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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

sim37053 runs
negative feedback thyroid hormone metabolism biology
#2

Extinction Vortex

sim24939 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
sim7459 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

Evolving Bits N=40

sim1957 runs
evolution bits receptor substrate
#7

Chaos Theory: Strange Attractor

Manipulate the main variables of the Lorenz equation.
sim1382 runs
chaos theory Lorenz attractor manifold
#8

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
#9

Pattern with recessive single band

sim59731 runs
genetics
#10

Grant Finches Mobile

sim15 runs
#11

HPV and Adaptive Immune Response

sim4793 runs
HPV Antibodies feedback loops vaccine
#12

Oxytocin-P

sim15 runs
Biology
#13

Steady State in Freshwater Ecosystems

sim27645 runs
#14

Cell Cycle Simulation

sim1544 runs
Biology
#15

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
#16

Fruit Fly with variable sample size

sim43 runs
#17

GLUT and Insulin

sim20 runs
#18

Photosynthesis Simulation - Simplified

sim32 runs
Environment Biology Science Ecology Education
#19

Extinction

sim
#20

Predator Prey Model - Mobile

sim50 runs
Biology
#21

Carbon in the Atmosphere - Graphic Input constant

sim28 runs
#22

Beta Cell Membrane Transport - Insulin Regulation

sim227 runs
Insulin Glucose Beta Cell
#23

Tryptophan Operon: A repressible system

sim51102 runs
#24

Recombination and Gene Linkage

sim71731 runs
#25

Exponential Growth

sim6312 runs
Biology Ecology
#26

HPV with Influenza A Humoral Immunity

Immune response of HPV
sim15322 runs
HPV antibodies biology Immunity
#27

Oxytocin and Child Birth

sim140649 runs
#28

Beta Cell Simulation - Split story

sim29640 runs
#29

Guppy Evolution

sim91405 runs
evolution biology genes
#30

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.
sim3044 runs
logistic growth carrying capacity
#31

Fruit Fly Choice

Simulation to model random behavior in a fruit fly choice chamber
sim750 runs
randomness random
#32

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
#33

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)
sim13650 runs
system dynamics carbon climate
#34

SIR COVID-19 Coronavirus Simulation

sim11681 runs
Environment Biology Science Education SIR
#35

Catastrophic Regime Change in Aquatic Ecosystems

sim48807 runs
Ecology
#36

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.
sim13128 runs
Biology Science Education transformation DNA
#37

Illusions and Assumptions

sim103 runs
Biology Science
#38

The dynamics of photosynthesis - variable sample size

The dynamics of photosynthesis - variable sample size
sim87471 runs
photosynthesis sample size biology
#39

Photosynthesis Simulation with Variance

sim207819 runs
#40

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
#41

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.
sim103883 runs
diffusion surface area volume radius
#42

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?
sim88960 runs
Genetics
#43

Population dynamics of white footed mouse

sim495218 runs
#44

Lactase with Variable Sample Sizes

Arrayed Lactase Model
sim561685 runs
Lactase array sample size biology
#45

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.
sim90169 runs
transformation DNA biology
#46

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.)
sim1373 runs
flows dynamic phosphorus
#47

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.
sim129958 runs
negative feedback loop Lotka-Volterra homeostasis predator-prey
#48

Evolution and Natural Selection

sim220698 runs
#49

Cell Cycle - Simpler 2020

sim36409 runs
Biology Science Education
#50

Position, Velocity, and Acceleration Simulation

sim281 runs
Science
#51

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.
sim1816 runs
Environment Biology Science Ecology Education
#52

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.
sim7040 runs
evolution biology natural selection
#53

Cardiovascular Model

sim397 runs
#54

Evolution of LAP Allele in Mussels

sim55801 runs
Evolution Natural Selection Cline
#55

Photosynthesis Model

sim924517 runs
#56

Simple Genetics

sim72071 runs
#57

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.
sim64295 runs
metabolism respriation ATP biology
#58

Tesing Unknown Enzymes

sim147276 runs
enzymes
#59

Circadian Clock in the Mouse

Transcriptional Translational Feedback Loop in the Mouse
sim22776 runs
Mouse Circadian Clock
#60

Lac Operon with Monod Bump

sim120567 runs
Lac Operon Gene Regulation mRNA
#61

Genotyping with Electrophoresis

sim29588 runs
biology inheritance DNA restriction enzyme
#62

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.
sim66874 runs
limiting nutrients ecosystem biology logistic growth
#63

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.
sim8410 runs
asynchrony timing phenology climate change butterfly
#64

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?
sim195185 runs
Genetics
#65

Water Potential and Osmosis

Factors that affect the flow across a semi-permeable membrane.
sim246420 runs
#66

Lactase Enzyme Simulation with Data Analysis

sim6537002 runs
#67

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.
sim63037 runs
Biology Science Ecology Education
#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.
sim110334 runs
infromation processing neurophysiology biology
#69

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.
sim391352 runs
cellular respiration aerobic respiration ATP biology
#70

ATP Hydrolysis

sim2538 runs
Science ATP Free Energy Entropy
#71

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.
sim180725 runs
growth factors cyclins cell cycle cancer
#72

Photosynthesis with Variable Sample Sizes

Sample sizes of Photosynthesis stocks in an array
sim38514 runs, 59 downloads
Download Model
#73

Enzyme Diversity: Enzymes, Products, and Substrates

sim567579 runs
enzymes substrates products DNA trypsin
#74

Enzyme Diversity

sim285790 runs
enzyme biology substrate pepsin indicators
#75

Comparing COVID-19 with xxx

This model was copied from Jon Darkow:
model180 downloads
Download Model
Environment Biology Education
#76

insulin secretion

model90 downloads
Download Model
Biology
#77

Limiting Nutrients Model

model224 downloads
Download Model
Environment Ecology Education
#78

TSH-TH Feedback

model96 downloads
Download Model
Biology
#79

Primary Candidate Election Model

model147 downloads
Download Model
Education
#80

Signal Transduction Example

model93 downloads
Download Model
Biology Science
#81

TH v2

model82 downloads
Download Model
Biology
#82

Cellular Respriation: ID process flows

model102 downloads
Download Model
#83

Natural Selection Model v1

model156 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.
model156 downloads
Download Model
Biology Physiology Feedback
#85

Pop Growth v3

model98 downloads
Download Model
#86

OT Feedback

model115 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.
model99 downloads
Download Model
Biology Science Education natural selection evolution
#88

CR and ATP coupled reaction

model95 downloads
Download Model
Biology
#89

Cardiac Myocytes

model147 downloads
Download Model
Biology Education
#90

Epinephrine Signal Transduction

model288 downloads
Download Model
Biology Science Education
#91

p53 and Cell Cycle

model135 downloads
Download Model
Biology
#92

Two Variations - Population Growth

model86 downloads
Download Model
Biology Science Ecology Education
#93

Pop Growth with Resources v2

model83 downloads
Download Model
#94

Stock and Flow Teaching

model69 downloads
Download Model
Education
#95

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

This model was copied from Jon Darkow:
model396 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:
model80 downloads
Download Model
Environment Biology Education
#97

Cellular Respiration Matter

model144 downloads
Download Model
#98

Logistic Growth Model

model576 downloads
Download Model
#99

Chapter 2.12

model327 downloads
Download Model
#100

Hormone Sample 1

model149 downloads
Download Model
#101

Exponential Growth in Population - AF

Chapter 2: Modeling the Environment
model501 downloads
Download Model
#102

SIR Model for Coronavirus (COVID-19)

model1058 downloads
Download Model
Environment Biology Education
#103

Chapter 2: Population Growth

Chapter 2 introduction
model439 downloads
Download Model
#104

Pop Growth v2

model66 downloads
Download Model
#105

TH v3

model84 downloads
Download Model
Biology
#106

CLD Example

diagram148 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™.