Jon Darkow's Work


We found 122 items
Include in results:
#1

Lactase Enzyme Simulation with Data Analysis

sim14,628,693 runs
3221585.8
#2

Enzyme Diversity: Enzymes, Products, and Substrates

sim1,320,535 runs
enzymes substrates products DNA trypsin
1661802.5
#3

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.
sim842,100 runs
cellular respiration aerobic respiration ATP biology
814826.2
#4

Enzyme Diversity

sim553,933 runs
enzyme biology substrate pepsin indicators
739463.2
#5

Photosynthesis Model

sim3,151,036 runs
674982
#6

Lactase with Variable Sample Sizes

Arrayed Lactase Model
sim980,748 runs
Lactase array sample size biology
587883.4
#7

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.
sim391,502 runs
infromation processing neurophysiology biology
453955.44
#8

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.
sim375,137 runs
negative feedback loop Lotka-Volterra homeostasis predator-prey
388908.1
#9

Population dynamics of white footed mouse

sim2,305,529 runs
387055.9
#10

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.
sim358,535 runs
growth factors cyclins cell cycle cancer
289023.75
#11

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.
sim272,237 runs
Biology Science Ecology Education
211153.06
#12

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.
sim160,225 runs
Inhibition negative feedback biology lactose operon
169403.22
#13

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.
sim159,048 runs
limiting nutrients ecosystem biology logistic growth
141999.88
#14

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?
sim344,070 runs
Genetics
140387.88
#15

Lac Operon with Monod Bump

sim235,824 runs
Lac Operon Gene Regulation mRNA
122395.766
#16

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.
sim158,641 runs
diffusion surface area volume radius
120021.12
#17

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.
sim151,077 runs
transformation DNA biology
109729.13
#18

Water Potential and Osmosis

Factors that affect the flow across a semi-permeable membrane.
sim459,290 runs
106117.35
#19

Evolution and Natural Selection

sim421,897 runs
95384.78
#20

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.
sim130,198 runs
metabolism respriation ATP biology
89551.28
#21

Guppy Evolution

sim218,900 runs
evolution biology genes
86349.36
#22

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?
sim218,686 runs
Genetics
84112.09
#23

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.
sim46,458 runs
Neurophysiology toxins sarin VX TTX
81203.625
#24

Thyroid Hormone - Negative Feedback

sim93,486 runs
negative feedback thyroid hormone metabolism biology
79402.14
#25

Tesing Unknown Enzymes

sim311,712 runs
enzymes
75203.06
#26

The dynamics of photosynthesis - variable sample size

The dynamics of photosynthesis - variable sample size
sim95,178 runs
photosynthesis sample size biology
65991.375
#27

Oxytocin and Child Birth

sim283,231 runs
63825.72
#28

Photosynthesis with Variable Sample Sizes

Sample sizes of Photosynthesis stocks in an array
sim226,654 runs, 295 downloads
Download Model
58994.63
#29

Photosynthesis Simulation with Variance

sim211,053 runs
54340.92
#30

Evolution of LAP Allele in Mussels

sim90,344 runs
Evolution Natural Selection Cline
53709.094
#31

Recombination and Gene Linkage

sim186,682 runs
39001.18
#32

Genotyping with Electrophoresis

sim51,128 runs
biology inheritance DNA restriction enzyme
38798.375
#33

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.
sim32,839 runs
Biology Science Education transformation DNA
37834.348
#34

Simple Genetics

sim146,263 runs
34626.42
#35

Catastrophic Regime Change in Aquatic Ecosystems

sim146,282 runs
Ecology
30083.44
#36

SIR COVID-19 Coronavirus Simulation

sim21,733 runs
Environment Biology Science Education SIR
28623.08
#37

Cell Cycle - Simpler 2020

sim66,933 runs
Biology Science Education
28445.02
#38

Neurophysiology and Information Processing 2022

sim24,689 runs
Biology information processing neuron neurotransmission neurophysiology
25742.98
#39

Pattern with recessive single band

sim100,068 runs
genetics
24803.88
#40

Tryptophan Operon: A repressible system

sim102,146 runs
23229.58
#41

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.
sim14,861 runs
asynchrony timing phenology climate change butterfly
21939.643
#42

Beta Cell Simulation - Split story

sim92,527 runs
21075.22
#43

HPV with Influenza A Humoral Immunity

Immune response of HPV
sim30,025 runs
HPV antibodies biology Immunity
18466.504
#44

Extinction Vortex

sim80,896 runs
16713.46
#45

Circadian Clock in the Mouse

Transcriptional Translational Feedback Loop in the Mouse
sim33,149 runs
Mouse Circadian Clock
15130.539
#46

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)
sim17,603 runs
system dynamics carbon climate
12848.22
#47

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.
sim12,910 runs
Environment Biology Science Ecology Education
11845.566
#48

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.
sim13,642 runs
evolution biology natural selection
10058.2
#49

HPV and Adaptive Immune Response

sim15,404 runs
HPV Antibodies feedback loops vaccine
9121.76
#50

Steady State in Freshwater Ecosystems

sim39,165 runs
9119.38
#51

Cardiovascular Model

sim34,573 runs
7448.1
#52

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.
sim3,211 runs
Environment Science Education Bathtub hydrodynamics
7211.918
#53

Evolution with Heterozygous Advantage

Evolution of Populations: Genetic Drift, Natural Selection, and Mutations
sim7,697 runs
evolution natural selection genetic drift
6654.491
#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.
sim7,104 runs
logistic growth carrying capacity
4879.967
#55

Exponential Growth

sim16,795 runs
Biology Ecology
4241.42
#56

ATP Hydrolysis

sim8,451 runs
Science ATP Free Energy Entropy
4061.85
#57

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.)
sim4,297 runs
flows dynamic phosphorus
2522.6843
#58

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.
model1,393 downloads
Download Model
Biology Science Education natural selection evolution
2346.709
#59

Epinephrine Signal Transduction

model4,644 downloads
Download Model
Biology Science Education
2146.24
#60

Chaos Theory: Strange Attractor

Manipulate the main variables of the Lorenz equation.
sim3,140 runs
chaos theory Lorenz attractor manifold
1950.7034
#61

Evolving Bits N=40

sim3,107 runs
evolution bits receptor substrate
1831.88
#62

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.
sim1,723 runs
Diversity Selection Evolution Receptor Antigen
1695.075
#63

SIR Model for Coronavirus (COVID-19)

model2,590 downloads
Download Model
Environment Biology Education
1465.4
#64

Mechanical Energy Model

model1,025 downloads
Download Model
Science Physics Acceleration Velocity Potential Energy
1294.4166
#65

Understanding Linear Motion

Understand linear motion with automated feedback.
sim1,484 runs
Science Education physics motion velocity
1195.4983
#66

Modeling Constant Acceleration

model1,295 downloads
Download Model
Science Education Physics Acceleration Velocity
1133.7
#67

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.
model1,293 downloads
Download Model
Biology Physiology Feedback
960.799
#68

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

This model was copied from Jon Darkow:
model1,561 downloads
Download Model
Environment Biology Education
953.6
#69

Position, Velocity, and Acceleration Simulation

sim5,069 runs
Science
850.86
#70

Two Variations - Population Growth

model1,370 downloads
Download Model
Biology Science Ecology Education
850.7
#71

Projectile Motion Physics

model589 downloads
Download Model
Science Education physics science position
850.49
#72

Limiting Nutrients Model

model1,457 downloads
Download Model
Environment Ecology Education
830.92
#73

Comparing COVID-19 with xxx

This model was copied from Jon Darkow:
model1,324 downloads
Download Model
Environment Biology Education
811.4
#74

Soybean and Aphid Population Dynamics

sim5,128 runs
Biology Science
753.62
#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.
sim1,128 runs
circadian clock feedback loop
750.176
#76

SIR Model for COVID-19

This model was copied from Jon Darkow: This model was copied from Jon Darkow:
model1,121 downloads
Download Model
Environment Biology Education
698.7573
#77

Cell Cycle Simulation

sim2,561 runs
Biology
655.14
#78

Uniform Circular Motion

sim1,031 runs
Science Education Circular Motion Physics
640.8
#79

Cardiac Myocytes

model1,779 downloads
Download Model
Biology Education
620.79
#80

Mechanical Energy and Kinematics

sim593 runs
Science Physics Energy Acceleration Velocity
618.4867
#81

Gravitational Attraction of Three Bodies

sim767 runs
Science Education Forces Gravitation Physics
475.4
#82

Logistic Growth Model

model1,760 downloads
Download Model
457.6
#83

CLD Example

diagram1,534 downloads
Download Model
Biology
398.64
#84

Fruit Fly Choice

Simulation to model random behavior in a fruit fly choice chamber
sim1,053 runs
randomness random
391.09167
#85

Exponential Growth in Population - AF

Chapter 2: Modeling the Environment
model1,459 downloads
Download Model
381.09
#86

OT Feedback

model1,452 downloads
Download Model
Biology
377.52
#87

Chapter 2: Population Growth

Chapter 2 introduction
model1,438 downloads
Download Model
374.98
#88

TSH-TH Feedback

model1,363 downloads
Download Model
Biology
354.38
#89

Signal Transduction Example

model1,229 downloads
Download Model
Biology Science
345.02335
#90

Stock and Flow Teaching

model1,316 downloads
Download Model
Education
342.16
#91

p53 and Cell Cycle

model1,265 downloads
Download Model
Biology
328.9
#92

Natural Selection Model v1

model1,244 downloads
Download Model
Biology
328.44
#93

Pop Growth with Resources v2

model1,262 downloads
Download Model
328.12
#94

Something

model1,198 downloads
Download Model
311.48
#95

Pop Growth v3

model1,185 downloads
Download Model
308.1
#96

Cellular Respiration Matter

model1,180 downloads
Download Model
306.8
#97

CR and ATP coupled reaction

model1,156 downloads
Download Model
Biology
300.56
#98

insulin secretion

model1,144 downloads
Download Model
Biology
297.44
#99

Hormone Sample 1

model1,143 downloads
Download Model
297.18
#100

Cellular Respriation: ID process flows

model1,133 downloads
Download Model
294.58
#101

Pop Growth v2

model1,090 downloads
Download Model
283.4
#102

Force and Position

model981 downloads
Download Model
Science physics
276.41
#103

Illusions and Assumptions

sim1,516 runs
Biology Science
259.77
#104

Model1

model972 downloads
Download Model
252.72
#105

model1-mrd

model904 downloads
Download Model
235.04
#106

Ball Bet Code Generators for Answer Keys

sim846 runs
Education
203.98
#107

Soybean and Aphid Dynamics

sim174 runs
Environment Biology Science Economics Ecology
131.2
#108

Beta Cell Membrane Transport - Insulin Regulation

sim375 runs
Insulin Glucose Beta Cell
122.84
#109

Body Temperature Regulation with Scatter Plot

sim5,206 runs
Biology Science Education Health
105.27333
#110

Photosynthesis Simulation - Simplified

sim167 runs
Environment Biology Science Ecology Education
65.9
#111

Pendulum Model

sim50 runs
Science Education Physics Simple Harmonic Motion Pendulum
45.3
#112

Stock, Inflow, and Outflow with Atrazine

Simple stock and flow diagram. Flows linear.
sim98 runs
stock flow atrazine
33.688
#113

Predator Prey Model - Mobile

sim370 runs
Biology
24.12
#114

Ball Bet for Metacognition - Random

sim110 runs
Education
11.84
#115

Slider Bets and Metacognition

sim89 runs
Education
7.94
#116

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

sim84 runs
6.64
#117

Fruit Fly with variable sample size

sim43 runs
-4.02
#118

Oxytocin-P

sim38 runs
Biology
-5.84
#119

Carbon in the Atmosphere - Graphic Input constant

sim28 runs
-7.92
#120

GLUT and Insulin

sim20 runs
-10
#121

Grant Finches Mobile

sim15 runs
-11.3
#122

Ball Bet 3.0.2

sim2 runs
-14.68
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™.