Chin J Plant Ecol ›› 2017, Vol. 41 ›› Issue (3): 378-385.DOI: 10.17521/cjpe.2016.0067
• Method and Technology • Previous Articles
Ji-Ye ZENG1, Zheng-Hong TAN2,*(), Nobuko SAIGUSA1
Online:
2017-03-10
Published:
2017-04-12
Contact:
Zheng-Hong TAN
About author:
KANG Jing-yao(1991-), E-mail: Ji-Ye ZENG, Zheng-Hong TAN, Nobuko SAIGUSA. Using approximate Bayesian computation to infer photosynthesis model parameters[J]. Chin J Plant Ecol, 2017, 41(3): 378-385.
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URL: https://www.plant-ecology.com/EN/10.17521/cjpe.2016.0067
Fig. 1 Comparison of the temperature correction models. Solid line is the curve of von Caemmerer et al. (2009) when S = 710 and H = 220 000; dotted line is the curve when S is increased by 10% (S=790, H=220 000); dashed line is the curve calculated according to our new response curve (Cm = 0.3, Tm = 37).
符号 Symbol | 单位 Units | 注释 Remark | 参考值 Reference value |
---|---|---|---|
A | μmol·m-2·s-1 | 净光合速率 Net photosynthesis rate | |
Ac | μmol·m-2·s-1 | Rubisco酶限制下的光合速率 Rubisco activity limited net photosynthesis rate | |
Aj | μmol·m-2·s-1 | RuBP再生限制的光合速率 Electron transport limited net photosynthesis rate | |
Rd | μmol·m-2·s-1 | 呼吸速率 Respiration rate | |
Ci | μbar | 胞内CO2分压 Intercellular CO2 partial pressure | |
Ca | μbar | 大气CO2分压 Air CO2 partial pressure | |
Cs | μbar | 叶面CO2分压 Leaf-surface CO2 partial pressure | |
Γ* | μbar | CO2补偿点 CO2 compensation point | |
Vcmax | μmol·m-2·s-1 | 最大羧化速率 Maximal rubisco carboxylase rate | |
Jmax | μmol·m-2·s-1 | 最大电子传输速率 Maximal electronic transport rate | |
J | μmol·m-2·s-1 | 电子传输速率 Electronic transport rate | |
I2 | μmol·m-2·s-1 | 电子传输速率 Electronic transport rate through photosystem II | |
I0 | μmol·m-2·s-1 | 光照强度 Photon flux density | |
f | 光谱校正常数 Fraction of effective photon flux | 0.15 | |
α | 转化率 Conversion efficiency | 0.15 | |
Oi | mbar | 胞内氧分压 Intercellular O2 partial pressure | 210 |
Ko | mbar | 氧化酶的动力学常数 Michaelis-Menten constant of Rubisco for O2 | |
Kc | μbar | 羧化酶的动力学常数 Michaelis-Menten constant of Rubisco for CO2 | |
gb | mol·m-2·s-1 | 边界层导度 Boundary-layer conductance | |
gs | mol·m-2·s-1 | 气孔导度 Stomatal conductance | |
g0 | mol·m-2·s-1 | 气孔最小导度 Minimum stomatal conductance | 0.01 |
g1 | 气孔导度常数 Sensitivity coefficient of stomatal conductance | 10.0 | |
hs | 叶面相对湿度 Relative humidity on leaf surface | ||
WS | m·s-1 | 风速 Wind speed | |
LeafW | m | 叶片宽度 Leaf width | |
V25, J25, Kc25, Ko25, Rd25, Γ*25 | 相应参数在25 ℃的值 Values at 25 °C | 分别为80, 160, 260, 165, 1, 38 respectively | |
Ea | J·mol-1 | 活化能 Activation energy | 分别为58 500, 37 000, 59 400, 36 000, 66 400, 23 400 respectively |
TK | K | 温度 Temperature | |
TC | °C | 温度 Temperature | |
R | J·K-1·mol-1 | 气体常数 Gas constant | 8.314 |
S | J·K-1·mol-1 | 电子传输速率的温度参数 Entropy term | 650 |
H | J·mol-1 | 曲率参数 Deactivation energy | 200 000 |
Cm | °C-1 | 温度修正参数 Temperature modification constant | |
Tm | °C | 温度修正参数 Temperature modification constant | |
VTm | μmol·m-2·s-1 | 羧化速率参数 Rubisco carboxylase rate | |
JTm | μmol·m-2·s-1 | 电子传输速率参数 Potential rate of electron transport | |
NEE | μmol·m-2·s-1 | 有效净生态系统CO2交换率 Net ecosystem exchange | |
PPFD | μmol·m-2·s-1 | 有效光量子流密度 Photosynthetic photon flux density | |
P2 | kPa | 大气压 Air pressure | |
LAI | 叶面积指数 Leaf area index |
Table 2 Variables and parameters used in the photosynthesis model and their reference values mainly from Caemmerer et al. (2009)
符号 Symbol | 单位 Units | 注释 Remark | 参考值 Reference value |
---|---|---|---|
A | μmol·m-2·s-1 | 净光合速率 Net photosynthesis rate | |
Ac | μmol·m-2·s-1 | Rubisco酶限制下的光合速率 Rubisco activity limited net photosynthesis rate | |
Aj | μmol·m-2·s-1 | RuBP再生限制的光合速率 Electron transport limited net photosynthesis rate | |
Rd | μmol·m-2·s-1 | 呼吸速率 Respiration rate | |
Ci | μbar | 胞内CO2分压 Intercellular CO2 partial pressure | |
Ca | μbar | 大气CO2分压 Air CO2 partial pressure | |
Cs | μbar | 叶面CO2分压 Leaf-surface CO2 partial pressure | |
Γ* | μbar | CO2补偿点 CO2 compensation point | |
Vcmax | μmol·m-2·s-1 | 最大羧化速率 Maximal rubisco carboxylase rate | |
Jmax | μmol·m-2·s-1 | 最大电子传输速率 Maximal electronic transport rate | |
J | μmol·m-2·s-1 | 电子传输速率 Electronic transport rate | |
I2 | μmol·m-2·s-1 | 电子传输速率 Electronic transport rate through photosystem II | |
I0 | μmol·m-2·s-1 | 光照强度 Photon flux density | |
f | 光谱校正常数 Fraction of effective photon flux | 0.15 | |
α | 转化率 Conversion efficiency | 0.15 | |
Oi | mbar | 胞内氧分压 Intercellular O2 partial pressure | 210 |
Ko | mbar | 氧化酶的动力学常数 Michaelis-Menten constant of Rubisco for O2 | |
Kc | μbar | 羧化酶的动力学常数 Michaelis-Menten constant of Rubisco for CO2 | |
gb | mol·m-2·s-1 | 边界层导度 Boundary-layer conductance | |
gs | mol·m-2·s-1 | 气孔导度 Stomatal conductance | |
g0 | mol·m-2·s-1 | 气孔最小导度 Minimum stomatal conductance | 0.01 |
g1 | 气孔导度常数 Sensitivity coefficient of stomatal conductance | 10.0 | |
hs | 叶面相对湿度 Relative humidity on leaf surface | ||
WS | m·s-1 | 风速 Wind speed | |
LeafW | m | 叶片宽度 Leaf width | |
V25, J25, Kc25, Ko25, Rd25, Γ*25 | 相应参数在25 ℃的值 Values at 25 °C | 分别为80, 160, 260, 165, 1, 38 respectively | |
Ea | J·mol-1 | 活化能 Activation energy | 分别为58 500, 37 000, 59 400, 36 000, 66 400, 23 400 respectively |
TK | K | 温度 Temperature | |
TC | °C | 温度 Temperature | |
R | J·K-1·mol-1 | 气体常数 Gas constant | 8.314 |
S | J·K-1·mol-1 | 电子传输速率的温度参数 Entropy term | 650 |
H | J·mol-1 | 曲率参数 Deactivation energy | 200 000 |
Cm | °C-1 | 温度修正参数 Temperature modification constant | |
Tm | °C | 温度修正参数 Temperature modification constant | |
VTm | μmol·m-2·s-1 | 羧化速率参数 Rubisco carboxylase rate | |
JTm | μmol·m-2·s-1 | 电子传输速率参数 Potential rate of electron transport | |
NEE | μmol·m-2·s-1 | 有效净生态系统CO2交换率 Net ecosystem exchange | |
PPFD | μmol·m-2·s-1 | 有效光量子流密度 Photosynthetic photon flux density | |
P2 | kPa | 大气压 Air pressure | |
LAI | 叶面积指数 Leaf area index |
参数 Parameter | 参数值下限 Lower value | 参数值上限 Upper value | 实际模拟值 Inversed value | |
---|---|---|---|---|
Vcmax | Vopt | 10 | 500 | 374 |
Ea | 10 000 | 70 000 | 21 287 | |
Jmax | Jopt | 10 | 500 | 310 |
Ea | 10 000 | 50 000 | 10 000 | |
Rd | Rd25 | 0 | 10 | 10 |
Ea | 10 000 | 70 000 | 10 033 | |
Cm | 0.25 | 0.50 | 0.28 | |
Tm | 20.0 | 50.0 | 26.9 | |
g1 | 0.0 | 10.0 | 3.7 |
Table 3 Initial parameter ranges and modeled values
参数 Parameter | 参数值下限 Lower value | 参数值上限 Upper value | 实际模拟值 Inversed value | |
---|---|---|---|---|
Vcmax | Vopt | 10 | 500 | 374 |
Ea | 10 000 | 70 000 | 21 287 | |
Jmax | Jopt | 10 | 500 | 310 |
Ea | 10 000 | 50 000 | 10 000 | |
Rd | Rd25 | 0 | 10 | 10 |
Ea | 10 000 | 70 000 | 10 033 | |
Cm | 0.25 | 0.50 | 0.28 | |
Tm | 20.0 | 50.0 | 26.9 | |
g1 | 0.0 | 10.0 | 3.7 |
对每一个APMC粒子 For all particles for k = 1 to Nobs do(对所有的观测数据) For all observations 用APMC粒子选定的V25, J25, Rd25, g1, Ea, Cm, Tm Use parameter values selected by AMPC 计算Vcmax, Jmax, Rd, gb Estimate target model parameters 设t = 1 (Ci的迭代计算次数) At initial time 设\(C_i^0=0.7C_a\) Set the intercellular CO2 equal to 70% of air CO2 设\(\Delta C_i >1\) Set the intercellular CO2 not in equilibrant While \(\Delta C_i >1 \) do 计算 Ac, Aj Compute the two rate. 计算\(A=\frac{A_c+A_j-\sqrt{(A_c+A_j)^2-4\times 0.98A_cA_j}}{2\times 0.98} \\ Compute the joint rate 计算\\ C_i^t=C_a-\frac{A}{g_b}-\frac{g_bC_aA-A^2}{g_bg_1h_sA-g_0A+g_0Ag_bg_oC_a}\) Compute the intercellular CO2 \( \Delta C_i=|C_i^t-C_i^{t-1}|\) Check equilibrant state 设t = t + 1 Advance time end while end for 将|A-NEE|的平均值作为APMC粒子的r Calculate the difference between modeled photosynthesis rate and the observed rate |
Appendix I Model entity in the APMC
对每一个APMC粒子 For all particles for k = 1 to Nobs do(对所有的观测数据) For all observations 用APMC粒子选定的V25, J25, Rd25, g1, Ea, Cm, Tm Use parameter values selected by AMPC 计算Vcmax, Jmax, Rd, gb Estimate target model parameters 设t = 1 (Ci的迭代计算次数) At initial time 设\(C_i^0=0.7C_a\) Set the intercellular CO2 equal to 70% of air CO2 设\(\Delta C_i >1\) Set the intercellular CO2 not in equilibrant While \(\Delta C_i >1 \) do 计算 Ac, Aj Compute the two rate. 计算\(A=\frac{A_c+A_j-\sqrt{(A_c+A_j)^2-4\times 0.98A_cA_j}}{2\times 0.98} \\ Compute the joint rate 计算\\ C_i^t=C_a-\frac{A}{g_b}-\frac{g_bC_aA-A^2}{g_bg_1h_sA-g_0A+g_0Ag_bg_oC_a}\) Compute the intercellular CO2 \( \Delta C_i=|C_i^t-C_i^{t-1}|\) Check equilibrant state 设t = t + 1 Advance time end while end for 将|A-NEE|的平均值作为APMC粒子的r Calculate the difference between modeled photosynthesis rate and the observed rate |
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