Archive for May 2013

Welcome to our three Google Summer of Code students

May 28th, 2013 by Cynthia McIntyre

Google Summer of Code 2013Three international students will spend the summer coding for our open source projects. Through Google Summer of Code (GSoC), they’ll earn stipends from Google, plus get a coveted GSoC t-shirt and certificate.

Expansion of SPARKS HTML5 circuit simulator

Our HTML5 breadboard simulator allows students to experiment with basic DC and AC circuits using linear components (resistors, capacitors, inductors) and to perform measurements with a function generator, a digital multimeter and an oscilloscope.

Sabareesh Nikhil C, from Hyderabad, India, will extend our existing circuit-solving code to handle non-linear components such as diodes, op amps and transistors. Instead of treating each circuit as a lumped impedance and computing its response to a single frequency, the new code will perform a more realistic time-based computation, which will enable it to model the behavior of more complex circuits. Sabareesh also plans to implement a communication protocol that will enable circuits on different computers to communicate with each other.

Sabareesh will work with Concord Consortium mentors Paul Horwitz, Sam Fentress and Richard Klancer.

Probe your browser!

Science classrooms use probes and sensors to enable real-time data collection by students. Currently we use Java applets to support communication between sensors and web-based applications in the browser. Increasingly limited support for Java is making it difficult to integrate probes and sensors that use Java software for use in the classroom.

Lingliang Zhang from New York, NY, and Abu Dhabi, United Arab Emirates, will design a native application for desktops, which will make the data from probes and sensor hardware available to our browser-based JavaScript applications. The native application will use an embedded webserver to connect to our existing sensor library. This approach will enable browsers on desktops and laptops to use our currently supported Pasco and Vernier sensor devices without a Java applet.

He will work under the mentorship of our Senior Software Engineer Scott Cytacki.

Port HTML5 interactives to phones and tablets

Our HTML5 interactives are rendered using a semantic layout system. With a modified UI, they could work on phones, allowing students to interact with them on multiple devices. Additionally, with an iOS and Android application created using Cordova, users could install the interactives and use them offline. This app could also allow parts of the engine behind the interactives to run natively in order to get better performance on these devices.

Apoorv Narang from New Delhi, India, will measure performance on various devices to determine which of our HTML5 interactives can be run on these devices. He will improve our lab framework, which is the system that displays and runs interactives, with the goal of making our interactives look—and run!—better on phones.

Director of Technology Stephen Bannasch will mentor Apoorv.


During summer 2012, we were fortunate to have two fabulous GSoC students, including Piotr Janik, who continues coding for us as a consultant. Watch Piotr describe his experience with Google Summer of Code.

We can’t wait to see the code that our three new GSoC students will develop this summer!


Solar urban design using Energy3D: Part III

May 22nd, 2013 by Charles Xie
Figure 1
In Part I and II, we discussed how solar simulations in Energy3D can be used to decide where to erect a new building in a city block surrounded by existing buildings. Now, what about putting multiple buildings in the block? The optimization problem becomes more complex because students will have to deal with more variables while searching for an optimal solution.
Figure 2
Suppose students have to decide the locations of two new constructions A and B that have identical shapes. Now they have six options to layout
the two new constructions. Figure 1 shows the results of the solar simulations for all these six layouts in the winter. Placing the buildings in the northeast and northwest parts (the first in the first row of Figure 1) seems to be the best solution for receiving solar heating in the winter. This is not surprising because this layout creates large south-facing areas for both buildings that will get a lot of solar energy in the winter and there are not shadowed very much by the surrounding buildings.

Switch the season to the summer.  Figure 2 shows the results of the solar simulations for all these six layouts in July. Placing the buildings in the southeast and southwest parts (the first in the second row of Figure 2) seems to be the best solution for avoiding solar heating in the summer.

To make a trade-off between winter heating and summer cooling, it seems the southeast and southwest locations are the optimal solution: In the winter the solar heating on the two buildings is the second best (which is not much lower than the highest) and in the summer the solar heating on them is the lowest (which is much lower than the contender).


Share and embed—easily!

May 22nd, 2013 by Cynthia McIntyre

One of the key features of our Next-Generation Molecular Workbench is the ability to easily share and embed interactives in blog posts, learning management systems, emails and more—wherever you can paste a weblink or HTML code. Just two simple steps will have you sharing your favorite interactives with all your friends and colleagues in no time flat!

  1. Click the Share link at the top of an interactive.
  2. Copy and paste the link into Facebook, Google+, Twitter, Pinterest or wherever you want to share the interactive.

Want to embed the interactive in your own blog or web page instead?

  1. Click the Share link at the top of an interactive.
  2. Copy the HTML and paste the iframe code where you want the interactive to appear.

Sharing and embedding Next-Generation Molecular Workbench interactives

Learn more about how easy it is to share interactives.

We want to make it easy for you to learn and teach with accurate scientific models.  We’ve gotten it down to two steps. Now it’s up to you to share your favorite interactives far and wide. :-)

Explore currently available interactives.

Share with us: which are your favorite interactives and why? What interactives do you want to see?


Solar urban design using Energy3D: Part II

May 18th, 2013 by Charles Xie
Figure 1
The sun is lower in the winter and higher in the summer. How does the sun path affect the solar radiation on the city block in our urban design challenge? Is solar heating different in different seasons? Let's find out using Energy3D's solar simulator. Energy3D has a nice feature that allows us to look at the 3D view exactly from the top. This kind of reduces the 3D problem to a 2D one once you complete your 3D construction and want to do some solar analysis. The 2D view is clearer and the drag-and-drop of buildings is easier.

Figure 2
First, we added a rectangular building to the city block and moved it to four different places -- northwest, northeast, southeast, and southwest -- in the city block and set the month to be January and the location to be Boston, MA (which is where we are close to). Not surprisingly, the solar radiation on the building is the lowest at the southeast location (Figure 1). This is because to the southeast of the block, there are three tall buildings that shadow the southeast part of the block --- you can see in the heat map that the southeast part is deep blue. At the southwest location, the building receives the highest solar energy. The northwest location seconds it with a slightly smaller number.

Figure 3
Next we set the month to be July and repeated the solar simulation.This time, the solar heating on the building at all locations increases (Figure 2). However, the location that receives the lowest solar heating, surprisingly, is not southeast but southwest! The location that receives the highest solar heating is northwest. The reason could be that there is a tall building next to the southwest location that provides a lot of shadow (Figure 3). This shadowing effect seems to be more significant than the shadowing effect from the three tall buildings around the southeast corner.
Figure 4
The conclusion is that the building of this particular shape receives the highest solar energy in the winter and the lowest in the summer at the southwest spot.

Now, what about the orientation of the building? Let's rotate the building 90 degrees and redo the solar analysis in January (Figure 4). The results show that the building receives higher solar energy at all locations. This is because the building has a larger south-facing side in this orientation than in the previous one. The southeast location remains the coldest spot, but the difference between southwest and northwest is less.


Solar urban design using Energy3D: Part I

May 17th, 2013 by Charles Xie

Figure 1
In sustainable architecture, passive solar design refers to searching for optimal strategies to maximize solar heating on a building in the winter and minimize solar heating in the summer in order to reduce heating and cooling costs of the building. A passive solar design challenge is a typical optimization problem that requires many steps of engineering design to solve, such as testing ideas, analyzing data, considering constraints, and making trade-offs.

Figure 2
For urban design, site layout has a big impact on passive solar heating in buildings as neighboring tall buildings can block low winter sun. Energy3D’s solar simulator can compute, visualize, and analyze solar radiation in obstructed situations commonly encountered in dense urban areas.

The solar urban design project we have developed challenges students to use Energy3D to construct a square city block surrounded by a number of existing buildings of different heights, with the goals to maximize solar access for new constructions and minimize obstruction of sunlight to existing buildings. The existing buildings, which cannot be modified by students, serve as constraints for the design challenge. This design challenge is an authentic engineering problem as it requires students to consider solar radiation as it varies over seasons and apply these math and science concepts to solve open-ended problems using a supporting analytic tool. This distinguishes it from common computer drafting activities in which students draw structures whose functions cannot or will not be verified or tested.

Figure 3
Energy3D can generate solar radiation heat maps on the walls of buildings and the ground (Figures 1 and 2). These heat maps show the cumulative heat of solar radiation on a surface over a certain period (a day or a month). They are calculated by summing up the solar energy projected onto each unit area of the surface while the sun moves cyclically in its path at the given location. The total solar heating result (in kWh), summing from all the unit areas of all the walls, is shown on top of each building. This number will go up and down as students move or reshape the building. This calculated result is more accurate than shadow and shading, which only reflects instantaneous solar heating at a particular moment.

The horizontal radiation heat map can be used to identify the hot and cold areas of the empty city block. With this heat map, students can find out where the new constructions should be in order to have maximal solar heating in the winter. Once they put in a new building, they can move the building around within the construction site to experiment how much solar energy the building will gain. As an example, Figure 3 shows that a rectangular high-rise building will receive the highest amount of solar radiation in January if it is placed at the southwestern part of the square and it will receive the lowest amount of solar radiation if it is placed at the southeastern part.

Such an analytic tool provides data for students to make their design decisions, creating plenty of opportunities of inquiry in design processes.


Classrooms on fire…with dragon genetics!

May 15th, 2013 by Frieda Reichsman

No smoke and mirrors here: dragons are getting kids all fired up about genetics. Geniverse software engages students with compelling reasons to solve genetics problems. As they rise through the ranks of the Drake Breeders Guild, students win stars and quills for efficient experimentation and for using their own experimental results as evidence for their scientific claims. Watch how students are learning genetics while having fun—using Geniverse! Want to get your students fired up about genetics, too? Sign up to use Geniverse in your classroom next year.

Solar heating simulations in Energy3D

May 14th, 2013 by Charles Xie
We are adding some new features to our Energy3D software that will allow the user to carry out passive solar design of one or multiple buildings (or even an entire city block). These new features will calculate the distribution of solar energy density over an area such as the vertical surface of a wall of a building or the horizontal surface area of open space. The results will be visualized as color heat maps overlaid to the surface. The information in these color maps can be used to help students make decisions when they are searching for optimal passive solar designs.

These new analytic tools will be used in our Passive Solar Urban Design Challenge that requires students to design a city block with new buildings that have maximal solar heating in the winter and minimal solar heating in the summer, without severely obstructing solar access of existing buildings in the neighborhood.

These new features are integral parts of the existing heliodon simulator in Energy3D, which allows the user to adjust the sun path. The video in this blog post demonstrates this.

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

Energy3D Version 2.0 released

May 9th, 2013 by Charles Xie
We are proud to release Energy3D version 2.0, available for download from our website. Energy3D is a computer-aided design and fabrication tool for making small model green buildings. This version added new energy assessment features that allow students to evaluate the energy performances of their  designs and investigate the effect of passive solar heating. Currently however, this energy assessment tool is limited to only 12 selected cities around the world.

The next release will feature powerful passive solar heating simulation that can be applied to a wide variety of settings ranging from a single family house to a dense urban area.

Energy3D runs on both Windows and Mac OS X. Java 7 is required. It may also run on Linux (some of our users actually got it to run on Linux), but it has not been thoroughly tested on Linux.