AramcoMech2.0__HAS_PLOG.xls

AramcoMech 2.0 detailed combustion mechanism (C0-C4 hydrocarbons, oxygenates) with pressure-dependent PLOG rate expressions and full Chemkin-style thermodynamic (therm) and transport (TRANSPORT) data. Built on the H2/O2 sub-mechanism.

Workbook note: AramcoMech 2.0, NUI Galway Combustion Chemistry Centre (Saudi Aramco funded), downloaded July 2016 from c3.nuigalway.ie. Built hierarchically from an H2/O2 sub-mechanism upward to characterise C1–C4 hydrocarbons and oxygenated fuels over a wide range of conditions.

Reference foundational mechanism for combustion reactor design and engine simulation. Used to predict ignition delay, laminar flame behavior and species profiles across the pressures/temperatures encountered in gas turbines and IC engines, where PLOG handles falloff between low- and high-pressure rate limits.

AramcoMech3.0__HAS_PLOG.xls

AramcoMech 3.0, the expanded successor mechanism with refined rate parameters and additional fuel sub-mechanisms, again carrying PLOG pressure dependence plus therm/transport tables.

Workbook note: NUI Galway AramcoMech series (the workbook's own text box was copied from the 2.0 file and still reads "AramcoMech 2.0"; the file name and contents are the 3.0 update).

State-of-the-art validation mechanism for combustion engineers: benchmarking burner, engine and flow-reactor models, and providing the kinetic backbone when reducing large mechanisms for CFD.

Combustion_H2_O2_cluster.xls

The branched-chain H2/O2 mechanism used as the dataset for Kintecus's clustering-analysis feature (the -cluster switch), here clustering on a correlation similarity matrix.

Workbook note: this example demonstrates the clustering-analysis feature in Kintecus V3.9 (the -cluster switch), here using a correlation similarity matrix.

Demonstrates kinetics-driven clustering analysis: grouping species/profiles by similarity of their concentration trajectories — a diagnostic for identifying co-evolving species and lumping candidates during mechanism reduction.

Combustion_H2_O2_scan.xlsm

Same H2/O2 mechanism set up to scan an input parameter (here the O2 initial concentration is bracketed for sweeping).

Workbook note: demonstrates the parameter-scanning feature (-scan:1 switch); here scanning a single parameter, the O2 concentration.

Parametric reactor study: sweeping feed stoichiometry/equivalence ratio to locate ignition thresholds and optimum operating windows, a standard combustion-engineering screening exercise.

Combustion_H2_O2_sensit.xlsm

H2/O2 mechanism configured for normalized sensitivity analysis of species concentrations with respect to each rate constant.

Workbook note: demonstrates normalized sensitivity analysis (NSA) plotting (-SENSIT switch, uppercase required).

Identifies the rate-controlling elementary steps so designers know which kinetics dominate ignition and heat release — the basis for rational mechanism reduction before CFD reactor modelling.

Combustion_H2_O2_sensit_AT_TEST.xlsm

H2/O2 sensitivity workbook with 31 stored SENSIT result sheets (time-resolved sensitivity coefficients) for post-processing.

Workbook note: NSA plotting at user-selected time intervals (see O_sens.txt).

Demonstrates time-dependent sensitivity output for combustion diagnostics, letting engineers see how the controlling reaction shifts through induction, branching and burnout phases.

Combustion_OH_DYNAMIC.xls

H2/O2 (OH-producing) mechanism with a dynamic-condition sheet driving time-varying temperature/volume during the run.

Workbook note: uses the Dynamic Kintecus worksheet (dyn_plot); only finalized, completed mechanisms should be placed in it.

Models combustion under non-isothermal, time-varying reactor conditions such as compression/expansion strokes or programmed heating — directly relevant to engine-cylinder and rapid-compression-machine simulation.

Combustion_workbook_OH.xlsm

Baseline H2/O2 OH-chemistry workbook with temperature and concentration output sheets; the reference template the other OH variants build on.

Teaching/working template for setting up an adiabatic or isothermal combustion batch reactor and reading out temperature and radical-pool evolution.

Combustion_workbook_OH_CONF.xlsm

OH combustion model with confidence-interval output sheets (CONCMIN/CONCMAX/CONCAVG/CONCSTD) from Monte-Carlo style runs.

Workbook note: confidence/uncertainty run; author notes the integrator accuracy may need tightening (~1e-8) on some processors.

Propagates rate-constant uncertainty into predicted concentration bands — essential for risk-aware combustor and safety-margin design.

Combustion_workbook_OH_enthalpy_fit.xlsm

OH combustion model set up to regress thermodynamic (enthalpy) parameters against data, with THERMOUT and FITPLOT sheets.

Workbook note: regresses the initial concentration of a species (O2 here) against the measured heat (enthalpy) output of an experiment.

Lets an engineer refine species thermochemistry (heats of formation / NASA polynomials) from measured profiles, improving energy-balance accuracy in reactor heat-release predictions.

Combustion_workbook_OH_multifit.xlsm

OH combustion model configured to fit several rate constants simultaneously against three datasets (d1/d2/d3, multi-plot).

Workbook note: multi-dataset fit of activation energies (Ea) across three datasets at different initial conditions (1000/1500/1700 K); see O_initconditions.txt.

Global kinetic parameter estimation from multiple experiments at once — the standard way to obtain self-consistent Arrhenius parameters for design-grade mechanisms.

Combustion_workbook_OH_props.xlsm

OH combustion model exporting derived properties: per-reaction rates (SPECRATE/RATESOUT), thermodynamic output and full system output (SYSOUT).

Workbook note: outputs full system thermodynamics and reaction properties via the -o:y:y:y:y switch.

Generates reaction-flux and thermochemical property tables used for flux analysis and reactor energy balances.

Combustion_workbook_OH_user_defined_functions.xlsm

OH combustion model where several rate laws are replaced with USER-defined symbolic expressions (custom k = f(T, concentrations)).

Shows how to embed non-standard or empirical rate forms (e.g. custom falloff, third-body weighting) — useful when a process exhibits kinetics outside the Arrhenius template.

Combustion_BIODIESEL2_CH3C10_C7_surrogate.xls

Biodiesel surrogate mechanism (methyl-decanoate-type ester + n-heptane co-fuel) with large C0-C10 hydrocarbon/oxygenate set, therm and transport data.

Workbook note: Herbinet, Pitz & Westbrook (LLNL), biodiesel surrogate = Methyl Decanoate + n-Heptane, v2, LLNL-MI-415050 (Combustion and Flame, 2009). ~5 h runtime on a Core i7.

Predicts ignition and emissions behavior of biodiesel blends for compression-ignition engine and burner design and renewable-fuel evaluation.

Combustion_BIODIESEL_CH3-9-C10_C7_surrogate.xls

Alternate biodiesel surrogate (methyl-ester + n-heptane) detailed mechanism in explicit forward/reverse Arrhenius form.

Workbook note: Herbinet, Pitz & Westbrook (LLNL), surrogate = Methyl-9-Decenoate + Methyl Decanoate + n-Heptane, LLNL-MI-415050 (Combustion and Flame, 2009). ~2 h runtime.

Companion biodiesel surrogate for comparing fuel-structure effects on autoignition and soot precursors in engine combustion studies.

Combustion_C8_to_C16_alkanes.xls

Detailed oxidation mechanism spanning C8-C16 normal alkanes (n-decane representative fuel) with TROE falloff and transport data.

Workbook note: Westbrook, Pitz, Herbinet, Curran & Silke, "A Detailed Chemical Kinetic Reaction Mechanism for n-Alkane Hydrocarbons from n-Octane to n-Hexadecane," Combust. Flame (2008); LLNL n-alkane mechanisms v2.

Surrogate kinetics for kerosene/jet and diesel-range fuels; used to design and optimize gas-turbine and diesel combustors and to study cetane behavior.

Combustion_DIESEL_surrogate.xls

Full diesel surrogate combustion mechanism (large-alkane + aromatic blend) with explicit reverse reactions, therm and transport tables.

Workbook note: detailed low- and high-T mechanism for species up to C12 + xylenes; Mehl, Sarathy, Westbrook & Pitz (LLNL), Xylene+C12_v1.mech, 2012.

Engine-relevant diesel autoignition and emissions modelling for compression-ignition combustion-chamber design.

Combustion_DIESEL_surrogate_reduced_model.xls

A reduced (skeletal) version of the diesel surrogate mechanism with original Chemkin lines retained as comments for traceability.

Workbook note: downloaded from LLNL (combustion.llnl.gov diesel-surrogate detailed-and-reduced) July 2016.

Demonstrates mechanism reduction — trimming species/reactions to a CFD-affordable skeletal model while preserving ignition behavior, a core combustion-engineering task.

Combustion_GASOLINE_surrogate.xls

Gasoline surrogate mechanism built around iso-octane (IC8H18) and companion reference fuels, with therm/transport data.

Workbook note: Mehl, Pitz, Westbrook & Curran, "Kinetic Modeling of Gasoline Surrogate Components and Mixtures under Engine Conditions," Proc. Combust. Inst. 33 (2011) 193-200; LLNL gasoline surrogate v1.0.

Spark-ignition engine knock and octane-rating studies; surrogate-fuel modelling for SI combustion-chamber optimization.

Combustion_isooctane3.xls

Iso-octane (2,2,4-trimethylpentane) detailed oxidation mechanism, the primary high-octane reference fuel.

Workbook note: Iso-octane Model 3, Mehl, Curran, Pitz & Westbrook (LLNL), 2009; LLNL-MI-421507.

Defines the knock-resistant end of the octane scale; used for SI-engine autoignition/knock prediction and as an RON reference in fuel design.

Combustion_methlycarbonate.xls

Dimethyl carbonate / methyl-carbonate oxygenated-fuel combustion mechanism.

Workbook note: Glaude, Pitz & Thomson, "Chemical Kinetic Modeling of Dimethyl Carbonate in an Opposed-Flow Diffusion Flame," Proc. Combust. Inst. 30 (2004) 1095-1102; UCRL-CONF-201358.

Evaluates oxygenated fuel additives that suppress soot; relevant to clean-diesel and additive-formulation engineering.

Combustion_methlydecanoate.xls

Methyl decanoate combustion mechanism — a realistic methyl-ester representative of biodiesel.

Workbook note: Herbinet, Pitz & Westbrook (LLNL), Methyl Decanoate v2, LLNL-MI-415050 (Combustion and Flame, 2009). ~3 h runtime on a Core i7.

Benchmark biodiesel-component kinetics for renewable-fuel combustor and engine design.

Combustion_Organophosphates.xls

Hydrocarbon combustion mechanism extended with organophosphorus chemistry (H/O/C1/C2 core plus P-species).

Workbook note: Glaude, Melius, Pitz & Westbrook, "Detailed Chemical Kinetic Reaction Mechanisms for Incineration of Organophosphorus and Fluoro-Organophosphorus Compounds," Proc. Combust. Inst. 29 (2002) 2469-2476; UCRL-JC-146563.

Models flame inhibition/suppression by phosphorus agents and incineration of organophosphate compounds — fire-suppression and hazardous-waste-destruction engineering.

Combustion_TNT_and_RDX.xls

Combustion/decomposition mechanism for energetic materials (TNT and RDX) built on a C/H/O/N hydrocarbon core.

Workbook note: Pitz & Westbrook, "A detailed chemical kinetic model for gas phase combustion of TNT," Proc. Combust. Inst. 31 (2007) 2343-2351; LLNL mechanism tnt_v1j_tol_v6k_rdx_1a_c4_2c.mech.

Energetic-material decomposition and afterburn modelling for propulsion, demilitarization and explosion-safety analysis.

Ethanol_Combustion.xls

Ethanol oxidation mechanism (Marinov-type rate data) with LIN/falloff third-body handling.

Bioethanol and flex-fuel combustion modelling for engine and burner design with a renewable oxygenate.

Dimethylether_combustion.xlsm

Dimethyl ether (DME) wide-range oxidation mechanism (Curran et al.) with TROE falloff and free-format thermo.

Workbook note: DME combustion example (~10 min on a Pentium IV).

DME is a clean compression-ignition fuel; this models its low-temperature ignition for alternative-fuel engine design.

Dimethoxy_model.xlsm

Dimethoxymethane (DMM/methylal) oxidation mechanism (Daly thesis) with free-format thermodynamic data.

Workbook note: dimethoxymethane combustion example (~3 min on a Pentium IV).

Oxygenated diesel-additive combustion modelling aimed at soot reduction in compression-ignition engines.

Heptane_Combustion_Pitz.xlsm

n-Heptane counterflow ignition/extinction mechanism (Seiser/Pitsch/Pitz/Curran).

Workbook note: uses -obeymaxint with a small maximum integration time for a smoother output curve (~3 min on a Pentium IV).

n-Heptane is the zero-octane diesel reference fuel; used for autoignition, ignition-delay and extinction-strain studies in CI-engine design.

n-buthane-combustion.xlsm

n-Butane oxidation mechanism (Marinov rate data, LIN third-body falloff).

LPG/butane combustion modelling for burners and small engines.

pitz_propane_model.xlsm

Detailed propane oxidation mechanism (Curran/Pitz/Westbrook) in explicit forward/reverse form.

Propane/LPG combustor and flame modelling; a common reference for C3 oxidation kinetics.

GRI_MECH_30.xlsm

GRI-Mech 3.0 — the 53-species/325-reaction natural-gas (methane) combustion mechanism with NOx, third-body efficiencies and its own thermo file.

Workbook note: the gritherm.dat Chemkin thermodynamic database was converted into the O_gritherm.dat worksheet using the -OF switch.

The industry-standard methane/natural-gas mechanism for gas-turbine, boiler and burner design and for validating CFD combustion codes.

GRMECH_with_compression.xlsm

GRI-Mech 3.0 driven by a sinusoidal volume profile (O_sine1.txt) simulating piston compression.

Workbook note: GRI-Mech 3.0 with compression (~20 min on a Pentium IV).

Couples detailed methane kinetics to engine-cylinder volume change — homogeneous-charge / HCCI-style engine autoignition modelling.

GRMECH_with_compression_heat_loss.xlsm

As above but adding an external wall-temperature profile (O_externtemp.txt) for heat loss during compression.

Workbook note: GRI-Mech 3.0 with compression and heat loss (~15 min on a Pentium IV).

Adds non-adiabatic heat transfer to the engine-compression model — more realistic cylinder energy balance for IC-engine simulation.

Kilpinen_97_NH3_ORG.xlsm

Kilpinen-97 detailed NH3/NO/O2 nitrogen-chemistry mechanism (Abo Akademi).

Workbook note: Kilpinen 97 NH3/NO/O2 scheme; author notes the integrator accuracy may need tightening on some processors.

Ammonia combustion and fuel/thermal-NOx formation modelling — central to carbon-free NH3 fuel engineering and combustion NOx control.

nox_model.xlsm

Marinov NO-NO2 conversion mechanism showing hydrocarbon promotion of NO oxidation in a flow reactor.

Flue-gas NOx chemistry for emissions prediction and abatement design in furnaces and engines.

H2-O2-Combustion-gas-liquid-catalytic-surface-tests.xlsm

H2/O2 combustion mechanism configured to test coupled gas-phase, liquid-phase and catalytic-surface reaction handling.

Demonstrates multiphase / heterogeneous-catalytic reaction modelling (gas + surface) relevant to catalytic combustors and surface-reaction reactor design.

Calculate_a_volume_factor_for_pistons.xls

A utility spreadsheet converting a measured piston swept-volume-vs-time profile into the per-step Kintecus volume factor.

Pre-processing tool that turns an engine/rapid-compression-machine volume trace into the time-dependent volume input a variable-volume reactor model needs.

Wolfrum_with_Temp_Program.xlsm

Temperature-programmed desorption of CO from a tungsten crystal (Houle & Hinsberg) using extended Arrhenius with a programmed temperature ramp (O_tempprof.txt).

Surface-science / heterogeneous-catalysis kinetics: extracting desorption activation energies from TPD — directly applicable to catalyst characterization and surface reaction engineering.

Fe(VI)+ABTS_Fe(IV)_involved_multiple_fitting_20180724_100mM phosphate_pH=7_ks3=1e6.xlsm

Ferrate(VI) oxidation of the ABTS probe via Fe(V)/Fe(IV) intermediates, fitted to four datasets simultaneously; this version in 100 mM phosphate buffer, pH 7.

Workbook note: bootstrapped error analysis of several rate parameters across multiple datasets/initial conditions; results in Huang et al. (ACS); 100 mM phosphate, pH 7 (~12 h runtime).

Quantifies high-valent iron oxidation kinetics used in ferrate-based drinking-water and wastewater treatment; the buffer/concentration variants probe matrix effects on disinfection/oxidation performance.

Fe(VI)+ABTS_Fe(IV)_involved_multiple_fitting_20180724_10mM phosphate_pH=7_ks3=1e6.xlsm

Same ferrate(VI)/ABTS Fe(IV)-involved kinetic model, 10 mM phosphate buffer, pH 7, multi-dataset fit.

Workbook note: same bootstrapped multi-dataset error analysis (Huang et al., ACS); 10 mM phosphate, pH 7 (~8 h runtime).

Tests buffer-strength (phosphate) effect on ferrate oxidation rates — water-treatment process design under realistic ionic conditions.

Fe(VI)+ABTS_Fe(IV)_involved_multiple_fitting_20180729_10mM borate_pH=7_ks3=1e6.xlsm

Ferrate(VI)/ABTS Fe(IV)-involved model in 10 mM borate buffer, pH 7, multi-dataset fit.

Workbook note: same bootstrapped multi-dataset error analysis (Huang et al., ACS); 10 mM borate, pH 7 (~17 h runtime).

Compares borate vs phosphate buffering on ferrate decay/oxidation — supports buffer selection and rate prediction in ferrate water-treatment trains.

Micropollutant Degradation by Ferrate FeVI-PAA.xlsm

Ferrate(VI) + peracetic acid (PAA) system with the full Fe(VI)/Fe(V)/Fe(IV)/Fe(III)/Fe(II) redox cycle and H2O2/O2 side chemistry degrading a micropollutant.

Workbook note: from Wang, Kim, Ashley, Sharma & Huang, "Peracetic Acid Enhances Micropollutant Degradation by Ferrate(VI)...," Environ. Sci. Technol. 56(16) 2022, 11683-11693.

Models an advanced ferrate/PAA oxidation process for removing trace organic micropollutants (pharmaceuticals, etc.) in water-treatment engineering.

Superfast degradation of micropollutants in water final.xlsm

Chlorine-dioxide / sulfite radical-chain advanced reduction-oxidation network (ClO2, SO3*-, SO4*-, ClO*, etc.) degrading micropollutants.

Workbook note: from Li et al., "Superfast degradation of micropollutants in water by reactive species generated from the reaction between chlorine dioxide and sulfite," Water Research 222 (2022) 118886.

Radical-based advanced oxidation/reduction process (AOP/ARP) design for rapid micropollutant destruction in water treatment.

UV_bromine_final_Lee et al., ES&T, 2020.xlsm

UV/bromine advanced-oxidation mechanism (Lee et al., ES&T 2020): photolysis of HOBr/OBr- generating reactive bromine and OH radicals.

Workbook note: from Lee, Lee, Allard, Ra, Han & Lee, "...UV254 Photolysis of Chlorine and Bromine Species in Water and Formation of Oxyhalides," Environ. Sci. Technol. 54(18) 2020; simulates oxidant decay, probe degradation and ClO3-/BrO3- formation.

Designs UV/bromine AOP and predicts reactive-bromine speciation and bromate formation risk in disinfection — key water-quality engineering concern.

UV_chlorine_final_Lee et al., ES&T, 2020.xlsm

UV/chlorine AOP mechanism (Lee et al., ES&T 2020): photolysis of HOCl/OCl-/ozone producing OH, Cl, O radicals and reactive species.

Workbook note: from Lee et al., Environ. Sci. Technol. 54(18) 2020 (same study as the UV/bromine workbook); simulates oxidant decay, probe degradation and oxyhalide formation.

Models the widely used UV/chlorine advanced-oxidation process for micropollutant removal and disinfection-byproduct prediction in potable-water treatment.

Water Purification HOCl_chlorite_model.xlsm

Aqueous chlorine/chlorite/chlorine-dioxide disproportionation and inter-conversion network (HOCl, OCl-, ClO2, ClO2-, ClO3-) with NOM terms, pH-fixed.

Workbook note: from Rougé, Lee, von Gunten & Allard, "Kinetic and mechanistic understanding of chlorite oxidation during chlorination...," Water Research 220 (2022) 118515.

Predicts chlorine-species speciation and chlorate/chlorite byproduct formation during disinfection — regulatory-compliance and disinfectant-dosing engineering.

Water Purification_phenol oxidation.xlsm

Phenol oxidation in water using USER-defined photolysis/oxidant rate laws spanning HSO5-, S2O8--, H2O2, HOCl, OCl-, HOBr competing for UV photons.

Workbook note: from Huang & Zhang, "A comprehensive kinetic model for phenol oxidation in seven advanced oxidation processes...," Water Research X 14 (2022) 100129.

Models competitive-oxidant phenol destruction under UV — process optimization for oxidant selection in contaminated-water remediation.

zhang_aerobic-Fitting_Multiple_Datasets.xlsm

Surface-bound Fe(III)/Fe(II) + ascorbate redox cycling under aerobic conditions with O2, fitted across six datasets.

Iron redox cycling at mineral/water interfaces with oxygen — relevant to iron-mediated contaminant transformation and natural attenuation in aerobic waters/sediments.

zhang_anoxic-Fitting_Multiple_Datasets.xlsm

The anoxic counterpart: surface Fe(III)/Fe(II)/ascorbate redox cycling without oxygen, multi-dataset fit.

Anoxic iron redox kinetics for groundwater/sediment geochemistry and contaminant fate under oxygen-limited conditions.

Oregonator_in_CSTR.xlsm

Modified Oregonator model of the Belousov-Zhabotinsky oscillating reaction with explicit flow through a CSTR (residence time set on every species).

Textbook nonlinear reaction-engineering case: oscillations, limit cycles and multiplicity in a continuous stirred-tank reactor — used to study reactor stability and dynamic control.

Pires and Faria Inorg Chem 2021 photochemical chlorate-iodide clock reaction.xlsm

Detailed chlorate-iodide photochemical clock-reaction mechanism (Pires & Faria, Inorg. Chem. 2021): iodine/chlorine oxy-species autocatalytic network.

Workbook note: from Pires & Faria, "The Photochemical Chlorate–Iodide Clock Reaction," Inorg. Chem. 61(2) 2022, 1178-1187.

Models clock/autocatalytic kinetics and induction-time control — reaction-engineering insight into autocatalysis and feedback that also underlies halogen water chemistry.

Chemnet_Pires and Faria Inorg Chem 2021 photochemical chlorate-iodide clock reaction.xlsm

The Pires & Faria chlorate-iodide photochemical clock mechanism configured to export a reaction network (chemnet/specnet, plus dot/circo graph layouts) for visualization.

Workbook note: network-graph (chemnet) version of the Pires & Faria chlorate-iodide clock model (Inorg. Chem. 2022); O_-prefixed sheets are written out as tab-delimited text on Run.

The network-graph version of the chlorate-iodide clock model: used to visualize and audit the autocatalytic halogen reaction pathways behind the clock behavior.

chlorate_iodine_JACS_FIG_1a.xlsm

Chlorate + iodide autocatalytic clock mechanism reproducing Figure 1a of the source JACS study (HOI/HIO2/I2/ClO2 network).

Workbook note: the Chlorate-Iodine clock reaction of Oliveira & Faria (JACS 2005, 127, 18022); this run replicates Figure 1a.

Reproduces a published clock-reaction figure; a validation/benchmark case for autocatalytic halogen kinetics modelling.

chiral_kinetic_resolution.xlsm

Dynamic kinetic resolution of chirally labile enantiomers (Noyori BINAP-Ru hydrogenation, Kitamura et al. JACS 1993): competing R/S substrate interconversion and stereoselective product formation.

Quantifies enantioselectivity vs substrate racemization rates — pharmaceutical/fine-chemical asymmetric-catalysis reactor design and optimization of %ee.

Chemnet_Enzyme_Inhibition_Model.xlsm

Non-competitive enzyme inhibition mechanism (E, S, ES, I, EI, EIS, P) with network-export (chemnet/specnet) sheets for reaction-graph visualization.

Bioreactor/biocatalysis kinetics with inhibition; the network export helps visualize and communicate enzyme-mechanism pathways for process and pharmacology work.

Enzyme_Cluster_Analysis.xls

The non-competitive enzyme inhibition mechanism used as input to Kintecus's clustering-analysis feature (-cluster switch) with a simple Euclidean-distance similarity matrix.

Workbook note: demonstrates the clustering-analysis feature in Kintecus V3.9 (-cluster switch) using a simple Euclidean-distance similarity matrix.

Shows clustering of reacting species by trajectory similarity (Euclidean metric) — used to find groups of kinetically similar species in a biochemical network.

Enzyme_Cluster_Analysis_2.xls

The same enzyme inhibition mechanism run through Kintecus clustering analysis but using a correlation similarity matrix.

Workbook note: the same clustering-analysis feature using a correlation similarity matrix instead of Euclidean distance.

Companion clustering-analysis case contrasting the correlation metric with the Euclidean metric for grouping kinetically similar species.

Enzyme_Regression_Fitting.xlsm

The core non-competitive-inhibition enzyme model with unknown rate constants flagged ('1?') for regression against FDATA/FITPLOT data.

Workbook note: baseline single-dataset rate-constant regression example (FDATA/FITPLOT).

Demonstrates fitting enzyme rate constants to a progress curve — the foundational parameter-estimation workflow for biocatalytic process kinetics.

Enzyme_Regression_Fitting_BOOTSTRAPPING.xlsm

Same enzyme fit using bootstrap resampling and thermodynamic linkage (k expressed via 1/Keq) to estimate parameter confidence.

Workbook note: demonstrates the BOOTSTRAP method for accurate standard errors of the fitted parameters.

Provides statistically rigorous confidence intervals on enzyme kinetic parameters — important for defensible bioprocess design.

Enzyme_Regression_Fitting_Constraints_fit5.xlsm

Enzyme fit with explicit bound constraints on rate constants (e.g. 1e3<k<1e9).

Workbook note: shows rate-constant constraints (model worksheet) with the newer -FIT:5 optimizer.

Shows constrained parameter estimation that keeps fitted enzyme constants physically realistic — a practical regression technique.

Enzyme_Regression_Fitting_Multi_Absorb.xlsm

Enzyme fit against multiple absorbance signals (multi-wavelength spectroscopic data, fitdata + fitdata2).

Workbook note: builds special outputs that are functions of concentrations/temperature (here four overlapping absorbance wavelengths) to regress against data when species absorbances overlap.

Fits kinetics to spectrophotometric data where several species absorb — typical of UV-Vis enzyme assays in bioanalytical engineering.

Enzyme_Regression_Fitting_Multiple_Datasets.xlsm

Enzyme model fitted simultaneously to three experimental datasets (d1/d2/d3, multi-plot).

Workbook note: multi-dataset fit of rate constants across three datasets at the same initial conditions.

Global fitting across experiments for one consistent enzyme parameter set — best practice for robust biocatalytic kinetic models.

Enzyme_Regression_Fitting_Multiple_Datasets_and_initial_conditions.xlsm

Multi-dataset enzyme fit that also varies initial conditions per dataset (O_initial_conditions.txt).

Workbook note: multi-dataset fit of rate constants where each dataset uses different initial conditions.

Handles experiments run at different starting concentrations in a single global fit — realistic for enzyme assay series at varied substrate loadings.

Enzyme_Regression_Fitting_WEIGHTS_TEST.xlsm

Enzyme regression demonstrating data weighting in the objective function.

Workbook note: demonstrates per-point data weighting in the fitdata file via values in parentheses, e.g. 2e-5(0.1).

Shows how measurement weighting (by uncertainty) affects fitted enzyme parameters — sound statistical practice in kinetic estimation.

Enzyme_Regression_Fitting_reverse_rate_fit.xlsm

Enzyme fit where reverse rate constants are tied to forward ones through equilibrium constants (k_rev = k_fwd / Keq).

Workbook note: constrains reverse constants kb to forward constants via the equilibrium constant (reducing 9 parameters to 5); use -FITSTAT:BOOT for errors.

Enforces thermodynamic consistency between forward/reverse steps while fitting — prevents physically impossible kinetics in reversible enzyme mechanisms.

Enzyme_Regression_Fitting_reverse_rate_fit_new_way.xlsm

Updated approach to the reverse-rate linkage using an explicit fit-links file (O_fit_links.txt) referencing reaction numbers.

Workbook note: the same forward/reverse linkage done through the fit_links mechanism (O_fit_links.txt).

A cleaner parameter-linking method for thermodynamically consistent reversible enzyme kinetics.

Enzyme_Regression_Molar_Extinct.xlsm

Enzyme fit that simultaneously regresses molar extinction coefficients alongside rate constants.

Workbook note: uses -FITWEIGHT:column#:guess to fit a molar extinction coefficient (Kintecus returns 1/epsilon) together with one rate constant.

Couples spectroscopic calibration (extinction coefficients) with kinetic fitting — needed when absorbance must be converted to concentration during the fit.

Enzyme_Uncertainty_Analysis.xlsm

Enzyme model with input uncertainty assigned to rate constants and initial concentrations (e.g. value(.2/1)? notation) for error propagation.

Workbook note: -CONF switch runs 100 kinetic runs with 2-4% Gaussian deviations; model/species cells override values via the number(stddev/1)? notation.

Propagates kinetic and concentration uncertainty into predicted enzyme behavior — quantitative risk assessment for bioprocess predictions.

Enzyme_scanning.xlsm

Enzyme model scanning a parameter (e.g. substrate from 0.01 to 0.10 M) with 23 stored CONC result sheets and a SCANPLOT.

Workbook note: uses the scan switch to generate a family of runs.

Generates a family of progress curves vs substrate loading — e.g. building a rate-vs-[S] saturation profile for Michaelis-Menten/inhibition characterization.

POLYMER_MULTIFIT_MULTICONDITIONS.xls

Free-radical MMA polymerization mechanism (initiation, propagation, termination by combination/disproportionation, chain transfer, inhibition) fitted across three conditions with external condition file.

Workbook note: multi-dataset rate-constant fit at three temperatures (300/325/350 K); initial conditions per dataset set in O_polymer_conditions.txt.

Models methyl-methacrylate radical polymerization and fits kinetics across multiple operating conditions — core polymer-reactor design and process-development kinetics.

POLYMER_MW_DISTRIBUTION_CALC.xlsm

The MMA polymerization mechanism with a dedicated molecular-weight-distribution calculation sheet.

Computes polymer molecular-weight distribution / dispersity from the kinetic run — directly tied to product-quality control in polymer manufacturing.

H2SO4_Equilibrium_Phase.xlsm

Equilibrium (eqtherm) calculation of the H2SO4(l)/SO2/SO3 system with a concentration-vs-temperature plot.

Predicts sulfuric-acid/SOx equilibrium speciation vs temperature — relevant to contact-process sulfuric-acid plants and SOx handling.

H2_O2_Equil_Phases.xlsm

Multi-phase equilibrium of the H2/O2/H2O system (eqtherm) with concentration-vs-temperature output.

Gibbs-energy-minimization style equilibrium of water formation/dissociation vs temperature — combustion-product and steam-system thermodynamics.

H2_O2_N2_Equilibrium.xlsm

Equilibrium composition of the H2/O2/N2 system including N-containing species (eqtherm).

Equilibrium NOx and combustion-product prediction in air — adiabatic-flame/equilibrium analysis for emissions and thermodynamic limits.

EGU_Atmos_Meas_2025_ClNO2.xlsm

Thermal dissociation of nitryl chloride (ClNO2 + M → Cl + NO2) coupled to a detailed Cl / NOx / CH4 / chloromethane gas-phase sub-network (ClONO2, ClO, HOCl, HCl, CH3Cl, CH2Cl2, CHCl3, etc.). Rate data are drawn from atmospheric-kinetics databases (Baulch, Atkinson, IUPAC, JPL/DeMore — including a JPL5/Troe falloff form). Concentrations are in molecules cm⁻³ and a heated temperature profile (O_ClNO2temp-450.txt) drives the run; a chemnet/specnet network export is included.

Workbook note: replicates Figure 2 of Halfacre et al., “The determination of ClNO2 via thermal dissociation–tunable infrared laser direct absorption spectroscopy,” Atmos. Meas. Tech. 18 (2025) 3799-3818.

Simulates the heated inlet of a thermal-dissociation tunable-infrared-laser direct-absorption spectrometer (TD-TILDAS) used to quantify atmospheric ClNO2. From a process standpoint it is a heated flow-reactor model used to design and interpret an analytical trace-gas instrument — a process-analytical / atmospheric-measurement chemistry application — reproducing Figure 2 of the source paper.

Kintecus_workbook.xls

The blank master Kintecus workbook (empty model/species with full CONTROL, PARM, therm, fitdata sheets and embedded help).

The starting template for building any new kinetic simulation — the blank reactor 'form' an engineer copies and fills in.

Kintecus_graphs_templates.xls

Pre-built graphing templates (CONC and CONCeq plot sheets) for visualizing kinetic and equilibrium output.

Workbook note: graph templates copied into a workbook via right-click > Move or Copy; Kintecus recognizes "ctemplate" (concentration plots) and "ttemplate" (temperature plots).

Reusable plotting layouts for presenting concentration-time and equilibrium results — reporting/visualization aid.

Kintecus_10_products_test.xlsm

A stress/validation case with one reaction producing many products with non-integer stoichiometry (A+B+C ==> D+E+F+2G+3.566H+...).

Verification model checking that the solver handles many products and fractional stoichiometric coefficients correctly — software QA.

Kintecus_MCM_examples.xls

Examples of special rate-law directives (TDBR, MTD, MCM, CHEB third-body/temperature-pressure forms) drawn from the Master Chemical Mechanism conventions.

Workbook note: examples of the special MCM/TDBR/MTD/CHEB third-body and temperature/pressure rate directives.

Reference for encoding complex pressure/temperature-dependent and Master-Chemical-Mechanism rate expressions — used in atmospheric/tropospheric chemistry modelling.

MCM import macro_v0.4.1_beta.xlsm

A VBA macro tool that imports Master Chemical Mechanism (MCM) reaction sets and translates their rate expressions into Kintecus format.

Workbook note: macro to import an MCM model from a spreadsheet.

Automation/tooling that ingests large published atmospheric mechanisms — a productivity utility for air-quality and tropospheric-chemistry modelling.

Kintecus_multiwell_cheb_tests.xls

Test workbook for Chebyshev (CHEB) pressure/temperature-dependent rate representations (multiwell rate surfaces) with SYSOUT.

Workbook note: Kintecus V5.5+ supports Chebyshev expansions (Venkatesh) for pressure falloff and T-dependent rates of multiple-well reactions via the CHEB keyword and a chebdata.txt file.

Validates Chebyshev-polynomial rate handling used for complex falloff/multiwell reactions — important for accurate pressure-dependent combustion/atmospheric kinetics.

Chemnet_Simple_Mechanism_Validations.xlsm

Simple A/B/C interconversion mechanisms implementing the validation cases of Stanbury & Hoffman (2019) with network export.

Teaching/validation set illustrating thermodynamically legal vs illegal mechanism cycles — trains correct mechanism construction and detailed-balance checking.

Chemnet_Visualize_mechanism_validation_1.xlsm

Iodate/iodide (Dushman-type) mechanism set up to export a reaction network (chemnet/specnet) for graphical visualization.

Demonstrates turning a kinetic mechanism into a species/reaction graph — a communication and mechanism-auditing aid.

ChemNet_Combustion_workbook_OH.xlsm

The H2/O2 OH combustion mechanism configured to export chemnet/specnet reaction-network files.

Shows reaction-flux/network visualization applied to a combustion mechanism — pedagogical and diagnostic for pathway analysis.

Disease_spread_Endemic.xlsm

An SI-type epidemiological model (Healthy/Infected/Dead with births) cast as chemical reactions reaching an endemic steady state.

Pedagogical use of chemical-kinetics machinery for population/epidemic dynamics — illustrates that mass-action ODE solvers apply to any rate process, including endemic-equilibrium analysis.

Disease_spread_Epidemic.xlsm

An SIR-type model (Healthy/Infected/Recovered/Dead) as reactions producing an epidemic peak-and-decay curve.

Teaching example mapping epidemic outbreak dynamics onto chemical rate equations — analogy for autocatalytic/chain processes.

Disease_spread_Epidemic_error_analysis.xlsm

The SIR epidemic model with uncertainty on initial populations and confidence-band output (CONCMIN/MAX/AVG/STD).

Combines the epidemic analogy with Monte-Carlo uncertainty propagation — teaches both dynamic modelling and error analysis.

AstroBiology_Ross.xlsm

A stepwise oligomerization/polymerization network (A1+A1->A2, A2+A1->A3, ...) with paired forward/reverse rates and thermodynamic (delta-G/Keq) annotations, modelling prebiotic chain growth.

Workbook note: from Ross & Deamer, "Prebiotic Oligomer Assembly: What Was the Energy Source?", Astrobiology 19(4), 2019.

Physical-chemistry/astrobiology model of abiotic monomer-to-polymer assembly — illustrates sequential equilibrium polymerization and free-energy-controlled chain growth.