Jon Darkow's Profile
Number of items: 124
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
SIR COVID-19 Coronavirus Simulation
sim
⋮ 17442 runs
Environment
Biology
Science
Education
SIR
#2
Student Model (X. Hicks and J. Margraf) - HIV
sim
⋮ 81 runs
#3
Stock, Inflow, and Outflow with Atrazine
Simple stock and flow diagram. Flows linear.
sim
⋮ 72 runs
stock
flow
atrazine
#4
Evolving Bits N=40
sim
⋮ 2473 runs
evolution
bits
receptor
substrate
#5
Grant Finches Mobile
sim
⋮ 15 runs
#6
Oxytocin-P
sim
⋮ 28 runs
Biology
#7
Steady State in Freshwater Ecosystems
sim
⋮ 31630 runs
#8
Cell Cycle Simulation
sim
⋮ 2552 runs
Biology
#9
Fruit Fly with variable sample size
sim
⋮ 43 runs
#10
GLUT and Insulin
sim
⋮ 20 runs
#11
Extinction
sim
#12
Predator Prey Model - Mobile
sim
⋮ 58 runs
Biology
#13
Carbon in the Atmosphere - Graphic Input constant
sim
⋮ 28 runs
#14
Beta Cell Membrane Transport - Insulin Regulation
sim
⋮ 255 runs
Insulin
Glucose
Beta Cell
#15
Illusions and Assumptions
sim
⋮ 561 runs
Biology
Science
#16
Photosynthesis Simulation with Variance
sim
⋮ 208331 runs
#17
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
#18
Uniform Circular Motion
sim
⋮ 526 runs
Science
Education
Circular
Motion
Physics
#19
Mechanical Energy and Kinematics
sim
⋮ 173 runs
Science
Physics
Energy
Acceleration
Velocity
#20
Oxytocin and Child Birth
sim
⋮ 207614 runs
#21
Evolution with Heterozygous Advantage
Evolution of Populations: Genetic Drift, Natural Selection, and Mutations
sim
⋮ 7647 runs
evolution
natural selection
genetic drift
#22
Fruit Fly Choice
Simulation to model random behavior in a fruit fly choice chamber
sim
⋮ 943 runs
randomness
random
#23
ATP Hydrolysis
sim
⋮ 5137 runs
Science
ATP
Free Energy
Entropy
#24
Chaos Theory: Strange Attractor
Manipulate the main variables of the Lorenz equation.
sim
⋮ 1893 runs
chaos theory
Lorenz
attractor
manifold
#25
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
⋮ 9692 runs
evolution
biology
natural selection
#26
Ball Bet for Metacognition - Random
sim
⋮ 50 runs
Education
#27
Ball Bet 3.0.2
sim
⋮ 1 run
#28
Photosynthesis Simulation - Simplified
sim
⋮ 55 runs
Environment
Biology
Science
Ecology
Education
#29
Extinction Vortex
sim
⋮ 46297 runs
#30
Tesing Unknown Enzymes
sim
⋮ 212610 runs
enzymes
#31
Simple Genetics
sim
⋮ 110555 runs
#32
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
⋮ 15507 runs
system dynamics
carbon
climate
#33
Slider Bets and Metacognition
sim
⋮ 79 runs
Education
#34
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
⋮ 5857 runs
Environment
Biology
Science
Ecology
Education
#35
Guppy Evolution
sim
⋮ 147591 runs
evolution
biology
genes
#36
Cell Cycle - Simpler 2020
sim
⋮ 51818 runs
Biology
Science
Education
#37
Position, Velocity, and Acceleration Simulation
sim
⋮ 1460 runs
Science
#38
Exponential Growth
sim
⋮ 9460 runs
Biology
Ecology
#39
Ball Bet Code Generators for Answer Keys
sim
⋮ 345 runs
Education
#40
Pattern with recessive single band
sim
⋮ 83242 runs
genetics
#41
Beta Cell Simulation - Split story
sim
⋮ 53938 runs
#42
Tryptophan Operon: A repressible system
sim
⋮ 76641 runs
#43
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
⋮ 1120 runs
circadian
clock
feedback loop
#44
Catastrophic Regime Change in Aquatic Ecosystems
sim
⋮ 88377 runs
Ecology
#45
The dynamics of photosynthesis - variable sample size
The dynamics of photosynthesis - variable sample size
sim
⋮ 89920 runs
photosynthesis
sample size
biology
#46
HPV with Influenza A Humoral Immunity
Immune response of HPV
sim
⋮ 24004 runs
HPV
antibodies
biology
Immunity
#47
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
⋮ 4003 runs
logistic growth
carrying capacity
#48
Genotyping with Electrophoresis
sim
⋮ 39591 runs
biology
inheritance
DNA
restriction enzyme
#49
Photosynthesis with Variable Sample Sizes
Sample sizes of Photosynthesis stocks in an array
#50
Neurophysiology and Information Processing 2022
sim
⋮ 5796 runs
Biology
information processing
neuron
neurotransmission
neurophysiology
#51
HPV and Adaptive Immune Response
sim
⋮ 9241 runs
HPV
Antibodies
feedback loops
vaccine
#52
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
⋮ 1630 runs
Diversity
Selection
Evolution
Receptor
Antigen
#53
Water Potential and Osmosis
Factors that affect the flow across a semi-permeable membrane.
sim
⋮ 338179 runs
#54
Understanding Linear Motion
Understand linear motion with automated feedback.
sim
⋮ 572 runs
Science
Education
physics
motion
velocity
#55
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
⋮ 270944 runs
Genetics
#56
Enzyme Diversity
sim
⋮ 421422 runs
enzyme
biology
substrate
pepsin
indicators
#57
Recombination and Gene Linkage
sim
⋮ 111408 runs
#58
Evolution and Natural Selection
sim
⋮ 299906 runs
#59
Enzyme Diversity: Enzymes, Products, and Substrates
sim
⋮ 909672 runs
enzymes
substrates
products
DNA
trypsin
#60
Photosynthesis Model
sim
⋮ 1917916 runs
#61
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
⋮ 264987 runs
growth factors
cyclins
cell cycle
cancer
#62
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
⋮ 25377 runs
Biology
Science
Education
transformation
DNA
#63
Lactase Enzyme Simulation with Data Analysis
sim
⋮ 9880976 runs
#64
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.
sim
⋮ 582212 runs
cellular respiration
aerobic respiration
ATP
biology
#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
⋮ 130523 runs
Inhibition
negative feedback
biology
lactose
operon
#66
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
⋮ 93656 runs
metabolism
respriation
ATP
biology
#67
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
⋮ 216881 runs
infromation processing
neurophysiology
biology
#68
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
⋮ 10885 runs
asynchrony
timing
phenology
climate change
butterfly
#69
Lactase with Variable Sample Sizes
Arrayed Lactase Model
sim
⋮ 718485 runs
Lactase
array
sample size
biology
#70
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?
sim
⋮ 146528 runs
Genetics
#71
Evolution of LAP Allele in Mussels
sim
⋮ 70364 runs
Evolution
Natural Selection
Cline
#72
Cardiovascular Model
sim
⋮ 17410 runs
#73
Thyroid Hormone - Negative Feedback
sim
⋮ 63467 runs
negative feedback
thyroid hormone
metabolism
biology
#74
Circadian Clock in the Mouse
Transcriptional Translational Feedback Loop in the Mouse
sim
⋮ 26999 runs
Mouse
Circadian
Clock
#75
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
⋮ 2450 runs
flows
dynamic
phosphorus
#76
Soybean and Aphid Population Dynamics
sim
⋮ 7 runs
Biology
Science
#77
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.
sim
⋮ 130900 runs
Biology
Science
Ecology
Education
#78
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
⋮ 119417 runs
transformation
DNA
biology
#79
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
⋮ 98595 runs
limiting nutrients
ecosystem
biology
logistic growth
#80
Lac Operon with Monod Bump
sim
⋮ 176570 runs
Lac Operon
Gene Regulation
mRNA
#81
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.
sim
⋮ 208677 runs
negative feedback loop
Lotka-Volterra
homeostasis
predator-prey
#82
Population dynamics of white footed mouse
sim
⋮ 905171 runs
#83
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
⋮ 131191 runs
diffusion
surface area
volume
radius
#84
Pendulum Model
sim
⋮ 14 runs
Science
Education
Physics
Simple Harmonic Motion
Pendulum
#85
#86
#87
#88
#89
#90
#91
#92
Comparing COVID-19 with xxx
This model was copied from Jon Darkow:
#93
#94
Exponential Growth in Population - AF
Chapter 2: Modeling the Environment
#95
#96
#97
#98
#99
#100
#101
SIR Model for Coronavirus (COVID-19) - with social distancing
This model was copied from Jon Darkow:
#102
#103
#104
#105
#106
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.
#107
Modeling Constant Acceleration
#108
#109
#110
Two Variations - Population Growth
#111
#112
#113
#114
SIR Model for COVID-19
This model was copied from Jon Darkow:
This model was copied from Jon Darkow:
#115
#116
Mechanical Energy Model
#117
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.
#118
SIR Model for Coronavirus (COVID-19)
#119
#120
#121
#122
#123
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™.