Archive for June 2013

First research paper using the Molecular Workbench submitted to arXiv

June 30th, 2013 by Charles Xie
Credit: M. Rendi, A.S. Suprijadi, & S. Viridi
Researchers from Institut Teknologi Bandung, Indonesia recently submitted a paper "Modeling Of Blood Vessel Constriction In 2-D Case Using Molecular Dynamics Method" to arXiv (an open e-print repository), in which they claimed: "Blood vessel constriction is simulated with particle-based method using a molecular dynamics authoring software known as Molecular Workbench. Blood flow and vessel wall, the only components considered in constructing a blood vessel, are all represented in particle form with interaction potentials: Lennard-Jones potential, push-pull spring potential, and bending spring potential. Influence of medium or blood plasma is accommodated in plasma viscosity through Stokes drag force. It has been observed that pressure p is increased as constriction c is increased. Leakage of blood vessel starts at 80 % constriction, which shows existence of maximum pressure that can be overcome by vessel wall."

This blog article is not to endorse their paper but to use this example to illustrate the point that a piece of simulation software that was originally intended to be an educational tool can turn out to be also useful to scientists. If you are a teacher, don't you want your students to have such a tool that assumes no boundary to what they can do? The science education community has published numerous papers about how to teach students to think and act like a scientist, but much less has been done to actually empower them with tools they can realistically use.

More things, more people, more easily

June 24th, 2013 by MW Team
“The most exciting thing about the Next-Generation Molecular Workbench is that it lets us to do more things for more people, more easily.” -Chad Dorsey, CEO & President of the Concord Consortium

Have you seen the latest Next-Generation MW interactives? We’ve taken the physics-based interactive simulations and made them better. The Next-Generation Molecular Workbench is accessible to anyone with a browser and works on multiple devices (desktops, laptops, tablets and phones).

With our easy-to-share interactives (just click the “Share” link in the top right corner of any interactive), you can develop your own activities on your blog or teacher page. CK-12¬†and edX already have!

And best of all, the code is free and open source. Want to change the model? You can get access to the code and tweak it.

Learn more in our latest video from the Molecular Workbench team!

Solar urban design and data mining in the classroom

June 23rd, 2013 by Charles Xie
Image usage permitted by students.
Image usage permitted by students.
In the past two weeks, seventy ninth graders in three physics classes of Arlington High School (MA) each used our Energy3D CAD software to solve the Solar Urban Design Challenge (which I blogged earlier). I observed them for three days. I didn't have experience with these students before, but according to their teacher, they were exceptionally engaged. Most students hadn't "run out of steam" even after 4-5 days of continuous work on the design project. As anyone who works in schools knows, it is hard to keep students interested in serious science projects for that long, especially near the end of a semester. These students seemed to have enjoyed this learning experience. This is a good sign that we must have done something right. I suppose the colorful 3D solar visualization provides some eye candies to keep them curious for a while.

Image usage permitted by students.
CAD tools are probably not new things in classrooms these days, at least not for Arlington High School that uses SketchUp and AutoCAD for years. What is cool about our CAD tool is that all these students' actions were recorded behind the scene -- at a frequency of every two seconds! That is to say, the computer was "watching" every move of every student. This sounds like a little concerning if you have heard in the news about a secret governmental project called the Prism that is probably "watching" me writing this blog article at this time. But rest assured that we are using this data mining technology in a good way. Our mission is not to spy on students but to figure out how to help them learn science and engineering in a more fruitful way. This is probably equally important -- if not more -- to our national security if we are to maintain our global leadership in science and technology.

Solar urban design using Energy3D: Part IV

June 1st, 2013 by Charles Xie
In Part I, II, and III, we mainly explored the possible layouts of buildings in the city block and their solar energy outputs in different seasons. In those cases, the solar radiation on a new construction is mostly affected by other new constructions and existing buildings in the neighborhood. We haven't explored the effect of the shape of a building. The shape of a building is what makes architecture matter, but it also has solar implications. In this blog post, we will explore these implications.

Figure 1: Compare solar heating of three different shapes in two seasons.
Let's start with a square-shaped tall building and make two variations. The first one is a U-shaped building and the second is a T-shaped one. In both variations, the base areas and the heights are identical to those of the original square-shaped building. Let's save these buildings into separate files and don't put them into the city block. We just want to study the solar performance of each individual building before we put them in a city.

The U-shaped building has a larger surface area than the square-shaped and the T-shaped ones (which have an identical surface area). Having a larger surface means that the building can potentially receive more solar radiation. But the two wings of the U-shaped building also obstruct sunlight. So does the U-shaped building get more or less energy? It would have been very difficult to tell without running some solar simulations, which tell us that this particular U-shaped building gets more solar energy than the square-shaped one both in the winter and in the summer.

In comparison, the T-shaped building gets the least amount of solar energy in both seasons. This is not surprising because its surface is not larger than the square-shaped one but its shape obstructs sunlight to its western part in the morning and to its eastern part in the afternoon, resulting in a reduction of solar heating.

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