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Molecular Workbench: An Interface to the Molecular World
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You can download most materials at once to accelerate online browsing and enable offline browsing, using the "Option>Prefetch to Cache" menu. After you have prefetched them, you do not need an Internet connection in order to use asdfthis program --- simply select "File>Work Offline" and the software will not check updates if it finds a cached version. If the last time you prefetched is a long time agoasdfafs we also suggest that you prefetch again, as we keep adding and updating stuff. If you expect to have very bad connection or no connection at all in the classroom, or prefer using the software on a CD, you may request a free CD.
This program delivers visual, interactive molecular simulations that are specifically designed for science education. In addition to many existing simulations and materials offered at this site, which you may choose to use as they are, the software also gives you the entire power to make new ones. Technology-savvy users may find it useful in designing interactive computational experiments for studying abstract concepts in physics, cdasdfasdfasfdhemistry and biology. Educational researchers may be interested in a built-in system of embedded assessment for studying the effectiveness of using models and simulations to teach science. A rich set of useful tools is seamlessly integrated into a versatile, easy-to-use authoring environment (former Program Officer Liz Dorland at the National Science Foundation called it Word for Molecules!). With such a flexible system, you can create your own simulation-based lessons, set up your own assessment freely, and collect and analyze student data on your own. If your interest is beyond molecular modeling, this extensible system also allows you to write a Java plug-in that can leverage many services it provides as a platform.
An online User's Manual with several hundred pages and numerous working examples is provided. Hundreds of pre-made models and model-based activities, which can be opened in exactly the same way as a web page is opened with a browser, are freely available for you to use or adapt. The model-builders (2D and 3D) can also be set up to be used directly by students to do hands-on virtual experiments to test different "what-if" scenarios.
This free, open-source software is based upon work supported by the National Science Foundation under grant numbers REC-9980620, ESI-0242701 and EIA-0219345. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
The content created using this program and published in the concord.org domain is licensed under Creative Commons Attribution-NonCommercial-ShareAlike 2.0, which is detached from the GPL license of the software.
Three-dimensional rendering is powered by the Jmol Graphics Library developed by the Jmol Development Team. Mathematical expression evaluation is powered by the JEP Parser developed by Singular Systems.
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Selected models and simulations
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<font size="2"><b>Molecular Rover:</b></font> <font size="2"><a href="student/fly/index.cml">Tour
inside molecules</a></font><br><font size="2"><b>ZoomIt:</b></font> <font size="2" face="Verdana"><a href="part2/ZoomIt/main.cml">Up
and down the scale</a></font><br><font size="2"><b>Interactive Essays:</b></font>
<font size="2" face="Verdana"><a href="student/fluid/pressureconveyance1.cml">Fluid
mechanics</a></font><br><font size="2"><b>Self-Running Demos:</b></font> <font size="2" face="Verdana"><a href="tutorial/BuildMolecule.cml">Make
molecules</a></font><br><font size="2"><b>Analysis Tools:</b></font> <font size="2" face="Verdana"><a href="tutorial/script_mvd.cml">Speed
distribution analysis</a></font><br><font size="2"><b>Tree of Life:</b></font>
<font size="2" face="Verdana"><a href="part2/TreeOfLife/treeoflife1.cml">Exploring
macromolecules</a></font><br><font size="2"><a href="part1/facs/facsIndex.cml">Fluorescence
Activated Cell Sorting </a></font><img src="New.gif"><font size="2"><br><a href="student/classic/machine/suspensionbridge.cml">Suspension
bridge</a></font><img src="New.gif"><font size="2"><br><a href="student/motionandforce/sticky.cml">Shapes
and charges</a><br><a href="student/fly/hemoglobin2.cml">Exploring
hemoglobin</a><br><a href="student/organic/ethane.cml">Stereochemistry:
ethane</a><br><a href="student/fly/diffgear2.cml">Navigating in a nano gear</a><br><a href="student/fly/benzeneorbitals.cml">Touring
molecular orbitals</a><br><a href="student/fly/ghg.cml">Greenhouse gases</a><br><a href="student/fly/gas2.cml">An
atom's perspective of gas dynamics</a><br><a href="student/nano/nanocar2.cml">Nano
car </a><br><a href="student/nano/waterrace.cml">Water race in nanotubes</a><br><a href="student/organic/threebenzene.cml">Benzene
tango</a><br><a href="student/motionandforce/debyesphere.cml">Debye sphere</a><br><a href="student/stateofmatter/latentheat2.cml">Heat
capacity and latent heat</a><br><a href="student/reverseosmosis/reverse.cml">Desalination:
reverse osmosis</a><br><a href="student/nano/planetarygear.cml">Molecular
planetary gears</a><br><a href="student/nano/conveyor.cml">Nano conveyor
belt</a><br><a href="part1/polymer/polymersPage1.cml">Polymerization</a><br><a href="student/fluid/pascal.cml">Hydraulic
lever</a><br><a href="student/nano/alcvd.cml">Atomic layer chemical vapor
deposition</a><br></font><font size="2" face="Verdana"><a href="part1/xray/intro.cml">X-ray
crystallography</a></font><font size="2"><br><a href="part1/eric/selfassembly/self_assembly1.cml">Self
assembly</a><br><a href="student/classic/machine/SliderCrank.cml">Slider-crank</a><br><a href="student/electrostatics/twocharges.cml">Visualizing
electric fields</a><br><a href="part1/elisa/elisa1.cml">ELISA</a><br><a href="part1/dna2protein/DNAtoProteins1.cml">DNA
to proteins</a><br><a href="part1/dan/dnahybrid/intro.cml">DNA
hybridization</a><br><a href="part1/dan/brownian/newBrownianPage1.cml">Brownian
motion</a><br><a href="student/chemicalreaction/equilibrium.cml">Chemical
equilibria</a><br><a href="student/chemicalreaction/catalysis1.cml">Homogenous
catalysis</a><br><a href="student/nano/dock.cml">Docking</a> </font>
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<font size="3">Click the above links to enter.</font>
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org.concord.modeler.text.LineIcon444002210<html><font face="Verdana" size="2" color="#666666"><center>© 2004-2007. Concord Consortium, Inc., Concord, Massachusetts, USA.<br> <a href="http://www.concord.org">http://www.concord.org</a></center></font></html>-f37c02020
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