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Issues in Ecology, Issue 08: Effects of Aquaculture on World Fish Supply
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This report discusses the negative and positive aspects of aquaculture as an ...

This report discusses the negative and positive aspects of aquaculture as an alternative to harvesting wild stocks of fish. The report defines aquaculture and describes its recent growth, as well as its ecological impact. Practices to sustain aquaculture operations, such as habitat modification and the use of wild-caught seedstock are discussed. Changes to ocean food webs, the introduction of non-native fish and pathogens, and nutrient pollution from wastes are presented as negative consequences of aquaculture operations. The report discusses strategies to improve aquaculture, such as reducing fish meal and oil in fish feed, integrating production systems, and promoting sustainability within the industry. Issues in Ecology is an ongoing series of reports designed to present major ecological issues in an easy-to-read manner. This Issue summarizes the consensus of a panel of scientific experts based on the information that was current and available at the time of its publication in 2001.

Subject:
Computing and Information
Life Science
Ecology
Forestry and Agriculture
Material Type:
Reading
Provider:
BiosciEdNet (BEN): Digital Library Portal for Teaching and Learning in the Biological Sciences
Provider Set:
BiosciEdNet (BEN): Digital Library Portal for Teaching and Learning in the Biological Sciences
Author:
Rosamond Naylor
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
EJS CSM Textbook Chapter 1: Introduction to modeling
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We introduce the <i>Easy Java Simulations</i> (EJS) edition of <i>An Introduction to ...

We introduce the <i>Easy Java Simulations</i> (EJS) edition of <i>An Introduction to Computer Simulation Methods</i> and discuss the importance of computers in physics and the nature of computer simulation. Various computer languages are considered and we show how the EJS modeling and authoring tool allows us to separate the model into logical parts and to separate the model from the view. Students learn the logic of computer modeling using loops and control structures as they study algorithms used in professional practice. Students are also introduced to object-oriented programming concepts by using object properties and methods when they create user interfaces. However, little user-interface coding is required because the user interface is created automatically by EJS. <i>Easy Java Simulations</i> is built using the <a href="http://www.compadre.org/osp/">Open Source Physics</a> code library and produces XML-based source code. The use of XML is important because it enables users to describe and store the model at a high level of abstraction, thereby leaving the Java implementation to EJS. A tutorial at the end of Chapter 1 describes this process.

Subject:
Computing and Information
Physics
Material Type:
Textbook
Provider:
ComPADRE Digital Library
Provider Set:
ComPADRE: Resources for Physics and Astronomy Education
Author:
Wolfgang Christian
Synaptic Plasticity (1)
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Professor Tom O'Dell discusses synaptic plasticity - the strengthening and weakening of ...

Professor Tom O'Dell discusses synaptic plasticity - the strengthening and weakening of synaptic connections between neurons.

Subject:
Engineering
Computing and Information
Life Science
Chemistry
Physics
Material Type:
Lecture
Provider:
BiosciEdNet (BEN): Digital Library Portal for Teaching and Learning in the Biological Sciences
Provider Set:
BiosciEdNet (BEN): Digital Library Portal for Teaching and Learning in the Biological Sciences
Author:
Amy Nisselle REV
Caren Gough TITLE
Danielle Sixsmith NOTE;ENCODING=QUOTED-PRINTABLE
David Micklos (Cold Spring Harbor Laboratory;DNA Learning Center X-AUDIENCE)
John Connolly (Cold Spring Harbor Laboratory;DNA Learning Center X-AUDIENCE)
Laura Maitland (Mepham High School TITLE)
Mary Colvard TITLE
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
Point Charge Forces in 1D Model
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The Point Charge Forces in One-Dimension model investigates the electric force that ...

The Point Charge Forces in One-Dimension model investigates the electric force that one charged particle exerts on another. The electric force is shown in three ways. First, particle 2 can be dragged left or right to sample the force at various locations - the force on each particle is shown with an arrow. Second, the numerical value of each force is shown in the table at the bottom. Third, you can check the box at the top of the menu to plot a graph of the electric force as a function of position. For the graph (and the numerical values), we define positive force as a force pointing to the right, and negative force as a force pointing to the left. The Point Charge Forces in One-Dimension was created using the Easy Java Simulations (EJS) modeling tool. It is distributed as a ready-to-run (compiled) Java archive. Double clicking the ejs_bu_Point_Charge_Force_1D.jar file will run the program if Java is installed.

Subject:
Computing and Information
Education
Physics
Material Type:
Full Course
Interactive
Provider:
ComPADRE Digital Library
Provider Set:
ComPADRE: Resources for Physics and Astronomy Education
Author:
Andrew Duffy
Point Charge Electric Field in 1D Model
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The Point Charge Electric Field in 1D model investigates the electric field ...

The Point Charge Electric Field in 1D model investigates the electric field at various positions along a line, when there are either one or two charged particles on that line. The electric field is represented in two ways. First, there is a movable positive test charge that you can move along the line to sample the field at various locations - the direction of the force on that test charge is the same as the direction of the electric force on the test charge. The second way to represent the electric field is to plot a graph of the electric field as a function of position. For the graph, we define positive field as a field pointing to the right, and negative field as a field pointing to the left.

Subject:
Computing and Information
Physics
Material Type:
Full Course
Interactive
Provider:
ComPADRE Digital Library
Provider Set:
ComPADRE: Resources for Physics and Astronomy Education
Author:
Andrew Duffy
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:
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.
Ejs Intro 1D Motion Lab Model
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The Introductory Physics 1D Motion Lab asks students to develop a computer ...

The Introductory Physics 1D Motion Lab asks students to develop a computer model for a ball moving vertically under the influence of gravity. When the file is opened, it is initially programmed with a mass moving at constant velocity. It is assumed that students have first collected data of a basketball or volleyball bouncing under a motion detector. The lab instructions fully explain how to build the computer model using Easy Java Simulations modeling tool. The students will learn how to modify the model to simulate a bouncing ball, define variables, calculate relationships, and change the properties for plotting the graph. The calculus is done for the student. <i>Editor's Note: The Easy Java Simulation tool greatly reduces the amount of programming required to develop computer models. Exercises in student-generated modeling are becoming much more widespread in physics education because of the opportunities for students to test and apply their own prototypes to explain and predict physical phenomena.</i> This resource is distributed as a ready-to-run (compiled) Java archive. In order to modify the simulation (and see how it is designed), users must install the <i>Easy Java Simulations Modeling and Authoring Tool</i>. <b>SEE RELATED MATERIALS</b> for a link to install the EJS modeling tool.

Subject:
Computing and Information
Technology
Education
Physics
Material Type:
Activity/Lab
Full Course
Interactive
Provider:
ComPADRE Digital Library
Provider Set:
ComPADRE Classroom-Ready Resources
ComPADRE: Resources for Physics and Astronomy Education
Author:
Anne Cox
Mario Belloni
National Science Foundation
Wolfgang Christian
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.
Random Walk 1D Continuous Model
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The EJS Random Walk 1D Continuous Model simulates a 1-D random walk ...

The EJS Random Walk 1D Continuous Model simulates a 1-D random walk with a variable step size. You can change the number of walkers and probability of going right and left. You can modify this simulation if you have Ejs installed by right-clicking within the plot and selecting “Open Ejs Model” from the pop-up menu item. The Random Walk 1D Continuous Model was created using the Easy Java Simulations (Ejs) modeling tool. It is distributed as a ready-to-run (compiled) Java archive. Double clicking the ejs_stp_RandomWalk1D.jar file will run the program if Java is installed. Ejs is a part of the Open Source Physics Project and is designed to make it easier to access, modify, and generate computer models. Additional Ejs models are available. They can be found by searching ComPADRE for Open Source Physics, OSP, or Ejs.

Subject:
Computing and Information
Mathematics
Physics
Material Type:
Activity/Lab
Provider:
ComPADRE Digital Library
Provider Set:
ComPADRE: Resources for Physics and Astronomy Education
Author:
Wolfgang Christian
Atlas of Science Literacy, Volumes 1 and 2
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Atlas of Science Literacy is a two-volume collection of conceptual strand maps--and ...

Atlas of Science Literacy is a two-volume collection of conceptual strand maps--and commentary on those maps--that show how students' understanding of the ideas and skills that lead to literacy in science, mathematics, and technology might develop from kindergarten through 12th grade.Atlas is part of a coordinated set of tools developed by Project 2061 to help educators understand and use specific goals for student learning. The maps in Atlas are built from the K-12 learning goals presented in Project 2061's Benchmarks for Science Literacy. Benchmarks was derived from the recommendations for adult science literacy proposed in Project 2061's landmark report Science for All Americans.

Subject:
Computing and Information
Education
Material Type:
Diagram/Illustration
Lecture Notes
Provider:
BiosciEdNet (BEN): Digital Library Portal for Teaching and Learning in the Biological Sciences
Provider Set:
BiosciEdNet (BEN): Digital Library Portal for Teaching and Learning in the Biological Sciences
Author:
AAAS, Project 2061 (;)
Gases : OzoneMolcsFromppm (10 Variations)
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Although ozone is an important component of the upper atmosphere, long-term exposure ...

Although ozone is an important component of the upper atmosphere, long-term exposure to ozone in the air we breathe can cause inflammation of the lung, impairment of lung defense mechanisms, and irreversible changes in lung structure. The EPA has set an 8 hour limit for ozone of 0.08 ppm as an air quality standard for cities. At the EPA limit, how many ozone molecules are present in 5.0 liters of air at 25 o C and 0.967 atm? (Hint: assume that air is an ideal gas and calculate the total number of molecules there are in 5.0 L. Then use the definition of ppm.)

Subject:
Computing and Information
Education
Chemistry
Physics
Material Type:
Assessment
Provider:
Chemical Education Digital Library
Provider Set:
Chemical Education Digital Library (ChemEd DL)
Author:
Chemical Education Digital Library
Matter_and_Measurement : ConvertUnits (10 Variations)
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Your textbook is approximately 8.75 inches by 10.25 inches. What are these ...

Your textbook is approximately 8.75 inches by 10.25 inches. What are these measurements in centimeters?

Subject:
Computing and Information
Education
Mathematics
Chemistry
Material Type:
Assessment
Provider:
Chemical Education Digital Library
Provider Set:
Chemical Education Digital Library (ChemEd DL)
Author:
Chemical Education Digital Library