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Number of items: 107
Date joined: Apr 04 2016

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. Hide full description


Jon Darkow's Work

#1

Thyroid Hormone - Negative Feedback

sim36800 runs
negative feedback thyroid hormone metabolism biology
#2

Extinction Vortex

sim24762 runs
#3

Student Model (X. Hicks and J. Margraf) - HIV

sim42 runs
#4

Evolution with Heterozygous Advantage

Evolution of Populations: Genetic Drift, Natural Selection, and Mutations
sim7427 runs
evolution natural selection genetic drift
#5

Stock, Inflow, and Outflow with Atrazine

Simple stock and flow diagram. Flows linear.
sim64 runs
stock flow atrazine
#6

ATP Hydrolysis

sim2214 runs
Science ATP Free Energy Entropy
#7

Chaos Theory: Strange Attractor

Manipulate the main variables of the Lorenz equation.
sim1380 runs
chaos theory Lorenz attractor manifold
#8

Evolving Bits N=40

sim1954 runs
evolution bits receptor substrate
#9

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.
sim1079 runs
circadian clock feedback loop
#10

Pattern with recessive single band

sim59605 runs
genetics
#11

Grant Finches Mobile

sim15 runs
#12

HPV and Adaptive Immune Response

sim4682 runs
HPV Antibodies feedback loops vaccine
#13

Oxytocin-P

sim15 runs
Biology
#14

Steady State in Freshwater Ecosystems

sim27644 runs
#15

Cell Cycle Simulation

sim1544 runs
Biology
#16

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.
sim1544 runs
Diversity Selection Evolution Receptor Antigen
#17

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.
sim1768 runs
Environment Biology Science Ecology Education
#18

Fruit Fly with variable sample size

sim43 runs
#19

GLUT and Insulin

sim20 runs
#20

Photosynthesis Simulation - Simplified

sim32 runs
Environment Biology Science Ecology Education
#21

Extinction

sim
#22

Predator Prey Model - Mobile

sim50 runs
Biology
#23

Carbon in the Atmosphere - Graphic Input constant

sim28 runs
#24

Beta Cell Membrane Transport - Insulin Regulation

sim227 runs
Insulin Glucose Beta Cell
#25

Tryptophan Operon: A repressible system

sim51096 runs
#26

Exponential Growth

sim6120 runs
Biology Ecology
#27

Recombination and Gene Linkage

sim71167 runs
#28

HPV with Influenza A Humoral Immunity

Immune response of HPV
sim15278 runs
HPV antibodies biology Immunity
#29

Oxytocin and Child Birth

sim137530 runs
#30

Beta Cell Simulation - Split story

sim28595 runs
#31

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.
sim179945 runs
growth factors cyclins cell cycle cancer
#32

Guppy Evolution

sim88614 runs
evolution biology genes
#33

Fruit Fly Choice

Simulation to model random behavior in a fruit fly choice chamber
sim743 runs
randomness random
#34

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.
sim2918 runs
logistic growth carrying capacity
#35

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)
sim13539 runs
system dynamics carbon climate
#36

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.
sim102974 runs
Inhibition negative feedback biology lactose operon
#37

Catastrophic Regime Change in Aquatic Ecosystems

sim46054 runs
Ecology
#38

SIR COVID-19 Coronavirus Simulation

sim11533 runs
Environment Biology Science Education SIR
#39

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.
sim12085 runs
Biology Science Education transformation DNA
#40

Illusions and Assumptions

sim100 runs
Biology Science
#41

The dynamics of photosynthesis - variable sample size

The dynamics of photosynthesis - variable sample size
sim87456 runs
photosynthesis sample size biology
#42

Photosynthesis Simulation with Variance

sim207816 runs
#43

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.
sim46458 runs
Neurophysiology toxins sarin VX TTX
#44

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.
sim98632 runs
diffusion surface area volume radius
#45

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.
sim382877 runs
cellular respiration aerobic respiration ATP biology
#46

Population dynamics of white footed mouse

sim482790 runs
#47

Lactase with Variable Sample Sizes

Arrayed Lactase Model
sim529717 runs
Lactase array sample size biology
#48

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?
sim88568 runs
Genetics
#49

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.
sim89927 runs
transformation DNA biology
#50

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?
sim194636 runs
Genetics
#51

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.)
sim1320 runs
flows dynamic phosphorus
#52

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.
sim122685 runs
negative feedback loop Lotka-Volterra homeostasis predator-prey
#53

Photosynthesis with Variable Sample Sizes

Sample sizes of Photosynthesis stocks in an array
sim32717 runs, 59 downloads
Download Model
#54

Water Potential and Osmosis

Factors that affect the flow across a semi-permeable membrane.
sim227266 runs
#55

Cell Cycle - Simpler 2020

sim36305 runs
Biology Science Education
#56

Evolution and Natural Selection

sim218780 runs
#57

Position, Velocity, and Acceleration Simulation

sim212 runs
Science
#58

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.
sim6971 runs
evolution biology natural selection
#59

Cardiovascular Model

sim37 runs
#60

Evolution of LAP Allele in Mussels

sim53443 runs
Evolution Natural Selection Cline
#61

Lactase Enzyme Simulation with Data Analysis

sim6242899 runs
#62

Enzyme Diversity

sim273691 runs
enzyme biology substrate pepsin indicators
#63

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.
sim61611 runs
Biology Science Ecology Education
#64

Simple Genetics

sim71894 runs
#65

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.
sim59980 runs
metabolism respriation ATP biology
#66

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.
sim109670 runs
infromation processing neurophysiology biology
#67

Circadian Clock in the Mouse

Transcriptional Translational Feedback Loop in the Mouse
sim22727 runs
Mouse Circadian Clock
#68

Enzyme Diversity: Enzymes, Products, and Substrates

sim526065 runs
enzymes substrates products DNA trypsin
#69

Photosynthesis Model

sim860973 runs
#70

Tesing Unknown Enzymes

sim138465 runs
enzymes
#71

Lac Operon with Monod Bump

sim120349 runs
Lac Operon Gene Regulation mRNA
#72

Genotyping with Electrophoresis

sim29525 runs
biology inheritance DNA restriction enzyme
#73

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.
sim65981 runs
limiting nutrients ecosystem biology logistic growth
#74

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.
sim8406 runs
asynchrony timing phenology climate change butterfly
#75

Comparing COVID-19 with xxx

This model was copied from Jon Darkow:
model175 downloads
Download Model
Environment Biology Education
#76

insulin secretion

model86 downloads
Download Model
Biology
#77

Limiting Nutrients Model

model216 downloads
Download Model
Environment Ecology Education
#78

Primary Candidate Election Model

model142 downloads
Download Model
Education
#79

TSH-TH Feedback

model91 downloads
Download Model
Biology
#80

Signal Transduction Example

model88 downloads
Download Model
Biology Science
#81

TH v2

model78 downloads
Download Model
Biology
#82

Cellular Respriation: ID process flows

model98 downloads
Download Model
#83

Natural Selection Model v1

model151 downloads
Download Model
Biology
#84

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.
model149 downloads
Download Model
Biology Physiology Feedback
#85

Pop Growth v3

model94 downloads
Download Model
#86

OT Feedback

model111 downloads
Download Model
Biology
#87

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.
model94 downloads
Download Model
Biology Science Education natural selection evolution
#88

CR and ATP coupled reaction

model91 downloads
Download Model
Biology
#89

Cardiac Myocytes

model141 downloads
Download Model
Biology Education
#90

Epinephrine Signal Transduction

model279 downloads
Download Model
Biology Science Education
#91

p53 and Cell Cycle

model131 downloads
Download Model
Biology
#92

Two Variations - Population Growth

model81 downloads
Download Model
Biology Science Ecology Education
#93

Pop Growth with Resources v2

model79 downloads
Download Model
#94

Stock and Flow Teaching

model65 downloads
Download Model
Education
#95

SIR Model for Coronavirus (COVID-19) - with social distancing

This model was copied from Jon Darkow:
model392 downloads
Download Model
Environment Biology Education
#96

SIR Model for COVID-19

This model was copied from Jon Darkow: This model was copied from Jon Darkow:
model75 downloads
Download Model
Environment Biology Education
#97

Cellular Respiration Matter

model141 downloads
Download Model
#98

Chapter 2.12

model324 downloads
Download Model
#99

Logistic Growth Model

model571 downloads
Download Model
#100

Hormone Sample 1

model145 downloads
Download Model
#101

Exponential Growth in Population - AF

Chapter 2: Modeling the Environment
model496 downloads
Download Model
#102

SIR Model for Coronavirus (COVID-19)

model1045 downloads
Download Model
Environment Biology Education
#103

Chapter 2: Population Growth

Chapter 2 introduction
model435 downloads
Download Model
#104

Pop Growth v2

model63 downloads
Download Model
#105

TH v3

model79 downloads
Download Model
Biology
#106

CLD Example

diagram144 downloads
Download Model
Biology
X

Sim App (Sim)

An interface that allows users to interact with a model.

Image of a sim

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.

Image of a model

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.

Image of a CLD

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™.