MATLAB: Fluctuations in Simbiology

fluctuationsSimBiology

Hi,

I try to run a simulation in Simbiology in which a parameter fluctuates during the simulation. I have a few reactions which are not of mass-action type so I can't use the stochastic solver, I believe. How can I simulate with a fluctuating parameter?

Thanks in advance.

Razvan

Best Answer

Hi Razvan,

I think the answer will ultimately depend on what you know about the fluctuations and what sort of questions you're trying to answer. Can you share more details about why you need to model fluctuations and what the fluctuations represent?

In any case, let me see if I can make some guesses and suggestions for how to model your problem in SimBiology.

Are the fluctuations ultimately due to the presence of a small number of molecules of some species participating in a reaction? If so, can you refine the mechanism of your model so that you can write the model in terms of mass action reactions and events? Then, you would be able to use one of the stochastic solvers. (Note that the ssa solver does support events, if that is helpful.)

If you can find some way to convert all your reactions to mass action kinetics, then you will need to take another approach. However, your question does raise some concerns. If something about the model fluctuates during the simulation, do you think it is reasonable to model the reaction kinetics as ODEs? For example, if the parameters fluctuate slowly relative to the time scale of the reactions, then perhaps it is reasonable to model the reactions with ODEs. Let's assume so for now.

Depending on what you know about the fluctuations, I can suggest two approaches, both of which assume the fluctuations are relatively low frequency:

Model the fluctuations as discrete step changes using events.
Model the fluctuations as continuous changes to the parameters that are done via a repeated assignment rule that uses a smooth function (for example, an interpolant like interp1) to determine the parameter values. If you use this approach, you may need to set the MaxStep on the configset's SolverOptions to some time scale that is smaller than the frequency of the fluctuations to ensure that the solver "sees" these fluctuations.

Let me know if you need more details about any of these approaches.

Good luck!

-Arthur

Related Solutions

MATLAB: Redefine mass action kinetics

It's not currently possible to create a custom kinetic law that depends on the reaction's stoichiometry. You will need to manually write each reaction rate.

Based on the form of your reaction rate, I suspect you're trying to model a system containing a small numbers of reacting molecules. Have you considered using one of SimBiology's stochastic solvers? That would likely be a better model of your system than using deterministic solver with the reaction rates you describe.

MATLAB: Problems with a simbiology model

Question 1: First, a little background. In SimBiology, parameters can be associated either with a model (sometimes called "model-scoped parameters") or with a kinetic law of a reaction ("reaction-scoped parameters"). A model-scoped parameter is visible throughout the model and can be used in any reaction, event, or rule. A reaction-scoped parameter can only be used in the rate of the reaction that it's associated with.

get(modelObj1,'Parameters'), or equivalently modelObj1.Parameters, only lists model-scoped parameters. You can get the parameters associated with a particular reaction with code like modelObj1.Reactions(1).KineticLaw.Parameters, or the equivalent

reactionObjs = get(modelObj1, 'Reactions')
kineticLawObj = get(reactionObjs(1), 'KineticLaw')
parameterObjs = get(kineticLawObj, 'Parameters')

If you'd like a simple way to get all the parameters used in a model, you can use use sbioselect function as follows:

allParameterObjs = sbioselect(modelObj, 'Type', 'parameter')

Question 2: I'm a developer on the SimBiology team, and I would need to know more details to assist you with diagnosing a crash. For example, what version of MATLAB are you using? What operating system? Can you provide the crash log? Can you provide reproduction steps? I will try to contact you to obtain this information.

Best Answer

Related Solutions

MATLAB: Redefine mass action kinetics

MATLAB: Problems with a simbiology model

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