Sunday, 15 June 2014

Onehunga high school visit to the Photon Factory

Here are some notes for the students coming from Onehunga High School to take part in practical science projects. Below is a list of the different projects.

During the course of the day we are going to be drawing up some slides about the project you have chosen including:
  • Background research
  • Design of the device
  • Building the device and testing
  • The questions will you ask with what you have made
Clean drinking water using natural microorganisms
3.4 million people die every year from water-related diseases. This is largely due to pathogens living and breeding in the water. There are many different ways to clean water of microorganisms; filters and solar precipitators to name just a couple. However, there is a way to filter out microorganisms using other microorganisms. Using a biosand filter (a bucket full of sand) that slowly empties, water can be sanitised simply and naturally. A thick biofilm forms on the surface of the sand and breaks down bacteria. Then the sand allows for filtering of water and provides a dark place where the bacteria die from lack of food. How the biofilm and each different element work is still not fully understood. We will make a biosand filter and look at what experiments can be done to improve our understanding of the biosand filter.

Timelapse images for long term changes in nature
The climate is changing due to an increase in greenhouse gases in the atmosphere. This rapid change is going to have a huge impact on the environment around us, particularly on plants which are dependent on the weather cycles to survive. Due to the slow movement of plants it is hard to look at trends in their behaviour. Using special time lapse photography we can watch the long term movements of plants using a simple webcam and computer software. By stitching the images together  using software a video can be made and analysed. We will be building an enclosure for a webcam to be set up outside to collect images of plants growth. We will also look into using algorithms to exaggerate the movement of plants to observe subtle changes in the plants as they grow.
Revealing Invisible Changes In The World - YouTube

3d printed spectrometer using a CD grating and a cell phone
Have you ever wondered why something appears blue or red? What determines a material's colour? A spectrometer is a device that can measure the light that comes off an object. We are going to make one of these using a normal CD which has lots of small pits in its surface which allow it to reflect light of different colours in only one direction. This means that if white light enters in at a particular angle, the colours spread out at different angles and can be measured individually. These have been used to look at the different chemicals are in stars and on planets. They are also used to detect contaminants in water. In the Photon Factory we use this to look at how energy moves around molecules and we are working on making artificial leaves that turn sunlight into energy. You will build your own spectrometer and attach it to a cellphone to find out how you can help the world by conducting experiments with your own spectrometer.

Invisible light camera reveals when plants are stressed
We can see from blue light (~400 nanometers) to red light (~600 nanometers). Outside this range we are blind, however continuing past the red end of our vision will show signatures in plants that would otherwise be invisible. Plants absorb red and blue light but reflect green light. But what about the invisible light? Plants reflect near infrared light (NIR) (~700nm - ~1200nm) very well also. However, when they are under stress the part of the plant that reflects the NIR becomes damaged and the plant reduces its reflectance. This can happen when there is a pest invasion or when the plant is not getting the right nutrients or water. Using a simple webcam we will remove the infrared filter from the camera to see the invisible light, then add a red filter. This replaces the red channel with the infrared to show stress in the plants.

Biochar and efficient stoves for safer cooking conditions and carbon sequestration
The majority of the world still uses open fires for cooking food. This presents a health risk due to smoke inhalation and also leads to pollutants in the environment. Using a different way of burning wood, a highly efficient stove (gasifier) can be built that firstly turns the wood into a gas and then burns that gas in another part of the burner. This gasifier can then burn the fuel more efficiently with fewer harmful emissions. One of the byproducts from this process is charcoal, a solid form of carbon, that is very difficult to break down. When wood grows it uses and stores carbon dioxide, a greenhouse gas, and when it dies microbes break down the wood and the carbon dioxide is released. By heat-treating the wood carbon can be trapped in the ground for thousands of years. The application of charcoal to the soil (this type of charcoal is known as biochar) was first done with soils along the Amazon. Ancient Amazonians would put food waste and charcoal together to produce a very potent fertiliser. We will build a gasifier out of a can and a computer fan, then design some experiments to test out the effects of the charcoal on different plants and soils.

This is just the beginning. If you want to continue doing the project you were assigned or another group's, then you can enter the high school science fair.

Friday, 10 January 2014

Floating raisins and sad shellfish

The floating raisin is a classic Christmas kitchen experiment. A raisin is dropped into a carbonated beverage (often champagne) and after a minute or so the raisin rises to the top of the drink and then sinks back to the bottom to repeat the process. I posted a video on Facebook of the experiment and had a few people ask me how it works.

Why is champagne bubbly? The bubbles in champagne and other carbonated drinks are bubbles of carbon dioxide gas (CO2).
These bubbles of CO2 are formed by tiny yeast microbes during a second fermentation step in producing champagne. During this step, the yeast eats the sugar breaking it down into carbon dioxide.

Why don't we see bubbles of CO2 when champagne is corked? This is due to a dynamic equilibrium inside a closed system - dynamic in that chemicals are always moving from one state to another (in this case carbon dioxide in solution and carbon dioxide gas) and an equilibrium in that the rate of change going from the liquid to the gas phase is the same as going from the gas into the liquid. No bubbles form, as that would indicate more carbon dioxide moving from the liquid to the gas and the system would be out of equilibrium.
Another time you may have come across this is when you leave your drink bottle in the car on a hot day with a little bit of water in the bottom. When you come back to open the bottle you hear a release of gas when the lid is opened. This is due to the water in the gas phase which is in equilibrium with liquid water until you open the bottle. We call this vapour pressure in chemistry. Below is a video of water at the gas-liquid interface.

So we know the bubbles come from CO2 escaping due to a non-equilibrium open system.  

Considering that CO2 is usually thought of as a gas (at room temperature) how is it stable in water? Hydrogen bonding holds the answer to CO2 stability in water. In this case, oxygen is electronegative (has higher negativity) than hydrogen, which is comparatively more positive. When oxygen comes near the small positive hydrogen, the positive and negative attract to form a very strong intermolecular (between molecules) bond. This stabilises the CO2 in water, stopping it from grouping together and forming a bubble.

CO2 in an 18-molecule water dodecahedral cluster
The bonding H2O around CO2 [1], [2]
However, it is important to keep in mind that due to thermal energy (temperature) there is always change at a molecular level. This perfectly bonded sphere is the representation of an average of these bonds, which are themselves constantly changing.

When the cork is popped the pressure at the top is released and so there is no gas pushing on the liquid. Without this pressure, the gas at room temperature will push the water molecules apart and form a bubble.

Co2 water

Above you can see a bubble of CO2 with water on either side. However, water is quite heavy and will push on this bubble until the CO2 goes back into the water and no bubbles form in the liquid. [4]

If no bubbles can form in a liquid how do they form in champagne? This is due to microscopic dirt and scratches on the inside of the glass on which the bubbles can form. Only on a solid, where CO2 forms weak bonds with the surface, can enough CO2 molecules get together to form a bubble. When this bubble reaches about 1 micron (a hair being about 100 microns in diameter) it is large enough to continue to grow by itself in the liquid. [5-7]
Above is a bubble formed on a cotton fibre. It can be seen to form, grow and then detach and continue to grow as it travels through the liquid. Champagne bottles and glasses can be scratched using lasers or mechanically to tune just how quickly the champagne will stay bubbly. This video explains it with some simple experiments.

Coming back to the raisin in the champagne, it is easy to see how bubbles can form on its wrinkled surface.

Why do the bubbles grow larger than a micron on a raisin and actually stick to it? In short, the bubble of CO2 likes the sugary surface of the raisin more than it wants to float. As a result, the raisin is pulled up to the top of the glass due to the buoyancy of the bubbles. Once at the surface there is no liquid to hold the gas in bubbles so it escapes into the air and the raisin sinks again.

Super-heated water
A dangerous example of the need for impurities on which bubbles can form is super-heated water. (Don't try this at home - after this I have an experiment you can try at home.) Pure water (with a complete lack of impurities) can be heated above boiling in the microwave for a few minutes. When it comes in contact with a spoon (as my father found out while flatting to disastrous consequences) or sugar (as the video below shows) it explodes as gas is released.

Super-cooled water
Instead of this rather dangerous experiment, what you can try at home is super-cooling water. If you put purified water into the freezer it will cool below freezing until either the introduction of an impurity or a shockwave (for example, hitting the bottle) starts the ice crystal formation.

The really important research that is going on in this area is to do with CO2 storage. Due to the blanket of CO2 around the earth, our atmosphere is heating up. Something slowing down this increase in CO2 are the oceans, which are absorbing excess CO2. However, this presents two long-term problems - firstly, as the earth heats up further less CO2 can be stored in the oceans, so this is a finite solution, and secondly, it acidifies the ocean making it very difficult for shellfish to make their shells.

Sebastian is sad because his shell is slowly dissolving in the ocean's acidity.

The picture below shows pteropod shells that have already started dissolving in the Southern Ocean.

A shell placed in seawater with increased acidity slowly dissolves over 45 days.<div class='credit'><strong>Credit:</strong> A shell placed in seawater with increased acidity slowly dissolves over 45 days.</div>
A more scientific representation of a sad shellfish.
Ocean Acidification Illustration

Shellfish use calcium carbonate to form their shells. The shell is made out of calcium with the carbonate ions helping to make sure the calcium isn't dissolved in water. But by flooding the oceans with CO2 we are removing carbonate and forming bicarbonate, therefore removing the molecules needed for shells to not dissolve. 

This is why the study of CO2 in water and also trapping CO2 by adsorbing them onto solids is of great importance to the earth and why the chemistry of floating raisins is much more interesting and important than you could have imagined.

[1] H. Sato, N. Matubayasi, M. Nakahara and F. Hirata, Which carbon oxide is more soluble? Ab initio study on carbon monoxide and dioxide in aqueous solution, Chem. Phys. Lett. 323 (2000) 257 - 262.

[2] G. K. Anderson, Enthalpy of dissociation and hydration number of carbon dioxide hydrate from the Clapeyron equation, J. Chem. Thermodynamics 35 (2003) 1171-1183.

[3] G.A. Gallet, F. Pietrucci, W. Andreoni, J. Chem. Theory Comput. 8, 4029-4039 (2012)

[4] W. L. Ryan et al., J. Coll. Interf. Sci. 1993, 157, 312. DOI: 10.1006/jcis.1993.1191

[5] G. Liger-Belair et al., Langmuir 2004, 20, 4132. DOI: 10.1021/la049960f

[6] G. Liger-Belair et al., J. Phys. Chem B, 2005, 109, 14573. DOI: 10.1021/jp051650y

[7] G. Liger-Belair et al., J. Phys. Chem B, 2006, 110, 21145. DOI: 10.1021/jp0640427

For more of the physics behind champagne check out this great review:

Tuesday, 24 December 2013

Back story to laser engraved poetry

A presentation for the Poetry off the Page project where I explain some of the back story of why we decided to machine poetry on everyday objects in the Photon Factory at the University of Auckland.

Thursday, 17 October 2013

Learn Python for free with edX

There is still time to enrol for the free course in python offered by MITx on 

This is a great course and how I first got introduced to Python two years ago when I watched the lectures for this course on MIT open courseware.

It started a few days ago so there is still time to get involved. I am currently working though the Quantum computation course which is a lot of fun as well.