Decapentaene pi orbitals - Particle in a box

While tutoring in physical chemistry this year I wanted to show the students how simple models like the particle in a box can come quite close to describing the electron motion in real molecules. So I used molcalc a great tool that lets you build molecules and then run calculations in Gamess and display the orbitals in the browser. I plotted the solutions in python for comparison.

Shrinking down chemical analysis - microTAS 2014

Just got back from microTAS conference 2014 (micro total analysis systems). The conference was all about miniaturised chemical detectors. A lot of what was shown was lab-on-a-chip devices which makes use of semiconductor chip technology to fabricate channels in plastics to automate lab work.

Prof. Dino Di Carlo's Young Innovator Award presentation at #MicroTAS https://t.co/bgpkgLOK5Q pic.twitter.com/GboYNdYDA1

— Thomas Levario (@ThomasLevario) October 28, 2014

One of the questions I often get when I show off microfluidic chips is "What's so amazing about that?". Most people don't have a macroscale reference to see how amazing fluid moves in small channels. So the day before we had to leave for San Antonio we decided to do an experiment for the video competition (very quickly!!) where we went from a macrofluidic mixer to a microfluidic mixer. We ended up placing in the top 3 videos at microTAS the only educational video.


Just to give a taster as to what was at microTAS here are some of the amazing devices that were being shown off.

Digital microfluidics
A.H.C. Ng gave a presentation on a digital microfluidic system from the wheeler lab from the University of Toronto that automated the synthesis of gold nanoparticles with DNA bound only on one side of the nanoparticle which can then self assemble into structures.

I was surprised to find out that the digital microfluidics platform they developed is open source and is available online. All is needed is a high voltage power supply and some pcbs and an arduino. They also got a video into the top three videos at microTAS which shows off their open source digital microfluidic device Dropbot.

Droplet to digital microfluidics
Steve C. C. Shih presented a talk on his new droplet to digital system from the Joint Bioenergy Institute USA. A droplet maker was used to put single yeast cells into each drop. These were then transferred over to a digital microfluidic device that mixed the droplets with an ionic liquid. The idea was to see how ionic liquids damage the yeast. As ionic liquids can be used to help convert cellulose into sugars for biofuel production. However the ionic liquids can damage the yeast cells which are meant to eat the sugars.

They designed and made the whole system using arduino's. The device really leveraged the best out of both technologies and has been published in lab on a chip last week

 

Inertial microfluidics
I went to a workshop run by Assoc. Prof. Di Carlo on inertial microfluidics. Two main forces dictate if a microfluidic flow will be laminar (Steady and predictable) or turbulent (unsteady and difficult to model); inertial forces, which relates to the momentum of the fluid and viscous forces, where the fluid resists being sheared. Often when modelling microfluidics we ignore inertia and arrive at Stokes flow. However a recent review by Assoc. Prof. Di Carlo looked at including these effects and the different phenomenon that can be observed.

You are also able to arrange particles in a flow due to the way the particles deform the flow. This deformation is felt by other particles and leads to nicely ordered particles in channels.

http://biomicrofluidics.com/research.php

You can use this to put individual particles or cells into single droplets which is super useful for doing lots of cell based analysis.

http://biomicrofluidics.com/research.php

It can also be used to align particles along a channel.

As fluid moves around a corner or around a barrier you get vortices set up which allow you to more easily mix solutions. Which as I showed with the mixer at the beginning of this post is quite difficult.

 uFlow was demonstrated a program written in python that allows for calculation of the flow pattern at the outlet. If you were to do this with a finite element modelling program it would take hours to run each time. To reduce this time they calculated advection maps (transport map) for pillars at different places in the channel and operated on the concentration profile by these maps to make the simulation run in real time. This was a really interesting way to speed up simulations in microfluidics and I am thinking about what else could be simulated in this way.

http://biomicrofluidics.com/software.php

Nanotech wedding ring

New Zealand is known for the Lord of the Rings trilogy and so I took the opportunity recently when I got married to make the precious. But I couldn't resist including some nanotechnology in the design.

Shane Hartdegen a great teacher and designer of jewellery made both my wife and my wedding rings and I wanted to explain the design as we had a lot of fun with the materials. There are four concentric rings of different metals.

From the outside in there is electrochemically recycled gold, followed by white gold which was made from forged gold and palladium, then a copper layer giving a nice orange colour and inside is titanium which would normally be grey in appearance but by heating it in the flame a very thin layer of titanium oxide is formed that allows light to interfere and produce this blue-purple colour.

I was intrigued about how a grey metal could produce so many amazing colours. It all comes down to a small layer of oxide that is formed when you heat treat the metal. This nanocoating is on the order of the wavelength of light.

Figure of a 50 nm in (a) and (b), 550 nm in (c) and (d), 750 nm in (e) and (f), layer of Titanium dioxide grown on a layer of indium tin oxide a conductive film. The layer was grown with atomic layer deposition and is as close as I could find to oxide growth on Titanium metal however you would probably not get such a porous structure.

http://iopscience.iop.org/0957-4484/23/12/125707/article 

What optical effect causes some colours to be reflected (such as blue and purple in this case) but not other colours such as yellow. The phenomenon responsible is called interference and occurs as the light bouncing off the top of the oxide layer and off the oxide metal interface interfere. Only certain wavelengths will constructively interfere and be reflected. 

http://www.valhallaarms.com/wyvern/titanium/anodizing.htm

To work out what wavelengths will be reflected you can use similar formulas to Bragg's law which is used for measuring the thickness of layer of crystals, however that require much shorter wavelength x-rays.

http://harryysherwood.wordpress.com/2013/11/25/proof-by-anodisation/

This effects allows us to determine the thickness of the layer by determining the colour of the film (as has been done by harry sherwood on his blog)

A more common way to deposit the oxide layer is by using electricity through a process called electrolysis where titanium ions in the solution are neutralised by the electrons given from the anode allowing for the depositing of the metal. This method allows for a wide range of colours to be created.

 

http://www.valhallaarms.com/wyvern/titanium/anodizing.htm

Electrolysis was the method used to recycle the gold used in the ring. Most gold is made through dissolving rocks in cyanide solutions. These are harmful for the environment. We decided to recycle gold from old jewelery. First the jewelery was dissolved in an acid solution followed by electrolysis onto the anode and finally smelting it to form the metals needed.

Shane has gone on to do more with this multi-component design and I recommend checking out more of his work.