Posts Tagged ‘next-generation-MW’

Modeling Physical Behavior with an Atomic Engine

May 13th, 2013 by Sara Remsen

Our Next-Generation Molecular Workbench (MW) software usually models molecular dynamics—from states of matter and phase changes to diffusion and gas laws. Recently, we adapted the Molecular Dynamics 2D engine to model macroscale physics mechanics as well, including pendulums and springs.

In order to scale up the models from microscopic to macroscopic, we employ specific unit-scaling conventions. The Next-Generation Molecular Workbench (MW) engine simulates molecular behavior by treating atoms as particles that obey Newton’s laws. For example, the bond between two atoms is treated as a spring that obeys Hooke’s law, and electrostatic interactions between charged ions follow Coulomb’s Law.

Dipole-dipole interactions simulated using Coulomb’s Law.

At the microscale, the Next-Generation MW engine calculates the forces between molecules or atoms using atomic mass units (amu), nanometers (10−9 meters) and femtoseconds (10-15 seconds), and depicts their motion. To simulate macroscopic particles that follow the same laws, we can imagine them as microscopic particles with masses in amu, distance in nanometers, and timescales measured in femtoseconds. Once the Next-Generation MW engine calculates the movement of these atomic-scale particles, we simply multiply the length, mass and time units by the correct scaling factors. This motion satisfies the same physical laws as the atomic motion but is now measured in meters, kilograms and seconds.

In the pendulum simulation below, the Next-Generation MW engine models the behavior of a pendulum by treating it as two atoms connected by a very stiff bond with a very long equilibrium length. The topmost atom is restrained to become a “pivot” while the bottom atom “swings” because of the stiff bond. Once the engine has calculated the force using the atomic-scale units, it converts the mass, velocity and acceleration to the appropriate units for large, physical objects like the pendulum.

Large-scale physical behavior simulated with a molecular dynamics engine.

In order to appropriately model the physical behavior of a pendulum or a spring, we use specific scaling constants. Independent scaling constants for mass, distance and time enable us to convert nanometers to meters, atomic mass units to kilograms and femtoseconds to model seconds. Using the same scaling constants, we can derive other physical conversions, such as elementary charge unit to Coulomb. In order to make one model second pass for every real second, we adjusted the amount of model time between each page refresh. We also chose to simulate a gravitation field—a feature usually absent in molecular dynamics simulators—because it is relevant to macroscopic phenomena.

From microscale to macroscale, the Next-Generation Molecular Workbench engine is a powerful modeling tool that we can use to simulate a wide variety of biological, chemical, and physical phenomena.  Find more simulations at

Exhibit Booth at BCCE Conference and free MW buttons

August 10th, 2012 by Dan Damelin

Just got back from the Biennial Conference on Chemical Education (BCCE 2012), where I participated in a symposium titled “Web-Based Resources for Chemical Education.” About 60 people attended to learn about Molecular Workbench and other online tools and resources. One of the audience questions was about future availability of Molecular Workbench on the iPad and other tablets. Our latest work on the HTML5/JavaScript next-generation MW project, generously funded by, will address exactly this. We’ll be bringing much of the Java-based Classic MW to the browser, so that any device running a modern Web browser will be able to run our newest interactives and activities.

I didn’t get to attend many of the other sessions at BCCE because much of my time was spent staffing Concord Consortium’s exhibit booth to disseminate our free software. Jeanne Hurtz and I spoke with hundreds of people who stopped by our booth to hear about the current MW capabilities and see a next-generation MW model running on a tablet. We gave away about 350 MW buttons, but have a few left. If you’d like one of your own, please stop by our office at 25 Love Lane in Concord, MA, to pick one up!

It was great to share the excitement of MW’s potential and versatility with so many new people. We heard from many (surprised) guests at our booth: “This is free?”  Yes! And so is the button.

Embedding Next-Generation Molecular Workbench

June 7th, 2012 by Dan Barstow

The next-generation Molecular Workbench has a fundamental feature that is both simple and profound: MW models will be embeddable directly in Web pages. This simple statement means that anyone will be able to integrate these scientifically accurate models into their own work—without having to launch a separate application. Teachers will embed MW models and activities into their own Web pages. Textbook publishers will embed them in new e-books.  There is much room for creativity and partnerships here.

The significance of this advance struck me at a recent conference on educational technology sponsored by the Software & Information Industry Association. Many creative people and companies attended, from large publishers to innovative startups. Throughout the presentations and conversations, I envisioned ways these potential partners might use MW to enhance their products and services.

Ron Dunn, CEO of Cengage, gave a keynote describing their new digital textbooks and aligned homework helpers and other digital resources. He pointed out that 35% of their sales are “digitally driven,” and that technology is essential to their future. Other major publishers echoed those messages. When publishers embed Molecular Workbench models and activities throughout their e-books as a consistent modeling environment, students will be able to investigate fundamental principles of chemistry, physics and biology more deeply than the simple animations and videos now so typical in e-books.

SmartScience is a startup, developing supplemental science education activities. Their idea to link videos of science phenomena with corresponding graphing tools is clever. For example, in a time-lapse video of rising and falling tides, students mark the ocean height and automatically see their data in a graph in order to understand both the scientific phenomena and the graph output. Augmenting reality is great, and we love the idea of integrating videos of physical, chemical and biological processes at the macroscopic scale with MW models to show what happens at the microscopic scale.

Karen Cator, Director of the Office of Educational Technology at the U.S. Department of Education, discussed a new framework for evaluating the effectiveness of educational technology projects. Software can monitor how students work their way through online problems, providing teachers with deeper insights on student learning, especially in terms of scientific thinking and problem-solving skills. Teachers can focus on students’ higher-level thinking skills, and provide useful, real-time feedback to identify strengths, progress and areas in need of help. We agree whole-heartedly and have been working on ways to capture student data in real time and provide feedback loops for teachers. Our next-generation Molecular Workbench will record what students do as they explore the models and make that information available to teachers and researchers.

Partnerships with creative teachers, publishers, and software developers will help us ignite large-scale improvements in teaching and learning through technology. That’s our mission and our goal for Molecular Workbench. Thanks to Google funding, we’re working to increase access to the incredibly powerful next-generation Molecular Workbench.