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Oscar Schofield (oscar@ imcs .rutgers.edu ) 932-6555 x 548, you are better off just walking in if you need help, if I can’t I will let you know, but it is quicker then trying to make a formal appointment, ask Judy I am a schedule-organization disaster……
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Dec 17, 2015

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Page 1: Oscar Schofield (oscar@imcs.rutgers.edu)oscar@imcs.rutgers.edu 932-6555 x 548, you are better off just walking in if you need help, if I can’t I will.

Oscar Schofield ([email protected])932-6555 x 548, you are better off just walking in if you need help, if I can’t I will let you know, but it is quicker then trying to make a formal appointment, ask Judy I am a schedule-organization disaster……

Page 2: Oscar Schofield (oscar@imcs.rutgers.edu)oscar@imcs.rutgers.edu 932-6555 x 548, you are better off just walking in if you need help, if I can’t I will.

Light and PhotosynthesisLight and Photosynthesis

1) Light in the OceanI) IntensityII) ColorIII) Inherent Optical PropertiesIV) Apparent Optical PropertiesV) Remote Sensing

2) PhotosynthesisI) Light AbsorptionII) Light ReactionsIII) Dark Reactions

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For satellite remote sensing the wavelength is the key to what

you want to measure.

c = = hhc

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Figure 6

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I) Light

Z (meters)

Irradiance Intensity

Lambert Beers LawEd2 = Ed1e-z*Kd

Ed2

Ed1z1

z2

z

1) Because of Lambert Beers Lawthe ocean is dim

2) Plant life is dependent on light

3) The 1% light levelfor the majority of the is 100 m or less?

2500 2500 mol photons mmol photons m-2-2 s s-1-1

5.0 5.0 mol photons mmol photons m-2-2 s s-1-1

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Alexander the Great

Early Optics

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The color of the sea shows a great deal of variability from the deep violet-blue of the open ocean to degrees of green and brown in coastal regions. Before the advent of sensitive optical instruments, color was determined by visual comparison against standard reference standards such as the Forel Ule Color scale.

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Your future will include robots patrolling the watersfor you as optical instruments are now small

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74:10 74:00 73:50 73:40 73:30 73:20 73:10

16-Sep-2004 15:00:53 - 23-Sep-2004 11:57:27

Temperature

bb(532)/c(532)

bb532

10

30

50

70

90

110

10

30

50

70

90

110

10

30

50

70

90

110

Now we can study during storms

Depth-Averaged CurrentsSurface Currents

Tropical Storm Ivan

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What kind of measurements are there?What kind of measurements are there?

Inherent Optical PropertiesInherent Optical Properties: Those optical properties that are : Those optical properties that are fundamental to the piece of water, not dependent on the geometric fundamental to the piece of water, not dependent on the geometric structure of the light field. (absorption, scattering, attenuation) structure of the light field. (absorption, scattering, attenuation)

Apparent Optical PropertiesApparent Optical Properties: Those optical properties that are : Those optical properties that are fundamental to the piece of water and are dependent on the geometric fundamental to the piece of water and are dependent on the geometric structure of the light field. (light intensity, reflectance) structure of the light field. (light intensity, reflectance)

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Why IOP Measurements?

• Absorption, a color• Scattering, b clarity• Beam attenuation, c (transmission)

a + b = c

The IOPs tell us something about the particulate anddissolved substances in the aquatic medium; how we measure them determines what we can resolve

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Why IOP Measurements?Why IOP Measurements?

• Absorption, a colorAbsorption, a color

Photo S. EtheridgePhoto S. Etheridge

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Why IOP Measurements?• Absorption, a• Scattering, b

clarity

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Review of IOP Theory

o

IncidentRadiant Flux

No attenuation

TransmittedRadiant Flux

t

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Review of IOP Theory

Attenuation

to

IncidentRadiant Flux

TransmittedRadiant Flux

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Loss due to absorption

a Absorbed Radiant Flux

o

IncidentRadiant Flux

t

TransmittedRadiant Flux

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Loss due to scattering

b Scattered Radiant Flux

o

IncidentRadiant Flux

t

TransmittedRadiant Flux

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Loss due to beam attenuation

(absorption + scattering)

a Absorbed Radiant Flux

b Scattered Radiant Flux

to

IncidentRadiant Flux

TransmittedRadiant Flux

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Conservation of radiant flux

a Absorbed Radiant Flux

b Scattered Radiant Flux

o = t + a + b

to

IncidentRadiant Flux

TransmittedRadiant Flux

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Beam Attenuation Measurement Theory

t

a

b

c = fractional attenuance per unit distance, attenuation coefficient

c = C/x

c x = -/

c x = -ln(t/o)

c (m-1) = (-1/x)ln(t/o)

o

x

0 c dx = -0 d/x x

c(x-0) = -[ ln(x)-ln(0)]

c x = -[ ln(t)-ln(o)]

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1m 1m

Underwater Eye ChartUnderwater Eye Chart

11:4011:40

TIMETIME

Optical MooringOptical Mooring

c532c532

13:4013:4015:4015:4018:2018:20

19:2519:25

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Phytoplankton

CDOM-Rich Water

SuspendedSediments

Benthic Plants1/Kd1/Kd

Optically-ShallowOptically-ShallowOptically-DeepOptically-Deep

Micro-bubbles

Whitecaps

Shallow Ocean Floor

1) Collect a signal, about 95% of the signal is determined by the atmosphere.

2) Relate the reflectance to the physics, chemistry, and/or biology in the water.

R = Bb/(a+Bb)

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-0.1

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

400 450 500 550 600 650 700

wavelength (nm)

Ab

sorp

tion

(1/

m)

Phytoplankton Dissolved organics

Changing the relative Changing the relative proportions of materialsproportions of materials

in the water column also impacts in the water column also impacts color of the watercolor of the water

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Distance (km)

0 1Absorption (m-1)

0 0.03Backscatter (m-1)

Dep

th (

m)

0

12

6

0 2 4 6 8 10

Dep

th (

m)

0

12

6

Distance (km)0 2 4 6 8 10

Distance (km)0 2 4 6 8 10

Distance (km)0 2 4 6 8 10

Dep

th (

m)

0

12

6

Dep

th (

m)

0

12

6

Bb488 Bb589

a490 a550

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a490/a5500.5

1

1.5

2

0 5 10

Bb488/Bb589

Distance (km)

Rat

io

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That Pristine Blue NJ WaterThat Pristine Blue NJ Water

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Courtesy of Hans Graber, Rich Garvine, Bob Chant, Andreas Munchow, Scott Glenn and Mike Crowley

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Target 3 mTarget 3 mBased on Surface Based on Surface

Values Values

Influence of OpticalInfluence of OpticalProperties on Properties on

Laser Performance Laser Performance

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Changes in the color of the reflectance as theChanges in the color of the reflectance as theload of material changes in the water column.load of material changes in the water column.

Water Leaving RadianceWater Leaving Radiance ReflectanceReflectance

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Color variability at multiple scales

around Tasmaniafrom CZCS image

Causes?Strong winds,

strong currents,bottom togography,

etc.

GSFC, NASA

Tasmania

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a z c z aph ii

n

i' ( , ) ( ) ( ) = ⋅=

∗∑1

a z c z aph ii

n

i' ( , ) ( ) ( ) = ⋅=

∗∑1

0

0.1

0.2

0.3

400 500 600 700

wavelength (nm)wavelength (nm)

ph

ytop

lan

kto

n a

bso

rpti

on (

m-1)

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0.0

0.02

0.04

0.06

0.08

400 450 500 550 600 650 700

chl a

chl b

chl c

PSC

PPC

wavelength (nm)

abso

rpti

on c

oeff

icie

nt

(m2 m

g-1)

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0

5

10

15

20

400 450 500 550 600 650 700

Wavelength (nm)

Spectral Irradiance (

W cm

-2 nm-1)

chl a chl achl b

chl cchl b

carotenoids

phycobilins

0

0.25

0.50

0.75

1.0

1.25

Rel

ativ

e A

bsor

ptio

n

chl a-chl c-carotenoidschl a-chl b-carotenoidschl a-phycobilins

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Chlorophyll a : all phytoplankton (used as a measure of concentrations)

Chlorophyll b : green algae

Chlorophyll c : chromophytes (dinoflagellates, diatoms, coccolithophorrids)

Carotenoids : fucoxanthin (dinoflagellates, diatoms, coccolithophorrids)19’-hexanoyfucoxanthin (coccolithophorrids)alloxanthin (cryptophytes)peridinin (dinoflagellates)

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Ene

rgy

hv

GroundState

DifferentExcitation

OrbitalsIn a molecule

Heat Fluorescence

Photosynthesis

Energy gained

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PAR

Light-Harvesting PigmentsLight-Harvesting Pigments

RC II RC I

e -

Q

A

QB 2H+

PQH2

2H+

FdCO

2CH2O

P680+

z

2H2O O2 + 4H+

FluorescenceFluorescence

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THYLAKOID THYLAKOID MEMBRANEMEMBRANE

STROMASTROMA

CYTOSOLCYTOSOL

LHCLHC LHCLHC

1/2 O2 + 2H+H2O

4Mn Yze-

2H+

PQ

PQPQ

PQPQ

Qb

Qb

Cyt

och

rom

e b 6-

f-F

e nn

2H+

2H+2H+

PC/cyt c6

Ph

otos

yste

m I

CHLOROPLASTCHLOROPLAST

P700

A0

Fx

Fa/ Fb

Fd

AT

P s

ynth

ase

com

plex

CF0

CF1

3/2ADP + 3/2Pi 3/2ATP + 3/2Pi

NADPHH+ + NADP+6H+

1/2CH2O + 3/2ADP + 3/2PiH+ + 1/2CO2

THYLAKOID LUMENTHYLAKOID LUMEN

EP680

Pheo

e-

e-

Ph

otos

yste

m I

ID2D1

E

Qa

Qb

2 x e-

PH

Min

ute

s to

Hou

rs

NUCLEUSNUCLEUS

PLHC geneLHC gene

Repressor proteins

Day

s to

Wee

ks

fluorescence

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light intensitylight intensity

oxyg

en

evolu

tion

oxyg

en

evolu

tion

0

0.5

1.5

2.5

3.5

0 50 100 150 200 250 3000

0.02

0.04

0.06

0.08

qu

an

tum

yie

ld o

f oxyg

en

evolu

tion

qu

an

tum

yie

ld o

f oxyg

en

evolu

tion

Pmax

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Irradiance Intensity

Z (meters)

Ik

Photosynthesis

BiomassNutrients