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Revision as of 15:19, 1 November 2017
Modelling
Physics 101 - Light
Electromagnetic radiation is energy travelling as waves or photons. This is not the place or the time to go into this discussion [1] but Einstein and Infeld said it well:
"But what is light really? Is it a wave or a shower of photons? There seems no likelihood for forming a consistent description of the phenomena of light by a choice of only one of the two languages. It seems as though we must use sometimes the one theory and sometimes the other, while at times we may use either. We are faced with a new kind of difficulty. We have two contradictory pictures of reality; separately neither of them fully explains the phenomena of light, but together they do."
- Albert Einstein and Leopold Infeld, The Evolution of Physics, pg. 262-263.
Light, or the visible light spectrum range from \( \in [400 - 700] \) nm in the electromagnetic radiation spectrum. XX insert picture of Elmag spectrum here XX.
Above, with higher wavelengths, you will find infrared radiation (also known as IR), and under you will find the ultraviolet radiation (also known as UV). We call it visible light due to the fact that our eyes can only "pick up" these wavelengths. For this project we will mostly focus on light \( \lambda \in [470,520] \) nm region.
You have probably heard that nothing can travel faster than light? But not that many (non-physicist) remembers what velocity light actually travels with. In most cases it's enough to say that light travels in \( \sim 3.0 \cdot 10^{8}\) m/s in vacuum or \( \sim 6.7 {\cdot 10^{8}} \)mph.
When talking about light there is a couple of expressions that is good to know the meaning of
- Monochromatic
- Coherent
- Wavelength
- Optical Path
Physics 101 - LED
The light from a light-emitting diode, LED for short, can be viewed by the human eye as monochromatic. This means it appears to only light up as one color. From theory we know that a LED cannot be monochromatic, thus proving one of the biggest differences between a LED and a laser. More importantly, the light from a LED is not coherent, meaning that the light waves do not have the same frequency. A LED loses little energy to heat as it applies most of its energy to light up the diode. This is a very useful property.
To create a simple LED-circuit you only need a couple of components: a LED, a resistance, some wires, a circuit board and a voltage source. We used a blue LED lamp with the properties 20mA and 3.2V, a resistance of 1kΩ and a PHYWE power supply that allowed us to vary our voltage between 0-30V. The LED and the resistance were mounted to the circuit board using a soldering iron, before the wires were soldered to each side of the board (insert figure).
Physics 101 - Wavelength
The given wavelength \(\lambda \) for a lightsource can be found using the following formula:
\begin{align}
\lambda = d sin(\theta)
\end{align}
Where \(d\) is the grid spacing and \(\theta\) is the angle.
Continuing this part we will refer to light as waves. As shown in the picture above, visible light ranges around ∈[400−700] nm. This is known as the wavelength of the light, and to label it we use the symbol \(\lambda\). To better understand the physics we will start by using the rainbow as an example. Most people have had the pleasure to see this magnificent phenomenon in their life. To understand what happens to the light, we need to introduce the term refraction index. In short terms, this means that light will behave differently in different mediums if hit with an angle different than zero from the optical path. For air, the refraction index is simply \(1\), but for water it is \(1.33\), both in vacuum. Using Snell’s law and the fact that the light travels from air to water we can see that the angle with which the light will be emitted can be found by:
\begin{align}
n_1 sin\theta_1 = n_2 sin\theta_2
\end{align}
Physics 101 - (Bio)laser
What is a laser?
A laser is a device that emits monochromatic light amplificated by stimulated emission of electromagnetic radiation, hence the name (“Light Amplification by Stimulated Emission of Radiation”).
The first laser was built in 1960 by Theodore H. Maiman, based on theoretical work by Charles Hard Townes and Arthur Leonard Schawlow. What makes a laser different from other light sources is the fact that it emits its light coherently. This means that the stream of light will stay narrow over a long distance and can also be focused in a tight spot, like for example for laser cutting or a laser pointer.
A laser consists mainly of five parts: the gain medium, the laser pumping energy, the high reflector, an output coupler and a laser beam. The gain medium is a material which allows light to amplify. This is usually located in an optical cavity. What this means is that there is a mirror on either side of the medium, in order to make the light bounce back and forth. This amplifies the light, as it passes through the gain medium each time. One of the mirrors is usually not 100% reflective, since there will a small output (the laser beam). For anything to happen within the optical cavity we need a power source that allows the gain medium to amplify the light. This energy is supplied through a process called pumping and is usually either light or an electrical current.
The biolaser
When we use the term biolaser we refer to a biological component that posesses the same qualities as a laser. What we mean by this, is that the gain medium is now the biological component.
Physics 101 - The Setup
As observed in figure (?), our setup is made up of the following components: LED-circuit, lenses, filters, mirrors, spectrometre and CCD-camera.
The purpose of the lenses is to focuse the light into a thin beam. Not only will this make the LED-light more similar to a laser, but it will make sure we have a higher intensity concentrated on a smaller radius.
In order to make the LED more similar to a laser (monochromatic) we need to filter out quite a bit of its specter. Like mentioned before, LED is not monochromatic, so we will use a blue filter in order to remove all the wavelength we do not wish to use for the GFP or yeast. It is worth mentioning that even though we use filters and lenses to focuse the light, we still have to keep the LED at a maximum of 20V and hopefully the intensity is high enough for lasing to happen.
Ideally, the mirrors we use should be 98% reflective and the last 2% would be emitted light that we could detect. Unfortunately, we have not been able to acquire mirrors of that sort, which is why our setup looks a bit different from that of a regular laser. The mirrors we used had a ??????.
The solution (both GFP or yeast) will go between the mirrors, in order to increase the effect of the light emitted from the solution. In order to gather the light emitted from the GFP, which will be emitted in all directions, we place a big lense next to it which will focus the green light right into a filter that picks out the wavelengths we want to see.
Physics 101 - The spectre
To know if we have achieved laser effect we need to measure the spectre of the light waves emitted from the solution we are working with. The spectre of the GFP is a broad peak as opposed to the laser, which is a clear peak. What we were looking for was the laserpeak, in order to prove we had gotten the proteins to lase.
We were operating a CCD camera that did not include a lense, it only had the detector in place. In order to know if we will get an image we can see and work with (given that the rest of the setup works), we calculated how big the detected image would be.
We are working with wavelengths that go roughly from 505 nm-515 nm, so we wish to calculate the angle between the two waves when they pass through the slit of the spectrometre. We also know that 4000 bars occupy a space of 2.5 cm, so we can calculate \(d\):
\begin{align}
d = 2.5 \cdot 10^{-3} / 4000 = 6.25 \cdot 10^{-6} m \\
\theta = sin^{-1} \left(\frac{505 \cdot 10^{-9}m}{6.25 \cdot 10^{-6}m}\right) = 0.081 rad \\
\phi = sin^{-1} \left(\frac{515 \cdot 10^{-9} m}{6.25 \cdot 10^{-3}}\right) = 0.082 rad
\end{align}
The distance from the grid to the tip of the spectrometre (where we would out our camera) is 0.3m.
So, the space between the two waves (and so, the size of our image) is:
\begin{align}
(0.082 - 0.081) \cdot 0.3m = 0.3mm
\end{align}
It is also worth mentioning that the angle at which the waves pass through the grid is more or less 5 degrees.
To check if this works with our camera, we take the number of pixels pr 5 mm, and get:
\begin{align}
\frac{0.005 m}{750 px} = 6.67 \cdot 10^{-6} = 7 \mu m
\end{align}
Anything bigger than 7 \(\mu \) m should be easily observed, and our image should project at around 0.3 mm, so we are good to go!
This is where the spectrometre and the CCD camera come into play. By knowing more or less the angle at which the spectre will be emitted we can place the camera where the spectre is sure to appear, and get a good measure of the spectre on screen.
![](https://static.igem.org/mediawiki/2017/f/f8/T--UiOslo_norway--modelling_spectrum.png)
![](https://static.igem.org/mediawiki/2017/5/52/T--UiOslo_norway--modelling_LEDcircuit.png)
![](https://static.igem.org/mediawiki/2017/9/99/T--UiOslo_norway--modelling_set_up.png)