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Biological Modeling - Coggle Diagram
Biological Modeling
1
Random Walks and Turing Patterns
zebra stripes?
Random Walk Theorem
After n steps of unit length in a random walk, a particle will on average find itself a distance from its origin that is proportional to \( \sqrt{n} \).
consider more than one type of particle are randomly walking
Reaction-Diffusion System
parameters
kill rate ( \( k \) )
\( \frac{d[B]}{dt} = k [B] \)
predator-prey rate ( \( r \) )
\( A + 2B \rightarrow 3B\)
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feed rate ( \( f \) )
\( \frac{d[A]}{dt} = f \)
diffusion rate ( \( d_A \) )
if we raise the diffusion rate \( \rightarrow \) more of the reaction A + 2B → 3B.
if f = 2k we can see zebra stripes
we want to simulate system
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concentration of a particle
\( [ A ] \)
the emergent patterns are called
Turing patterns
2
Network of Proteins
model protein interactions
network
biological networks has
network motifs
frequently recurring structures hidden within biological networks
central dogma
regulation
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3
chemotaxis
How does a simple organism like E. coli sense an
attractant
or
repellent
in its environment?
The movement of organisms like E. coli in response to a chemical stimulus is called
chemotaxis
.
E. coli and other bacteria
move toward
attractants
like glucose and electron acceptors
move away from
repellents
like \(\text{Ni}^{2+}\) and \(\text{Co}^{2+}\)
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4
Analyzing the Coronavirus Spike Protein
2003
severe acute respiratory syndrome, or
SARS
This mysterious new disease had crossed the Pacific Ocean within a week of entering Hong Kong.
SARS was deadly, killing close to 10% of those who became sick.
2017
researchers published the results of sampling horseshoe bats for five years in a cave in Yunnan province. They found that these bats harbored coronaviruses with remarkable genetic similarity to the virus causing SARS.
but no body cares 😭
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5
Classifying White Blood Cells
what are blood cells?
red blood cell (RBC)
transport oxygen via the hemoglobin protein
white blood cell (WBC)
identify and attack foreign cells as part of your immune system
divide into families based on their structure and function
monocytes
lymphocytes
granulocytes
have a multilobular nucleus
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How Are Blood Cells Counted?
classic method
device
hemocytometer
a technician filters a small amount of blood onto a gridded slide
counts the number of cells of each type in the squares on the grid
estimate the number of each type of cell per volume
computational methods
identify WBC by color threshold
a
binarized image
not bad!
How to classify them?
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