Jon Darkow's Profile
Number of items: 121
Date joined: Apr 05 2016
Website: www.jondarkow.com
Jon Darkow has taught a variety of biology courses at the high school and college level for the past ...Read more Jon Darkow has taught a variety of biology courses at the high school and college level for the past 15 years at Seneca East High School and through Bowling Green State University. Currently, Jon teaches Biology, AP Biology, and Anatomy and Physiology. Additionally, he teaches Instructional Technologies to educators in Seneca County. Jon has a diverse academic training with a B.A. in Sociology from Ohio State University in 2000. He has a post-bachelors in Life Science Education and an M.Ed. in Curriculum and Instruction from Ashland University where he received The Most Outstanding Professional Educator Award in 2007. Jon Darkow was the 2016 recipient of the Outstanding Biology Teacher Award from the National Association of Biology Teachers. Jon is most interested in teaching scientific reasoning and systems thinking using system dynamics modeling.
Jon Darkow's Work
#1
Photosynthesis Model
sim
⋮ 2062959 runs
#2
Tesing Unknown Enzymes
sim
⋮ 240694 runs
enzymes
#3
The dynamics of photosynthesis - variable sample size
The dynamics of photosynthesis - variable sample size
sim
⋮ 91681 runs
photosynthesis
sample size
biology
#4
Oxytocin and Child Birth
sim
⋮ 216821 runs
#5
Population dynamics of white footed mouse
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⋮ 1088040 runs
#6
HPV and Adaptive Immune Response
sim
⋮ 9627 runs
HPV
Antibodies
feedback loops
vaccine
#7
Slider Bets and Metacognition
sim
⋮ 82 runs
Education
#8
Stock, Inflow, and Outflow with Atrazine
Simple stock and flow diagram. Flows linear.
sim
⋮ 76 runs
stock
flow
atrazine
#9
Neurophysiology and Information Processing 2022
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⋮ 10397 runs
Biology
information processing
neuron
neurotransmission
neurophysiology
#10
Extinction
sim
#11
Evolving Bits N=40
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⋮ 2572 runs
evolution
bits
receptor
substrate
#12
Lotka-Volterra Predator-Prey Model
Explore my favorite aspect of system dynamics and a historic example. The homeostasis generated by t
... Read more
Explore my favorite aspect of system dynamics and a historic example. The homeostasis generated by the interconnections of a negative feedback loop governs much of life.
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⋮ 241157 runs
negative feedback loop
Lotka-Volterra
homeostasis
predator-prey
#13
Genotyping with Electrophoresis
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⋮ 41383 runs
biology
inheritance
DNA
restriction enzyme
#14
Thyroid Hormone - Negative Feedback
sim
⋮ 66496 runs
negative feedback
thyroid hormone
metabolism
biology
#15
SIR COVID-19 Coronavirus Simulation
sim
⋮ 18202 runs
Environment
Biology
Science
Education
SIR
#16
Chaos Theory: Strange Attractor
Manipulate the main variables of the Lorenz equation.
sim
⋮ 2102 runs
chaos theory
Lorenz
attractor
manifold
#17
Simple Genetics
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⋮ 115543 runs
#18
ATP Hydrolysis
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⋮ 5529 runs
Science
ATP
Free Energy
Entropy
#19
Evolution with Heterozygous Advantage
Evolution of Populations: Genetic Drift, Natural Selection, and Mutations
sim
⋮ 7647 runs
evolution
natural selection
genetic drift
#20
Photosynthesis Simulation with Variance
sim
⋮ 208684 runs
#21
Photosynthesis Simulation - Simplified
sim
⋮ 60 runs
Environment
Biology
Science
Ecology
Education
#22
Cell Cycle - Simpler 2020
sim
⋮ 54356 runs
Biology
Science
Education
#23
Illusions and Assumptions
sim
⋮ 671 runs
Biology
Science
#24
Evolution of Antibiotic Resistance Simulation
Evolution of Antibiotic Resistance Simulation. This model tracks the accumulation of 40 colonies of
... Read more
Evolution of Antibiotic Resistance Simulation. This model tracks the accumulation of 40 colonies of bacteria. The main purpose of the model is to show that new adaptations are not caused by an environmental factor, like antibiotics. Rather, new adaptations are the selection of available variations. In this model you can increase variations by increasing the UV dose. The UV dose increases the mutation rate with a Monte Carlo function.
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⋮ 149277 runs
Biology
Science
Ecology
Education
#25
Evolving Bits
Diversity and selection for the basis of evolution. This simple model tries to illustrate these conc
... Read more
Diversity and selection for the basis of evolution. This simple model tries to illustrate these concepts.
sim
⋮ 1648 runs
Diversity
Selection
Evolution
Receptor
Antigen
#26
Position, Velocity, and Acceleration Simulation
sim
⋮ 1915 runs
Science
#27
Predator Prey Model - Mobile
sim
⋮ 84 runs
Biology
#28
Carbon in the Atmosphere - Graphic Input constant
sim
⋮ 28 runs
#29
Guppy Evolution
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⋮ 160622 runs
evolution
biology
genes
#30
Lactase Enzyme Simulation with Data Analysis
sim
⋮ 10616970 runs
#31
Water Potential and Osmosis
Factors that affect the flow across a semi-permeable membrane.
sim
⋮ 357498 runs
#32
Beta Cell Simulation - Split story
sim
⋮ 56786 runs
#33
Ball Bet Code Generators for Answer Keys
sim
⋮ 532 runs
Education
#34
Enzyme Diversity: Enzymes, Products, and Substrates
sim
⋮ 953615 runs
enzymes
substrates
products
DNA
trypsin
#35
HPV with Influenza A Humoral Immunity
Immune response of HPV
sim
⋮ 26750 runs
HPV
antibodies
biology
Immunity
#36
Mechanical Energy and Kinematics
sim
⋮ 235 runs
Science
Physics
Energy
Acceleration
Velocity
#37
Evolution: Grants Finches
Models the effects on population sizes of ground finches with different beak sizes in response to di
... Read more
Models the effects on population sizes of ground finches with different beak sizes in response to different amounts of annual precipitation.
sim
⋮ 11547 runs
evolution
biology
natural selection
#38
Ball Bet for Metacognition - Random
sim
⋮ 70 runs
Education
#39
White-Eyed Genetics
White-eyed is an allele that results in a fly white eyes. Wild-type variants have red eyes.
The
... Read more
White-eyed is an allele that results in a fly white eyes. Wild-type variants have red eyes.
The goal of this simulation is to determine the pattern of inheritance for the white-eyed phenotype. Is yellow body dominant or recessive? Sex-linked or autosomal? Complete, incomplete, or codominant?
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⋮ 159036 runs
Genetics
#40
Cell Cycle Simulation
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⋮ 2554 runs
Biology
#41
Transformation Experiment with Controls
Simulation allows users to test the bacterial transformation principle discovered by Frederick Griff
... Read more
Simulation allows users to test the bacterial transformation principle discovered by Frederick Griffith.
sim
⋮ 27051 runs
Biology
Science
Education
transformation
DNA
#42
Enzyme Diversity
sim
⋮ 428775 runs
enzyme
biology
substrate
pepsin
indicators
#43
Grant Finches Mobile
sim
⋮ 15 runs
#44
Student Model (X. Hicks and J. Margraf) - HIV
sim
⋮ 84 runs
#45
Ball Bet 3.0.2
sim
⋮ 1 run
#46
Oxytocin-P
sim
⋮ 28 runs
Biology
#47
Exponential Growth
sim
⋮ 10710 runs
Biology
Ecology
#48
Circadian Clock in the Mouse
Transcriptional Translational Feedback Loop in the Mouse
sim
⋮ 29135 runs
Mouse
Circadian
Clock
#49
Beta Cell Membrane Transport - Insulin Regulation
sim
⋮ 259 runs
Insulin
Glucose
Beta Cell
#50
Photosynthesis with Variable Sample Sizes
Sample sizes of Photosynthesis stocks in an array
#51
Catastrophic Regime Change in Aquatic Ecosystems
sim
⋮ 98664 runs
Ecology
#52
Pattern with recessive single band
sim
⋮ 86218 runs
genetics
#53
Limiting Nutrients in Aquatic Ecosystems
Experiment with a variety of nutrients that are limited by different degrees in four different ecosy
... Read more
Experiment with a variety of nutrients that are limited by different degrees in four different ecosystems.
sim
⋮ 111843 runs
limiting nutrients
ecosystem
biology
logistic growth
#54
Logistic Growth Model and the Butterfly Effect
Model allows users to test the starting population size (N), the carrying capacity of the populatio
... Read more
Model allows users to test the starting population size (N), the carrying capacity of the population (K), and the intrinsic rate of growth (r max).
Iterations are discrete, not continuous.
sim
⋮ 4393 runs
logistic growth
carrying capacity
#55
Understanding Linear Motion
Understand linear motion with automated feedback.
sim
⋮ 658 runs
Science
Education
physics
motion
velocity
#56
Recombination and Gene Linkage
sim
⋮ 115428 runs
#57
Evolution and Natural Selection
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⋮ 320984 runs
#58
Neurophysiology and Neurotoxicity
The main dependent variable measured in the model is the membrane potential (millivolts) of a motor
... Read more
The main dependent variable measured in the model is the membrane potential (millivolts) of a motor neuron and the muscle fiber it innervates. You will be able to add excitatory and inhibitory neurotransmitters, and compare how neurotransmitters modulate the electrical impulses of the motor neuron and the muscle fiber.
Additionally, you will be able to compare the effects of four neurotoxins: Tetrodotoxin, botulinum toxin, sarin nerve gas, and VX. While extremely lethal, these toxins are very instructive in understanding neurons because of the specific way the toxins act. Each toxin modifies or inhibits a specific molecule in neurons that help process and transmit information.
sim
⋮ 46458 runs
Neurophysiology
toxins
sarin
VX
TTX
#59
Apterous Genetics
Apterous is an allele that results in a fly without wings. Wild-type variants have normally function
... Read more
Apterous is an allele that results in a fly without wings. Wild-type variants have normally functioning wings.
The goal of this simulation is to determine the pattern of inheritance for the apterous phenotype. Is apterous dominant or recessive? Sex-linked or autosomal? Complete, incomplete, or codominant?
sim
⋮ 275819 runs
Genetics
#60
Lactase with Variable Sample Sizes
Arrayed Lactase Model
sim
⋮ 760685 runs
Lactase
array
sample size
biology
#61
Soybean and Aphid Dynamics
sim
⋮ 55 runs
Environment
Biology
Science
Economics
Ecology
#62
Fruit Fly with variable sample size
sim
⋮ 43 runs
#63
Growth Factors, Cyclins, and Cancer
Explores the feedback loops that regulate the cell cycle. Model focuses on manipulating stimuli (gro
... Read more
Explores the feedback loops that regulate the cell cycle. Model focuses on manipulating stimuli (growth factors), to stimulate the cell cycle feedback loops.
sim
⋮ 269390 runs
growth factors
cyclins
cell cycle
cancer
#64
Tryptophan Operon: A repressible system
sim
⋮ 78365 runs
#65
Lactose Operon: An Inducible System
In this simulation users explore the negative feedback system of the Lactose Operon found in bacteri
... Read more
In this simulation users explore the negative feedback system of the Lactose Operon found in bacteria. Lactose induces the system by inhibiting and inhibitor.
sim
⋮ 133287 runs
Inhibition
negative feedback
biology
lactose
operon
#66
Steady State in Freshwater Ecosystems
sim
⋮ 33842 runs
#67
Body Temperature Regulation with Scatter Plot
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⋮ 49 runs
Biology
Science
Education
Health
#68
Information Processing and Neurophysiology Model
The main dependent variable measured in the model is the membrane potential (millivolts) of two diff
... Read more
The main dependent variable measured in the model is the membrane potential (millivolts) of two different neurons in a series. You will be able to add excitatory and inhibitory neurotransmitters, and compare how these modulate electrical impulses of the two neurons.
Additionally, you will be able to compare the effects of three neurotoxins: Tetrodotoxin, botulinum toxin, and sarin nerve gas. While extremely lethal, these toxins are very instructive in understanding neurons because of the specific way the toxins act. Each toxin modifies or inhibits a specific molecule in neurons that help process and transmit information.
sim
⋮ 271127 runs
infromation processing
neurophysiology
biology
#69
System Dynamics of Carbon Budget
Simulation of the system dynamics of the global carbon dioxide budget based on the work on systems d
... Read more
Simulation of the system dynamics of the global carbon dioxide budget based on the work on systems dynamics based on John Sternman (MIT) and Krytyna Stave (University of Nebraska)
sim
⋮ 16095 runs
system dynamics
carbon
climate
#70
Extinction Vortex
sim
⋮ 53459 runs
#71
Uniform Circular Motion
sim
⋮ 599 runs
Science
Education
Circular
Motion
Physics
#72
GLUT and Insulin
sim
⋮ 20 runs
#73
Cellular Respiration Inquiry
Model of the dynamics of the metabolism of one mole of glucose. Randomness is built into the computa
... Read more
Model of the dynamics of the metabolism of one mole of glucose. Randomness is built into the computations.
sim
⋮ 95577 runs
metabolism
respriation
ATP
biology
#74
Carbon Cycle Simulation
Simulation tracks the movement of carbon to and from the atmosphere in Gt C (and Gt CO2). Users can
... Read more
Simulation tracks the movement of carbon to and from the atmosphere in Gt C (and Gt CO2). Users can manipulate with graphical inputs the changes in fossil fuel emissions, land-use, and ocean sinks.
sim
⋮ 7889 runs
Environment
Biology
Science
Ecology
Education
#75
Cellular Respiration Accounting Model
The purpose of the model is to understand how glucose is metabolized, and how the energy stored in i
... Read more
The purpose of the model is to understand how glucose is metabolized, and how the energy stored in its chemical bonds is transfered.
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⋮ 610143 runs
cellular respiration
aerobic respiration
ATP
biology
#76
Transformation Simulation
Simulation allows students to test the transformation principle. Two major goals of the experiment a
... Read more
Simulation allows students to test the transformation principle. Two major goals of the experiment are:
1. Allow users to see that supernatant from heat-killed bacteria can transform the genes of another bacterium.
2. What transforms the inheritance of the bacteria is DNA, not RNA or proteins.
sim
⋮ 122514 runs
transformation
DNA
biology
#77
Cardiovascular Model
sim
⋮ 19201 runs
#78
Evolution of LAP Allele in Mussels
sim
⋮ 73158 runs
Evolution
Natural Selection
Cline
#79
Phosphorus in Lake: Changes to Flows in a Dynamic System
This model allows users to experiment with a very simple dynamic system: one stock (Phosphorus in a
... Read more
This model allows users to experiment with a very simple dynamic system: one stock (Phosphorus in a lake), an inflow (added P/day), and an outflow (removed P/day).
The flows can either be constant throughout the simulation run, or dynamic (changing throughout the simulation run.)
sim
⋮ 2730 runs
flows
dynamic
phosphorus
#80
Diffusion of a Spherical Cell
Why are cells small? This model allows users to see how the size of a sphere affects the rate of dif
... Read more
Why are cells small? This model allows users to see how the size of a sphere affects the rate of diffusion.
sim
⋮ 136601 runs
diffusion
surface area
volume
radius
#81
Tick Tock: The Biological Clock and Circadian Rhythm
Explore gene expression of the transcriptional-translational feedback loop (TTFL) of the mouse circa
... Read more
Explore gene expression of the transcriptional-translational feedback loop (TTFL) of the mouse circadian rhythm.
sim
⋮ 1128 runs
circadian
clock
feedback loop
#82
Fruit Fly Choice
Simulation to model random behavior in a fruit fly choice chamber
sim
⋮ 982 runs
randomness
random
#83
Soybean and Aphid Population Dynamics
sim
⋮ 384 runs
Biology
Science
#84
Phenology of the Karner Blue Butterfly
Karner Blue butterfly is an endangered species. Habitat loss and climate change are contributing fac
... Read more
Karner Blue butterfly is an endangered species. Habitat loss and climate change are contributing factors to the reduction in the butterflies' population sizes. Climate change can alter the timing of lifecycles. When climate change disproportionally affects the timing of life cycles of species in an ecosystem asynchrony within a food web occurs.
sim
⋮ 11309 runs
asynchrony
timing
phenology
climate change
butterfly
#85
Lac Operon with Monod Bump
sim
⋮ 180276 runs
Lac Operon
Gene Regulation
mRNA
#86
Pendulum Model
sim
⋮ 17 runs
Science
Education
Physics
Simple Harmonic Motion
Pendulum
#87
#88
#89
SIR Model for COVID-19
This model was copied from Jon Darkow:
This model was copied from Jon Darkow:
#90
Mechanical Energy Model
#91
#92
SIR Model for Coronavirus (COVID-19)
#93
#94
Exponential Growth in Population - AF
Chapter 2: Modeling the Environment
#95
#96
#97
#98
Modeling Constant Acceleration
#99
#100
Two Variations - Population Growth
#101
#102
#103
#104
#105
#106
#107
#108
SIR Model for Coronavirus (COVID-19) - with social distancing
This model was copied from Jon Darkow:
#109
#110
#111
Endocrine System Dynamics
This model shows how FSH regulates the reproductive cycle in females, and how diseases may emerge fr
... Read more
This model shows how FSH regulates the reproductive cycle in females, and how diseases may emerge from underproduction and excess production of the hormone.
This model was developed for a high school Anatomy and Physiology class.
#112
#113
Differential Reproduction, Natural Selection Model
This is the fourth model in a sequence of models to show the logic of natural selection, formalized
... Read more
This is the fourth model in a sequence of models to show the logic of natural selection, formalized by Earnst Mayr.
Mayr E. The growth of biological thought. Cambridge: Harvard University Press; 1982.
#114
#115
#116
#117
#118
#119
Comparing COVID-19 with xxx
This model was copied from Jon Darkow:
#120
Uploading a Bundle from Zip
Instead of creating bundles, categories, and assemblies one by one, you can upload a single zip file that contains all of your bundle's content. To create your zipped bundle, make a folder with your bundle's name and add subfolders with your categories' names. The folder tree should have the same structure that you want the categories to have in your bundle. Place your assembly .stmx files in the appropriate category folders, then zip your bundle folder and upload it using the Upload Bundle from Zip link above.
Assemblies, Bundles, and Categories
Assemblies are self contained models that demonstrate common ways to connect together building blocks and that can be used as parts of other models. This is analogous to using prefabricated wall and roof pieces to construct a house.
Bundles are groups of assemblies with a common use or theme. For example, a Health Care bundle might contain a variety of assemblies that aid in creating health care models. When you download assemblies from the isee Exchange™, you download an entire bundle, rather than individual assemblies.
Categories are subgroups of assemblies within a bundle. For example, a Health Care bundle might contain a Funding category for assemblies related to the management of hospital funds. All assemblies must be assigned to a category—they cannot be assigned to the root of a bundle.
Assemblies, bundles, and categories can be created and uploaded to the isee Exchange™ via the options on the Manage My Assemblies page. To learn more, visit our help pages, or take our assemblies tutorial.
Sim App (Sim)
An interface that allows users to interact with a model.
Sim apps allow users to interact with a model using buttons, sliders, knobs, tables, graphs, and storytelling. These interactions help users understand how parts of a system interact.
Interfaces are created by model authors in the Stella desktop software and can be uploaded to the isee Exchange™.
Model
A diagram that represents how elements in a system influence one another.
Models are mathematical representations of how elements in a system are connected and interact (e.g., ecosystems, organizations, supply chains). When running models on the isee Exchange™, results can be viewed in output devices like graphs and tables.
Models appear in the isee Exchange™ directory when authors upload them from the Stella® desktop software or create them with Stella Online™.
Causal Loop Diagram (CLD)
A map that represents the feedback structure of a system.
CLDs are high-level maps that represents the feedback structure of a system and easily communicate the essence of a model. They appear in the isee Exchange™ when authors upload them from the Stella desktop software or create them with Stella Online™.