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    Free Online Textbook
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    2018-Eduardo-Sontag-Lecture_Notes_on_Mathematical_Systems_Biology
    I am often asked if it is OK to use these notes in courses at other universities. The answer is “of course!” though I strongly suggest that a link to my website be provided, so that students can always access the current version.
    biologytextbooksystemsdyanmical system
    Modeling Scenario
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    3-010-EnergyInSpringMassSystem-ModlingScenario
    As a way to synthesize the effects of damping and forcing terms, this activity is meant to encourage students to explore how different forcing terms will change the total energy in a mass-spring system.
    energymass-spring systemkinetic energypotential energytotal energy
    Technique Narrative
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    5-012-LinearSystemConjecture-TechniqueNarrative
    Students go from the solution for y'(t) = k*y(t) to a natural extension to the solution conjecture of a system of two constant coefficient, homogeneous, linear differential equations introducing eigenvalues and eigenvectors through student...
    discovery learningconjecturesolutionsubstitution
    Modeling Scenario
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    3-101-SpringMassFirstTry-NoResistance-ModelingScenario
    Students build a model based on their perceptions of what the solution should look like for a simple spring mass system with no damping.
    frequencymassoscillationundampedspring constantspring\Single Degree of Freedom System
    Modeling Scenario
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    3-102-SpringMassDamped-ModelingScenario
    Students build a model based on their perceptions of what the solution should look like for a simple spring mass system with damping.
    frequencymassoscillationstiffnessspring constantspring\dampedSingle Degree of Freedom Systemcoefficient
    Modeling Scenario
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    1-137-SheepGraze-ModelingScenario
    In this activity, students will apply graphical analysis (such as phase lines) to determine the long-term predictions of a differential equation model for pasture grass using two different formulas for the herbivore consumption rate.
    herbivoreplantphase linesbifurcationoverexploitationsheepgraze
    Modeling Scenario
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    3-091-SpringModeling-ModelingScenario
    In this lab students will collect data on their spring mass systems and compare their empirical models to their theoretical ones—giving them an opportunity to actually test a model against data.
    datalaboratoryLoggerProVerniermass-spring systemmodel validationempirical modeltheoretical model
    Modeling Scenario
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    5-001-LSD-ModelingScenario
    We describe the use of a two compartment model of a linear system of first order linear differential equations to model lysergic acid diethylamide (LSD) in the body. We provide the data from the literature.
    LSDSpanishcompartmentpharmacokineticslysergic acid diethylamide
    Modeling Scenario
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    5-022-ColdPill-ModelingScenario
    A model for the flow of a cold pill drug through the gastrointestinal compartment to the bloodstream compartment of a human subject is proposed. Students solve the system of differential equation model, use known parameter values, and plot solutions.
    ratesmedicinedrug discoverycompartmentcold pillgastrointestinalbloodstream
    Article or Presentation
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    SIMIODE Spring 2024 Webinars - Insightmaker
    We discuss the use of the FREE system dynamics software Insightmaker (https://insightmaker.com/) in a first course in Ordinary Differential Equations (with a modeling emphasis).
    modelingsimulationSoftwarepythonsystemsInsightMakerflowCategory Theorystockstock-flow
    Modeling Scenario
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    3-130-MatterOfSomeGravity-ModelingScenario
    This project introduces the concept of an inverse problem (or parameter estimation), in the context of the simple linearized pendulum ordinary differential equation.
    gravityinverse problemacceleration
    Modeling Scenario
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    3-060-DataToDifferentialEquation-ModelingScenario
    Students use knowledge of second-order linear differential equations in conjunction with physical intuition of spring-mass systems to estimate the damping coefficient and spring constant from data.
    Association & Data Fittingmassspring-mass systemspring\total distancenumerical differentiation
    Modeling Scenario
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    1-132-DigoxinElimination-ModelingScenario
    We model the concentration of digoxin eliminated from the human body at a rate proportional to the concentration. This is a ``first-order reaction'' in the language of pharmacokinetics -- the study of how drugs move in the body.
    nullclinespharmacokineticsdigoxindrug eliminationtwo compartment
    Modeling Scenario
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    1-190-IntroClass-ModelingScenario
    Students go through development of ideas in mathematical modeling with differential equations. They encounter fundamental ideas of unlimited population growth, limited population growth and a predator prey system.
    population dynamicspredator-preylogisticexponentialgraphical interpretationsqualitative analysis
    Modeling Scenario
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    3-001-SpringMassDataAnalysis-ModelingScenario
    We offer data on position of a mass at end of spring over time where the spring mass configuration has damping due to taped flat index cards at the bottom of the mass. Modeling of a spring mass configuration and estimation of parameters are the core.
    datadampingspring-mass systemNewton's Second Law of Motionspring constantHooke's Law
    Modeling Scenario
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    3-051-ProjectileMotions-ModelingScenario
    We consider several instances of projectile flight without resistance, one on level ground and one from edge of cliff to determine maximum distance and placement.
    trajectorylaunching radiantprojectile motionprojectileno resistanceangle of launch
    Modeling Scenario
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    1-131-CaffeineElimination-ModelingScenario
    We model the concentration of caffeine eliminated from the human body at a rate proportional to the concentration. This is a ``first-order reaction'' in the language of pharmacokinetics -- the study of how drugs move in the body.
    caffeineeliminationpharmacokineticsdrug
    Modeling Scenario
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    5-024-PhGreatLakes
    In this teaching modeling scenario, we demonstrate how lessons on salt-tank compartmental modeling can be used to predict phosphorus levels in the Great Lakes.
    Great Lakeslimnologycomparmentpollutioncompartmental modelsphosphorous
    Modeling Scenario
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    3-026-SpringInverseProblem-ModelingScenario
    We are given data on the position of a mass in an oscillating spring mass system and we seek to discover approaches to estimating an unknown parameter.
    datamassinverse problemspring\parameter estimate
    Modeling Scenario
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    3-035-StadiumDesign-ModelingScenario
    For a given baseball playing field outline how high must the outfield fence be at each point in order to make a homerun equally likely in all fair directions?
    projectile motionbaseballparametric equationstadiumhome runno reistantfairnessno resistance