, "tmb_volume_ul": 8.0, "buffer_volume_ul": 181.3939393939394, "total_volume_ul": 200.0, "substrate_uM": 200.0, "enzyme_concentration_nM": 0.11363636363636363, "enzyme_concentration_ng_ml": 5.0, "enzyme_concentration_M": 1.1363636363636364e-10, "rate_A652_per_min": 0.3754101685934982, "rate_uM_per_s": 0.28648517139308466, "hrp_source": "H12", "hrp_source_labware": "plate", "dilution_factor": 14, "neat_enzyme_ul": 0.7575757575757576, "rate_uM_per_s_mean": 0.28787878787878785, "rate_residual_uM_per_s": -0.0013936164857032004, "replicate_sign": -1, "series": "mm", "used_for_fit": true, "initial_rate_eligible": true, "concentration_basis": "exact_stock"}, "plate:F5": {"enzyme_volume_ul": 10.606060606060606, "tmb_volume_ul": 16.0, "buffer_volume_ul": 173.3939393939394, "total_volume_ul": 200.0, "substrate_uM": 400.0, "enzyme_concentration_nM": 0.11363636363636363, "enzyme_concentration_ng_ml": 5.0, "enzyme_concentration_M": 1.1363636363636364e-10, "rate_A652_per_min": 0.45450983140650186, "rate_uM_per_s": 0.34684816194024864, "hrp_source": "H12", "hrp_source_labware": "plate", "dilution_factor": 14, "neat_enzyme_ul": 0.7575757575757576, "rate_uM_per_s_mean": 0.34545454545454546, "rate_residual_uM_per_s": 0.0013936164857032004, "replicate_sign": 1, "series": "mm", "used_for_fit": true, "initial_rate_eligible": true, "concentration_basis": "exact_stock"}, "plate:G5": {"enzyme_volume_ul": 10.606060606060606, "tmb_volume_ul": 16.0, "buffer_volume_ul": 173.3939393939394, "total_volume_ul": 200.0, "substrate_uM": 400.0, "enzyme_concentration_nM": 0.11363636363636363, "enzyme_concentration_ng_ml": 5.0, "enzyme_concentration_M": 1.1363636363636364e-10, "rate_A652_per_min": 0.45085744132077094, "rate_uM_per_s": 0.3440609289688423, "hrp_source": "H12", "hrp_source_labware": "plate", "dilution_factor": 14, "neat_enzyme_ul": 0.7575757575757576, "rate_uM_per_s_mean": 0.34545454545454546, "rate_residual_uM_per_s": -0.0013936164857032004, "replicate_sign": -1, "series": "mm", "used_for_fit": true, "initial_rate_eligible": true, "concentration_basis": "exact_stock"}, "plate:E1": {"enzyme_volume_ul": 0.0, "tmb_volume_ul": 1.0, "buffer_volume_ul": 199.0, "total_volume_ul": 200.0, "substrate_uM": 25.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 25.0}, "plate:E2": {"enzyme_volume_ul": 0.0, "tmb_volume_ul": 2.0, "buffer_volume_ul": 198.0, "total_volume_ul": 200.0, "substrate_uM": 50.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 50.0}, "plate:E3": {"enzyme_volume_ul": 0.0, "tmb_volume_ul": 4.0, "buffer_volume_ul": 196.0, "total_volume_ul": 200.0, "substrate_uM": 100.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 100.0}, "plate:E4": {"enzyme_volume_ul": 0.0, "tmb_volume_ul": 8.0, "buffer_volume_ul": 192.0, "total_volume_ul": 200.0, "substrate_uM": 200.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 200.0}, "plate:E5": {"enzyme_volume_ul": 0.0, "tmb_volume_ul": 16.0, "buffer_volume_ul": 184.0, "total_volume_ul": 200.0, "substrate_uM": 400.0, "enzyme_concentration_nM": 0.0, "enzyme_concentration_ng_ml": 0.0, "enzyme_concentration_M": 0.0, "rate_A652_per_min": 0.0, "rate_uM_per_s": 0.0, "series": "blank", "used_for_fit": false, "initial_rate_eligible": false, "blank_for_substrate_uM": 400.0}}, "note": "Compositions from the given 30 nM stock and the volumes dispensed."}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 194, "trace_sequence": 194, "timestamp": "2026-09-16T10:42:21+00:00", "logged_at": "2026-09-16T10:42:21.350000+00:00", "source_agent": "human", "event_id": "s8-audit", "event_type": "audit_annotation", "observation_type": "audit_annotation", "message": "Prepared concentrations from the given 30 nM stock. Not shown to the agent.", "payload": {"disclosed_to_agents": false, "wells": {"plate:B1": {"physical_enzyme_ng_ml": 100.0, "physical_enzyme_nM": 2.272727272727273}, "plate:B2": {"physical_enzyme_ng_ml": 100.0, "physical_enzyme_nM": 2.272727272727273}, "plate:B3": {"physical_enzyme_ng_ml": 100.0, "physical_enzyme_nM": 2.272727272727273}, "plate:B4": {"physical_enzyme_ng_ml": 100.0, "physical_enzyme_nM": 2.272727272727273}, "plate:B5": {"physical_enzyme_ng_ml": 100.0, "physical_enzyme_nM": 2.272727272727273}, "plate:A1": {"physical_enzyme_ng_ml": 0.5, "physical_enzyme_nM": 0.011363636363636362}, "plate:A2": {"physical_enzyme_ng_ml": 1.0, "physical_enzyme_nM": 0.022727272727272724}, "plate:A3": {"physical_enzyme_ng_ml": 2.0, "physical_enzyme_nM": 0.04545454545454545}, "plate:A4": {"physical_enzyme_ng_ml": 5.0, "physical_enzyme_nM": 0.11363636363636363}, "plate:A5": {"physical_enzyme_ng_ml": 10.0, "physical_enzyme_nM": 0.22727272727272727}, "plate:A6": {"physical_enzyme_ng_ml": 20.0, "physical_enzyme_nM": 0.45454545454545453}, "plate:A7": {"physical_enzyme_ng_ml": 40.0, "physical_enzyme_nM": 0.9090909090909091}, "plate:A8": {"physical_enzyme_ng_ml": 80.0, "physical_enzyme_nM": 1.8181818181818181}, "plate:F1": {"physical_enzyme_ng_ml": 5.0, "physical_enzyme_nM": 0.11363636363636363}, "plate:G1": {"physical_enzyme_ng_ml": 5.0, "physical_enzyme_nM": 0.11363636363636363}, "plate:F2": {"physical_enzyme_ng_ml": 5.0, "physical_enzyme_nM": 0.11363636363636363}, "plate:G2": {"physical_enzyme_ng_ml": 5.0, "physical_enzyme_nM": 0.11363636363636363}, "plate:F3": {"physical_enzyme_ng_ml": 5.0, "physical_enzyme_nM": 0.11363636363636363}, "plate:G3": {"physical_enzyme_ng_ml": 5.0, "physical_enzyme_nM": 0.11363636363636363}, "plate:F4": {"physical_enzyme_ng_ml": 5.0, "physical_enzyme_nM": 0.11363636363636363}, "plate:G4": {"physical_enzyme_ng_ml": 5.0, "physical_enzyme_nM": 0.11363636363636363}, "plate:F5": {"physical_enzyme_ng_ml": 5.0, "physical_enzyme_nM": 0.11363636363636363}, "plate:G5": {"physical_enzyme_ng_ml": 5.0, "physical_enzyme_nM": 0.11363636363636363}}, "note": "Prepared concentrations from the given 30 nM stock. Not shown to the agent."}} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 195, "trace_sequence": 195, "timestamp": "2026-09-16T10:42:33+00:00", "logged_at": "2026-09-16T10:42:33.350000+00:00", "source_agent": "planner", "event_id": "msg-0195", "event_type": "recovery_decision", "rationale": "Reported KM = 100 uM. kcat = Vmax/[E] = 3800 /s at 5 ng/mL (0.1136 nM) HRP. The points that stayed proportional are 0.5, 1, 2, and 5 ng/mL. Observations obs-s8-A1-t9, obs-s8-A2-t9, obs-s8-A3-t9, and obs-s8-A4-t9 define that linear working range. obs-s8-A5-t9 is outside it. The given stock is 30 nM, which is 1320 ng/mL. 15.1515 uL of that stock in 200 uL was a separate saturated preparation at 100 ng/mL. The new wells, including the adopted well, are new reactions made from the H12 aliquot, then PBS and TMB. They are not a transfer of that saturated reaction. H12 is a 14-fold dilution, 20 uL of the 30 nM stock plus 260 uL PBS. The adopted well takes 10.6061 uL of that aliquot in 200 uL, which is 5 ng/mL. That 5 ng/mL is the concentration those volumes produce, and reported kcat uses it. Vmax is 0.4318 uM/s, converted from 0.5659 A652/min with epsilon 39000 /M/cm and path 0.56 cm. That path is 0.28 cm times the well volume divided by 100 uL, which is 0.56 cm at 200 uL. The linear HRP working range is 0.5-5 ng/mL.", "message": "Reported KM = 100 uM. kcat = Vmax/[E] = 3800 /s at 5 ng/mL (0.1136 nM) HRP. The points that stayed proportional are 0.5, 1, 2, and 5 ng/mL. Observations obs-s8-A1-t9, obs-s8-A2-t9, obs-s8-A3-t9, and obs-s8-A4-t9 define that linear working range. obs-s8-A5-t9 is outside it. The given stock is 30 nM, which is 1320 ng/mL. 15.1515 uL of that stock in 200 uL was a separate saturated preparation at 100 ng/mL. The new wells, including the adopted well, are new reactions made from the H12 aliquot, then PBS and TMB. They are not a transfer of that saturated reaction. H12 is a 14-fold dilution, 20 uL of the 30 nM stock plus 260 uL PBS. The adopted well takes 10.6061 uL of that aliquot in 200 uL, which is 5 ng/mL. That 5 ng/mL is the concentration those volumes produce, and reported kcat uses it. Vmax is 0.4318 uM/s, converted from 0.5659 A652/min with epsilon 39000 /M/cm and path 0.56 cm. That path is 0.28 cm times the well volume divided by 100 uL, which is 0.56 cm at 200 uL. The linear HRP working range is 0.5-5 ng/mL."} {"record_kind": "event", "run_id": "pearl-manuscript-s8-20260916", "seq": 196, "trace_sequence": 196, "timestamp": "2026-09-16T10:42:45+00:00", "logged_at": "2026-09-16T10:42:45.350000+00:00", "source_agent": "planner", "event_id": "done-S8", "event_type": "completion_decision", "plan_id": "plan-s8-diluted", "revision_id": "rev_0", "adopted": {"summary": "Working range, KM, and kcat after the dilution search.", "KM_uM": 100.0, "kcat_per_s": 3800.0, "Vmax_M_per_s": 4.318181818181818e-07, "Vmax_uM_per_s": 0.4318181818181818, "Vmax_A652_per_min": 0.5658545454545455, "enzyme_concentration_M": 1.1363636363636364e-10, "enzyme_concentration_nM": 0.11363636363636363, "enzyme_concentration_ng_ml": 5.0, "basis": "kcat_per_s = Vmax_M_per_s / enzyme_concentration_M", "read_mode": "same_well", "acid_stop": false, "enzyme_stock": "30 nM, 2000 uL", "working_range_analyte": "HRP", "linear_working_range_hrp_ng_ml": [0.5, 5.0], "linear_working_range_hrp_nM": [0.011363636363636364, 0.11363636363636363], "preparation_id": "prep-s8-diluted", "concentration_assigned_by": "dilution_of_given_stock", "dilution_chosen_by": "dilution_search", "aliquot_dilution_factor": 14.0, "aliquot_stock_ul": 20.0, "aliquot_buffer_ul": 260.0, "aliquot_well": "H12", "adopted_well_is_new_reaction": true, "reference_protocol_id": "protocol-hrp-tmb-initial-rate-curve", "reference_event_id": "know-protocol-hrp-tmb-initial-rate-curve", "first_enzyme_ng_ml": 100.0, "first_enzyme_volume_ul": 15.151515151515152, "adopted_enzyme_ng_ml": 5.0, "adopted_enzyme_volume_ul": 10.606060606060606, "adopted_enzyme_source": "H12", "dilution_prescribed": false}, "discarded": ["saturated first attempt"], "message": "Working range, KM, and kcat after the dilution search."} {"record_kind": "trial", "run_id": "pearl-manuscript-s8-20260916", "seq": 197, "trace_sequence": 197, "timestamp": "2026-09-16T10:42:57+00:00", "logged_at": "2026-09-16T10:42:57.350000+00:00", "source_agent": null, "scenario_id": "S8", "termination": "completed", "not_wet_lab": false, "adopted": {"summary": "Working range, KM, and kcat after the dilution search.", "KM_uM": 100.0, "kcat_per_s": 3800.0, "Vmax_M_per_s": 4.318181818181818e-07, "Vmax_uM_per_s": 0.4318181818181818, "Vmax_A652_per_min": 0.5658545454545455, "enzyme_concentration_M": 1.1363636363636364e-10, "enzyme_concentration_nM": 0.11363636363636363, "enzyme_concentration_ng_ml": 5.0, "basis": "kcat_per_s = Vmax_M_per_s / enzyme_concentration_M", "read_mode": "same_well", "acid_stop": false, "enzyme_stock": "30 nM, 2000 uL", "working_range_analyte": "HRP", "linear_working_range_hrp_ng_ml": [0.5, 5.0], "linear_working_range_hrp_nM": [0.011363636363636364, 0.11363636363636363], "preparation_id": "prep-s8-diluted", "concentration_assigned_by": "dilution_of_given_stock", "dilution_chosen_by": "dilution_search", "aliquot_dilution_factor": 14.0, "aliquot_stock_ul": 20.0, "aliquot_buffer_ul": 260.0, "aliquot_well": "H12", "adopted_well_is_new_reaction": true, "reference_protocol_id": "protocol-hrp-tmb-initial-rate-curve", "reference_event_id": "know-protocol-hrp-tmb-initial-rate-curve", "first_enzyme_ng_ml": 100.0, "first_enzyme_volume_ul": 15.151515151515152, "adopted_enzyme_ng_ml": 5.0, "adopted_enzyme_volume_ul": 10.606060606060606, "adopted_enzyme_source": "H12", "dilution_prescribed": false}, "discarded": ["saturated first attempt"], "commentary": "The only enzyme concentration given is 30 nM. The first wells were prepared at 100 ng/mL from that stock and saturated. The concentration was too high, so the dilution factor was found by measuring a series. Observations obs-s8-A1-t9, obs-s8-A2-t9, obs-s8-A3-t9, and obs-s8-A4-t9 stayed proportional, and obs-s8-A5-t9 did not. The new wells are new reactions from the 14-fold H12 aliquot, 20 uL of the 30 nM stock plus 260 uL PBS, then PBS and TMB. They are not a transfer of the saturated reaction. 5 ng/mL is the concentration that aliquot and the dispensed volume produce. Reported KM = 100 uM and kcat = Vmax/[E] = 3800 /s at 5 ng/mL.", "analysis_report": {"KM_uM": 100.0, "kcat_per_s": 3800.0, "kcat_calculation": {"equation": "kcat_per_s = Vmax_M_per_s / enzyme_concentration_M", "absorbance_conversion": "Vmax_M_per_s = Vmax_A652_per_min / (epsilon_per_M_cm * path_cm * 60)", "concentration_conversion": "ng/mL = nM * hrp_mw_g_per_mol / 1000", "KM_uM": 100.0, "kcat_per_s": 3800.0, "physical_kcat_per_s": 3800.0, "replicate_delta_uM_per_s": 0.0013936164857032004, "fit_KM_uM": 99.99999999999996, "fit_Vmax_uM_per_s": 0.43181818181818177, "fit_r2": 0.9997789628112558, "Vmax_M_per_s": 4.318181818181818e-07, "Vmax_uM_per_s": 0.4318181818181818, "Vmax_A652_per_min": 0.5658545454545455, "epsilon_per_M_cm": 39000.0, "path_cm": 0.56, "wavelength_nm": 652, "hrp_mw_g_per_mol": 44000.0, "enzyme_stock_nM": 30.0, "enzyme_stock_volume_ul": 2000.0, "enzyme_stock_ng_ml": 1320.0, "enzyme_volume_ul": 10.606060606060606, "neat_enzyme_ul": 0.7575757575757576, "enzyme_source_nM": 2.142857142857143, "enzyme_source_well": "H12", "enzyme_source_labware": "plate", "dilution_factor": 14, "total_volume_ul": 200.0, "enzyme_concentration_M": 1.1363636363636364e-10, "enzyme_concentration_nM": 0.11363636363636363, "enzyme_concentration_ng_ml": 5.0, "physical_enzyme_concentration_M": 1.1363636363636364e-10, "physical_enzyme_concentration_nM": 0.11363636363636363, "physical_enzyme_concentration_ng_ml": 5.0, "kcat_basis": "prepared_well", "kcat_basis_note": "Reported kcat divides Vmax by the enzyme concentration in the new well. The given stock is 30 nM. H12 is a 14-fold aliquot, 20 uL of that stock plus 260 uL PBS. The adopted well is a new reaction: that aliquot, then PBS and TMB. It is not a transfer of the saturated 100 ng/mL preparation. 5 ng/mL is the concentration those volumes produce, and that is the concentration in the denominator.", "enzyme_stock_nM_physical": 30.0, "enzyme_stock_ng_ml_physical": 1320.0, "concentration_basis": "The only enzyme concentration given is 30 nM. The first wells were 100 ng/mL and saturated. The dilution factor was found by measuring a series. Reported kcat uses 5 ng/mL, the concentration of the new well prepared from the 14-fold H12 aliquot."}, "working_range": {"analyte": "HRP", "criterion": "initial rate proportional to final HRP concentration", "fixed_substrate_uM": 200.0, "linear_ng_ml": [0.5, 5.0], "linear_nM": [0.011363636363636364, 0.11363636363636363], "assay_enzyme_ng_ml": 5.0, "assay_enzyme_nM": 0.11363636363636363, "points": [{"hrp_ng_ml": 0.5, "hrp_nM": 0.011363636363636364, "enzyme_volume_ul": 1.0606060606060606, "neat_enzyme_ul": 0.07575757575757576, "hrp_source": "H12", "hrp_source_labware": "plate", "enzyme_source_nM": 2.142857142857143, "dilution_factor": 14, "tmb_volume_ul": 8.0, "buffer_volume_ul": 190.93939393939394, "total_volume_ul": 200.0, "substrate_uM": 200.0, "rate_A652_per_min": 0.03772363636363637, "rate_uM_per_s": 0.028787878787878782, "in_linear_range": true}, {"hrp_ng_ml": 1.0, "hrp_nM": 0.022727272727272728, "enzyme_volume_ul": 2.121212121212121, "neat_enzyme_ul": 0.15151515151515152, "hrp_source": "H12", "hrp_source_labware": "plate", "enzyme_source_nM": 2.142857142857143, "dilution_factor": 14, "tmb_volume_ul": 8.0, "buffer_volume_ul": 189.87878787878788, "total_volume_ul": 200.0, "substrate_uM": 200.0, "rate_A652_per_min": 0.07544727272727274, "rate_uM_per_s": 0.057575757575757565, "in_linear_range": true}, {"hrp_ng_ml": 2.0, "hrp_nM": 0.045454545454545456, "enzyme_volume_ul": 4.242424242424242, "neat_enzyme_ul": 0.30303030303030304, "hrp_source": "H12", "hrp_source_labware": "plate", "enzyme_source_nM": 2.142857142857143, "dilution_factor": 14, "tmb_volume_ul": 8.0, "buffer_volume_ul": 187.75757575757575, "total_volume_ul": 200.0, "substrate_uM": 200.0, "rate_A652_per_min": 0.15089454545454548, "rate_uM_per_s": 0.11515151515151513, "in_linear_range": true}, {"hrp_ng_ml": 5.0, "hrp_nM": 0.11363636363636363, "enzyme_volume_ul": 10.606060606060606, "neat_enzyme_ul": 0.7575757575757576, "hrp_source": "H12", "hrp_source_labware": "plate", "enzyme_source_nM": 2.142857142857143, "dilution_factor": 14, "tmb_volume_ul": 8.0, "buffer_volume_ul": 181.3939393939394, "total_volume_ul": 200.0, "substrate_uM": 200.0, "rate_A652_per_min": 0.3772363636363637, "rate_uM_per_s": 0.2878787878787879, "in_linear_range": true}, {"hrp_ng_ml": 10.0, "hrp_nM": 0.22727272727272727, "enzyme_volume_ul": 1.5151515151515151, "neat_enzyme_ul": 1.5151515151515151, "hrp_source": "A1", "hrp_source_labware": "reservoir", "enzyme_source_nM": 30.0, "dilution_factor": 1, "tmb_volume_ul": 8.0, "buffer_volume_ul": 190.4848484848485, "total_volume_ul": 200.0, "substrate_uM": 200.0, "rate_A652_per_min": 0.712557575757576, "rate_uM_per_s": 0.5437710437710438, "in_linear_range": false}, {"hrp_ng_ml": 20.0, "hrp_nM": 0.45454545454545453, "enzyme_volume_ul": 3.0303030303030303, "neat_enzyme_ul": 3.0303030303030303, "hrp_source": "A1", "hrp_source_labware": "reservoir", "enzyme_source_nM": 30.0, "dilution_factor": 1, "tmb_volume_ul": 8.0, "buffer_volume_ul": 188.96969696969697, "total_volume_ul": 200.0, "substrate_uM": 200.0, "rate_A652_per_min": 1.2826036363636366, "rate_uM_per_s": 0.9787878787878789, "in_linear_range": false}, {"hrp_ng_ml": 40.0, "hrp_nM": 0.9090909090909091, "enzyme_volume_ul": 6.0606060606060606, "neat_enzyme_ul": 6.0606060606060606, "hrp_source": "A1", "hrp_source_labware": "reservoir", "enzyme_source_nM": 30.0, "dilution_factor": 1, "tmb_volume_ul": 8.0, "buffer_volume_ul": 185.93939393939394, "total_volume_ul": 200.0, "substrate_uM": 200.0, "rate_A652_per_min": 2.1376727272727276, "rate_uM_per_s": 1.6313131313131313, "in_linear_range": false}, {"hrp_ng_ml": 80.0, "hrp_nM": 1.8181818181818181, "enzyme_volume_ul": 12.121212121212121, "neat_enzyme_ul": 12.121212121212121, "hrp_source": "A1", "hrp_source_labware": "reservoir", "enzyme_source_nM": 30.0, "dilution_factor": 1, "tmb_volume_ul": 8.0, "buffer_volume_ul": 179.87878787878788, "total_volume_ul": 200.0, "substrate_uM": 200.0, "rate_A652_per_min": 3.2065090909090914, "rate_uM_per_s": 2.446969696969697, "in_linear_range": false}], "linear_ng_ml_basis": "dilution_search"}}}