Category Archives: Molecular Workbench

Book review: "Simulation and Learning: A Model-Centered Approach" by Franco Landriscina

Interactive science (Image credit: Franco Landriscina)
If future historians were to write a book about the most important contributions of technology to improving science education, it would be hard for them to skip computer modeling and simulation.

Much of our intelligence as humans originates from our ability to run mental simulations or thought experiments in our mind to decide whether it would be a good idea to do something or not to do something. We are able to do this because we have already acquired some basic ideas or mental models that can be applied to new situations. But how do we get those ideas in the first place? Sometimes we learn from our experiences. Sometimes we learn from listening to someone. Now, we can learn from computer simulation, which was carefully programmed by someone who knows the subject matter well and is typically expressed by a computer through interactive visualization based on some sort of calculation. In the cases when the subject matter is entirely alien to students such as atoms and molecules, computer simulation is perhaps the most effective form of instruction. Given the importance of mental simulation in scientific reasoning, there is no doubt that computer simulation, bearing some similarity with mental simulation, should have great potential in fostering learning.

Constructive science (Image credit: Franco Landriscina)
Although enough ink has been spilled on this topic and many thoughts have existed in various forms for decades, I found the book "Simulation and Learning: A Model-Centered Approach" by Dr. Franco Landriscina, an experimental psychologist in Italy, is a masterpiece that I must have on my desk and chew over from time to time. What Dr. Landriscina has accomplished in a book less than 250 pages is amazingly deep and wide. He starts with fundamental questions in cognition and learning that are related to simulation-based instruction. He then gradually builds a solid theoretical foundation for understanding why computer simulation can help people learn and think by grounding cognition in the interplay between mental simulation (internal) and computer simulation (external). This intimate coupling of internalization and externalization leads to some insights as for how the effectiveness of computer simulation as an instructional tool can be maximized in various cases. For example, Landriscina's two illustrations, embedded in this blog post, represent how two ways of using simulations in learning, which I coined as "Interactive Science" and "Constructive Science," differ in terms of the relationships among the foundational components in cognition and simulation.

This book is not only useful to researchers. Developers should benefit from reading it, too. Developers tend to create educational tools and materials based on the learning goals set by some education standards, with less consideration on how complex learning actually happens through interaction and cognition in reality. This succinct book should provide a comprehensive, insightful, and intriguing guide for those developers who would like to understand more deeply about simulation-based learning in order to create more effective educational simulations.

SimBuilding on iPad

SimBuilding (alpha version) is a 3D simulation game that we are developing to provide a more accessible and fun way to teach building science. A good reason that we are working on this game is because we want to teach building science concepts and practices to home energy professionals without having to invade someone's house or risk ruining it (well, we have to create or maintain some awful cases for teaching purposes, but what sane property owner would allow us to do so?). We also believe that computer graphics can be used to create some cool effects that demonstrate the ideas more clearly, providing complementary experiences to hands-on learning. The project is funded by the National Science Foundation to support technical education and workforce development.

SimBuilding is based on three.js, a powerful JavaScript-based graphics library that renders 3D scenes within the browser using WebGL. This allows it to run on a variety of devices, including the iPad (but not on a smartphone that has less horsepower, however). The photos in this blog post show how it looks on an iPad Mini, with multi-touch support for navigation and interaction.

In its current version, SimBuilding only supports virtual infrared thermography. The player walks around in a virtual house, challenged to correctly identify home energy problems in a house using a virtual IR camera. The virtual IR camera will show false-color IR images of a large number of sites when the player inspects them, from which the player must diagnose the causes of problems if he believes the house has been compromised by problems such as missing insulation, thermal bridge, air leakage, or water damage. In addition to the IR camera, a set of diagnostics tools is also provided, such as a blower-door system that is used to depressurize a house for identifying infiltration. We will also provide links to our Energy2D simulations should the player become interested in deepening their understanding about heat transfer concepts such as conduction, convection, and radiation.

SimBuilding is a collaborative project with New Mexico EnergySmart Academy at Santa Fe. A number of industry partners such as FLIR Systems and Building Science Corporation are also involved in this project. Our special thanks go to Jay Bowen of FLIR, who generously provided most of the IR images used to create the IR game scenes free of charge.

Complete undo/redo support in Energy2D

In Version 2.3 of Energy2D, I have added full support of undo/redo for most actions. With this feature, you can undo all the way back to your starting point and redo all the way forward to your latest state. This is not only a must-have feature for a design tool with a reasonable degree of complexity, but also a simple -- yet powerful -- mechanism for reliably collecting very fine-grained data for understanding how a user interacts with the software.

Why are we interested in collecting these action data?

From the perspective of software engineering, these action data provide first-hand information for quality assurance (QA). QA engineers can analyze these data to measure the usability of the software, to identify behavior patterns of users, and to track results from version to version to gauge if an adjustment has led to better user experience.

From the perspective of education and training, these action data encode users' cognitive processes. Any interaction with the software, especially with a piece of highly visual and responsive software like Energy2D, is automatically a process of cognition. A fundamental thesis in learning science is to understand how we can design interactive materials that maximize learning for all students. These precious fine-grained action data may hold an important key to that understanding.

This idea of using the stack of actions stored in the undo manager of a piece of software to record and replay the entire process of interaction is a unique feature that has been implemented in our Energy2D and Energy3D software and proven a non-obtrusive, high-fidelity, and low-bandwidth technique for data collection.

Energy2D video tutorials in English and Spanish

Many users asked if there is any good tutorial of Energy2D. I apologize for the lack of a User Manual and other tutorial materials (I am just too busy to set aside time for writing up some good documentations).


So Carmen Trudell, an architect who currently teaches at the School of Architecture of the University of Virginia, decided to make a video tutorial of Energy2D for her students. It turned out to be an excellent overview of what the software is capable of doing in terms of illustrating some basic concepts related to heat transfer in architectural engineering. She also kindly granted permission for us to publish her video on Energy2D's website so that other users can benefit from her work.

If you happen to come from the Spanish-speaking part of the world, there is also a Spanish video tutorial made by Gabriel Concha based on an earlier version of Energy2D.

Comparing two smartphone-based infrared cameras

Figure 1
With the releases of two competitively priced IR cameras for smartphones, the year 2014 has become a milestone for IR imaging. Early in 2014, FLIR unveiled the $349 FLIR ONE, the first IR camera that can be attached to an iPhone. Months later, a startup company Seek Thermal released a $199 IR camera that has an even higher resolution and is attachable to most smartphones. In addition, another company Therm-App released an Android mobile thermal camera that specializes in long-range night vision and high-resolution thermography, priced at $1,600. The race is on... Into 2015, FLIR announced a new version of FLIR ONE that supports both Android and iOS and will probably be even more aggressively priced.

Figure 2
All these game changers can take impressive IR images just like taking conventional photos and record IR videos just like recording conventional videos, and then share them online through an app. The companies also provide a software developers kit (SDK) for a third party to create apps linked to their cameras. Excited by these new developments, researchers at several Swedish universities and I have embarked an international collaboration towards the vision that IR cameras will one day become as necessary as microscopes in science labs.

Figure3
To test these new IR cameras, I did an easy-to-do experiment (Figure 1) that shows a paradoxical warming effect on a piece of paper placed on top of a cup of (slightly cooler than) room-temperature water. This seemingly simple experiment actually leads to very deep science at the molecular level, as blogged before.

I took images using FLIR ONE (Figure 2) and SEEK (Figure 3), respectively. These images are shown to the right for comparison. As you can see, both cameras are sensitive enough to capture the small temperature rise caused by water absorption and condensation underside the paper.

The FLIR ONE has a nice feature that contextualizes the false-color IR image by overlaying it on top of the edges (where brightness changes sharply) of the true-color image taken at the same time by the conventional camera of the smartphone. With this feature, you can see the sharp edges of the paper in Figure 2.

Energy2D recommended in computational fluid dynamics textbook

Computational fluid dynamics (CFD) is an important research method that uses numerical algorithms to solve and analyze problems that involve fluid flows. Computers are used to perform the calculations required to simulate the interaction of liquids and gases with surfaces defined by boundary conditions. Today, almost every branch of engineering rely on CFD simulations for conceptual design and product design.

A recent textbook "Computational Fluid Dynamics, Second Edition: A Practical Approach" by Profs. Jiyuan Tu, Guan Heng Yeoh, and Chaoqun Liu has recommended Energy2D as "Shareware CFD" for beginners. Here is a quote from their excellent book:
"Nevertheless, first-time CFD users may wish to search the Internet to gain immediate access to an interactive CFD code. (Users may be required to register in order to freely access the interactive CFD code.) The website is http://energy.concord.org/energy2d/index.html provides simple CFD flow problems for first time users to solve and allows colorful graphic representation of the computed results."

Happy New Year from Energy2D

In the year 2014, Energy2Dhas incorporated a radiation simulation engine and a particle simulation engine, expanding its modeling capacity and making it a truly multiphysics simulation package. To celebrate the New Year, I made some simulations that demonstrate these multiphysics features using objects shaped after the numbers of 2015.

These simulations feature the fluid dynamics engine, the heat conduction engine, the thermal radiation engine, and the particle dynamics engine. If you are curious enough, you can click this link to run the simulations.


These shapes were drawn using Energy2D's polygon and ring tools, which allow users to create a wide variety of arbitrary 2D shapes. Many users probably do not know how versatile the polygon tool actually is (the original triangle icon on the tool bar probably misleads some to think it is only good for drawing triangles -- so I changed it to look like a cross-section of an I-beam). The polygon tool allows one to easily draw a polygon with maximally 256 control points for adjusting its shape later. One can draw an approximate shape and then drag these control points to get it to the exact shape. To modify a shape even further, one can also insert a control point by double-clicking on an existing point. A new point will be added to the adjacent position, which you can then drag around. To delete a control point, just hold down the SHIFT key while double-clicking on it. In addition, a polygon can be rotated, twisted, compressed, or elongated using the corresponding fields in its property window (there is currently no graphical user interface for doing those things, however).

As for the New Year's resolutions, in 2015, the ring shape will be enhanced into a new tool called the shape subtractor, which allows users to subtract a shape from another to make a hollow one.

On the numerical simulation side, we will continue to improve the accuracy of the existing simulation engines by adding an explicit solver as an option for users to overcome some of the problems related to the implicit solvers.

On the multiphysics modeling side, we will try to support multiple fluids, which seems simple at first glance but has turned out to be a very difficult mathematical problem. With the capacity of multiple fluids, we will also be able to add an electromagnetism solver in order to model effects such as electrorheological fluids (fluids whose viscosity changes with respect to an applied electric field).

We wish all Energy2D users a very successful new year!

European scientists use Energy2D to simulate submarine eruptions

The November issue of the Remote Sensing of Environment published a research article "Magma emission rates from shallow submarine eruptions using airborne thermal imaging" by a team of Spanish scientists in collaboration with Italian and American scientists. The researchers used airborne infrared cameras to monitor the 2011–2012 submarine volcanic eruption at El Hierro, Canary Islands and used our Energy2D software to calculate the heat flux distribution from the sea floor to the sea surface. The two figures in the blog post are from their paper.

According to their paper, "volcanoes are widely spread out over the seabed of our planet, being concentrated mainly along mid-ocean ridges. Due to the depths where this volcanic activity occurs, monitoring submarine volcanic eruptions is a very difficult task." The use of thermal imaging in this research, unfortunately, can only detect temperature distribution on the sea surface. Energy2D simulations turn out to be a complementary tool for understanding the vertical body flow.

Their research was supported by the European Union and assisted by the Spanish Air Force.

Although Energy2D started out as an educational program, we are very pleased to witness that its power has grown to the point that even scientists find it useful in conducting serious scientific research. We are totally thrilled by the publication of the first scientific paper that documents the validity of Energy2D as a research tool and appreciate the efforts of the European scientists in adopting this piece of software in their work.

Beautiful Chemistry


It is hard for students to associate chemistry with beauty. The image of chemistry in schools is mostly linked to something dangerous, dirty, or smelly. Yet Dr. Yan Liang, a collaborator and a materials scientist with a Ph.D. degree from the University of Minnesota, is launching a campaign to change that image. The result of his work is now online at beautifulchemistry.net.

To bring the beauty of chemistry to the general public, Dr. Liang uses 4K UltraHD cameras and special lenses to capture chemical reactions in astonishing detail and advanced computer graphics to render stunning images of molecular structures.

Using the beauty of science to interest students has rarely been taken seriously by educators. The federal government has invested billions of dollars in instructional materials development. But from a layman's point of view, it is hard to imagine how children can be engaged in science if they do not fall in love with it. Beautiful Chemistry represents an attempt that could inspire a whole new genre of high-quality educational materials based on breathtaking scientific visualizations. How about Beautiful Physics and Beautiful Biology?

Our work is well aligned with this vision. Our interactive, visual Energy2D simulations bring a beautiful world of heat and mass flow to students like never seen before; our Energy3D software creates splendid 3D scenes based on scientific calculations; and our infrared visualization of the real world has uncovered a beautiful hidden universe through an IR lens. These materials demonstrate computational and experimental ways to marry science and beauty and have resulted in great enticements in science classrooms.

BTW, Dr. Liang is the artist who designed the splash panes of Energy2D and Energy3D.

Simulating cool roofs with Energy3D

Fig. 1: Solar absorption of colors.
Cool roofs represent a simple solution that can save significant air-conditioning cost and help mitigate the urban heat island effect, especially in hot climates. Nobel Prize winner and former Secretary of Energy Steven Chu is a strong advocate of cool roofs. It was estimated that painting all the roofs and pavements around the world with reflective coatings would be "equivalent to getting 300 millions cars off the road!"

With Version 4.0 of Energy3D (BTW, this version supports 200+ worldwide locations -- with 150+ in the US), you can model cool roofs and evaluate how much energy you can save by switching from a dark-colored roof to a light-colored one. All you need to do is to set the colors of your roofs and other building blocks. Energy3D will automatically assign an albedo value to each building block according to the lightness of its color.

Figure 1 shows five rectangles in different gray colors (upper) and their thermal view (lower). In this thermal view, blue represents low energy absorption, red represents high energy absorption, and the colors in-between represents the energy absorption at the level in-between.

Now let's compare the thermal views of a black roof and a white roof of a cape code house, as shown in Figure 2. To produce Figure 2, the date was set to July 1st, the hottest time of the year in northern hemisphere, and the location was set to Boston.

Fig. 2: Compare dark and white roofs.
How much energy can we save if we switch from a perfectly black roof (100% absorption) to a perfectly white roof (0% absorption)? We can run the Annual Energy Analysis Tool of Energy3D to figure this out in a matter of seconds. The results are shown in Figure 3. Overall, the total yearly energy cost is cut from 6876 kWh to 6217 kWh for this small cape code house, about 10% of saving.

Figure 3 shows that the majority of savings comes from the reduction of AC cost. The reason that the color has no effect on heating in the winter is because the passive solar heat gains through the windows in this well-insulated house is enough to keep it warm during the sunshine hours. So the additional heat absorbed by the black roof in the same period doesn't offset the heating cost (it took me quite a while to figure out that this was not a bug in our code but actually the case in the simulation).

Fig. 3: Compare heating and AC costs (blue is white roof).
Of course, this result depends on other factors such as the U-value and thermal mass of the roof. In general, the better the roof is insulated, the less its color impacts the energy cost. With Energy3D, students can easily explore these design variables.

This new feature, along with others such as the heat flux visualization that we have introduced earlier, represents the increased capacity of Energy3D for performing function design using scientific simulations.

Here is a video that shows the heating effect on roofs of different colors.