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Scientific Computing

New Year's Resolutions
New Year's resolutions for scientific computing.
A (Digital) Letter To Santa
This is a letter to Santa, asking for some scientific computing toys.
Economic Simulation Models
This article discusses the "Lemonade Stand" and "Tradebot" economic models.
The Economy as An Ecosystem
This article discusses some of the philosophy behind the Bionomics approach to economic system modeling.
The Economy as An Ecosystem
This article discusses how the economy may be viewed as an ecosystem.
A Buffet of Scientific Computing
This article offers a sampling of scientific computing web sites.
Environmental Modeling Is Like a Simile
This article descibes the "Simile" environmental simulation software package.
Green Acres with Greenhat
This article describes crop simulation programs available from Greenhat Software.
A Remote Location : Down On The Farm
This article discusses the use of remote sensing in farm modeling.
Surveying The Remote Sensing Webscape
This article presents some web sites with copious information on remote sensing.
Remote Sensing Basics
This article discusses the basic principles of remote sensing.
Waterway Pollution Simulation
This article discusses environmental simulation software developed at McMaster University in Ontario.
Environmental Simulation with ESP
This article discusses ESP, a software product for simulating aqueous systems.
Massively Parallel Ecosystem Simulations
This article discusses a parallel protocol for studying ecosystems.
Ecosystem Simulation in Practice
This article describes a web-based ecosystem simulation software package.
Scientific Computing and Security
This article briefly discusses how high-performance computing may be used in the future in security-enhancing efforts.
More Ecosystem Simulation Models
This article discusses ecosystem simulation methods with particular application to modern life.
Ecosystem Simulation Models
This article discusses some of the models used in the simulation of various ecosystems.
Ecosystem Simulation
This article is an introductory discussion of ecosystem simulation.
Simulation of Collisional and Collisionless Matter
This article discusses methods for combining collisional and collisionless matter simulation.
Methods for Simulating Collisionless Matter
This article discusses numerical methods for simulating systems of collisionless matter.
Methods for Simulating Collisional Matter
This article discusses methods for simulating systems of collisional matter.
Astrophysical Simulation Basics
This article describes the difference between collisional and collisionless matter and begins to discuss numerical methods for studying them.
Simulating Galaxy Cluster Collisions
This article discusses COSMOS, an astronomical simulation code.
Colliding Galaxy Clusters
This article discusses the collision of galaxy clusters.
Networking with Starlink
This article discusses Starlink, a community of astronomers in the UK working to make standardized analysis software available to others.
Finding Tools Of the Trade
This article discusses simulation software packages available from SoftSim.
N-Body Simulation Methods
This article discusses N-body simulation methods.
Analyzing Astronomical Data With AIPS++
This article discusses the AIPS++ software package for analyzing radio telescope data.
Analyzing Astronomical Data Can Drive You (to) AIPS!
This article discusses AIPS, a scientific visualization software package for radio telescopy.
Studying the Planets' Magnetic Fields with MHD
A short discussion of the magnetospheres of planets and their simulation via magnetohydrodynamics.
Codes for MHD Simulation
A quick look at the Zeus suite of MHD simulation codes.
An Aside on MHD
This article is a short introduction to magnetohydrodynamics, a branch of fluid dynamics with wide applicability.
Into the Wild Blue Yonder ...
This article describes some phenomena near black holes that have been the focus of recent simulation studies.
Computer Simulation in Molecular Biomedicine
This article discusses trends in molecular biomedical simulation research.
An Oldie But a Goodie
This piece describes a 1994 proposal for biological simulation.
The BioPSE Project
This article describes some of the features of the biolectric field PSE , BioPSE, developed at the NIH.
Taking a BioPSE of Bioelectric Field Studies
This article describes some problems with simulation in the bioelectric field area and discusses a related Problem Solving Environment from the NIH.
Real-World Biomedical Simulations
This article discusses the work of the "Virtual Reality in Medicine and Biology Group", based at the University of Sheffield in the United Kingdom.
More On DNA Simulation
This article discusses some DNA simulation studies being carried out in Sweden.
Simulating DNA
This article discusses a recent simulation study of DNA.
Molecular Dynamics Simulation of Ionic Channels
This article discusses recent molecular dynamics studies conducted to gain a better understanding of ionic channels in lipid bilayers.
Other Problems in Biological Simulation
This article discusses the study of lipid membranes via computer simulation.
Reviewing Protein Folding
This article reviews simulation work done on the protein folding problem by researchers at Columbia University in New York.
Proteins Behaving Badly
This article discusses protein misfolding, which is at the root of many disabling diseases.
Parallel Protein Folding
This article discusses a recent study which made strides in simulating protein folding.
Simulation Studies of Protein Folding
This article discusses the special challenges presented by studying protein folding via computer simulation.
Quantum Simulation of Alkanes and Proteins
This piece discusses different types of quantum calculations used to study small biological molecules, namely alkanes and proteins.
Simulating Biological Building Blocks
This article discusses simulation methods used in the study of chemical systems with biological importance.
Computer Simulation of Biological Systems
This article represents a starting point for surveying recent efforts in biological simulations.
Extended Collaborative Visualization Models
This article discusses the extended collaborative visualization model developed under the CSCV project at the University of Leeds.
Collaborative Visualization Models
This article discusses the basic models of collaborative visualization.
New Toys for a New Millennium
This article discusses some of Sun's Java innovations that may be used in scientific computing applications in the near future.
The 12 Sites of Christmas
This article contains brief synopses of 12 useful scientific computing links.
Computer Supported Collaborative Visualization
This article discusses the spatial-temporal requirements of scientific visualization and how this problem might be approached.
Collaborative Scientific Visualization
A short discussion of the increasing focus on collaboration in scientific visualization is the purpose of this article
The WBCSim PSE
This article reviews the WBCSim Problem Solving Environment, a product of researchers at the Virginia Polytechnic Institute and State University in Blacksburg, VA
Giving Thanks to the Tech Gods
This article briefly reviews some of the really good things that have happened to scientific computing in the last couple of decades (or so).
The Virtual Handshake
This article discusses the Virtual Collaboratorium (tm) effort at Indiana University, which focuses on enabling geographically distributed collaboration.
Are You Solving Your Problems in the Right Environment?
This article begins a survey of Problem Solving Environment systems with a look at the PSEware project at Indiana University.
Java and PSE's
This article discusses how the use of Java to wrap existing scientific applications has helped lead to the development of Problem Solving Environments.
Using Java to Enhance Your Legacy
This article describes how Java may be used to create a user interface for existing scientific code.
Everything Old Is New Again
This article begins a discussion of how Java may be used to interface with legacy codes.
More on Java-Based Molecular Dynamics
This article reviews the Java-based molecular dynamics codes developed at Boston University's Center for Polymer Studies.
Molecular Modeling ... a Cup of Joe?
This article describes MDModel, one of the earliest Java-based molecular dynamics applications.
Object-Oriented Chemistry
This article describes how object-oriented programming concepts may be applied to computational codes.
OOhh ... It's Java!
This article briefly describes some of the features of the Java programming language.
Object-Oriented Simulation
This article briefly describes some of the advantages of object-oriented program design.
You Can SEE the Results
This article discusses the Solar System Simulator, a project at NASA's Jet Propulsion Laboratory
Where to Learn More
This article reviews a website, maintained at the University of Baltimore by Professor Hossein Arsham, which may prove to be a useful tool for learning about simulation techniques.
Wrapping Up the Planets
This article concludes a several-weeks-long look at an example solar system simulation problem.
What We Get Out, Part 2
This article discusses the techniques used to compute static and dynamic properties from a classical dynamics simulation.
So, What's It Good For, Anyway?
This article begins a discussion of how to obtain meaningful results from a classical simulation.
More on Periodic Boundary Conditions
This article concludes a two-part series about the use of periodic boundary conditions in classical simulations.
Out One Side and In the Other -- Periodic Boundary Conditions
This article begins describing the advantages of employing periodic boundary conditions in classical simulations.
Welcome to the Neighborhood ... Hope You Don't Stay Long
This article describes the basic principles involved in using a neighbor list to reduce computational time in a classical simulation.
Won't You Be My Neighbor?
This article begins a discussion of how the use of neighbor lists can significantly reduce the computational cost of a planetary simulation.
A Compelling Force
This article develops the expressions used to calculate the forces in a planetary system model.
Integrating Newton's Equations
This article describes the requirements for an integration algorithm and the advantages of the Verlet version of the software.
Moving the Planets
This article describes the setup of a model planetary system. It goes on to discuss the equations of motion governing this example system.
Tools of the Trade -- The Planets Problem
This article begins a discussion of the problem of modeling a planetary system as a means of illustrating the basics of scientific simulation.
CML Today, Part 2
This article describes a molecular viewer which supports CML formatting.
CML Today
This article begins to explore the advances made to CML since the specifications were laid out a few years ago. In particular, a CML browser, JUMBO, is reviewed.
The Chemical Markup Language
This article outlines the specifications of the Chemical Markup Language and discusses some of the potential applications of CML as described by its developers.
... And XML Begat CML ...
This article discusses the basic features of XML and its advantages in an information-management setting.
Chemical Information Management with CML
This article talks about some of the frustrations of file format manipulation in computational science and introduces a CML, a possible unifying language.
Medical Imaging with the Pulse-Coupled Neural Network
This piece continues to look at the use of PCNN's in the enhancement of various medical imaging schemes.
(Artificial) Mental Imagery
This article introduces work at the Battelle Memorial Institute in the area of neural networks for medical imaging.
If It Smells Like a Rose ... Maybe You're a Neural Network
The "Electronic Nose" application of artificial neural networks is examined as an introduction to real-world problems being approached in this field.
More on Neural Networks
This article describes the basic form and function of neural networks and briefly touches on the concept of a "percepton."
The Ubiquitous Neural Network
This article begins a discussion about the possible uses of neural networks in scientific simulation work.
Storm Water Management with the SDBay Modeling Project
This piece concludes our look at the San Diego Bay modeling project by examining its Storm Water Management Model.
Back to the Bay
This article continues the discussion of the San Diego Bay ecological modeling project with a look at the three-dimensional hydrodynamic model being used in the work.
Irish Eyes Are Smiling Over Green Computing
This article examines the San Diego Bay Modeling project, which employs state of the art ecological simulation methods to study the water in and around the San Diego Bay.
SDSC : A Pearl in the Cyber Ocean
This article discusses the San Diego Supercomputer Center.
Necessary Tools for Successful SBA
This article describes the hardware setup of the new SIMAF facility at Wright-Patterson Air Force Base in Dayton, OH.
The Computer Hangar
This article begins to examine the Simulation and Analysis Facility recently completed at Wright-Patterson Air Force Base in Dayton, OH.
Maybe You CAN Be Two Places at Once
This article discusses the ambitious Tele-Immersion project being undertaken within Internet2 efforts.
Information Control on the Internet2
This article describes the ongoing efforts in the Internet2 project to increase internet bandwidth in an attempt to enhance performance and capabilities.
Teaching on the Internet2
This article discusses the distributed education standards and utilities being developed under the auspices of the Internet2 project.
Will You Be Part of the Internet2, Too?
This article begins a discussion of Internet2, a network aimed at the development of new networking technologies.
Keep a Clear Head with ClearCase
This article describes the use of the ClearCase software configuration management tool.
Shelf-Control : How to Manage Those Development Projects
This article begins to look at the use of configuration management tools in scientific software development environments.
Didn't You Used to Be ... ?
This piece covers the recent developments at Chemical Abstract Services in the area of information dissemination.
All I Wanted for Christmas Was an Abacus
This article describes the readiness of the scientific computing community as the Year 2000 descends upon us.
Yesterday's Christmas Tree
This is just a light-hearted piece dealing with some of the hassles of programming in the yesteryear.
A Cycle is a Terrible Thing to Waste
This article details Globus, a project at Argonne National Labs which strives to develop the technology to take advantage of geographically-distributed computer resources.
Stuck in the Middle with You
This article describes the goals and structure of a middleware product, WebFlow
Web-Based High Performance Computing
This article talks about the need for web-based access to high-performance computing resources and the components which comprise such a scheme.
Mining Plastic
This article describes one effort to use modeling and data mining for composite materials candidate indentification and screening.
Rocketing into the New Millenium On the Nanotube
This article examines a simulation study of carbon nanotubes conducted by NASA physicists.
Soccer Balls and Bucky Tubes
This article briefly describes how carbon nanotubes have evolved as candidates for some of the most exciting materials applications being considered today. As well, a brief introduction into modeling efforts in this area is given.
Nano-nano : Simulation at the Microscopic Level and Smaller
This article discusses the overall trend toward miniaturization and how computational techniques are playing a role in this development.
Guns and Ammo : Real-World Impact of Computational Chemistry
This article describes the efforts and successes of a group of computational chemists in studying the problem of erosion in rifle-barrel erosion for the U.S. Army.
Real-World Contributions from Scientific Computing
This article serves as an introduction to a series of pieces that will document some of the accomplishments in scientific computing.
The Changing Face of Scientific Communication
This article describes how web publishing has revolutionized information dissemination in scientific fields in the last few years.
Oh say can you C?
This article describes some of the features of the C and C++ languages that make them attractive to scientific researchers.
How to Avoid Spaghetti Code
This article describes how code with jumbled logical control can come into being and how to avoid it.
Fortran in the Next Century
This article describes factors that led to fortran's prominence in the scientific community.
What Language Do YOU Speak?
This piece provides a short survey of the programming languages most prevalent in scientific computing.
Security and Science -- Research Under Wraps
This article describes some of the security measures in use today as scientists seek to protect their work from would-be information thieves.
Integrated Applications in Scientific Computing
This article describes how one company, MSI, has developed a chemistry simulation package that incorporates many of the important technologies available in scientific computing today.
The Use of the World Wide Web in Scientific Computing
This article describes some of the areas in scientific computing in which the internet is having the biggest impact.
Linux - Potential Applications
This article looks at a couple of potential applications for the Linux operating system.
Linux - Coupling Flexibility and Cost-Control
This article continues the series of pieces looking at operating systems for use by computational scientists and begins to look at how Linux is making waves in the industry.
Unix - Putting Scientists in Control
This article takes a look at the Unix operating system, and how it can provide control to the computational scientist.
Is Windows a Suitable Computing Environment for Scientists?
This article discusses the pros and cons of Windows™ as an operating system for scientific computing.
Operating Systems -- Looking out the Windows
This article begins to explore the operating system needs present in scientific computing.
"Poor Man's Supercomputer" -- The Buffalo Project
This article provides a specific example of workstation clustering.
Clustered Workstations : Block-by-Block Supercomputers
This article describes the concept of workstation clustering to mimick a supercomputer.
Supercomputer Centers : High Performance for the Average Joe
This article describes the general structure of supercomputer centers and gives a specific example.
Scientific Visualization - Taming the masses
This article deals with specific types of scientific visualization packages available to chemistry researchers.
The Cryogenic Challenge : A "Real-Life" Parallel Application
This article describes how one chemistry research project was rescued from the ages by parallel computing.
Chemistry in the Fast Lane
This piece describes, in general terms, one of the more common applications of parallel computing techniques to chemistry simulation research. In addition, several URL's are provided which include vivid examples of the power of parallelism for computational chemists.
A Parallel Universe
This article provides an introduction to the world of parallel computing as a lead-in to applications to computational chemistry.
Computational Chemistry - Electrons to Airplanes
This article describes the basic types of calculations performed in the study of chemistry and briefly mentions the types of problems suitable to each.
Computer Simulation : Meat and Potatoes of Scientific Computing
This article looks at the basic premises of scientific computer simulation and discusses applications in biology and chemistry as example cases.
The Categorization of Scientific Computing
This article outlines the categories most prevalent in Scientific Computing and provides a descriptive definition for each. It is these categories that will form the basis for future work.
Scientific Computing : Catalyst for Technology Explosion
This piece is a short introduction to scientific computing. It asserts that the use of computers are helping to fuel greater scientific discovery, and it outlines the works to come.