SimulateKinetics

SimulateKinetics[ReactionModel, InitialCondition, SimulationDuration]⟹Trajectory

performs kinetic simulation of reaction network described by ReactionModel, starting from initial condition InitialCondition, until the time SimulationDuration.

SimulateKinetics[InitialCondition, SimulationDuration]⟹Out

generates a mechanism from initial condition and then simulates its kinetics until the time SimulationDuration.

Details

There are two different injection models: slow and fast/instantaneous. Fast injections have the form {TimeP,Species,Volume,Concentration} | {TimeP,Species,Volume,Null,Concentration} where in the latter case Null implies instantaneous injection of the full volume. Slow injections have the form {TimeP,Species,Volume,Rate,Concentration}. The full form is for a list of injections, one for each species added.

Input

Output

General Options

Examples

Example Setup

These expressions are used in the examples to follow:

Basic Examples (6)

Allows list of numeric initial conditions:

Input can be specified as a ReactionMechanism object:

Simulate a hybridization reaction for 60 seconds:

Simulate an irreversible reaction for 60 seconds:

Simulate the kinetics of the a mechanism from the given initial state:

Simulation time without units defaults to seconds:

Additional Examples (4)

A first order irreversible reaction can have multiple products:

A second order irreversible reaction can have multiple products:

Given differential equation directly:

Return the final state:

Options (22)

AccuracyGoal (1)

Increase accuracy:

Injections (3)

Comparing the injections and slow injection models by overlaying trajectories on the same plot:

Injections to the system can be fully specified with FlowRate:

Without specifying FlowRate the injections are treated as instantaneous:

MaxStepFraction (1)

Increase max step fraction:

Method (3)

Compare deterministic and stochastic simulation by overlaying the trajectories from both methods on top of each other:

Use analytic solution instead of stochastic simulation, which is only available for certain types of reaction networks:

Use the stochastic method to simulate the concentration changes:

Noise (3)

A specified concentration value will be used as the standard deviation in a NormalDistribution with zero mean:

Specify a noise distribution and it will be sampled and injected into the simulation output:

Specify noise as a percentage of the maximum value in the initial state:

NumberOfPoints (1)

Specify number of points to sample solution at (which decides the sampling interval) when using Analytic solution method:

NumberOfTrajectories (1)

Conduct 3 stochastic simulations of the same system and overlay them in the same plot:

ObservedSpecies (1)

Specify species that are observed and recorded in the returned trajectory:

PrecisionGoal (1)

Increase precision:

Temperature (3)

Periodic heating and cooling causes weaker structures to slow get consumed by the stronger structures:

Simulate the kinetics of the mechanism at specified temperature:

Temperature can be a function of time, which varies along with the simulation:

Template (2)

A template simulation (Object Reference) whose methodology should be reproduced in running this simulation. Option values will be inherited from the template simulation, but can be individually overridden by directly specifying values for those options to this simulation function:

A template simulation (Object) whose methodology should be reproduced in running this simulation. Option values will be inherited from the template simulation, but can be individually overridden by directly specifying values for those options to this simulation function: