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Number of items: 121
Date joined: Apr 05 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

Photosynthesis Model

sim2062959 runs
#2

Tesing Unknown Enzymes

sim240694 runs
enzymes
#3

The dynamics of photosynthesis - variable sample size

The dynamics of photosynthesis - variable sample size
sim91681 runs
photosynthesis sample size biology
#4

Oxytocin and Child Birth

sim216821 runs
#5

Population dynamics of white footed mouse

sim1088040 runs
#6

HPV and Adaptive Immune Response

sim9627 runs
HPV Antibodies feedback loops vaccine
#7

Slider Bets and Metacognition

sim82 runs
Education
#8

Stock, Inflow, and Outflow with Atrazine

Simple stock and flow diagram. Flows linear.
sim76 runs
stock flow atrazine
#9

Neurophysiology and Information Processing 2022

sim10397 runs
Biology information processing neuron neurotransmission neurophysiology
#10

Extinction

sim
#11

Evolving Bits N=40

sim2572 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.
sim241157 runs
negative feedback loop Lotka-Volterra homeostasis predator-prey
#13

Genotyping with Electrophoresis

sim41383 runs
biology inheritance DNA restriction enzyme
#14

Thyroid Hormone - Negative Feedback

sim66496 runs
negative feedback thyroid hormone metabolism biology
#15

SIR COVID-19 Coronavirus Simulation

sim18202 runs
Environment Biology Science Education SIR
#16

Chaos Theory: Strange Attractor

Manipulate the main variables of the Lorenz equation.
sim2102 runs
chaos theory Lorenz attractor manifold
#17

Simple Genetics

sim115543 runs
#18

ATP Hydrolysis

sim5529 runs
Science ATP Free Energy Entropy
#19

Evolution with Heterozygous Advantage

Evolution of Populations: Genetic Drift, Natural Selection, and Mutations
sim7647 runs
evolution natural selection genetic drift
#20

Photosynthesis Simulation with Variance

sim208684 runs
#21

Photosynthesis Simulation - Simplified

sim60 runs
Environment Biology Science Ecology Education
#22

Cell Cycle - Simpler 2020

sim54356 runs
Biology Science Education
#23

Illusions and Assumptions

sim671 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.
sim149277 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.
sim1648 runs
Diversity Selection Evolution Receptor Antigen
#26

Position, Velocity, and Acceleration Simulation

sim1915 runs
Science
#27

Predator Prey Model - Mobile

sim84 runs
Biology
#28

Carbon in the Atmosphere - Graphic Input constant

sim28 runs
#29

Guppy Evolution

sim160622 runs
evolution biology genes
#30

Lactase Enzyme Simulation with Data Analysis

sim10616970 runs
#31

Water Potential and Osmosis

Factors that affect the flow across a semi-permeable membrane.
sim357498 runs
#32

Beta Cell Simulation - Split story

sim56786 runs
#33

Ball Bet Code Generators for Answer Keys

sim532 runs
Education
#34

Enzyme Diversity: Enzymes, Products, and Substrates

sim953615 runs
enzymes substrates products DNA trypsin
#35

HPV with Influenza A Humoral Immunity

Immune response of HPV
sim26750 runs
HPV antibodies biology Immunity
#36

Mechanical Energy and Kinematics

sim235 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.
sim11547 runs
evolution biology natural selection
#38

Ball Bet for Metacognition - Random

sim70 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?
sim159036 runs
Genetics
#40

Cell Cycle Simulation

sim2554 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.
sim27051 runs
Biology Science Education transformation DNA
#42

Enzyme Diversity

sim428775 runs
enzyme biology substrate pepsin indicators
#43

Grant Finches Mobile

sim15 runs
#44

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

sim84 runs
#45

Ball Bet 3.0.2

sim1 run
#46

Oxytocin-P

sim28 runs
Biology
#47

Exponential Growth

sim10710 runs
Biology Ecology
#48

Circadian Clock in the Mouse

Transcriptional Translational Feedback Loop in the Mouse
sim29135 runs
Mouse Circadian Clock
#49

Beta Cell Membrane Transport - Insulin Regulation

sim259 runs
Insulin Glucose Beta Cell
#50

Photosynthesis with Variable Sample Sizes

Sample sizes of Photosynthesis stocks in an array
sim149483 runs, 121 downloads
Download Model
#51

Catastrophic Regime Change in Aquatic Ecosystems

sim98664 runs
Ecology
#52

Pattern with recessive single band

sim86218 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.
sim111843 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.
sim4393 runs
logistic growth carrying capacity
#55

Understanding Linear Motion

Understand linear motion with automated feedback.
sim658 runs
Science Education physics motion velocity
#56

Recombination and Gene Linkage

sim115428 runs
#57

Evolution and Natural Selection

sim320984 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.
sim46458 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?
sim275819 runs
Genetics
#60

Lactase with Variable Sample Sizes

Arrayed Lactase Model
sim760685 runs
Lactase array sample size biology
#61

Soybean and Aphid Dynamics

sim55 runs
Environment Biology Science Economics Ecology
#62

Fruit Fly with variable sample size

sim43 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.
sim269390 runs
growth factors cyclins cell cycle cancer
#64

Tryptophan Operon: A repressible system

sim78365 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.
sim133287 runs
Inhibition negative feedback biology lactose operon
#66

Steady State in Freshwater Ecosystems

sim33842 runs
#67

Body Temperature Regulation with Scatter Plot

sim49 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.
sim271127 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)
sim16095 runs
system dynamics carbon climate
#70

Extinction Vortex

sim53459 runs
#71

Uniform Circular Motion

sim599 runs
Science Education Circular Motion Physics
#72

GLUT and Insulin

sim20 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.
sim95577 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.
sim7889 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.
sim610143 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.
sim122514 runs
transformation DNA biology
#77

Cardiovascular Model

sim19201 runs
#78

Evolution of LAP Allele in Mussels

sim73158 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.)
sim2730 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.
sim136601 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.
sim1128 runs
circadian clock feedback loop
#82

Fruit Fly Choice

Simulation to model random behavior in a fruit fly choice chamber
sim982 runs
randomness random
#83

Soybean and Aphid Population Dynamics

sim384 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.
sim11309 runs
asynchrony timing phenology climate change butterfly
#85

Lac Operon with Monod Bump

sim180276 runs
Lac Operon Gene Regulation mRNA
#86

Pendulum Model

sim17 runs
Science Education Physics Simple Harmonic Motion Pendulum
#87

Epinephrine Signal Transduction

model1109 downloads
Download Model
Biology Science Education
#88

Cellular Respiration Matter

model757 downloads
Download Model
#89

SIR Model for COVID-19

This model was copied from Jon Darkow: This model was copied from Jon Darkow:
model654 downloads
Download Model
Environment Biology Education
#90

Mechanical Energy Model

model562 downloads
Download Model
Science Physics Acceleration Velocity Potential Energy
#91

CR and ATP coupled reaction

model703 downloads
Download Model
Biology
#92

SIR Model for Coronavirus (COVID-19)

model1920 downloads
Download Model
Environment Biology Education
#93

Something

model506 downloads
Download Model
#94

Exponential Growth in Population - AF

Chapter 2: Modeling the Environment
model1038 downloads
Download Model
#95

Signal Transduction Example

model634 downloads
Download Model
Biology Science
#96

Pop Growth with Resources v2

model680 downloads
Download Model
#97

Pop Growth v2

model652 downloads
Download Model
#98

Modeling Constant Acceleration

model654 downloads
Download Model
Science Education Physics Acceleration Velocity
#99

Chapter 2: Population Growth

Chapter 2 introduction
model964 downloads
Download Model
#100

Two Variations - Population Growth

model706 downloads
Download Model
Biology Science Ecology Education
#101

Pop Growth v3

model735 downloads
Download Model
#102

insulin secretion

model670 downloads
Download Model
Biology
#103

p53 and Cell Cycle

model720 downloads
Download Model
Biology
#104

model1-mrd

model445 downloads
Download Model
#105

Cellular Respriation: ID process flows

model651 downloads
Download Model
#106

Stock and Flow Teaching

model736 downloads
Download Model
Education
#107

Cardiac Myocytes

model997 downloads
Download Model
Biology Education
#108

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

This model was copied from Jon Darkow:
model1050 downloads
Download Model
Environment Biology Education
#109

Natural Selection Model v1

model781 downloads
Download Model
Biology
#110

TSH-TH Feedback

model680 downloads
Download Model
Biology
#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.
model713 downloads
Download Model
Biology Physiology Feedback
#112

Hormone Sample 1

model707 downloads
Download Model
#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.
model765 downloads
Download Model
Biology Science Education natural selection evolution
#114

Logistic Growth Model

model1138 downloads
Download Model
#115

OT Feedback

model728 downloads
Download Model
Biology
#116

Force and Position

model512 downloads
Download Model
Science physics
#117

Limiting Nutrients Model

model814 downloads
Download Model
Environment Ecology Education
#118

Model1

model406 downloads
Download Model
#119

Comparing COVID-19 with xxx

This model was copied from Jon Darkow:
model760 downloads
Download Model
Environment Biology Education
#120

CLD Example

diagram765 downloads
Download Model
Biology
X

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.

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™.