kaijaks.co.uk

VEGASmagic

VEGASmagic is a program for converting files produced by the VEGAS simulation code for medium energy ion scattering spectroscopy (MEIS) for visualisation. It was written for 32-bit Windows (95/98/ME/NT/2000) and developed as part of my doctoral work.

It extracts atomic position information from VEGAS input, output and crystal files, and writes new crystal files. It can also read and write Tripos' Alchemy and Brookhaven Data Bank format (PDB) files. The latter ability is particularly useful as it enables VEGAS models to be viewed in macromolecular visualization software, such as RasMol.

The program is provided as is. Full (but simple) conditions are described within the zipfile.
Version 1.21a, 26 March 2000, 226K

Once a Physicist…

I've a PhD in Physics, from the University of Warwick. My thesis, submitted in 2000, was on ion scattering spectroscopy of III-V semiconductor surfaces. Semiconductors like this are used in optoelectronics like the lasers in Blu-Ray players. All this clever tech relies on carefully manufactured crystal structures, like layers of Lego—only on a nano-scale.

I was exploring how atoms arrange themselves in the top few layers of atoms on crystals of these semiconductors. This page gives a brief overview of how. Since it was originally written, Wikipedia and Britney Spears' Guide to Semiconductor Physics have been invented, which I’ve linked to give you options to learn more. If you want the full monty, you can even find a link to my thesis below.

Semiconductor surfaces 101

Inside a crystal

Deep inside a crystal (in the bulk), each atom is completely surrounded by other atoms. Like someone squashed in the middle of a festival crowd, each atom experiences similar forces acting from all sides. Because every atom experiences similar forces, they all behave the same way, and that's why they tend to line up to form a nearly perfect regular crystal structure, like the salt crystals you probably saw in science class as a kid.

Surfaces are special

However, atoms at surfaces behave differently from atoms deep within a crystal. At the top surface, the atoms don't have forces acting from above. To stick with the festival analogy, it's like the people at the back of a crowd who are relatively free to wander off. Without the balancing forces from atoms above them, the surface atoms naturally tend to re-organize themselves or reconstruct. They tend to lie in regular patterns on top of the surface. To stretch the analogy, imagine synchronised swimmers at our festival, who decide to crowd-surf—staying in a pattern together above the crowd below. Understanding these reconstructions is useful if you want to design small-scale electronic and optical devices. It's the atomic structure that fixes the physical (and so the electronic) properties of the material.

What’s the frequency, Kenneth?

There are many reconstructions which are relatively stable. The actual pattern depends on how they are created (for instance you often see different reconstructions which are stable at different temperatures). Most reconstructions have their structure repeating at simple multiples of the bulk crystal pattern (or unit cell). You see these described by shorthands such as 4x4 or 1x3 (where the pattern repeat is three times less frequent in one direction than the other). However, whilst the dimensions may be simple multiples of the bulk structure, the actual arrangement of atoms within many of these reconstructions is unknown or only partly understood. You may be able to see that there is a pattern, but not what it is.

Four years in four paragraphs

My work used surface science analytical techniques which are sensitive only to the top few atomic layers of crystals, such as low energy electron diffraction (LEED) and Auger electron spectroscopy (AES). These techniques require an ultra-high vacuum (UHV) of around one millionth of a millionth of an atmosphere (give or take) to keep the surfaces free from contamination, and to ensure that the electrons and ion beams used can move without being affected by the atoms of the air itself.

However, most of my work was performed using two separate UHV systems to perform ion-scattering spectroscopy (ISS). One was the CAICISS system (pronounced kye-siss), of the Surface Physics group in the Department of Physics at the University of Warwick. CAICISS is a low-energy ion-scattering spectroscopic technique, described in detail elsewhere. The other main system was at the MEIS facility at Daresbury Laboratory. This was the UK's central facility for medium-energy ion-scattering spectroscopy until its funding was withdrawn in 2010. My work was funded by a studentship from the EPSRC.

These analytical techniques don’t give you a direct picture of the surface’s structure. You only get second-hand information which you can use to try to infer the structure—like trying to tell what someone looks like if you can only see their shadow. In the case of ISS, you create a computer model of what you think the surface structure is, simulate the scattering experiment, and compare to the results of the real experiment to see whether your model is a good fit.

The materials were prepared in vacuo using atomic hydrogen cleaning (AHC) at different temperatures to create clean, reconstructed surfaces. Using ISS, I identified conditions required to create a number of specific reconstructions using AHC. I identified some novel reconstructions, and proposed some structures that might cause them.

The end

I was admitted to the degree of Doctor of Philosophy in Physics, of the University of Warwick, on 12 January 2001. My doctoral thesis is available for download in PDF format (screen-resolution, 3.42M). If you read it, please let me know! Since then, I have gained the professional qualifications of Chartered Scientist, Chartered Physicist, and full membership of the Institute of Physics. So, I'm now Dr Nick Kaijaks, CSci CPhys MInstP. Yay me!