Posts Tagged ‘Molecular Simulation’

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.

A mixed-reality gas lab

February 12th, 2013 by Charles Xie
In his Critique of Pure Reason, the Enlightenment philosopher Immanuel Kant asserted that “conception without perception is empty, perception without conception is blind. The understanding can intuit nothing, the senses can think nothing. Only through their unison can knowledge arise.” More than 200 years later, his wisdom is still enlightening our NSF-funded Mixed-Reality Labs project.

Mixed reality (more commonly known as augmented reality) refers to the blending of real and virtual worlds to create new environments where physical and digital objects co-exist and interact in real time to provide user experiences that are impossible in only real or virtual world. Mixed reality provides a perfect technology to promote the unison of perception and conception. Perception happens in the real world, whereas conception can be enhanced by the virtual world. Knitting the real and virtual worlds together, we can build a pathway that leads perceptual experiences to conceptual development.

We have developed and perfected a prototype of mixed reality for teaching the Kinetic Molecular Theory and the gas laws using our Frame technology. This Gas Frame uses three different types of sensors to translate user inputs into changes of variables in a molecular simulation on the computer: A temperature sensor is used to detect thermal changes in the real world and then change the temperature of the gas molecules in the virtual world; a gas pressure sensor is used to detect gas compression or decompression in the real world and then change the density of the gas molecules in the virtual world; a force sensor is used to detect force changes in the real world and then change the force on a piston in the virtual world. Because of this underlying linkage with the real world through the sensors, the simulation appears to be "smart" enough to detect user actions and react in meaningful ways accordingly.

Each sensor is attached to a physical object installed along the edge of the computer screen (see the illustration above). The temperature sensor is attached to a thermal contact area made of highly conductive material, the gas pressure sensor is attached to a syringe, and the force sensor is attached to a spring that provides some kind of force feedback. These three physical objects provide the real-world contextualization of the interactions. In this way, the Gas Frame not only produces an illusion as if students could directly manipulate tiny gas molecules, but also creates a natural association between microscopic concepts and macroscopic perception. Uniting the actions of students in the real world and the reactions of the molecules in the virtual world, the Gas Frame provides an unprecedented way of learning a set of important concepts in physical science.

Pilot tests of the Gas Frame will begin at Concord-Carlisle High School this week and, collaborating with our project partners Drs. Jennie Chiu and Jie Chao at the University of Virginia, unfold at several middle schools in Virginia shortly. Through the planned sequence of studies, we hope to understand the cognitive aspects of mixed reality, especially on whether perceptual changes can lead to conceptual changes in this particular kind of setup.

Acknowledgements: My colleague Ed Hazzard made a beautiful wood prototype of the Frame (in which we can hide the messy wires and sensor parts). The current version of the Gas Frame uses Vernier's sensors and a Java API to their sensors developed primarily by Scott Cytacki. This work is made possible by the National Science Foundation.

Constructive chemistry funded by the National Science Foundation

January 17th, 2013 by Charles Xie
One of the most effective pedagogies in science education is to challenge students to design and construct something that performs a function, solves a problem, or proves a hypothesis. Learning by design is a very compelling way of engaging students to learn science profoundly. Given the extensive incorporation and emphasis of engineering design across disciplines in the Next Generation Science Standards, design-based learning will only grow more important in US science education.

The problem, however, is that many science concepts are related to things that are too small, too big, too complex, too expensive, or too dangerous to be built in the classroom realistically. (If you are a LEGO fan, you may argue that LEGO can be used to build anything, but most LEGO models simulate the appearance but not the function -- a LEGO bike probably cannot roll and LEGO molecules probably do not assemble themselves. To scientists and engineers, functions are all that matters.)

Three approaches of using science models.
A good solution is to have students design computer models that work in cyberspace. This virtualization allows students to take on any design challenge without regard to the expense, hazard, and scale of the challenge. If the computer modeling environment is supported by computational science derived from fundamental laws, it will have the predictive power that permits anyone to design and test any model that falls within the range governed by the laws. Software systems that provide user interfaces for designing, constructing, testing, and evaluating solutions iteratively can potentially become powerful learning systems as they create an abundance of opportunities to motivate students to learn and apply the pertinent science concepts actively. This is the vision of "Constructive Science" that I had dreamed about almost four years ago. This constructive approach opens up a much larger learning space that can result in deeper and broader learning--beyond simply observing and interacting with existing science simulations that were created to assist teaching and learning.

This dream got a shot in the arm today by a small grant awarded by the National Science Foundation. This TUES Type-1 grant will support a collaboration with Bowling Green State University and Dakota County Technical College to pilot test the idea of "Constructive Chemistry" at the college level. Choosing chemistry as a test bed to explore this Constructive Science approach is most appropriate, as chemistry is all about atoms and molecules that are just too small to make any design-based learning option other than computational modeling viable. Decades of research in computational chemistry has developed the computational power needed to make the science right. We believe that using these computational methods should yield chemistry simulations that are sufficiently authentic for teaching and learning.

Think Molecularly: An Infrared Imaging Experiment Opens a Door to Deep Scientific Explorations

October 20th, 2012 by Charles Xie
Figure 1
The most fascinating part of science is the search of answers to strange phenomena. In the past nine months, I have posted more than fifty IR videos on my Infrared YouTube channel. These experiments are all very easy to do, but not all of them are easy to explain. In this blog post, I will try to explain one of those experiments, with one of my other skills -- molecular simulation.

This simple IR experiment concerns with putting a piece of paper above a cup of room temperature (nearly) water (Figure 1). I hear you saying, what is the big deal of it? You have probably done that several times in your life, for whatever reasons.

If you happen to have an IR camera and you look at this process through it, you may be surprised. Many of you know that water in an open cup is slightly cooler ( 1-2°C lower) than room temperature because of evaporative cooling: constant evaporation of water molecules from liquid water brings away thermal energy from the cup and causes it to remain a bit cooler than the room environment (which is why you feel cold when you step out of a swimming pool). You may think that the paper would also cool down because at room temperature paper is a bit warmer than the water in the cup and, based on what your science teacher has told you, heat would flow from the warmer paper to the cooler water, causing the paper to cool down.

Figure 2 (Watch it in YouTube)
But the result is exactly opposite -- the paper actually warms up (Figure 2)! And the warming appears to be pretty significant -- up to 2°C can be observed in a dry winter day. I don't know your reaction to this finding, but I was baffled when I saw it because I was expecting to see cooling and this effect appeared to be a violation of the Second Law of Thermodynamics (which, of course, is impossible)! In fact, the reason I did this experiment was to figure out how sensitive my IR camera could be. My intention was to exploit the small temperature difference resulting from evaporative cooling of water as a stable lower-temperature source. I was examining if the IR camera could catch the miniscule heat transfer between the water and the paper.

Figure 3 (Watch it in YouTube)
I quickly figured out that the culprit responsible for this strange heating phenomenon must come from the water vapor, which we cannot see with the naked eye. But what we can't see doesn't mean it doesn't exist. When water molecules in the vapor encounters the surface molecules of the paper, they will be captured. When more and more water molecules are captured and condense onto the paper surface, they will return to the liquid state and, according to the Law of Conservation of Energy, release the excessive energy they carry, which causes the paper to warm up. In other words, the paper somehow recovers the energy lost in the cup through evaporation. As you can see now, this is a pretty delicate thermodynamic cycle that connects two phase changes, evaporation and condensation, in two different places and their latent heats. The physicists among us would appreciate if I say that this shows entropy at work: evaporation is an entropic effect that is caused by water molecules wanting to maximize their entropy by leaving their more organized liquid state. The interaction between the vapor and the paper acts to reverse this process by returning the water molecules to the condensed liquid state and a certain amount of net energy can be extracted from this (known as the enthalpy of vaporization).

Figure 4: Sensor results.
At this point, I hope you have been enticed enough to want to try this out yourself. If you don't have an IR camera, you can use a temperature sensor or an IR thermometer as a substitution to observe this phenomenon (of course, nothing beats an IR camera in terms of seeing heat -- with a point thermometer you just need to be patient and be willing to do more tedious work).

But wait, this is not the end of the story!

If you keep observing the paper, you will see that this condensation heating effect will diminish in a few minutes (Figure 3). This trend is more clearly shown in Figure 4 in which the temperature of the paper was recorded for ten minutes using a fast-response surface temperature sensor. What happens?

Figure 5 (Watch it in YouTube)
The answer to this question can be illustrated using a schematic molecular simulation (Figure 5) I designed to explain the underlying molecular physics (in that simulation water molecules are simplified as single round particles). After water molecules condense onto the paper surface, a thin layer of condensate will form. When it becomes thick enough, water molecules will evaporate from it, too, just like from the surface layer of water in the cup. When the rate of evaporation equals the rate of condensation, there is no more net heating: The condensation heating and evaporative cooling will reach the "break-even" point. Reaching this equilibrium state doesn't mean that condensation and evaporation on the surface of the paper will stop. In fact, water molecules will keep condensing to the layer and evaporating from it. This is known as "dynamic equilibrium." If you move the paper, you will break this dynamic equilibrium. Figure 6 shows a pattern in which evaporative cooling and condensation heating occurred simultaneously on a single piece of paper after the paper had been shifted a bit. In Figure 6, evaporation dominated in the blue zone that was shifted out of the cup area, condensation dominated in the white zone that was shifted into the cup area, and the overlap zone in the middle remained close to the equilibrium state because it was the zone that still remained inside the cup area -- so business as usual.

Figure 6 (Watch it in YouTube)
As you can see, there is a lot of science in this "simple" experiment! Nothing we have done so far requires expensive materials or supplies. Everything needed to do this experiment is probably within the reach of your arm if you are reading this article at home (and you happen to have a digital thermometer, or better, an IR camera, nearby). If you are a science teacher, this experiment should fascinate you because you know this will be a perfect inquiry activity for your students. If you are a building professional, this experiment should fascinate you because you know how important hygrothermal dynamics is in driving moisture transport in the building envelope. If you are a scientist, this experiment should fascinate you because what I have shown you is in fact an atomic layer deposition experiment that anyone can do -- some Fermi calculation suggests that the thickness of the layer is in the nanometer range (only a few hundred layers of water molecules or 1/10,000th of the diameter of your hair). What we are seeing is in fact a signal from the nanoscale world! Isn't that cool?

Figure 7 (Watch it in YouTube)
Does our story end now? Absolutely no. The new questions you can ask will be practically endless if you keep "thinking molecularly." The following are six extended questions I have asked myself. You can try all of these without leaving your kitchen.

When will the paper cool down?

Returning to the original purpose of my experiment (looking for cooling due to heat transfer), can we find a situation in which we will indeed see cooling instead of heating? Yes, if the water is cold enough (Figure 7). When the water is cold, the evaporation rate drops. There will be less water molecules hitting the surface of the paper. The energy gain from weaker condensation heating cannot compensate the energy loss due to the heat transfer between the paper and the cold water. (By the way, I think the heat transfer in this case is mostly radiative, because air doesn't conduct heat well and natural convection acts against heat transfer in this situation.)

What if the paper has been atop the water for a long time?
Figure 8 (Watch it in YouTube)

If you leave the paper atop the cup of water for a few hours and you come back to examine it, you would probably be surprised again: The paper is now cooler than room temperature (Figure 8). I wouldn't be surprised if you are totally confused now: This heating and cooling business is indeed quite elusive -- even though everything we have done so far has been limited to manipulating paper and water. To keep the story short, I will tell you that this is because water molecules have traveled through the porous layer of the paper through capillary action and shown up on the other side of the paper (this molecular movement is often known as percolation in physics). Their evaporation from the upper side of the paper cools down the paper. The building science guys among us can use this experiment to teach moisture transport through materials. Can the temperature of the upper side be somehow used to gauge the moisture vapor transmission rate (MVTR) of a porous material? If so, this may provide a way to automatically measure MVTR of different materials. The American Society for Testing and Materials already has established a standard based on IR sensors. Perhaps this experiment can be related to that.

Different materials have different dew points?

Figure 9 (Watch it in YouTube)
Do water molecules condense to other materials such as plastic? We know plastic materials do not absorb water (which is why they are good vapor barriers). If plastic materials are not cold enough, water molecules do not condense to them. Figure 9 shows this difference by using a piece of paper half-covered by a transparency film taped to the underside. Heating was only observed in the paper part, indicating water molecules do not condense to the plastic film. This experiment raises an interesting question: The so-called dew point, the temperature below which the water vapor in the air at a constant barometric pressure will condense into liquid water, may not be an entirely reliable way to predict condensation. Condensation actually depends on the chemical property of the material surface. Hydrophobic (water-hating) materials like plastic tend to have a low dew point, whereas hydrophilic (water-loving) materials tend to have a high dew point. The porosity of the material should matter, too, because a more porous material will provide a large surface for interaction with water molecule -- paper happens to be such a material because of its fiber texture. If you are a building professional and you worry about moisture, you probably should have this in your mind.

Figure 10 (Watch it in YouTube)
Vapor pressure depression

What will happen if we add some salt (or baking soda or sugar) to the water? Figure 10 shows that the condensation heating effect becomes weaker. For our chemist friends, this is known as vapor pressure depression. The salt ions do not evaporate themselves, but their presence in a solution slows down the evaporation of water molecules.

A vapor column?

Figure 11 (Watch it in YouTube)
What will happen if the paper approaches the water from a different angle like in the vertical direction? How does the shape of the water vapor distribution above a cup of water look like? Does it look like a steam from a cup of coffee? Figure 11 could probably give you some clue.

What about alcohol?

So far we have used only water. What about other liquids? Alcohol is pretty volatile. So I tried some isopropyl alcohol (91%). Once again, I was baffled. Our experience with applying rubbing alcohol to our skin says that alcohol cools faster than water. So I expected that when the isopropanol  molecules condense, they would release more heat. But this is not what Figure 12 suggests! Given the fact that the enthalpies of vaporization of alcohol and water are 44 and 41 kJ/mol, respectively, the only sensible explanation may be that the heating effect is not only due to the condensation of the vapor molecules, but also the interaction between the vapor molecules and the surface molecules of the paper. If the interaction between an alcohol molecule and a paper molecule is weaker, then the adsorption of the alcohol molecule onto the paper surface will produce less heat. I don't know how to prove this now, but this could be a good topic to research.
Figure 12 (Watch it in YouTube)

Final words

Even if this is a lengthy blog post (and thanks for making it to the end), I am pretty sure that the scientific exploration does not stop here. There are other questions that you can ask yourself. For me, I have been intrigued by the fascinating thermodynamic cycle and have been wondering if that could be used to engineer something that can harvest that latent heat. In other words, could we turn a cup of water into a tiny power plant to charge my cell phone? The evaporation of water molecules from an open cup is a free gift of entropy from Nature. Perhaps something could be done about it.