rekinsim: a numerical platform for parameter estimation of
TRANSCRIPT
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ReKinSim: A numerical platform for parameter estimation of kinetically complex environmental systems
Mehdi Gharasoo, Martin Thullner, Martin Elsner
Institute of Groundwater Ecology, Helmholtz Zentrum München MICRODEGRADE
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Experimental data
Time
Mass
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Speculate, design and describe the kinetic model
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ReKinSim (GUI mode)
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Hypothetical test case
• Michealis-Menten reaction (Km and Vm)
• A second order reaction (k2)
• Another second order reaction (k3)
• A first order reaction (k4)
𝜕𝐶1𝜕𝑡
= −𝑉𝑚𝐶1
𝐶1 + 𝐾𝑚− 𝑘3𝐶1𝐶4
𝜕𝐶2𝜕𝑡
= +2𝑉𝑚𝐶1
𝐶1 + 𝐾𝑚− 𝑘2𝐶2𝐶3
𝜕𝐶3𝜕𝑡
= −𝑘2𝐶2𝐶3 − 𝑘4𝐶3
𝜕𝐶4𝜕𝑡
= +𝑘2𝐶3𝐶2 − 𝑘3𝐶1𝐶4
𝜕𝐶6𝜕𝑡
= +𝑘4𝐶3
𝜕𝐶5𝜕𝑡
= +2𝑘3𝐶1𝐶4 + 𝑘2𝐶3𝐶2
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• The actual values of parameters: Vm=1e-4[ML-3T-1], Km= .06[ML-3], k2=.02[M-1L3T-1], k3= .003[M-1L3T-1], k4= .005[T-1].
• Initial concentrations: C1=.3, C2=.3, C3=.8, C4=.5, C5=0 v, C6=0[ML-3]
• The solution over 1000 unit of time:
Hypothetical test case
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Hypothetical test case • noisy observations are artificially created from the model solution by
adding normally distributed pseudorandom errors.
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Vm=.71e-4±2.3e-5 Vm=1e-4 Km= .016±.042 Km= .06 k2=.019±1e-3 k2=.02 k3= .003±1e-4 k3= .003 k4= .0047±1.5e-4 k4= .005
Estimated values ± Stdv: Actual parameter values
Hypothetical test case
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KinTek Explorer test case
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Thermal isomerization of α-pinene
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Thermal isomerization of α-pinene
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Take away messages
• A parameter estimation platform for kinetically complex problems was introduced (ReKinSim)
• ReKinSim is shown by comparison in par or superior to other similarly oriented programs such as Aquasim and KinTek Explorer in terms of flexibility and adoptability.
• ReKinSim is offered in two different modes: • With a GUI • Code based