CSERD: Computational Science Education Reference Desk

The Computational Science Education Reference Desk (CSERD) features resources to help students learn about computational science and to help teachers incorporate it into the classroom. Computational science involves the appropriate use of a computational architecture or computing environment (a computer, calculator, abacus, dice, or the like) to apply some algorithm, or mathematical method, to solve some scientific application, or problem. This combination of application, algorithm, and architecture results in a model that can be used as a scientific tool. The Resources section of the CSERD site provides a permanent collection of materials developed especially for CSERD, including models (pieces of scientific software), activities (lessons or lesson plans that use models), tutorials (short courses designed to teach a specific topic), applications, algorithms, architectures, and several other categories. The Resources form part of a larger catalogue of computational science items gathered by CSERD from around the internet. The catalogue can be searched or browsed by subject, keyword, education level, audience, and resource type. The record for each item includes a link to the resource, title, brief description, education level, and other information.

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Optimization and Scalability Series - Part 1: Planning for Parallel
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This set of three modules describes how to analyze and optimize the ...

This set of three modules describes how to analyze and optimize the performance of an application on Ranger. It covers multiple scales, from collective MPI communication on thousands of nodes, down to individual threads on the AMD Barcelona processors.

Subject:
Computing and Information
Technology
Education
Material Type:
Full Course
Lecture Notes
Lesson Plan
Provider:
Shodor
Provider Set:
CSERD: Computational Science Education Reference Desk
Author:
Cornell University
The Journal of Computational Science Education Volume 1 Issue 1
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The Journal of Computational Science Education (JOCSE) promotes the use of computation ...

The Journal of Computational Science Education (JOCSE) promotes the use of computation in education through disseminating unique uses of computation in the classroom as well as research findings in computational science education, with submissions from both professionals and students. JOCSE utilizes internet technology and a web-based format to allow for enhanced interactivity in all publications.

Subject:
Computing and Information
Education
Provider:
Shodor
Provider Set:
CSERD: Computational Science Education Reference Desk
Author:
The Shodor Education Foundation, Inc.
Characterizing Ligand Interactions in Wild-type and Mutated HIV-1 Proteases
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A computational module has been developed in which students examine the binding ...

A computational module has been developed in which students examine the binding interactions between indinavir and HIV-1 protease. The project is a component of the Medicinal Chemistry course offered to upper level chemistry, biochemistry, and biology majors. Students work with modeling and informatics tools utilized in drug development research while evaluating wild-type and mutated forms of the HIV-1 protease in complex with the inhibitor indinavir. By quantifying the molecular interactions within protease-inhibitor complexes, students can characterize the structural basis for reduced efficacy of indinavir.

Subject:
Computing and Information
Technology
Education
Life Science
Mathematics
History, Law, Politics
Provider:
Shodor
Provider Set:
CSERD: Computational Science Education Reference Desk
Author:
Andy Watkins
Jordan Campbell
Leyte L. Winfield
Rosalind Gregory-Bass
Helium AtomSCF-LCAO Calculation of the (1s)2 Ground State of the
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Using a double-zeta basis of Slater-type orbitals [STOs], this Java applet calculates ...

Using a double-zeta basis of Slater-type orbitals [STOs], this Java applet calculates the single determinant singlet ground state 1s2 wavefunction of the helium atom. The doubly occupied orbital is expanded in terms of two basis functions, 1s and 1s`.

Subject:
Computing and Information
Physics
Provider:
Shodor
Provider Set:
CSERD: Computational Science Education Reference Desk
Understanding the Structural and Functional Effects of Mutations in HIV-1 Protease Mutants Using 100ns Molecular Dynamics Simulations
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The Human Immunodeficiency Virus type 1 protease (HIV-1 PR) performs a vital ...

The Human Immunodeficiency Virus type 1 protease (HIV-1 PR) performs a vital role in the lifecycle of the virus, specifically in the maturation of new viral particles. Therefore, delaying the onset of AIDS, the primary goal of HIV treatment, can be achieved by inhibiting this protease.[1] However, the rapidly mutating virus quickly develops drug resistance to current inhibitors, thus novel protease inhibitors are needed. Here, 100ns molecular dynamics (MD) simulations were done for the wild type and two mutant proteases to gain insight into the mechanisms by which the mutations confer drug resistance. Several different metrics were used to search for differences between the wild type and mutant proteases including: flap tip distance and root-mean-square deviation (RMSD), mutual information, and Kullback-Leibler divergence. Finally, it is found at the 100ns timescale there are not large differences in the structure, flexibility and motions of the wild type protease relative to the mutants, and longer simulations may be needed to identify how the structural changes imparted by the mutations affect the protease's functionality.

Subject:
Computing and Information
Education
Life Science
Chemistry
Provider:
Shodor
Provider Set:
CSERD: Computational Science Education Reference Desk
Author:
Christopher Savoie
David Mobley
The Journal of Computational Science Education Volume 3 Issue 1
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The Journal of Computational Science Education (JOCSE) promotes the use of computation ...

The Journal of Computational Science Education (JOCSE) promotes the use of computation in education through disseminating unique uses of computation in the classroom as well as research findings in computational science education, with submissions from both professionals and students. JOCSE utilizes internet technology and a web-based format to allow for enhanced interactivity in all publications.

Subject:
Engineering
Computing and Information
Technology
Education
Mathematics
History, Law, Politics
Provider:
Shodor
Provider Set:
CSERD: Computational Science Education Reference Desk
Author:
The Shodor Education Foundation, Inc.
GalaxSee HPC Module 1: The N-Body Problem, Serial and Parallel Simulation
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This module introduces the N-body problem, which seeks to account for the ...

This module introduces the N-body problem, which seeks to account for the dynamics of systems of multiple interacting objects. Galaxy dynamics serves as the motivating example to introduce a variety of computational methods for simulating change and criteria that can be used to check for model accuracy. Finally, the basic issues and ideas that must be considered when developing a parallel implementation of the simulation are introduced.

Subject:
Computing and Information
Physics
Space Science
Material Type:
Data Set
Lecture Notes
Provider:
Shodor
Provider Set:
CSERD: Computational Science Education Reference Desk
Author:
David Joiner
The Journal of Computational Science Education Volume 2 Issue 1
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The Journal of Computational Science Education (JOCSE) promotes the use of computation ...

The Journal of Computational Science Education (JOCSE) promotes the use of computation in education through disseminating unique uses of computation in the classroom as well as research findings in computational science education, with submissions from both professionals and students. JOCSE utilizes internet technology and a web-based format to allow for enhanced interactivity in all publications.

Subject:
Computing and Information
Education
Provider:
Shodor
Provider Set:
CSERD: Computational Science Education Reference Desk
Author:
The Shodor Education Foundation, Inc.
EngineSim Version 1.6e
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EngineSim is a Java-applet that visually simulates four types of jet propulsion ...

EngineSim is a Java-applet that visually simulates four types of jet propulsion systems. The user can change several parameters and observe the resulting visual feedback and other parameters changing.

Subject:
Computing and Information
Engineering
Physics
Space Science
Provider:
Shodor
Provider Set:
CSERD: Computational Science Education Reference Desk
Author:
Tom Benson, NASA Glenn Learning Technologies Project
2-D Waves Applet
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This java applet is a simulation that demonstrates scalar waves (such as ...

This java applet is a simulation that demonstrates scalar waves (such as sound waves) in two dimensions. It demonstrates the wave principles behind slit diffraction, zone plates, and holograms.

Subject:
Computing and Information
Physics
Provider:
Shodor
Provider Set:
CSERD: Computational Science Education Reference Desk
Author:
none listed
Paul Falstad
Stella2Java
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Stella2java models are java applets created from Stella equation files. In this ...

Stella2java models are java applets created from Stella equation files. In this process, initial conditions and converters of your choice can be replaced with slider bars, and your choice of stocks and converters can be shown in a graph, allowing for a more direct visualization of the result of dynamic models. Converters can be set by either a slider bar, or left as what they are in Stella. Initial conditions can be set by either a slider bar, or left at the Stella value.

Subject:
Computing and Information
Provider:
Shodor
Provider Set:
CSERD: Computational Science Education Reference Desk
Author:
David Joiner
Developed for the Computational Science Educational Reference Desk and the Envinronmental Protection Agency online course OS411 Computational Atmospheric Sciences
The Shodor Education Foundation, Inc.
The Journal of Computational Science Education Volume 3 Issue 2
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The Journal of Computational Science Education (JOCSE) promotes the use of computation ...

The Journal of Computational Science Education (JOCSE) promotes the use of computation in education through disseminating unique uses of computation in the classroom as well as research findings in computational science education, with submissions from both professionals and students. JOCSE utilizes internet technology and a web-based format to allow for enhanced interactivity in all publications.

Subject:
Computing and Information
Engineering
Technology
Education
Mathematics
History, Law, Politics
Provider:
Shodor
Provider Set:
CSERD: Computational Science Education Reference Desk
Author:
The Shodor Education Foundation, Inc.
Transmographer 2
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Build your own polygon and transform it in the Cartesian coordinate system. ...

Build your own polygon and transform it in the Cartesian coordinate system. Experiment with reflections across any line, rotations about any point, and translations in any direction. Parameters: Shape, x or y translation, x or y reflection, angle of rotation

Subject:
Computing and Information
Mathematics
Material Type:
Activity/Lab
Interactive
Lesson Plan
Student Guide
Provider:
NSDL Staff
Shodor
Provider Set:
NSDL Math Common Core
CSERD: Computational Science Education Reference Desk
Virtual Turing Machine 2
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A Turing machine is theoretical computer consisting of a finite set of ...

A Turing machine is theoretical computer consisting of a finite set of internal states, a finite alphabet that includes a blank symbol, and a finite set of instructions. It has a physical head and a physical infinitely long tape, which is divided into cells. The cell values consist of the alphabet. The tape has a finite number of non-blank cells. The head can read and write to the cells and move the tape one cell to the left and one cell to the right. The Virtual Turing Machine lets you input tape values and an instruction set to see the output of a turing machine.

Subject:
Computing and Information
Mathematics
Provider:
Shodor
Provider Set:
CSERD: Computational Science Education Reference Desk
Author:
Paul R. C. Ming