Jon Darkow's Work


We found 64 items
Include in results:
#1

Lactase Enzyme Simulation with Data Analysis

sim817518 runs
29851.5
#2

Photosynthesis Model

sim118759 runs
8271.7
#3

Evolution and Natural Selection

sim88382 runs
7445.6
#4

Population dynamics of white footed mouse

sim96352 runs
6427.2
#5

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.
sim68048 runs
infromation processing neurophysiology biology
4550.7
#6

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.
sim28829 runs
metabolism respriation ATP biology
2888.8
#7

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.
sim25757 runs
cellular respiration aerobic respiration ATP biology
2579.9
#8

Evolution of LAP Allele in Mussels

sim24466 runs
Evolution Natural Selection Cline
2411.5
#9

Lac Operon with Monod Bump

sim34294 runs
Lac Operon Gene Regulation mRNA
2326.1
#10

Lactase with Variable Sample Sizes

Arrayed Lactase Model
sim47469 runs
Lactase array sample size biology
1938.55
#11

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.
sim25744 runs
Inhibition negative feedback biology lactose operon
1470
#12

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.
sim17196 runs
limiting nutrients ecosystem biology logistic growth
1259.1
#13

Steady State in Freshwater Ecosystems

sim12317 runs
1218.7
#14

Water Potential and Osmosis

Factors that affect the flow across a semi-permeable membrane.
sim23579 runs
951.85
#15

Circadian Clock in the Mouse

Transcriptional Translational Feedback Loop in the Mouse
sim9192 runs
Mouse Circadian Clock
914.4
#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.
sim9934 runs
diffusion surface area volume radius
911.95
#17

Photosynthesis with Variable Sample Sizes

Sample sizes of Photosynthesis stocks in an array
sim7651 runs, 24 downloads
Download Model
763.05
#18

Thyroid Hormone - Negative Feedback

sim7907 runs
negative feedback thyroid hormone metabolism biology
637.3
#19

Recombination and Gene Linkage

sim27819 runs
631.8
#20

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.
sim8864 runs
transformation DNA biology
538.1
#21

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?
sim18597 runs
Genetics
326.9
#22

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.
sim2735 runs
asynchrony timing phenology climate change butterfly
297.9
#23

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?
sim59440 runs
Genetics
297.6
#24

Extinction Vortex

sim6641 runs
295.3
#25

Beta Cell Simulation - Split story

sim1923 runs
172.4
#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.
sim1406 runs
Diversity Selection Evolution Receptor Antigen
139.35
#27

Evolution with Heterozygous Advantage

Evolution of Populations: Genetic Drift, Natural Selection, and Mutations
sim3283 runs
evolution natural selection genetic drift
134.85
#28

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.
sim45212 runs
growth factors cyclins cell cycle cancer
118.85
#29

Catastrophic Regime Change in Aquatic Ecosystems

sim1340 runs
Ecology
111.1
#30

HPV and Adaptive Immune Response

sim4079 runs
HPV Antibodies feedback loops vaccine
110.9
#31

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.
sim1184 runs
negative feedback loop Lotka-Volterra homeostasis predator-prey
102.75
#32

Tryptophan Operon: A repressible system

sim13447 runs
87.8
#33

Guppy Evolution

sim3806 runs
evolution biology genes
79.7
#34

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.
sim791 runs
circadian clock feedback loop
74.6
#35

Pattern with recessive single band

sim13712 runs
genetics
60.8
#36

Evolving Bits N=40

sim1111 runs
evolution bits receptor substrate
50.3
#37

Tesing Unknown Enzymes

sim2951 runs
enzymes
45.8
#38

Logistic Growth Model

model368 downloads
Download Model
36.8
#39

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.
sim771 runs
logistic growth carrying capacity
31.3
#40

Exponential Growth in Population - AF

Chapter 2: Modeling the Environment
model287 downloads
Download Model
30.45
#41

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.
sim16883 runs
Neurophysiology toxins sarin VX TTX
28
#42

Chaos Theory: Strange Attractor

Manipulate the main variables of the Lorenz equation.
sim352 runs
chaos theory Lorenz attractor manifold
22.65
#43

Chapter 2: Population Growth

Chapter 2 introduction
model196 downloads
Download Model
20.7
#44

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.
sim1086 runs
evolution biology natural selection
18.9
#45

HPV with Influenza A Humoral Immunity

Immune response of HPV
sim186 runs
HPV antibodies biology Immunity
18.9
#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)
sim1309 runs
system dynamics carbon climate
16.25
#47

Chapter 2.12

model151 downloads
Download Model
15.1
#48

Genotyping with Electrophoresis

sim1465 runs
biology inheritance DNA restriction enzyme
14
#49

Enzyme Diversity: Enzymes, Products, and Substrates

sim24599 runs
enzymes substrates products DNA trypsin
13.9
#50

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.)
sim32 runs
flows dynamic phosphorus
12.05
#51

Enzyme Diversity

sim13405 runs
enzyme biology substrate pepsin indicators
8.2
#52

Beta Cell Membrane Transport - Insulin Regulation

sim211 runs
Insulin Glucose Beta Cell
4.4
#53

The dynamics of photosynthesis - variable sample size

The dynamics of photosynthesis - variable sample size
sim68 runs
photosynthesis sample size biology
0.65
#54

Stock, Inflow, and Outflow with Atrazine

Simple stock and flow diagram. Flows linear.
sim48 runs
stock flow atrazine
0.2
#55

Fruit Fly Choice

Simulation to model random behavior in a fruit fly choice chamber
sim153 runs
randomness random
-1.05
#56

Photosynthesis Simulation with Variance

sim37157 runs
-3.3
#57

Fruit Fly with variable sample size

sim39 runs
-8.7
#58

Simple Genetics

sim15752 runs
-9.5
#59

Carbon in the Atmosphere - Graphic Input constant

sim25 runs
-10
#60

Oxytocin and Child Birth

sim18739 runs
-10.3
#61

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

sim7 runs
-11.4
#62

GLUT and Insulin

sim10 runs
-11.7
#63

Grant Finches Mobile

sim10 runs
-12
#64

Cardiovascular Model

sim0 runs 0 views
-12
X

Sim App (Sim)

An interface that allows users to interact with a model.

Image of a sim

Sim apps allow users to interact with a model using buttons, sliders, knobs, tables, graphs, and storytelling. These interactions help users understand how parts of a system interact.

Interfaces are created by model authors in the Stella desktop software and can be uploaded to the isee Exchange.

Model

A diagram that represents how elements in a system influence one another.

Image of a model

Models are mathematical representations of how elements in a system are connected and interact (e.g., ecosystems, organizations, supply chains). When running models on the 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™.