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Team:Colombia Uniandes/Stochastic
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The biochemical reactions carried out in living systems, specifically in cells, follow in general a stochastic process. Transcription, signaling networks and systems within a cell can be modeled and simulated in time as Markovian processes. Gillespie algorithm (see references) gives a stochastic simulation method of these kinds of phenomena and offers a good resolution with an efficient use of computational resources. | The biochemical reactions carried out in living systems, specifically in cells, follow in general a stochastic process. Transcription, signaling networks and systems within a cell can be modeled and simulated in time as Markovian processes. Gillespie algorithm (see references) gives a stochastic simulation method of these kinds of phenomena and offers a good resolution with an efficient use of computational resources. | ||
| - | The advantage of this kind of modeling is that the differential equations that we use in the deterministic model can also be used in the stochastic model. However, in order to do the simulation for our Nickel Uptake system, we must start defining the parameters of the model in the correct units. For our purposes and the algorithm’s requirements, we need units of Molecules per unite of time (in our case, minutes). In the following table we show the parameters used for deterministic simulation and the stochastic parameters. The new parameters where obtained by using Avogadro`s number (6.02e23 molecules per mole) and an average cell volume of 10e-15liters | + | The advantage of this kind of modeling is that the differential equations that we use in the deterministic model can also be used in the stochastic model. However, in order to do the simulation for our Nickel Uptake system, we must start defining the parameters of the model in the correct units. For our purposes and the algorithm’s requirements, we need units of Molecules per unite of time (in our case, minutes). In the following table we show the parameters used for deterministic simulation and the stochastic parameters. The new parameters where obtained by using Avogadro`s number (6.02e23 molecules per mole) and an average cell volume of 10e-15liters. |
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Revision as of 17:03, 1 September 2013
Nickel removal system
The biochemical reactions carried out in living systems, specifically in cells, follow in general a stochastic process. Transcription, signaling networks and systems within a cell can be modeled and simulated in time as Markovian processes. Gillespie algorithm (see references) gives a stochastic simulation method of these kinds of phenomena and offers a good resolution with an efficient use of computational resources.
The advantage of this kind of modeling is that the differential equations that we use in the deterministic model can also be used in the stochastic model. However, in order to do the simulation for our Nickel Uptake system, we must start defining the parameters of the model in the correct units. For our purposes and the algorithm’s requirements, we need units of Molecules per unite of time (in our case, minutes). In the following table we show the parameters used for deterministic simulation and the stochastic parameters. The new parameters where obtained by using Avogadro`s number (6.02e23 molecules per mole) and an average cell volume of 10e-15liters.
