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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

Position, Velocity, and Acceleration Simulation

sim3278 runs
Science
#2

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.
sim6215 runs
logistic growth carrying capacity
#3

Tesing Unknown Enzymes

sim286467 runs
enzymes
#4

Photosynthesis with Variable Sample Sizes

Sample sizes of Photosynthesis stocks in an array
sim188045 runs, 152 downloads
Download Model
#5

Cell Cycle - Simpler 2020

sim61814 runs
Biology Science Education
#6

Pattern with recessive single band

sim95364 runs
genetics
#7

HPV and Adaptive Immune Response

sim12484 runs
HPV Antibodies feedback loops vaccine
#8

Slider Bets and Metacognition

sim89 runs
Education
#9

The dynamics of photosynthesis - variable sample size

The dynamics of photosynthesis - variable sample size
sim94313 runs
photosynthesis sample size biology
#10

Stock, Inflow, and Outflow with Atrazine

Simple stock and flow diagram. Flows linear.
sim92 runs
stock flow atrazine
#11

Neurophysiology and Information Processing 2022

sim20244 runs
Biology information processing neuron neurotransmission neurophysiology
#12

Extinction

sim
#13

Evolving Bits N=40

sim2760 runs
evolution bits receptor substrate
#14

Genotyping with Electrophoresis

sim44113 runs
biology inheritance DNA restriction enzyme
#15

Thyroid Hormone - Negative Feedback

sim80917 runs
negative feedback thyroid hormone metabolism biology
#16

SIR COVID-19 Coronavirus Simulation

sim19013 runs
Environment Biology Science Education SIR
#17

Chaos Theory: Strange Attractor

Manipulate the main variables of the Lorenz equation.
sim2406 runs
chaos theory Lorenz attractor manifold
#18

Evolution with Heterozygous Advantage

Evolution of Populations: Genetic Drift, Natural Selection, and Mutations
sim7692 runs
evolution natural selection genetic drift
#19

ATP Hydrolysis

sim7025 runs
Science ATP Free Energy Entropy
#20

Population dynamics of white footed mouse

sim1453996 runs
#21

Photosynthesis Simulation with Variance

sim209046 runs
#22

Photosynthesis Simulation - Simplified

sim85 runs
Environment Biology Science Ecology Education
#23

Illusions and Assumptions

sim973 runs
Biology Science
#24

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.
sim1675 runs
Diversity Selection Evolution Receptor Antigen
#25

Predator Prey Model - Mobile

sim116 runs
Biology
#26

Carbon in the Atmosphere - Graphic Input constant

sim28 runs
#27

Ball Bet Code Generators for Answer Keys

sim842 runs
Education
#28

Mechanical Energy and Kinematics

sim439 runs
Science Physics Energy Acceleration Velocity
#29

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.
sim12577 runs
evolution biology natural selection
#30

Ball Bet for Metacognition - Random

sim102 runs
Education
#31

HPV with Influenza A Humoral Immunity

Immune response of HPV
sim28072 runs
HPV antibodies biology Immunity
#32

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.
sim146309 runs
diffusion surface area volume radius
#33

Catastrophic Regime Change in Aquatic Ecosystems

sim115257 runs
Ecology
#34

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.
sim285931 runs
negative feedback loop Lotka-Volterra homeostasis predator-prey
#35

Grant Finches Mobile

sim15 runs
#36

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

sim84 runs
#37

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.)
sim3271 runs
flows dynamic phosphorus
#38

Ball Bet 3.0.2

sim1 run
#39

Oxytocin-P

sim36 runs
Biology
#40

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.
sim307910 runs
growth factors cyclins cell cycle cancer
#41

Exponential Growth

sim13618 runs
Biology Ecology
#42

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?
sim309230 runs
Genetics
#43

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?
sim190865 runs
Genetics
#44

Lactase with Variable Sample Sizes

Arrayed Lactase Model
sim850980 runs
Lactase array sample size biology
#45

Circadian Clock in the Mouse

Transcriptional Translational Feedback Loop in the Mouse
sim31187 runs
Mouse Circadian Clock
#46

Beta Cell Membrane Transport - Insulin Regulation

sim269 runs
Insulin Glucose Beta Cell
#47

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
#48

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.
sim130337 runs
limiting nutrients ecosystem biology logistic growth
#49

Understanding Linear Motion

Understand linear motion with automated feedback.
sim1118 runs
Science Education physics motion velocity
#50

Evolution of LAP Allele in Mussels

sim85387 runs
Evolution Natural Selection Cline
#51

Beta Cell Simulation - Split story

sim80672 runs
#52

Cell Cycle Simulation

sim2558 runs
Biology
#53

Soybean and Aphid Dynamics

sim125 runs
Environment Biology Science Economics Ecology
#54

Fruit Fly with variable sample size

sim43 runs
#55

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.
sim307572 runs
infromation processing neurophysiology biology
#56

Tryptophan Operon: A repressible system

sim89366 runs
#57

Steady State in Freshwater Ecosystems

sim35119 runs
#58

Body Temperature Regulation with Scatter Plot

sim150 runs
Biology Science Education Health
#59

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.
sim1458 runs
Environment Science Education Bathtub hydrodynamics
#60

Guppy Evolution

sim186750 runs
evolution biology genes
#61

Water Potential and Osmosis

Factors that affect the flow across a semi-permeable membrane.
sim399657 runs
#62

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.
sim192800 runs
Biology Science Ecology Education
#63

Lactase Enzyme Simulation with Data Analysis

sim12269500 runs
#64

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.
sim147024 runs
Inhibition negative feedback biology lactose operon
#65

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.
sim727951 runs
cellular respiration aerobic respiration ATP biology
#66

Recombination and Gene Linkage

sim146933 runs
#67

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)
sim16606 runs
system dynamics carbon climate
#68

Gravitational Attraction of Three Bodies

sim383 runs
Science Education Forces Gravitation Physics
#69

Oxytocin and Child Birth

sim245334 runs
#70

Uniform Circular Motion

sim846 runs
Science Education Circular Motion Physics
#71

GLUT and Insulin

sim20 runs
#72

Evolution and Natural Selection

sim363880 runs
#73

Cardiovascular Model

sim28598 runs
#74

Simple Genetics

sim132314 runs
#75

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
#76

Fruit Fly Choice

Simulation to model random behavior in a fruit fly choice chamber
sim1020 runs
randomness random
#77

Soybean and Aphid Population Dynamics

sim2693 runs
Biology Science
#78

Lac Operon with Monod Bump

sim206251 runs
Lac Operon Gene Regulation mRNA
#79

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.
sim30257 runs
Biology Science Education transformation DNA
#80

Extinction Vortex

sim61797 runs
#81

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.
sim135878 runs
transformation DNA biology
#82

Enzyme Diversity

sim481901 runs
enzyme biology substrate pepsin indicators
#83

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.
sim113607 runs
metabolism respriation ATP biology
#84

Enzyme Diversity: Enzymes, Products, and Substrates

sim1123815 runs
enzymes substrates products DNA trypsin
#85

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.
sim12572 runs
asynchrony timing phenology climate change butterfly
#86

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.
sim11074 runs
Environment Biology Science Ecology Education
#87

Photosynthesis Model

sim2576688 runs
#88

Pendulum Model

sim50 runs
Science Education Physics Simple Harmonic Motion Pendulum
#89

Cellular Respiration Matter

model872 downloads
Download Model
#90

Mechanical Energy Model

model683 downloads
Download Model
Science Physics Acceleration Velocity Potential Energy
#91

Something

model619 downloads
Download Model
#92

SIR Model for Coronavirus (COVID-19)

model2072 downloads
Download Model
Environment Biology Education
#93

Epinephrine Signal Transduction

model1337 downloads
Download Model
Biology Science Education
#94

CR and ATP coupled reaction

model814 downloads
Download Model
Biology
#95

Exponential Growth in Population - AF

Chapter 2: Modeling the Environment
model1157 downloads
Download Model
#96

Signal Transduction Example

model748 downloads
Download Model
Biology Science
#97

Pop Growth with Resources v2

model807 downloads
Download Model
#98

Pop Growth v2

model770 downloads
Download Model
#99

Modeling Constant Acceleration

model806 downloads
Download Model
Science Education Physics Acceleration Velocity
#100

Chapter 2: Population Growth

Chapter 2 introduction
model1092 downloads
Download Model
#101

Two Variations - Population Growth

model853 downloads
Download Model
Biology Science Ecology Education
#102

Pop Growth v3

model851 downloads
Download Model
#103

p53 and Cell Cycle

model888 downloads
Download Model
Biology
#104

insulin secretion

model804 downloads
Download Model
Biology
#105

model1-mrd

model568 downloads
Download Model
#106

Cellular Respriation: ID process flows

model772 downloads
Download Model
#107

Stock and Flow Teaching

model856 downloads
Download Model
Education
#108

Cardiac Myocytes

model1251 downloads
Download Model
Biology Education
#109

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

This model was copied from Jon Darkow:
model1182 downloads
Download Model
Environment Biology Education
#110

Natural Selection Model v1

model908 downloads
Download Model
Biology
#111

TSH-TH Feedback

model792 downloads
Download Model
Biology
#112

Hormone Sample 1

model821 downloads
Download Model
#113

Logistic Growth Model

model1252 downloads
Download Model
#114

OT Feedback

model857 downloads
Download Model
Biology
#115

Force and Position

model635 downloads
Download Model
Science physics
#116

Limiting Nutrients Model

model940 downloads
Download Model
Environment Ecology Education
#117

Model1

model527 downloads
Download Model
#118

Projectile Motion Physics

model118 downloads
Download Model
Science Education physics science position
#119

Comparing COVID-19 with xxx

This model was copied from Jon Darkow:
model870 downloads
Download Model
Environment Biology Education
#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.
model827 downloads
Download Model
Biology Physiology Feedback
#121

SIR Model for COVID-19

This model was copied from Jon Darkow: This model was copied from Jon Darkow:
model787 downloads
Download Model
Environment Biology Education
#122

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.
model902 downloads
Download Model
Biology Science Education natural selection evolution
#123

CLD Example

diagram899 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™.