Subject: Annoucement: Concord Modeler v1.0 - Molecular simulation software for education

From: [email-masked]
Date: Wed, 14 Aug 2002 14:07:23 -0400

Dear CCLers,

Molecular simulation methods are useful in solving R&D problems in chemical
and pharmaceutical industries. Techniques like molecular graphics, energy
minimization, Monte Carlo and molecular dynamics have become valuable
tools for materials and drug design.

Surprisingly, these techniques have been found particularly useful in K-12
education
in the US. Being a company pioneering on innovative educational technology, we
have
been developing molecular simulation tools specialized for education, and have
done extensive field tests in schools. Our research results show that kids have
significantly more cognitive gains by learning with interactive molecular models
put in an appropriate pedagogical context, than learning in a more traditional
way
involving use of non-modeling multimedia such as Flash animations.

There is constantly a gap between research and education in the history of
science.
This problem might be much less severe in Aristotle's time than in today, when
the
gap is unprecedentedly enlarging. Molecular simulation turns out to be one of
the few
fields that demonstrate an excellent opportunity to bridge the gap. This will be
a very
attractive research direction, considering the strategic importance of
molecular-level
science to the competitiveness of our future labor forces.

Many of the CCLers will ask the following question: What makes an educational
application different from a research one?

First of all, educational applications require high-level interactivities, which
in the
case of  molecular dynamics simulation are based on real-time computation,
real-time
user manipulation and dynamical visualization. In academic research, this type
of
computing is called interactive molecular simulation by, for example, Prof.
Klaus
Schulten's group. The difference here is that in an educaitonal setting,
everything has
to be done on a single microcomputer, and a user's action on a molecular system
must
be responded as promptly as possible. This requirement typically limits the
number of
atoms in a model to be in the hundreds in a classical molecular dynamics
simulation.

Second, educators always complain that monolithic applications such as the ones
molecular
simulation experts are using ( e.g. Cerius 2  or the lightweight WebLab Viewer,
etc.)
are too complicated to use, and lack the flexibility needed to organize models
in
an educational context (usually a sequence of guided activities with simplified
user
interfaces) and present them in an easy-to-understand form on various platforms.

Funded by the National Science Foundation, we have developed a tool called
Concord Modeler that we are pleased to share here. The Concord Modeler v1.0
can be downloaded at the following URL:

http://workbench.concord.org/modeler/index.html

The features of the Concord Modeler v1.0 are:

1) It is written in 100% Java, hence it runs on different platforms (currently
Red Hat
Linux and Windows OS).

2) It is, and will be, free and open-source, hence you can use the nuts and
bolts in
our API.

3) It is a Web browser which delivers models in XML format, hence it is
content-rich
and virus-proof. Because it is Web-based, your model will be seen and  commented
by visitors. Thus you can collaborate with other people on a simulation project.

4) It is an authoring tool which you can use to write your own curricula with
models
embedded in the context and publish on the Web.

5) You can do atomistic modeling using AMBER/CHARMm-like force fields, and
non-atomistic modeling using generalized Gay-Berne force fields. You can easily
create and manipulate objects. For example, a triatomic molecule can be
constructed
by assigning bond-stretching and angle-bending potentials to the three atoms.
The model
builder allows you to construct systems ranging from Lennard-Jones solids to
liquid
crystals and to polymers.

6) You can do NVE, NVT and NPT, and switch between these protocols.

7) Bond-crossing periodic boundary conditions in one or both directions are
supported.

8) You can exert electromagnetic and gravitational fields. You can use external
fields
to study, for example, electrolysis or ion transport in an electric field.

9) You can create a time series for any property of the model and plot them
instantly
using a graph tool integrated in the Concord Modeler.

10) You can record a simulation and save it as a  movie. The  movie is a
collection
of coordinate, velocity, and higher order time series, a mechanism that allows
you
to track a single object or property when playing back a recorded simulation.

11) You can save the whole simulation and preserve almost all settings, and
restore
them later. This feature is particularly useful when you embed a simulation in a
curriculum.

12) The molecular dynamics simulation engine is controlled by a task manager.
You can add a job to or remove a job from the task pool. This mechanism allows
you to create customized jobs.

...and much more.

Limitations:

1) It is 2D. ---- We have built our own molecular graphics engine using Java3D
and
will incorporate it into the Concord Modeler. In education, 2D models have
been proven very helpful because it shields students from the complexity of
stereo reasoning. What is more, many physical mechanisms can be simulated using
a cartoonized 2D model.

2) It is slow. ---- Yes, when you have a lot of particles. We focus on low-end
uses.

3) It does not do quantum mechanics. ---- Yes. Perhaps the tight-binding
approximation
(TBMD) would be a good solution.

In closing, students of today are scientists of tomorrow. The molecular
simulation and
modeling community will benefit if more of the beauty and power grown in the
field of
computational chemistry can be delivered to kids and deeply appreciated by them.

As the developer, we would greatly appreciate your support and help. Your
comments
and opinions are extremely important to helping us improve this product and
carry out
research in this directioin.

Q. Xie, PhD
The Concord Consortium Inc.
10 Concord Crossing, Suite 300
Concord, MA 01742