My Team Milestone 5

Melissa Checco, Michael Davis, Rachel LiGreci, Colleen O’Shea

December 3, 2014

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Contents
1 Introduction 3

2 Expectations 5

3 Experiments and Results 5

4 Model 11

5 Simulation 14

6 Conclusion 19

7 Future Work Plan 19

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1 Introduction
Heterosigma Akashiwo is a marine photoplankton that forms toxic surface aggregations under
certain conditions. Our team has focused on how Heterosigma Akashiwo form patterns due to
variations in position and intensity of light sources. While there has been some research on plank-
ton’s movement, it is mostly centered around their upward swimming behavior, the harmful algal
blooms, and the plankton as a group of organisms. Reaserch has not been conducted on the self-
assembled patterns plankton create when swimming. In this study we are mostly interested in
the vertical and horizontal patterns created. Therefore we have conducted our own controlled
experiments, holding temperature, flow of water, and salinity levels constant while changing the
intensity of the light sources, and analyzing the amount of time patterns take to form, as well as
how long the patterns are that form. Using a model based off of the Law of Conservation of Mass
and Energy we explain why the Heterosigma Akashiwo self-organize as observed in our experi-
ments. We are specifically looking at the interaction between plankton and light in our container
and how we can mathematically describe this natural phenomenon of pattern formation.
Self-assembly has a few requirements. One such requirement is that attractions and repulsions
will be balanced by steady-state positions. Balancing between aggregated and non-aggregated
states is ideal for pattern formations. In this sense, components will not stick together or bounce
off of each other and therefore can assemble into formations. It was also noted that changing
multiple parameters when studying self-assembly in living organisms is illogical when attempting
to monitor and model the behavior of the organisms [2]. We kept these requirements in mind while
doing our experiments and made sure to change only one variable at a time to ensure accurate
results.
Peter Franks, a phytoplankton ecologist, explored the patterns that are generated by internal
ocean waves and vertically swimming phytoplankton. He came up with models supporting the
claim that higher concentrations of plankton parallel to the shore are caused by these interactions
between the waves and the vertical swimming behavior of plankton [3]. Although this experiment
provides a model of pattern formation based on swimming behavior, it provides little to no expla-
nation of how light may affect these patterns. We attempted to fill in these holes by adding light
as a possible variable that affects the pattern formation of blooms. From an experiment conducted
by E.D.Tobin, D.Grunbaum, J. Patterson, and R.A. Cattolico, it was concluded that cell transition
between stages of life are largely regulated by temperature and light [9]. This information helps
us answer how the light has an impact on their pattern formations.
Conclusive evidence tells us that the toxicity levels and growth rates of Heterosigma Akashiwo
greatly depend on temperature and light intensity. Although research can identify the conditions
most suitable for toxicity or growth, it is evident that in natural environments, these levels can
vary frequently and simultaneously in any given sample [7]. Not much is known about the ef-
fects of the environment on their living habits. Given these circumstances, we foresee difficulties
making accurate generalizations with our findings. The inverse relationship between toxicity and
growth rate make us more curious about their response to environmental conditions. Since the
light intensity and temperature experiment was conducted without changes in light formation, it
is safe to presume that movement of light outside the sample is a valid parameter to test. It may

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very trivially mimic sun cycle-induced conditions in their natural habitat.
While light is a primary source of plankton’s energy, it is evident that an oversaturation of
light, known as photoinhibition, may begin to damage the cells faster than they may be able to
repair themselves [6]. As a result, oxygen is released, slowing the synthesis of repair proteins.
This restricts the amount of fluorescence (light and heat energy) that the Heterosigma Akashiwo
are able to give off. Consequently, the plankton beneath them react by adjusting their shape and
size to give off enough fluorescence to overcompensate for the deficiency in the affected top layer
of plankton facing the most direct light [10]. We are curious as to how this may affect the patterns
we have observed in the lab and would like to look into how photoinhibition at different light
intensities typically dictate plankton behavior.
When describing pattern formations in nature, scientists often study variations of Murrays
reaction-diffusion equation. According to Murray’s work, one morphogen u in the reaction is the
activator and the second morphogen v is the inhibitor [1]. In our case, the inhibitor would be the
light source (since its movement is inhibiting the plankton from maintaining their initial pattern
and we know that light can diffuse through water much more quickly than plankton can), and
plankton will be the activator. Turing’s research tells us that the inhibitor must diffuse through
space more quickly than the activator in order for pattern formation to occur. The reaction diffu-
sion model property of interactions between reaction and movement provide some explanation as
to why plankton species self organize to form patterns [4].
When considering how the concentration of plankton in a given volume change to form pat-
terns, we must consider the Law of Conservation of Mass and Energy. By definition, the law of
conservation in regards to mass and energy is the principle that, given a closed system, the mass
and energy are constant despite any internal changes [5]. With this understanding that matter
cannot be created or destroyed, the light energy and the mass of the plankton given a specific
volume will be unchanged despite the patterns that are formed [8].
Our concern with why Heterosigma Akashiwo self organize into distinct patterns due to light
sources has not been publically researched. We are interested in answering this question because
algal blooms, particularly of Heterosigma Akashiwo, are becoming a more prevalent toxin in bod-
ies of water around the globe. Any insight into their pattern formation and behavior may lead us
to understand more clearly how they directly react to their environment, how consistently these
reactions occur, and whether or not we can curb these reactions to minimize their harmful inter-
ference with the rest of the natural world.
In the lab, we have looked at the different patterns the plankton form at varying light inten-
sities. Given a lamp of fixed height and lumen, we shake the container of plankton so that the
plankton are in random starting positions, then take pictures of the patterns they form. Each
trial we move the lamp to a further distance, which has allowed us to analyze how varying light
intensity affects their patterns.

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2 Expectations
In terms of Heterosigma Akashiwo and light intensity, we hypothesize that plankton are drawn
to an optimal light intensity that will promote growth. Considering the law of conservation, the
light energy in the given volume must be conserved. We predict that as the light intensities vary
through the water in the flask, they induce the pattern formations we observe in our experiments.
Explaining why Heterosigma Akashiwo form patterns has positive and negative aspects. As
mentioned above, there is currently little research explaining how or why plankton form patterns.
This allows us to think freely about our problem and attempt methods that may be considered
out of the box, since we are not confined to existing research on the topic. However, this proves
difficult for our group since we don’t know what is reasonable for us to experiment and if what
we are hypothesizing will provide clear answers to the problem. In previous experiments, as
described in ”Self Assembly at All Scales”, satellites have been used to track movement and model
patterns in plankton formation [11]. Estimating depth and dispersion of plankton formations
visible to an observer has proven difficult for us to track in the laboratory, but we have tried to
overcome this challenge using photos and image processing.
In our experiment with altering the light intensity, we expect to see an inverse relationship
between distance of light and wavelengths of patterns. As the distance of the light increases,
hence the intensity of the light decreases, we expect that the plankton do not reach their saturation
level as quickly. Therefore, less plankton are ”hiding” in the shadows of other plankton, and are
therefore more dispersed throughout the flask, causing the patterns formed to have less plankton
and therefore be shorter wavelengths.
We also expect, for the same reasons, for the patterns to take longer to form. Since the plankton
are not quickly reaching their saturation level, they have no need to aggregate and form patterns
as quickly.
Through experimenting with different distances of light, calculating light intensities, timing
formations, and taking pictures of formations, we hope to be able to predict the time for a pattern
to form and the wavelengths of the patterns for a certain intensity of light. We will try to find a
relationship between light intensity and wavelengths of patterns by analyzing the images taken
using MATLAB image processing. If there is a relationship between the two we should be able to
fit a model to the data using the average wavelengths from various distances. We expect that this
experiment will confirm our predictions that wavelengths of patterns are shorter as light intensity
decreases.

3 Experiments and Results

In the lab, we have conducted several experiments hoping to better understand the relationship
between Heterosigma Akashiwo and light. Our experiments have focused on the intensity of the
light, which was changed by altering the distance between the lamp and our sample of plankton.
By varying the distances of the lamp, calculating the light intensities, and taking pictures of the
various patterns that form, we identified changes in the wavelengths of the patterns formed as the
distance of the light changed.

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Experiment Set Up & Expectations
Materials:
• CFL bulb of 1225 Lumens
• 2000mL flask of Heterosigma Akashiwo
• stopwatch
• iPhone 5c/5s
• a stand to hold the iPhone
To set up the experiment, we set the iPhone on the stand and placed the flask underneath so
that all photos were taken from the same height and angle in order to compare wavelengths. The
distance between the light and the flask was measured between the position of the bulb and the
bottom of the flask. Each time the light was moved to a further distance, the flask that holds the
plankton was shaken so that the experiment started at a diffused state with no existing patterns
formed.
We started with the light 2 inches away, turned it on, took a ”starting state” picture at time
0, and started the timer. When it looked like patterns had formed completely, we took a second
photo, and recorded the time. We continued to take photos at timed intervals while the plankton
continued to move. After about 10-15 minutes, we reset the experiment as before, at a new posi-
tion. In our first and second experiments, we repeated the experiment for the light source placed
at 2, 6, and 10 inches. After we had done this, we began to see a trend that the wavelengths got
shorter as the light moved further away. In later experiments, we tried to include more distances
to confirm this possible trend.
In the third experiment, we repeated the first and second experiments and hoped to include
more distances in order to collect more data. We wanted to use this data to see if we could possibly
fit a curve to the data and predict what happens as the light moves further away, or as the intensity
of the light decreases. However, the plankton were still very dull and hard to see, as seen in Figure
2. The results from the third experiment can be seen in Table 2.
We went back to the lab a fourth time in order to improve the experiment with more distances
of light. Finally, the plankton were forming patterns that were easy to see and we got some great
pictures and results that matched what we expected. Although we were only able to increase the
light to a distance of 22 inches, we used our pictures to obtain average wavelengths and to find
an equation that models the relationship between intensity of light and those wavelengths. Based
on our earlier experiments, we predicted to see a direct relationship between intensity of light and
wavelengths of patterns. That is, as the intensity of the light decreases, so should the length of the
patterns formed.

Results
The photos from the experiments can be seen in Figures 1, 2, 3, and 4 respectively. As you can see
in the photos, the patterns were much harder to see for a few experiments. We are not sure why

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this is the case, but we think that there are certain times in the lifecycle of the flask of plankton
at which the patterns they form are not as noticeable. Once a sample of the plankton were taken
out and fresh sea water was added, the patterns once again became more noticeable, as you can
see in Figure 4. In each of the photo sets, the light intensity is successively decreases. It appears
as though the wavelengths of the patterns decrease as the intensity decreases. We verify this
hypothesis using MATLAB image processing to measure the relative lengths of the patterns and
use Microsoft Excel to fit a model to that data.

Figure 1: First Experiment: Shows pattern formations at 2, 6, and 10 inches from left to right.

Figure 2: Second Experiment: Shows pattern formations at 2, 6, and 10 inches from left to right.
Clearly, the conditions changed for the second experiment and the patterns were much harder to
see.

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Figure 3: Third Experiment: Shows pattern formations at 2, 6, 10, and 12 inches from left to right.

Figure 4: Last Experiment: Shows pattern formations at 2, 4, 6, 10, 14, 18, and 22 inches from left
to right.

Analysis
We used MATLAB image processing in order to find an average wavelength of patterns at each
distance. Here is the code used for each picture to select different lengths and find an average:

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plankpic = imread(’filename.jpg’); % input image
imshow(plankpic) %figure1

[xscale yscale] = ginput(2); % set up length scale from ruler in image

lenscale = sqrt((xscale(2)-xscale(1))ˆ2+(yscale(2)-yscale(1))ˆ2); %scale

sum = 0;
for d=1:10
[x1 y1] = ginput(2); % find lengths of 10 lines
otherlength = sqrt( (x1(2)-x1(1))ˆ2+(y1(2)-y1(1))ˆ2 );
patternlength(d) = otherlength/lenscale
sum = sum+patternlength(d) % sum all 10 lengths
end

average = sum/10 % find average of 10 lengths

These results are shown in Tables 1, 2, and 3. The distances are relative, so there are no units.

Table 1: Experiments with 3 distances

first experiment second experiment
distance of light relative wavelength relative wavelength
2 inches 0.3375 0.2657
6 inches 0.2572 0.2026
10 inches 0.2496 0.1934

Table 2: Experiment with 4 distances

distance of light relative wavelength
2 inches 0.2214
6 inches 0.1935
10 inches 0.1487
12 inches 0.1188

From all of our experiments, we have observed that the lower the intensity of light (the further
away the light source is from the plankton), the shorter the wavelengths of the patterns formed.
This is possibly because as the light moves further away, the plankton don’t reach saturation
levels as quickly, and don’t need to “hide” from the intense light that is present when the lamp is
closer. From the data we have from the last experiment, shown in Table 3, we found a function
that best fits the data in order to predict what would happen as the light increases even further,

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 Table 3: Experiment with 7 distances
distance of light relative wavelength
2 inches 0.3866
4 inches 0.2759
6 inches 0.2678
10 inches 0.2403
14 inches 0.1805
18 inches 0.1910
22 inches 0.1522

and the intensity continues to decrease. The line shown in figure 5 shows a power fit, length =
0.4866 · distance−0.351 .

Wavelengths  of  Pa7erns  as  Light  

Intensity  Decreases  
0.45  
0.4  
Average  Wavelengths  (rela/ve)  

0.35  
0.3  
0.25  
0.2  
0.15  
0.1  
0.05  
0  
0   5   10   15   20   25  
Distance  of  light  (inches)  

Figure 5: Relationship between intensity of light and average wavelengths of patterns formed

There is a clear relationship between average wavelengths of patterns and intensity of light.
Since the intensity of the light decreases as the distance of light increases, the graph confirms our
expectations that the average lengths of patterns goes down as the intensity decreases. Since we
were only able to complete a successful experiment with enough distances to find a trendline once,
our power function is not completely accurate. Our wavelengths are also measured relatively,
so we can’t discern any lengths in a measurable unit. However, one could easily compare the
relative expected lengths at two different light intensities. Ultimately, our experiments, data, and
graph have shown that Heterosigma Akashiwo form different patterns under different conditions,

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specifically under different light intensities.
These results also help to confirm some of the reasoning that was included in our simula-
tion (see Section 5), that once they have reached a certain “saturation level”, the Heterosigma
Akashiwo will hide behind other plankton in order to receive less light. We believe that with a
lower light intensity, the plankton don’t reach that saturation level as quickly, and therefore not as
many plankton need to “hide” in the shadows of others, so the lines formed are not as long.

4 Model
As previously indicated, our primary goal is to describe how the concentration of Heterosigma
Akashiwo changes as they adjust to the positioning (and thus, intensity) of a singular light source
in time. We can see from our experiments that patterns are formed regardless of the light inten-
sity, but that the wavelengths of the patterns vary with varying intensity. While the experiment
confirms our expectations, we would also like to mathematically describe the pattern formations
of Heterosigma Akashiwo.

Assumptions
There are a few assumptions we need to make for our model:

1. We are working with an infinite body of water (no boundary conditions);

2. The plankton are aware of the light intensities in the positions surrounding them;

3. There is an optimal light intensity for Heterosigma Akashiwo and they will move to a posi-
tion closest to that intensity;

4. Temperature, flow of water, and salinity levels are all constant;

5. Heterosigma Akashiwo reach a ”saturation level” at which they can no longer absorb light;

6. The plankton are trying to find optimal positions and conditions in order to promote growth;
and,

7. Light intensity is not dependent on glass, water, or concentration of plankton between the
light source and the given area of interest.

To describe such a situation, we must use a conservation law in three dimensional volume.
Therefore, we are employing the model:
Z Z Z  
∂A
+ ∇(A~v ) dV = 0 (1)
∂t
where V is a fixed control volume (with bounds in the x, y, and z-plane), A is the density of plank-
ton in the given volume and ~v is the velocity of the Heterosigma Akashiwo (dependent on light
intensity). Keeping conservation of plankton in mind (since no amount of plankton is entering or

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leaving the flask during an experiment and matter in a given parameter must be conserved), our
integral must equal zero.
Since it is evident from the experiments that light is primarily inducing the movement of plank-
ton, we must incorporate the velocity of Heterosigma Akashiwo as a function of light intensity.
Heterosigma Akashiwo activity tends to peak at certain light intensities based on either their tox-
icity or growth patterns [7]. Since this plankton species is most toxic while feeding on prey, rather
than photosynthesis, we are assuming that in our case the species instinctually desires to grow.
Therefore, they will react most to their optimal light intensity for growth, denoted by I0 , which is
µE µE
100 2 , where 2 is a measurement of light intensity. [7]. The light intensity value I will
m ·s m ·s
thus represent the light intensity at any given position within our bounds. In an effort to simplify
these values, we are choosing to express light intensities in a relative manner.
Since we predict that the Heterosigma Akashiwo will swim closest to the surface where the
light intensity is optimal, we predict that the plankton will swim out of a given region to find this
optimal value for growth, creating a negative parabolic relationship with the surface of the water
in the flask. Therefore, we can use negative divergence to express plankton travelling out of the
region. Furthermore, we can describe ~v as

~v = −∇(I − I0 )2 (2)
Assuming we are working in a system with no glass or water, the light intensity at any given
point, I(x, y, z), is given by

Ib Ib
I(x, y, x) = p = (3)
2 2 2
( (x − xb ) + (y − yb ) + (z − zb ) ) 2 (x − xb ) + (y − yb )2 + (z − zb )2
2

where Ib represents the light intensity of the bulb, and (xb , yb , zb ) represent the position of
the bulb. For simplification purposes, we let the bulb be at position (0, 0, 0). Thus our equation
becomes I(x, y, x) = x2 +yIb2 +z 2 . Therefore, equation (2) becomes
 2
Ib
~v = −∇ − I0 (4)
x + y2 + z2
2

The optimal intensity for plankton in the water must be less than the intensity of light on the
surface of the bulb (since the light becomes less intense as you get further away). Assuming, for
simplicity, that the intensity of the bulb, Ib is 1, and the ratio of Ib to I0 is 3.5:1, we can expand
−∇v to
 2
3.5
~v = −∇ − 1 (5)
x2 + y 2 + z 2
which simplifies to
 
12.25 7
~v = −∇ − +1 (6)
(x2 + y 2 + z 2 )2 x2 + y 2 + z 2

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 Then, taking the gradient of (I(x, y, z) − I0 )2 we have

(−2)(12.25)(2x) 14x (−2)(12.25)(2y) 14y (−2)(2.25)(2z) 14z

~v = + 2 − + 2 − + 2 (7)
u3 u u3 u u3 u
which can be simplified to
−4x 14x −4y 14y −4z 14z
~v = + 2 + 3 + 2 + 3 + 2 (8)
u3 u u u u u
where u = (x2 + y 2 + z 2 ).
If equation (1) equals zero, we know that its integrand must also equal zero. Once we put ~v
into the integrand of equation (1), we can find a steady state density A.
We know that to find ∇A~v we would be looking for the expansion A∇~v + ~v ∇A. Using Maple
to calculate ∇~v , we found that

7(25x2 − 54xy − 54xz − 5y 2 − 5z 2 ) 21(3x2 + 10xy − 15y 2 − 18yz + 3z 2 )


∇(~v ) = , ,
(x2 + y 2 + z 2 )4 (x2 + y 2 + z 2 )4 (9)
21(3x2 + 10xz + 3y 2 − 18yz − 15z 2 )


(x2 + y 2 + z 2 )4

Therefore, ∇A~v is

7(25x2 − 54xy − 54xz − 5y 2 − 5z 2 ) 21(3x2 + 10xy − 15y 2 − 18yz + 3z 2 )


, ,
(x2 + y 2 + z 2 )4 (x2 + y 2 + z 2 )4
21(3x2 + 10xz + 3y 2 − 18yz − 15z 2 )

(A)
(x2 + y 2 + z 2 )4 (10)
 
∂x ∂y ∂z −49x 14x
+ + + 2 2 2 3
+ 2 ,
∂A ∂A ∂A (x + y + z ) (x + y 2 + z 2 )2

49y 14y 49z 14z
+ , +
(x2 + y 2 + z 2 )3 (x2 + y 2 + z 2 )2 (x2 + y 2 + z 2 )3 (x2 + y 2 + z 2 )2

We must now put this value in such a format that conveys the coordinates being observed as a
distance, r = x2 + y 2 + z 2 , from the light source at position (0, 0, 0). Putting our ∇A~v solution into
*~i +
a matrix by components ~j and extracting our distance component and factored coefficients,
~k
we express our final ∇A~v expansion as

 ∂x 
A(25x2 −54xy−54xz−5y 2 −5z 2 ) −7x ∂y ∂z
r2
+ (2x) + +
7   r   ∂A ∂A ∂A 
 3A(3x2 +10xy−15y2 −18yz+3z 2 )
r2
+ (2y) 7y ∂x ∂y ∂z 
r  ∂A + ∂A + ∂A  (11)
r2 

2 2 2

3A(3x +10xz+3y −18yz−15z ) ∂y
+ (2z) 7z ∂x ∂z


r2 r ∂A + ∂A + ∂A
.

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 Finally, we may use A, our density component, to solve the partial differential equation (as
previously discussed, at a steady state, our ∇A~v at any position and corresponding density will
equal zero). Upon completion, we anticipate our model (1) to predict how the concentration of
Heterosigma Akashiwo changes over time, given an (x, y, z) coordinate in space, a light intensity,
and time elapsed.

5 Simulation
In addition to the mathematical model, we also created a simulation of what is happening in
our model and our experiments. This simulation is an agent-based system in Java. We assume
a 500x500 pixel system, with 1000 individual Plankton starting at random positions. The light
is modeled throughout the system as if there is no water and no glass. In this sense, the light
intensity decreases as the distance from the source increases. The plankton are represented as
“agents” or “objects” - they are all individual entities which act independently of the others. The
combined “decisions” about where to move of each individual plankton ultimately represents the
behavior of the entire system that we can see in our experiments. The simulation acts as a way to
test the ideas in our model, and to confirm or disprove the accuracy of our model, by comparing
the simulation to the pictures taken during experiments.
In its simplest form, the steady state solution to our model in Equation (1) would have all of
the plankton lined up at the “sweet spot” of light intensity, their optimal intensity. With the in-
verse relationship between light intensity and distance from light source, this would look like a
semi circle around the light source. The concentration of plankton would be only along that semi-
circle, and zero elsewhere. When our simulation does not account for crowding and shadowing
of plankton, it represents that steady state solution as shown in Figure 6.
In our simple simulation of the steady state solution, each Plankton will “observe” the sur-
rounding pixels each moment, and the various light intensities. The light intensity at position
(x, y) is found by:

1. Calculating the distance between the pixel and the light source using the distance formula.

2. Subtracting that distance from the Intensity of the bulb. We chose a constant, 600, to repre-
sent the intensity of the bulb.

Similar to our ratio in the model, we chose an optimal light intensity that was 1/3 that of the
intensity of the bulb, 200. Finding the difference between each surrounding light intensity and the
optimal light intensity, a Plankton then chooses to move to the position which has a light inten-
sity closest to 200. After several moments, each Plankton has worked it’s way to the semicircle
representing optimal light intensity, as pictured in the screenshot of the simulation in Figure 6.
This steady state solution, however, is not representative of the actual behavior of the plankton.
Clearly, what we see in the simulation is not what we see in the experiments. What we really
expect the system to look like is shown in pictures from our experiments. Instead of forming a
circle around the light source, the plankton aggregate in several visible lines, as shown in Figures
1, 2, and 3. There are several ideas and hypotheses describing Heterosigma Akashiwo’s behavior

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Figure 6: Screenshot of the ”steady state” simulation. This state of the simulation accounts only
for the Plankton moving toward the optimal light source. It does not account for saturation levels
or shadowing of plankton.

that are not accounted for in the above simulation or in the model. The model would become too
complex if we tried to account for plankton reaching saturation levels, hiding in the shadows of
other plankton, or not being able to move to a position that is already occupied. However, these
are things that we can more easily handle in a simulation. Therefore, we add some of these ideas
to our existing simulation and test whether our hypotheses are true. Although these ideas are
still not accurately represented in a 2D simulation of a 3D system, they give us an opportunity to
explore and explain why the plankton are forming the patterns that we see in our experiments.
Since it is hard to explain every aspect of the system in our model, which leads to an inaccurate
solution as shown in Figure 6, we try to account for some of the ideas and factors that affect the
patterns formed in our simulation. In this more advanced simulation, we change the model of
light intensity to include an inverse square relationship between distance and intensity, as well as
to account for other Plankton blocking the light. The light intensity at any given position (x, y) is
now calculated by:

1. Calculating the distance between the pixel and the light source using the distance formula

2. Using the inverse squares relationship between light intensity and distance from source:
Io
Ir = 2 where Ir is the intensity at distance r, and Io is the intensity at light source, to find
r
the intensity given that there are no plankton blocking the light. We chose Io to be 1000, and
optimal light to be 400.

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 3. Finding the number of plankton between the light source and (x,y), and

4. decreasing the light intensity accordingly based on the number of plankton found in 3.

The plankton will again make a decision about where to move, based on the light intensities of
surrounding positions. There will be a constant representing the plankton’s optimal light intensity,
400, so the plankton will chose the surrounding position which has a light intensity closest to this
constant. Once a plankton reaches it’s ”saturation level,” it will look for a nearby plankton, and
stay in a position behind that other plankton until it again needs more light.
Some assumptions that are made in our new simulation are:

• OptimalLight = 200

• SaturationLevel = 2000

• No two Plankton can occupy the same location

• The light is a point source

• When a Plankton is not hiding, it absorbs all of the light at its current position

• When a Plankton is hiding from the light, it does not receive any light

• the amount of light absorbed by a Plankton decreases by 10 each moment while the plankton
is hiding from the light

The general algorithm that the plankton follow each moment is:
for all Plankton in the system do
find the position of the plankton, call this position (x,y)
check the surrounding positions for closest to optimal light: call this position (newx,newy)
if Plankton is not hiding then {plankton is not behind another plankton}
increase lightAbsorbed by amount of light at (x,y)
move plankton to (newx,newy)
else {plankton is hiding behind another plankton}
decrease light absorbed
if lightAbsorbed is less than half of the Saturation Level then
stop hiding {no longer sit behind another plankton}
end if
end if
if lightAbsorbed ≥ Saturation Level then
find closest plankton, closePlank
move to behind closePlank
set hiding to true for both plankton
end if
end for

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 This simulation represents a small 2D area where the plankton swim towards and aggregate at
the spot with optimal light intensity. After a few seconds, they begin to form lines moving toward
a smaller light intensity as they become oversaturated with light and choose to “hide” behind
nearby plankton. In Figure 7 you can see how one line in the pattern forms over time, and fans
out to be two lines.

Figure 7: Screenshots of the simulation in progress, from left to right, these photos show the
progression of pattern formation under the conditions and ”decision procedures” created by the
simulation.

There are still several issues with this simulation. Initially we were not sure why the Plankton
seem to be attracted to the light source itself, and start to aggregate at the light source. Although
we see some of what we expected, by seeing a line of plankton forming from plankton aggregating
and hiding behind one another, it is only one line, that seems to be too close to the light source.
We expect to see more lines forming and see these lines further from the actual light source.
Some helpful things that might improve the simualation are:

1. Change the light source to be a plane wave since the light in our experiments is not actually
a point source at the edge of the flask

2. Figure out how much light a plankton absorbs before it becomes ”oversaturated” and wants
to find a spot with less light

3. Decide how quickly the total light absorbed decreases from it’s saturation level down to
where the plankton would want to find a spot with more light

4. Make the system 3D

After studying code, we realized that the Plankton were aggregating so close to the light be-
cause we were using the pixel distance between the light source and the Plankton to calculate the
1000
intensity at any given point. So the intensity was given by Ir = where Ir is the intensity
r2

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at distance r, and 1000 is the intensity at light source, but the distance r could be as great as 500
pixels while we think of distances in terms of much larger units, like centimeters or inches. Thus,
the optimal light was actually very close to the light source. In a further simulation, we altered this
formula by dividing each ”pixel” distance by 100, so 500 pixels would be a distance of 5. Along
with this change, we altered the model of the light to represent more accurately the labratory set
up. When light travels through the glass of the flask, it is reflected and refracted, so there is not
one single point that is a light source. We change our simulation to model the light differently.
This is still a very elementary approach, because we are just modeling it as if there are multiple
point light sources, but it does in some way represent the way that light travels through water.
The light at any point (x, y) is now modeled as follows:
1. There are 9 “sources” of light with x value 700 and y values in the set lighty = {50, 100, 150, 200, 250, 300, 350,

2. The point (x, y) finds the closest of these light sources

3. Then it proceeds to model the light in a similar manner as before,

4. Uses the inverse square relationship between distance and light

Everything else remains the same in the simulation, and the simulation becomes slightly more
accurate and similar to what we see in the experiments. There are multiple lines of Plankton
moving toward the light source, but they are very short lines in comparison to the ones seen in the
experiment photos. You can see this in Figure 8.

Figure 8: Screenshot of the simulation in progress, once the light is modeled through water.

One very important thing that we are not accounting for in these simulations is the depth.
Simulating a 3D system in a 2D space is very limiting. One thing we believe is happening is
that the Plankton are hiding in the shadows of other Plankton. This is certainly not accurately
represented by Plankton hiding directly behind other Plankton at the same depth. Since the light
is coming from an angle above the water, the Plankton would realistically be slightly behind and
below the neighboring Plankton. This could explain why the patterns we see in our simulation

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are similar, but still inaccurate. Another thing the simulation assumes is that the Plankton hiding
directly behind another Plankton are not receiving any light. This is probably not actually the case,
because a microscopic Heterosigma Akashiwo cannot block all of the light from another. With this
in mind, we feel our simulation does a pretty good job of answering some of our questions. While
we made a lot of assumptions about the ratios between optimal light intensities and actual light
intensities, and how light travels through water, the simulation confirmed a few of our hypotheses
as to why Heterosigma Akashiwo will form lines in the presence of a light source. While it is nearly
impossible to model all of these factors in our mathematical model, our simulation made it easier
to test some of the ideas. With an elementary model of light through water, we see the Plankton
make decisions to hide behind other Plankton as they aggregate around the various “sweet spots”
of optimal light intensity and reach their saturation levels.

6 Conclusion
Heterosigma Akashiwo self organize in formations due to the presence of light. The plankton
self-assemble to maximize their absorption of light for photosynthesis and to protect against pho-
toinhibition. We hypothesized that they do this by sensing, and moving to, some optimal light
intensity. After reaching a certain saturation level, we believe they hide in the shadows of other
plankton to decrease the amount of light being absorbed. After creating a simulation to test this
hypothesis and comparing the results to our experimental data and the simple model shown in
Equation (1, we have confirmed our hypothesis. There is definitely a relationship between light
and plankton. As our simulation shows, the plankton will aggregate and form patterns at lo-
cations of optimal light intensity. The patterns also vary depending on light intensity since the
plankton’s absorption rate is dependent on the intensity of light present. We believe that this de-
pendency on light intensity is the reason that the wavelengths increase as the intensity increases.
With increasing light intensity, plankton reach saturation levels faster, and must hide in the shad-
ows of others, increasing the concentration of plankton in certain areas. So as the intensity of light
changes, individual plankton make adjustments to augment their absorption of light in order to
promote growth. The individual decisions of all the plankton combine to create the patterns that
we can see in the flask. Perhaps harmful algal blooms could be prevented if the light intensity in
high risk areas could be adjusted. For instance, since greater light intensity leads to longer pattern
formations, there are probably more Heterosigma Akashiwo aggregating in areas with more sun-
light. For areas along shorelines, it could be possible to plant trees or plants for shade, to decrease
the intensity of the light and hamper harmful algal blooms of Heterosigma Akashiwo.

7 Future Work Plan

Given an indefinite time frame, we would first analyze our steady solution further to check for
stability, as well as potential extraneous factors that may be affecting its stability. To look for solu-
tions as the plankton density changes in time, we may continue testing our plankton for situational
density, position, and light intensity data. With more specific in-lab observation combinations, we

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may be able to use boundary conditions and initial conditions to fit these values to our full model
and solve for ∂A ∂A
∂t . With multiple ∂t solutions completed, we may begin searching for outstanding
trends, and tailor new experiment trials to account for any information gaps. Such trends may
suggest the existence of valuable periodic solutions that may provide even further insight into the
behavior of Heterosigma akashiwo. A complete breadth of situational solutions for our full model
will presumably formulate a more accurate picture of what goes on when Heterosigma akashiwo
react to light in more natural environments as well.

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References
[1] Dartnel, Lewis How the leopard got its spots.. Plus Magazine (2004)Accessed October 13, 2014

[2] FalKowski, Paul The Role of Phytoplankton Photosynthesis in Global Biogeochemical Cycles Photo-
synthesis Research 39.3 (1994): 235?258. Web.

[3] Franks, Peter Spatial Patterns in Dense Algal Blooms sLimnology and Oceanography 42.5part2
(1997): 1297-305. Web.

[4] Levin, Simon A and Lee A. Segel Hypothesis for Origin of Planktonic Patchiness. Nature 259.5545
(1976): 659?659. Web.

[5] Mitchell, Sandra D. Dimensions of Scientific Law. Philosophy of Science. 67.2 (2000): 242. Web.
Accessed November 10, 2014.

[6] Murata, Norio, Shunichi Takashi, Yoshitaka Nishiyama, and Suleyman I. Allakhverdiev Pho-
toinhibition of Photosystem II under Environmental Stress. ScienceDirect, 19 Nov. 2006. Web. 27
Oct. 2014.

[7] Ono, K. Effects of Temperature and Light Intensity on the Growth and Toxicity of Heterosigma
Akashiwo 2008 - Aquaculture Research - Wiley Online Library. Accessed September 30, 2014.

[8] ZMEN, Haluk, and AYAS Alipaa. STUDENTSDIFFICULTIES IN UNDERSTANDING OF THE

CONSERVATION OF MATTER IN OPEN AND CLOSED-SYSTEM CHEMICAL REACTIONS.
Chemistry Education Research and Practice 4.3 (2003): 279290. Web. Accessed November 10,
2014.

[9] PLOS ONE Behavioral and Physiological Changes during Benthic-Pelagic Transition in the Harmful
Alga, Heterosigma Akashiwo: Potential for Rapid Bloom Formation. Accessed September 30, 2014.

[10] Sanders, Patrick, and Hach Hydromet. An Introduction to Algae Measurements Using In Vivo
Fluorescence. OTT. Web. 22 Oct. 2014.

[11] Whitesides, George M., and Bartosz Grzybowski. Self-Assembly at All Scales. Science 295.5564
(2002): 2418?2421. Web. 24 Sept. 2014.

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