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Number of items: 124
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

Population dynamics of white footed mouse

sim1236331 runs
#2

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?
sim301161 runs
Genetics
#3

Position, Velocity, and Acceleration Simulation

sim3033 runs
Science
#4

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?
sim179840 runs
Genetics
#5

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
#6

Catastrophic Regime Change in Aquatic Ecosystems

sim107381 runs
Ecology
#7

Cell Cycle - Simpler 2020

sim61115 runs
Biology Science Education
#8

Oxytocin and Child Birth

sim241965 runs
#9

Evolution and Natural Selection

sim332643 runs
#10

HPV and Adaptive Immune Response

sim11233 runs
HPV Antibodies feedback loops vaccine
#11

Slider Bets and Metacognition

sim86 runs
Education
#12

Stock, Inflow, and Outflow with Atrazine

Simple stock and flow diagram. Flows linear.
sim76 runs
stock flow atrazine
#13

The dynamics of photosynthesis - variable sample size

The dynamics of photosynthesis - variable sample size
sim93667 runs
photosynthesis sample size biology
#14

Neurophysiology and Information Processing 2022

sim17676 runs
Biology information processing neuron neurotransmission neurophysiology
#15

Extinction

sim
#16

Evolving Bits N=40

sim2642 runs
evolution bits receptor substrate
#17

Genotyping with Electrophoresis

sim42837 runs
biology inheritance DNA restriction enzyme
#18

Thyroid Hormone - Negative Feedback

sim77318 runs
negative feedback thyroid hormone metabolism biology
#19

SIR COVID-19 Coronavirus Simulation

sim18652 runs
Environment Biology Science Education SIR
#20

Chaos Theory: Strange Attractor

Manipulate the main variables of the Lorenz equation.
sim2261 runs
chaos theory Lorenz attractor manifold
#21

Evolution with Heterozygous Advantage

Evolution of Populations: Genetic Drift, Natural Selection, and Mutations
sim7686 runs
evolution natural selection genetic drift
#22

ATP Hydrolysis

sim6732 runs
Science ATP Free Energy Entropy
#23

Photosynthesis Simulation with Variance

sim208996 runs
#24

Photosynthesis Simulation - Simplified

sim74 runs
Environment Biology Science Ecology Education
#25

Illusions and Assumptions

sim828 runs
Biology Science
#26

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.
sim1664 runs
Diversity Selection Evolution Receptor Antigen
#27

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.
sim167138 runs
Biology Science Ecology Education
#28

Predator Prey Model - Mobile

sim97 runs
Biology
#29

Carbon in the Atmosphere - Graphic Input constant

sim28 runs
#30

Ball Bet Code Generators for Answer Keys

sim725 runs
Education
#31

Mechanical Energy and Kinematics

sim378 runs
Science Physics Energy Acceleration Velocity
#32

Ball Bet for Metacognition - Random

sim89 runs
Education
#33

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.
sim12126 runs
evolution biology natural selection
#34

HPV with Influenza A Humoral Immunity

Immune response of HPV
sim27191 runs
HPV antibodies biology Immunity
#35

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.
sim145192 runs
diffusion surface area volume radius
#36

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.
sim109787 runs
metabolism respriation ATP biology
#37

Lactase with Variable Sample Sizes

Arrayed Lactase Model
sim822180 runs
Lactase array sample size biology
#38

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.
sim266228 runs
negative feedback loop Lotka-Volterra homeostasis predator-prey
#39

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.
sim301610 runs
growth factors cyclins cell cycle cancer
#40

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

sim84 runs
#41

Grant Finches Mobile

sim15 runs
#42

Oxytocin-P

sim36 runs
Biology
#43

Ball Bet 3.0.2

sim1 run
#44

Exponential Growth

sim12423 runs
Biology Ecology
#45

Circadian Clock in the Mouse

Transcriptional Translational Feedback Loop in the Mouse
sim30038 runs
Mouse Circadian Clock
#46

Beta Cell Membrane Transport - Insulin Regulation

sim268 runs
Insulin Glucose Beta Cell
#47

Enzyme Diversity: Enzymes, Products, and Substrates

sim1066457 runs
enzymes substrates products DNA trypsin
#48

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.)
sim2986 runs
flows dynamic phosphorus
#49

Pattern with recessive single band

sim89705 runs
genetics
#50

Lactase Enzyme Simulation with Data Analysis

sim11960771 runs
#51

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.
sim5616 runs
logistic growth carrying capacity
#52

Understanding Linear Motion

Understand linear motion with automated feedback.
sim1086 runs
Science Education physics motion velocity
#53

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.
sim304276 runs
infromation processing neurophysiology biology
#54

Water Potential and Osmosis

Factors that affect the flow across a semi-permeable membrane.
sim395620 runs
#55

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.
sim700129 runs
cellular respiration aerobic respiration ATP biology
#56

Enzyme Diversity

sim469277 runs
enzyme biology substrate pepsin indicators
#57

Beta Cell Simulation - Split story

sim77588 runs
#58

Cell Cycle Simulation

sim2558 runs
Biology
#59

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.
sim28767 runs
Biology Science Education transformation DNA
#60

Fruit Fly with variable sample size

sim43 runs
#61

Soybean and Aphid Dynamics

sim81 runs
Environment Biology Science Economics Ecology
#62

Tryptophan Operon: A repressible system

sim83855 runs
#63

Steady State in Freshwater Ecosystems

sim34104 runs
#64

Body Temperature Regulation with Scatter Plot

sim101 runs
Biology Science Education Health
#65

Guppy Evolution

sim174127 runs
evolution biology genes
#66

Recombination and Gene Linkage

sim134159 runs
#67

Bathtub Dynamics

This simulation has three models. Model1 shows constant inflow and outflow into a bathtub. Model ... Read more
This simulation has three models. Model1 shows constant inflow and outflow into a bathtub. Model 2 shows constant inflow and nonlinear outflow based on the quantity of water in the bathtub. Model 3 shows constant inflow and nonlinear outflow based on the quantity of water in the bathtub. However, Model 3 uses Torricelli's law to calculate the flow rate based on physical principles. This law was formulated by Evangelista Torricelli, an Italian physicist, in the 17th century. It's an important principle in fluid dynamics and is closely related to Bernoulli's principle. Torricelli's law states that the speed (velocity) of efflux of a fluid through a hole under the force of gravity is proportional to the square root of the vertical distance (height) between the fluid surface and the center of the hole. The formula is given by efflux velocity = 2*g*ℎ​, where: g is the acceleration due to gravity (approximately 9.81 m/s² on Earth). ℎ is the height of the fluid column above the hole. The idea is that the fluid's potential energy due to its height is converted into kinetic energy as it falls. The higher the fluid, the greater its potential energy and thus the greater the speed at which it exits the hole. This principle is used in various applications, such as determining the flow rate of liquids from tanks, in hydrodynamics studies, and even in everyday situations like draining a bathtub. The law assumes an ideal fluid (incompressible and non-viscous) and neglects factors like air resistance and the viscosity of the fluid. It also assumes that the size of the hole is small compared to the depth of the fluid. The flow rate (the volume of fluid flowing per unit time) can be calculated by multiplying the cross-sectional area of the hole (A) by the velocity of the fluid (v), leading to the formula Q=A*v, where Q is the flow rate.
sim509 runs
Environment Science Education Bathtub hydrodynamics
#68

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)
sim16315 runs
system dynamics carbon climate
#69

Gravitational Attraction of Three Bodies

sim236 runs
Science Education Forces Gravitation Physics
#70

Tesing Unknown Enzymes

sim252131 runs
enzymes
#71

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.
sim117794 runs
limiting nutrients ecosystem biology logistic growth
#72

Uniform Circular Motion

sim741 runs
Science Education Circular Motion Physics
#73

Extinction Vortex

sim56964 runs
#74

GLUT and Insulin

sim20 runs
#75

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.
sim129503 runs
transformation DNA biology
#76

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.
sim9423 runs
Environment Biology Science Ecology Education
#77

Photosynthesis Model

sim2452310 runs
#78

Photosynthesis with Variable Sample Sizes

Sample sizes of Photosynthesis stocks in an array
sim176447 runs, 143 downloads
Download Model
#79

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.
sim11466 runs
asynchrony timing phenology climate change butterfly
#80

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.
sim141467 runs
Inhibition negative feedback biology lactose operon
#81

Cardiovascular Model

sim25193 runs
#82

Evolution of LAP Allele in Mussels

sim84828 runs
Evolution Natural Selection Cline
#83

Simple Genetics

sim125002 runs
#84

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
#85

Fruit Fly Choice

Simulation to model random behavior in a fruit fly choice chamber
sim1016 runs
randomness random
#86

Soybean and Aphid Population Dynamics

sim1716 runs
Biology Science
#87

Lac Operon with Monod Bump

sim196244 runs
Lac Operon Gene Regulation mRNA
#88

Pendulum Model

sim17 runs
Science Education Physics Simple Harmonic Motion Pendulum
#89

Cellular Respiration Matter

model823 downloads
Download Model
#90

SIR Model for COVID-19

This model was copied from Jon Darkow: This model was copied from Jon Darkow:
model720 downloads
Download Model
Environment Biology Education
#91

Mechanical Energy Model

model636 downloads
Download Model
Science Physics Acceleration Velocity Potential Energy
#92

Something

model570 downloads
Download Model
#93

SIR Model for Coronavirus (COVID-19)

model2008 downloads
Download Model
Environment Biology Education
#94

Epinephrine Signal Transduction

model1281 downloads
Download Model
Biology Science Education
#95

CR and ATP coupled reaction

model774 downloads
Download Model
Biology
#96

Exponential Growth in Population - AF

Chapter 2: Modeling the Environment
model1111 downloads
Download Model
#97

Signal Transduction Example

model708 downloads
Download Model
Biology Science
#98

Pop Growth with Resources v2

model760 downloads
Download Model
#99

Pop Growth v2

model722 downloads
Download Model
#100

Modeling Constant Acceleration

model750 downloads
Download Model
Science Education Physics Acceleration Velocity
#101

Chapter 2: Population Growth

Chapter 2 introduction
model1045 downloads
Download Model
#102

Two Variations - Population Growth

model803 downloads
Download Model
Biology Science Ecology Education
#103

Pop Growth v3

model799 downloads
Download Model
#104

p53 and Cell Cycle

model841 downloads
Download Model
Biology
#105

insulin secretion

model748 downloads
Download Model
Biology
#106

model1-mrd

model521 downloads
Download Model
#107

Cellular Respriation: ID process flows

model731 downloads
Download Model
#108

Stock and Flow Teaching

model812 downloads
Download Model
Education
#109

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.
model840 downloads
Download Model
Biology Science Education natural selection evolution
#110

Cardiac Myocytes

model1140 downloads
Download Model
Biology Education
#111

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

This model was copied from Jon Darkow:
model1127 downloads
Download Model
Environment Biology Education
#112

Natural Selection Model v1

model855 downloads
Download Model
Biology
#113

TSH-TH Feedback

model747 downloads
Download Model
Biology
#114

Hormone Sample 1

model778 downloads
Download Model
#115

Logistic Growth Model

model1205 downloads
Download Model
#116

OT Feedback

model804 downloads
Download Model
Biology
#117

Force and Position

model583 downloads
Download Model
Science physics
#118

Limiting Nutrients Model

model882 downloads
Download Model
Environment Ecology Education
#119

Model1

model477 downloads
Download Model
#120

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.
model785 downloads
Download Model
Biology Physiology Feedback
#121

Projectile Motion Physics

model67 downloads
Download Model
Science Education physics science position
#122

Comparing COVID-19 with xxx

This model was copied from Jon Darkow:
model828 downloads
Download Model
Environment Biology Education
#123

CLD Example

diagram829 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™.