ECL`

AnalyzeKinetics

AnalyzeKinetics[Trajectories, Reactions]⟹Object

solves for kinetic rates such that the model described by Reactions fits the training data Trajectories.

AnalyzeKinetics[KineticData, Reactions]⟹Object

fits to the trajectories in the given kinetics data objects or protocol.

Details

Uses least-squares optimization to solve for the unknown kinetic rates in the given reactions such that the predicted trajectories from the resulting mechanism best fit the training trajectories.
Global optimization uses NMinimize, while Local optimization uses FindMinimum.
Simulated trajectories are generated during optimization using SimulateKinetics, which uses NDSolve to numerically solve the differential equations describing the reaction network.

Input

Output

General Options

Method Options

Messages

PoorOptimization

Unable to determine optimal rate constants. Calculated rate constants may yield a bad fit, or be identical to the initial guess. This is typically caused by a bad initial guess, or data which cannot be described by the given reactions.

Examples

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Example Setup

These expressions are used in the examples to follow:

Basic Examples (5)

Fit fluorescence kinetics data to a single pairing reaction:

Fit kinetic trajectory data to a single folding reaction:

Fit to all kinetic data in a protocol:

Plot results of fitting catch-and-release data to ReactionMechanism with three reactions:

Specify kinetics equations to fit to:

Additional Examples (4)

Observed Species (1)

Trajectories can be observations on different species:

Reaction Specifications (3)

Reactions can be specified as implicit reactions or a ReactionMechanism:

Reactions can contain mixture of known numeric rates and unknown symblic rates:

Symbolic rate names are automatically generated if unspecified:

Options (22)

AssayWells (1)

Specify which data wells to fit to:

Domain (1)

Exclude from the fitting calculation any data points beyond 500 seconds:

InitialConcentration (1)

Specify the initial concentrations in each data well:

InitialSpecies (1)

Specify which species in the ReactionMechanism is in the wells initially:

InitialVolume (1)

Specify the initial volume for each data:

Injections (1)

Specify the injections corresponding to each input data:

ObservedSpecies (1)

Specify which species in the mechansim corresponds to the fluorescence datas:

OptimizationOptions (1)

Specify accuracy and precision of optimization:

OptimizationType (2)

Use global search with rate intervals:

Use local search with rate guesses:

PrimaryInjectionSpecies (1)

Specify which species in the ReactionMechanism is injected during primary injection:

Rates (3)

Specify guesses for the initial rates:

Specify intervals in which you expect to the true rate values to lie:

Use simulation object for initial guesses:

SecondaryInjectionSpecies (1)

Specify which species in the ReactionMechanism is injected during secondary injection:

StandardCurve (3)

Specify fit object containing standard curve:

Specify standard curve datas and concentrations:

Specify standard curve fluorescences and concentrations:

StandardCurveFitOptions (1)

Specify options for standard fitting:

StandardCurveFitType (1)

Fit a cubic standard curve:

Template (1)

Use resolved options from previous rate fitting analysis:

TertiaryInjectionSpecies (1)

Specify which species in the ReactionMechanism is injected during tertiary injection:

Messages (7)

InvalidAnalyzeKineticsOption (1)

Option lengths must match:

InvalidInjectionSpecies (1)

InvalidInjectionSpecies must exist in given ReactionMechanism:

InvalidObservedSpecies (1)

ObservedSpecies must exist in given ReactionMechanism:

NoAssayWells (1)

Protocol must have at least 1 well linked to data:

NoUnknownRates (1)

No unknown rates in the given ReactionMechanism:

PredictedValueOutOfDomain (1)

Warning if fluorescence data points lies outside of range of standard curve fit:

ReturningInitialGuess (1)

Data for which the rate constants cannot be optimized returns the initial guess:

Last modified on Wed 20 Aug 2025 14:33:27