Best Method

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Best Method

Post by ahmed.hamzah »

hi everyone

I am trying to solve the cable equation with set of concentration equations for Na, K and Ca. I read a discussion for solving a such system and someone said that the value of concentration was small and Ted told him to change the way of solution because that used way kill the concentration results and made it extremely small. My question is that what is the best way to use to get reasonable concentration results ?
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Re: Best Method

Post by ted »

The first question is whether your hypothesis, or the biological process that you are studying, requires you to do anything at all about ionic concentration. For most published models, the answer appears to be no; in such models, ionic concentrations and equilibrium potentials are assumed to be constant and can be represented by constant parameters.

Some models are used to study the response of a cell to an experimental manipulation such as an (experimenter-caused) change of extra- or intracellular ionic concentration or equilibrium potential. In those models, concentration (and/or equilibrium potential) is still a parameter, but the value of that parameter is changed once (or maybe a few times) in the course of a simulation.

Other models are used to examine how drugs or cellular activity affect ionic concentrations. For those models, the concentrations of the affected ionic species must be state variables, and in NEURON, this means that there must be an NMODL file that describes a mechanism that WRITEs the intra- and/or extracellular concentration of that ion. Such a mechanism is called an "ion accumulation mechanism." Models of this kind are difficult to work with for several reasons. First, ion accumulation is a slow process, so simulations can span hundreds if not thousands or tens of thousands of milliseconds of model time, and run times can be quite long. Second, such models usually require custom initialization because it is generally impossible to predict the steady state concentration of the involved ions, let alone the resting potential of the cell (and resting potential could even be nonuniform). Third, in real cells and tissues there are many processes that affect and regulate ionic concentrations--ion exchange mechanisms, pumps, buffers, diffusion, intracellular stores, uptake and release by satellite cells, just to name a few--and most of these are only partially characterized. This makes it difficult to implement models that avoid unjustifiable complications and still work properly.

Your best strategy is to start by looking in ModelDB for something that comes close to what you are interested in, and either reusing that after some modification, or using what you learn from that to implement your own model.
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