Volume 9 Issue 1 — May 2018

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Contents

Teaching Kinetics through Differential Equations Constructed with a Berkeley Madonna Flow Chart Model

Franklin M. Chen

pp. 2–12

https://doi.org/10.22369/issn.2153-4136/9/1/1

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BibTeX 
@article{jocse-9-1-1,
  author={Franklin M. Chen},
  title={Teaching Kinetics through Differential Equations Constructed with a Berkeley Madonna Flow Chart Model},
  journal={The Journal of Computational Science Education},
  year=2018,
  month=may,
  volume=9,
  issue=1,
  pages={2--12},
  doi={https://doi.org/10.22369/issn.2153-4136/9/1/1}
}
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The alias feature of the Berkeley Madonna platform allows this author to create a chemical kinetics project manual for students to create flow charts with rate equations consistent with their learning from physical chemistry textbooks. The platform used in this way becomes versatile and powerful that allow students to explore any chemical kinetics problems from simple (e.g. 1st or 2nd order kinetics) to complex (e.g. stratosphere ozone depletion, the Lotka-Volterra mechanism) bypassing complicate syntax that are required by most of the powerful mathematical programs. This kinetics manual has been successfully implemented in UW-Green Bay in the fall semester of 2017 with the students' success rate greater than 80%.

Motivating Computational Science with Systems Modeling

Holly Hirst

pp. 13–18

https://doi.org/10.22369/issn.2153-4136/9/1/2

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BibTeX 
@article{jocse-9-1-2,
  author={Holly Hirst},
  title={Motivating Computational Science with Systems Modeling},
  journal={The Journal of Computational Science Education},
  year=2018,
  month=may,
  volume=9,
  issue=1,
  pages={13--18},
  doi={https://doi.org/10.22369/issn.2153-4136/9/1/2}
}
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This paper describes introducing rate of change and systems modeling paradigms and software as tools to increase appreciation for computational science. A similar approach was used with three different audiences: freshman liberal arts majors, junior math education majors, and college faculty teaching introductory science courses. A description of the implementation used with each audience and their reactions to the material is discussed, along with some example problems that could be used in a variety of courses.

Building a MATLAB Graphical User Interface to Solve Ordinary Differential Equations as a Final Project for an Interdisciplinary Elective Course on Numerical Computing

Steve M. Ruggiero, Jianan Zhao, and Ashlee N. Ford Versypt

pp. 19–28

https://doi.org/10.22369/issn.2153-4136/9/1/3

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BibTeX 
@article{jocse-9-1-3,
  author={Steve M. Ruggiero and Jianan Zhao and Ashlee N. Ford Versypt},
  title={Building a MATLAB Graphical User Interface to Solve Ordinary Differential Equations as a Final Project for an Interdisciplinary Elective Course on Numerical Computing},
  journal={The Journal of Computational Science Education},
  year=2018,
  month=may,
  volume=9,
  issue=1,
  pages={19--28},
  doi={https://doi.org/10.22369/issn.2153-4136/9/1/3}
}
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A final project assignment is described for an interdisciplinary applied numerical computing upper division and graduate elective in which students develop a GUI for defining and solving a system of ordinary differential equations (initial value problems) and the associated explicit algebraic equations such as values for parameters. The primary task is to develop a GUI for MATLAB using GUIDE that takes a user-specified number of differential equations and explicit algebraic equations as input, solves the system of ODEs using \mcode{ode45}, returns the solution vector, and plots the solution vector components vs. the independent variable. The code for the GUI must be verified by showing that it returns the same results and the same figures as a system of ODEs with a known solution. The purpose of the final project assignment is threefold: (1) to practice GUI design and construction in MATLAB, (2) to verify code implementation, and (3) to review content covered throughout the course. The manuscript first introduces the course and the context and motivation for the project. Then the project assignment is detailed. Two student project submissions are described. The verification case study is also provided.

Modeling the Effects of Star Formation with a Volumetric Feedback Model

Claire Kopenhafer and Brian W. O'Shea

pp. 29–38

https://doi.org/10.22369/issn.2153-4136/9/1/4

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BibTeX 
@article{jocse-9-1-4,
  author={Claire Kopenhafer and Brian W. O'Shea},
  title={Modeling the Effects of Star Formation with a Volumetric Feedback Model},
  journal={The Journal of Computational Science Education},
  year=2018,
  month=may,
  volume=9,
  issue=1,
  pages={29--38},
  doi={https://doi.org/10.22369/issn.2153-4136/9/1/4}
}
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We implemented two new models for star formation and supernova feedback into the astrophysical code Enzo. These models are designed to efficiently capture the bulk properties of galaxies and the influence of the circumgalactic medium (CGM). Unlike Enzo's existing models, these do not track stellar populations over time with computationally expensive particle objects. Instead, supernova explosions immediately follow stellar birth and their feedback is deposited in a volumetric manner. Our models were tested using simulations of Milky Way-like isolated galaxies, and we found that neither model was able to produce a realistic, metal-enriched CGM. Our work suggests that volumetric feedback models are not sufficient replacements for particle-based star formation and feedback models.