Demonstrations Submitted:



Brian Coppola:

Beneath the Surface of the Chemical Article. First-Year Students use Technological Tools to Unpack the Original Literature. Beginning in 1996, a number of term-long projects were interwoven with the Structured Study Group program, in which first-year chemistry students earn honors credit. In one project, all of the students contribute to the construction of a written and HTML literature-driven resource on which their final examination is based. Ultimately, the multimedia text is fully owned by the students in the course, and they must seek out each other's expertise in order to examine their understanding.
 http://www.umich.edu/~chemh215

Peter Garik:

Quantum Explorer

The Quantum Explorer programs are intended to provide students with a first introduction to the way that molecules are built from atoms. The programs are in 2d and 3d and extend from models of atomic structure, to diatomic atoms, and finally to representations of polyatomic molecules. Requirements: I will bring to the meeting a program that we have developed. I can run it either on my laptop, or install it on another machine (requires NT or Windows 2000).

John Gelder:

A Web-based Molecular Level Inquiry Laboratory Activity This talk will present a new computer-based atomic level simulation of an ideal gas. The simulation is written in JAVA and is accessed by students through a web browser. This software is used in conjunction with a laboratory experiment write-up developed within the framework of an inquiry instructional strategy. This molecular level laboratory experiment is used in combination with a parallel macroscopic laboratory experiment.
We hypothesize that students exposed to these kinds of parallel activities will be better able to link their macroscopic, microscopic, and symbolic understanding of chemical concepts. Features of the software will be demonstrated and sample student responses will be discussed.

Eric Jakobbson:

Using Molecular Visualization to Demonstrate Principles of Protein Structure and conservation of Essential Function during Evolution. This demonstration will utilize a bioinformatics tool (the Biology Workbench) and a molecular visualization tool (Protein Explorer). The Workbench will be used to align sequences of homologous proteins from widely different organisms and Protein Explorer will be used to transform those alignments into 3-dimensional structural representations that illustrate functional conservation and principles of protein folding.

Bruce Koel:

Lessons Learned from the Consortium for Technology in Teaching Chemistry, (CTTC) Program at USC

The CTTC was started last year to establish a consortium for Southern California teachers and institutions who are interested in implementing computer technologies in their high school science classrooms, in order to pool resources, share ideas, develop strategies, and provide continuing education. I will report on some of the results of these interactions and workshops held at USC. I will also briefly mention how atomistic and molecular imaging using STM and AFM might be used to visualize chemistry and materials.

Bob Kozma:

ChemSense

ChemSense is a software environment that provides students with a variety of representational tools and resources that they can use to express their understanding of chemical phenomena. These tools allow students to create a variety of representations and use them in a community of learners to make predictions and explain the results of their laboratory investigations. These representations are both student-generated (e.g., molecular diagrams and animations) and generated by probes connected to student experiments (e.g., tabular data and real time graphs). Students work in a networked environment to comment and build on each other's work. I will demonstrate the tools and show examples of how these were used by chemistry students at both the high school and university levels.

Jeffry Madura:

Chemical Computing Groups software MOE and Proteins: Structure, Function and Dynamics CD

Peter Mahaffy:

Visualizing chemistry for majors and non-majors through molecular modeling. At The King's University College, chemistry students are introduced in their first year to HyperChem 5.1, a comprehensive PC-based molecular modeling software package. Molecular modeling is then used across the chemistry curriculum to visualize three- dimensional structures, understand molecular geometry and properties, visualize molecular orbitals and bonding, carry out thermodynamic calculations and conformational analysis, understand electronic and vibrational spectroscopy, and visualize simple reactions with molecular dynamics.

This demonstration will focus on integrated strategies, where molecular modeling is used along with experimental findings in investigative projects. Examples of models and animations used in non-majors chemistry, introductory chemistry, organic chemistry, environmental chemistry and spectroscopy will be available.

Neil Ostlund:

Palm, Pocket, and Handheld Devices for Molecular Modeling

Barry Rowe:

ChemViz -- A free WWW-based resource for high school teachers and students NCSA ChemViz has been available for over eight years to high school students and teachers, allowing them to explore more sophisticated models for atoms and molecules. Our goal has been to provide powerful computational opportunities so that students can use the same type of tools that working scientists use to visualize difficult atomic and molecular models.

Bob Tinker and Qian Xie:

Oslet

Oslet is the molecular simulation software being developed at the Concord Consortium since April 2000. Oslet can be used to build arbitrary 2D (for the time being) atomic- scale models ranging from gas, solids, surfaces, molecules to polymers, micelles and bilayers, run them using molecular dynamics engines, and analyze the results.

Oslet demonstrates its capability in explaining phenonmena like gas laws, osmosis, evaporation, condensation, melting, pressure-induced phase transformation, diffusion, polymerization, crystallization, clusterization, phase separation, thermal expansion, grain boundary, formation of molecular crystals, formation of ionic crystals, surface chemiadsorption, (off-lattice)protein folding, shock waves, bilayer lipid formation, and so on and so forth.

Oslet differs from some existing molecular dynamics software in the fact that it can not only do particle dynamics (typically with the Lennard-Jones potentials), but also build any kind of 2D molecular structure and investigate its dynamical behaviors. On the other hand, it differs from conventional chemistry visualization tools like Rasmol in the fact that it is being designed into a tool that as we hope will be used to study live molecules instead of exhibitions of static structures.

By using Oslet, the user can do molecular dynamics simulations under a variety of conditions, for instance, you can do NVE, NVT, NPT simulations, therefore theoretically you can draw a phase diagram; you can choose reflectory boundary conditions or periodic boundary conditions (the latter is useful in crystal simulations, when you deal with larger molecules or polymers, the former is always used)......

Oslet has powerful modelling environment with which the user can create/edit a structure. It enables the user to build molecules from scratch, i.e. building covalent bonds (radial and angular) out of a group of atoms, merge molecules such as building peptide bonds, delete anything you need to get rid of, translate/rotate/mutate molecules, drop atoms or molecules such as benzene into the simulation box, change temperature, change simulation time, adjust frames per second for animation, etc.. It is noteworthy that all the modelling actions are looked after by an undo/redo manager in order to allow the user to make mistakes, and any model created taken care by an energy minimization procedure in order to remove bad van der Waals contacts before it is actually executed by the molecular dynamics engines.

Oslet has a set of analysis tools with which the user can just-in-time analyze the on- screen structure. For instance, the user can plot an equipotential contour map and its companion, the so-called gradient vector paths, as well as the electron density map. An interesting thing is that using Oslet the user can reproduce the Boltzman-Maxwell velocities distribution in a 100% interactive way. While the design allows the user to prove that this theorem works no matter how complicated the force field is, it also enables the user to understand important concepts in statistical mechanics such as the ergodicity assumption and the Gibbs postulate, if he or she can.

Oslet has an energy landscape explorer under construction which enables the user to explore the potential energy surface so as to identify the saddle points, minima and the reaction paths between reactant and product.

Oslet has a fully functioning trajectory recorder/player that enables the user to save a simulation and play back with faster speed for demos or teaching. Any model created by Oslet can be exported in the Concord Molecular Modelling Language(CMML) format. The CMML is being designed as an analogue to markup languages (like XML) which encapsulates a Molecular Simulation Object (MSO). The MSO is a concept that we introduce to define a simulation that would be understood by the molecular dynamics engines, such that once loaded would spontaneously unfold the encapsulated model.

Olset employs robots to execute automated demos or carry out virtual instructions on how to use it and what it means scientifically.

The designer has some experience with Molecular Simulation Inc's mainstream product, the Cerius 2 platform. Oslet has used, actually, the most sophisticated and established force field (or Hamiltonian if this term is familiar to you). It uses similiar Hamiltonian with CHARMm and AMBER's, and is as a matter of fact sightly more verbose, because three-body non-bonded interactions can be optionally taken into account. Despite of this fact, everything can be done by just clicking, pulling sliders, drag-and-dropping. No numerical input or editing is needed at all.

Oslet is 100% pure-java, and therefore, cross-platform.

Oslet is still under development. We are currently working on the Corner type potentials like the popular Gay-Berne potential, among others.

The last thing, we believe that 2D models have particular educational value, because they are easier to manipulate with, and perfect for prototyping, and sometimes have profound scientific meanings as well. Nevertheless, we hope we would be able to come up with our 3D MSO before funding is terminated.

Bill Vining:

Interaction and Assignability

I will demonstrate software that shows a method for engaging students in their work with animations of molecular reaction mechanisms, moving toward a student-active approach to visualization. A minor point of this demonstration will touch on the use of letter-line drawings instead of 3D models as tools for following electron flow in organic mechanisms. I will also demonstrate the UMass OWL system, a web-based homework and tutoring system which we are in the process of extending for use with molecular models.

John Wintersteen:

MSI's ViewerPro - Integrated Molecular Visualization As the wealth of molecular information existing in public and private databases, or derived from tools based on new technologies continues to grow, the need to see and integrate results is now more important than ever. This demonstration will show how MSI's ViewerPro facilitates understanding through effective visual representation, and provides tools for integrating chemistry on the PC.


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