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STELLA Introduction

By Charlie Payne,2014-02-08 16:02
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STELLA Introduction

    Suggested Pathways through the Material with Notes and Assignments

    Introduction to Computational Science:

    Modeling and Simulation for the Sciences

    Angela B. Shiflet and George W. Shiflet

    Wofford College

    ? 2006 by Princeton University Press

    Suggestions

    Without explicitly covering Module 2.3 ("Rate of Change"), the calculus material necessary for the course can be considered with Modules 3.1 ("System Dynamics Tool: Tutorial 1") and 3.2 ("Unconstrained Growth and Decay").

    It is extremely helpful to take the class to a computer lab at least twice: To work through the first System Dynamics Tool Tutorial (Module 3.1) and the first Computational Toolbox Tutorial (Module 2.1). Work not completed during the closed lab time, can be finished outside of class. The Computational Toolbox Tutorials 1 and 2 (Modules 2.1 and 5.1, respectively) can be delayed until the second half of the course before consideration of Chapter 8. They can be done together in one lab session.

    Module 2.2 on "Errors" can be delayed to before consideration of Chapter 5 on "Simulation Techniques." Modules 5.2-5.4 on simulation methods can be covered at any time after Module 3.2 ("Unconstrained Growth and Decay").

    The ability to work well with an interdisciplinary team is important for a computational scientist, and project assignments provide good opportunities for teamwork. While a module, might develop one model for an application area, the projects section suggests many other refinements, approaches, and applications. Chapters 7 and 13 provide modules of additional, substantial projects from a variety of scientific areas that are particularly appropriate for teams of students. These modules indicate prerequisite text material, and earlier modules forward reference appropriate projects from Chapters 7 and 13.

    It is instructive for a project's team to present its model to the class. The team could be required to compose and print for the class five good questions that could be answered after hearing the presentation. The team could be graded on the quality of the questions. To help to assure attention during the presentation, the rest of the class could be required to write answers to one or several of the questions for homework or on a test.

    A course could cover both system dynamics models and cellular automaton simulations or just one of these two approaches to computational science problems. For a two-semester course, virtually all the modules can be covered in greater detail. For a computational biology course, applications in biology can be emphasized.

Syllabus 2

    Students tend to keep up better if there are daily short (5 minute) quizzes with questions taken directly from the Quick Review Questions. The website contains sample quizzes with answers.

    The following one-semester syllabus provides a week-by-week suggested pathway through the material with alternatives and possible assignments.

    Week 1

    Module 1.1 on "Overview of Computational Science"

    Module 1.2 on "The Modeling Process"

    Module 3.1 on "System Dynamics Tool: Tutorial 1" in computer lab the second class day.

    Hand in the tutorial by the end of the week.

    Module 3.2 on "Unconstrained Growth and Decay"

    Exercises 1, 3, 6, 8 with a system dynamics tool

    Project 1 except for Exercise 4 b with team to hand in towards the end of next week.

    It is easiest to make the flow tool a biflow so that the object can heat or cool.

    Week 2

    Module 3.3 on "Constrained Growth"

    Exercise 2

    Module 4.1 on "Modeling Falling and Skydiving"

    Exercises 1a, 2, 4

    Module 3.4 on "System Dynamics Tool: Tutorial 2" to do outside of class with partner.

    Hand in early next week.

    Week 3

    Module 3.5 on "Drug Dosage" (optional module)

    Exercises 4 (a, b, c), 5

    Early next week, hand in and present with a partner one of the projects below. The

    presentation should include material as described in Module 1.2 ("The Modeling

    Process"), the section "Report on the Model."

     Module 4.1 on "Modeling Falling and Skydiving" - Project 6 or 8

     Module 3.5 on "Drug Dosage" - Project 7

    Week 4

    Presentations as assigned in Week 3

    Module 6.1 on "Competition"

    Module 6.2 on "Spread of SARS" - only discussion of SIR model in class

    Exercises 1-11

    Early next week with a new partner, hand in a model for one of the projects below. Turn

    in a discussion of at least one paragraph, as requested in the project.

     Module 6.1 on "Competition " - Project 1 or 2

     Module 6.2 on "Spread of SARS" - Project 2 or 3

Syllabus 3

    Module 6.4 on "Predator-Prey Models"

    Week 5

    Module 2.2 on "Errors"

    Exercises 1-13 odd, 16, 17, 21, 24, 27, 29

    Hand in by the end of this week: Exercises 6, 18, 25, 28, 30 Early next week, hand in and present with a new partner one of the following project sets:

     Module 6.2 on "Spread of SARS" - Project 9, 10, or 11

     Module 6.3 on "Enzyme Kinetics" - Projects 2 and 3

     Module 6.3 on "Enzyme Kinetics" - Project 5

     Module 6.4 on "Predator-Prey Models" - Project 3

     Module 6.5 on "Modeling Malaria" - Projects 2 and 3 (optionally with 0)

    Week 6

    Presentations as assigned in Week 5

    Module 5.2 on "Euler's Method"

    Exercises 1, 3

    Hand in by the end of this week: Exercise 5

    Early next week, hand in and present with a new partner one of the following sets of

    projects:

    Module 7.3 on "Deep TroubleIdeal Gas Laws and Scuba Diving" - Projects 1, 5, 6,

    7

    Module 7.3 on "Deep TroubleIdeal Gas Laws and Scuba Diving" - Projects 1, 2, 3

    Module 7.5 on "A Heated DebateGlobal Warming" - Projects 1, 2, 3

    Module 7.8 on "Fueling Our CellsCarbohydrate Metabolism" - Projects 1, 2 (or 1-

    3)

    Module 7.9 on "Mercury PollutionGetting on Our Nerves" - Projects 1, 2

    Module 7.10 on "Managing to EatWhat’s the Catch? " - Projects 1, 5, 6, 7

    Module 7.10 on "Managing to Eat—What’s the Catch? " - Projects 1, 2, and 3

    Week 7

    Presentations as assigned in Week 6

    Module 5.3 on "Runge-Kutta 2 Method"

    Exercises 1, 3

    Hand in by early next week: Exercise 5

    Briefly mention Module 5.4 on "Runge-Kutta 4 Method"

    Week 8

    Review and test

    Week 9

    Module 2.1 on "Computational ToolboxTools of the Trade: Tutorial 1" and

Syllabus 4

     Module 5.1 on "Computational ToolboxTools of the Trade: Tutorial 2" in

    computer lab during class time. Hand in both tutorials by the end of the week. Hand in by early next week Module 8.1 on "Computational ToolboxTools of the Trade:

    Tutorial 3"

    Week 10

    Module 8.3 on "Empirical Models"

    Projects 2, 3, and 6 - not to hand in

    Hand in next week - Projects 4 and 9

    Week 11

    Module 9.2 on "Simulations" (optionally cover sections "Multiplicative Linear

    Congruential Method" and "Different Ranges of Random Numbers")

    If optional sections covered, do Exercises 1-4, 5, 9-11, 13-15 and hand in Exercises

    5, 12, 16

    Module 9.3 on "Area Through Monte Carlo Simulation" (optional)

    Exercises 1-11 - do not hand in

    Projects 1 and 3 using mean and standard deviation - do not hand in

    Hand in next week - Projects 2 and 4 using mean and standard deviation Hand in by early next week Module 9.1 on "Computational ToolboxTools of the Trade:

    Tutorial 4" through the section on loading a file and Module 10.1 on "Computational

    ToolboxTools of the Trade: Tutorial 5" (omit 3D point plotting)

    Week 12

    Module 10.2 on "Random Walk"

    Projects 2 and 4 - not to hand in

    Hand in next week with new partner - Project 6

    Hand in by early next week Module 11.1 on "Computational ToolboxTools of the

    Trade: Tutorial 6"

    Early next week, hand in and present with a new partner one of the following projects:

     Module 13.1 on "PolymersStrings of Pearls" - Project 1

     Module 13.2 on "Solidification—Let’s Make It Crystal Clear!" - Project 1 or 3

    Week 13

    Presentations as assigned last week

    Module 11.2 on "Spreading of Fire"

    Exercises 1-6

    Hand in early next week: Project 9

    By the end of next week, hand in and present with a new partner:

    Module 13.3 on "ForagingFinding a Way to Eat" - Project 7 applied to Project 1

    or Project 7 applied to Project 4

    Module 13.5 on "Mushroom Fairy RingsJust Going in Circles" - Project 1

    Module 13.7 on "HIVThe Enemy Within" - Project 1

Syllabus 5

    Module 13.9 on "CloudsBringing It All Together" - Project 1

    Week 14

    Presentations as assigned last week

    Module 11.3 on "Movement of Ants" (optional brief discussion)

    Week 15

    Chapter 12 on "High-Performance Computing" can be covered at any time.

    Module 12.1 on "Concurrent Processing"

    Exercises 2, 3, 5

    Module 12.2 on "Parallel Algorithms" up to the section on "Sequential Algorithm for N-

    Body Problem"

    Exercises 1, 5, 6, 7, 9, 10

    Week 16

    Test on material since the last test

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