Posts Tagged ‘visualization’

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 mw.concord.org/nextgen/interactives.

Video: Three Views of Molecular Workbench

May 29th, 2012 by The Concord Consortium

The Molecular Workbench has been downloaded over 800,000 times, making it Concord Consortium’s most popular single piece of software. We’re heading to a million and documenting in video both our history and our vision for the future.

Learn from Charles Xie, Senior Scientist and creator of the Molecular Workbench, about the computational engines that accurately simulate atomic motions, quantum waves, and atomic-scale interactions based on fundamental equations and laws in physics.

Amy Pallant, who researched student use of Molecular Workbench, describes the phone calls she made to students months after they’d used the software—and how impressed she was with their memory of the science of atoms and molecules.

Dan Damelin, Technology and Curriculum Developer, recalls his time as a classroom teacher and his frustration with trying to describe atoms and molecules to his students with words and pictures. He wanted more—and found it in Molecular Workbench!

Dan sums up the goal for Molecular Workbench: “It’s going to be just a given that this is a regular tool that will just be part of learning science.” We hope so.

We’re closing in on a million downloads and looking toward the next million.

If we build it, will they come? Feedback from the field.

May 22nd, 2012 by Amy Pallant

The Molecular Workbench team has a unique opportunity—take our wonderful software and increase access to it. But we know that this is no “Field of Dreams” task. If we build it, will they come?

We’re using The Lean Startup as a guide to optimize our software for the Web. It’s encouraging us to experiment to see which ideas are brilliant and which are crazy and get feedback from users early. We’re thinking about how not to assume we know what people want, but instead go and find out, and be prepared to shift our ideas. In short: Test. Iterate. Repeat.

So we held our first focus group with several Rhode Island teachers who have been loyal users of Molecular Workbench. Our goal was to get feedback on ways to make our new browser-based MW more valuable to them. We asked them to evaluate new designs (we invite you to take our survey, too). We also asked about tone and length of activities. And the teachers described ways they’d like to select and integrate MW models and activities into their classrooms.

Two major themes emerged: flexibility and student accountability. This confirmed what we knew about the classroom: teachers have limited time, a wide range of learners, a diversity of classes, and pressures around high-stakes tests. We’re now working on prototyping ways to incorporate teacher feedback into our Web-based MW models and activities. We’ll share our progress on our website.

And, of course, we’d love to hear your thoughts in the comments.

Video: Molecular Workbench Brings Science to Life in the Browser

May 15th, 2012 by Cynthia McIntyre

As we make our award-winning Molecular Workbench software more accessible and widely available, we’re documenting our story at the same time. Google’s grant to the Concord Consortium funds the conversion of MW from Java to HTML5 so it will run in modern Web browsers. This will reduce barriers for using the next generation MW in schools. Students will be able to access the software from a Web page on a school computer, iPad, or smartphone, giving them anywhere, anytime access to powerful science learning opportunities.

We’re creating videos to share our conversion story. We’ll describe Molecular Workbench, our technical development process, and the benefits of HTML5. We’ve teamed up with the excellent staff of Good Life Productions to produce these videos.

In the first video, Concord Consortium’s Director of Technology Stephen Bannasch describes the power of the modern Web browser to bring science to life. Enjoy.