leafbio

Leaf biochemical parameters

Initialized

select_input()

SCOPE.m

Variations

leafbio.Cca may be calculated as 25% of Cab: options.Cca_function_of_Cab

leafbio.fqe may be double (PSII only) or [2 x 1] double (PSI = 0.2 * PSII, PSII) if options.calc_PSI

leafbio.V2Z can be set to 0 with options.calc_PSI

Used

variable

user

Cab, Cca, V2Z, Cw, Cdm, Cs, Cant, Cp, Cbc, N, fqe
fluspect_B_CX() if options.calc_PSI
fluspect_B_CX_PSI_PSII_combined()

Type, BallBerrySlope, Rdparam, Tyear, Kn0, Knalpha, Knbeta, beta, qLs, kNPQs, stressfactor, Tparam, Vcmax25 -> biochem_in

ebal()

Vcmax25, Cab

load_timeseries()

rho_thermal, tau_thermal, fqe

SCOPE.m

Fields

Fields initialized in select_input() (read from input_data.xlsx)

variable

units

type

default

description

Cab

ug cm-2

double

80.0

Chlorophyll AB content

Cca

ug cm-2

double

20.0

Carotenoid content. Usually 25% of Cab if options.Cca_function_of_Cab

Cdm

g cm-2

double

0.012

Dry matter content

Cw

cm

double

0.009

leaf water equivalent layer

Cs

-

double

0.0

senescent material fraction

Cant

ug cm-2

double

0.0

Anthocyanins

Cp

ug cm-2

double

0.0

protein

Cbc

ug cm-2

double

0.0

?

N

-

double

1.4

leaf thickness parameters

Vcmax25

umol m-2 s-1

double

60.0

maximum carboxylation capacity (at optimum temperature of 25C, former Vcmo)

BallBerrySlope

double

8.0

slope of Ball-Berry stomatal conductance model (former m)

BallBerry0

double

0.01

intercept of Ball-Berry stomatal conductance model

Kn0

double

2.48

Kn0: parameter for empirical Kn (NPQ) model: Kn = Kno * (1+beta).*x.^alpha./(beta + x.^alpha);

Knalpha

double

2.83

alpha parameter for empirical Kn (NPQ) model: Kn = Kno * (1+beta).*x.^alpha./(beta + x.^alpha)

Knbeta

double

0.114

beta parameter for empirical Kn (NPQ) model: Kn = Kno * (1+beta).*x.^alpha./(beta + x.^alpha)

Type

-

int => char

0 (‘C3’)

Photochemical pathway: 0 => ‘C3’, 1 => ‘C4’

Tparam

ºK

[5 x 1] double

[0.2, 0.3, 281, 308, 328]

See PFT.xls. These are five parameters specifying the temperature response.

fqe

-

[1 x 1] | [2 x 1] double

0.01

fluorescence quantum yield efficiency at photosystem level

Rdparam

-

double

0.015

Respiration = Rdparam * Vcmcax

rho_thermal

-

double

0.01

broadband thermal reflectance

tau_thermal

-

double

0.01

broadband thermal transmittance

Tyear

ºC

double

15.0

mean annual temperature

beta

-

double

0.507

fraction of photons partitioned to PSII (0.507 for C3, 0.4 for C4; Yin et al. 2006 [11]; Yin and Struik 2012 [12])

kNPQs

s-1

double

0.0

rate constant of sustained thermal dissipation (Porcar-Castell 2011 [3])

qLs

-

double

1.0

fraction of functional reaction centres (Porcar-Castell 2011 [3])

stressfactor

-

double

1.0

optional input: stress factor to reduce Vcmax (for example soil moisture, leaf age)

Fields initialized in SCOPE.m

variable

units

type

default

description

V2Z

-

double

1.0

violaxantine to zeaxantine ratio. 0 if options.calc_PSI