The School of Physics in Edinburgh Is Home to One of the World’S Leading Colloid Physics Groups

School of Physics and Astronomy

BSc/MPhys Senior Honours Year

Physics Computational Physics Physics with Music Physics with Meteorology Astrophysics

Project Guide 2009/2010

September 2009

SENIOR HONOURS PROJECTS

The aim of the Senior Honours projects is to provide an introduction to a longer term and more open ended style of working which characterises Physics as it is practised at the professional level.

At the end of the course you should:

 have learnt how to conduct a comprehensive search of the literature relevant to a research topic and to select and summarise the crucial aspects of the relevant literature

 have gained experience of the organisation and completion of an extended project where the results and outcomes are not fully defined at the beginning

 have learnt how to organise, keep and use a comprehensive log book of the work done in the project

 have learnt how to write a full report including a concise summary of the relevant literature, the pertinent aspects of the method and a critical discussion of the results and conclusions

 have gained experience of the preparation of scientific posters and the oral reporting of results

Senior Honours Project Organiser

The Senior Honours Project Organiser is Prof. F. Muheim (5422 JCMB) e-mail [email protected] Telephone 650 5235. For Astrophysics Senior Honours Projects the local contact is Professor Andy Taylor (U15 ROE, [email protected]).

Selection of Project

Project work is a major element of the Senior Honours programme, both in terms of your time and in terms of its contribution to your final degree. Project work is your main chance to work on your own on a topic of interest to you and to show your own initiative and experimental or computational skill.

The projects in this booklet are arranged in four lists corresponding to the four degrees followed (Physics, Computational Physics, Physics with Music, and Physics with Meteorology).

It is essential that you discuss the proposed project with the supervisor and discuss what it involves prior to starting. Once you have selected a project, tell the supervisor and fill in the green Project Start Form (available from the Teaching Office, the Senior Honours laboratory technician or the Senior Honours Notice Board) which must be returned to the Teaching Office before you start the project. At the start of the semester a large number of people are trying to start projects, so try and make up your mind quickly.

Astrophysics Projects choices are available to view on the web at http://astroprojects.roe.ac.uk/bin/view/Projects/WebHome Astrophysics project are only available to Astrophysics students. Students will have a few days to review the projects and talk to potential supervisors before selecting their three top choices. Allocation will be on a first-come first-served basis. As many projects are oversubscribed, some discussion beforehand may be useful. Note that Astrophysics students should adhere to all the procedures and deadlines detailed below. More details will be given on the first day of this semester.

Please note that some projects rely on the operation of specialist equipment and, if located in a research laboratory, space being available. These projects are subject to cancellation at short notice. In most cases the original supervisor is able to offer an alternative project in that same subject area, but this cannot be guaranteed. If you book a project well ahead of time, check with the supervisor a week before you intend to start to ensure that the project is available.

The degree programme tables place the following constraints on your choices.

BSc Physics You must take one project from the Physics list (or the Science Education Placement). You may take a second project or substitute 20 points of other courses from Schedule Q.

BSc Computational Physics You must take one project from the Computational Physics list (or the Science Education Placement). You may take a second project or substitute 20 points of other courses from Schedule Q.

BSc Physics with Music You must take one project from the Musical Acoustics list. You may take a second project or substitute 20 points of other courses from Schedule Q.

BSc Physics with Meteorology You must take one project from the Physics with Meteorology list. You may take a second project or substitute 20 points of other courses from Schedule Q.

BSc Mathematical Physics You may take one project from the list.

BSc Astrophysics You must take one project from the Astrophysics list (or the Science Education Placement).

MPhys Physics You must take one project from the Physics list (or the Science Education Placement).

MPhys Computational Physics You must take one project from the Computational Physics list (or the Science Education Placement).

MPhys Mathematical Physics You may take one project from the list.

MPhys Astrophysics You must take one project from the Astrophysics list (or the Science Education Placement).

Background Reading

As with all aspects of science, the more background you know about the subject, the more likely you are to understand what is going on and the more likely that you will do a good project. A thorough search of the relevant literature and the selective presentation of the relevant material should form an important part of the introduction section of your report. Most projects have some initial references or background material, but this should be regarded as a starting point only, and it is your task to find other material, with the assistance of the supervisor, and by use of the library and through web databases such as Web of Knowledge (http://wok.mimas.ac.uk).

Background Skills

Some projects require specialist skills such as computing or electronics. In most cases these skills will be stated in the project synopsis, or will be identified for you by the supervisor. Remember that the levels of skills expected are not in excess of what is normally obtainable in your previous years of study. For example if a project asks for computing skills it is expected that you completed Computational Methods successfully, and well. If you are in any doubt, ask the supervisor - preferably before you actually start the project.

Planning the Project

All projects, even those that initially appear to be fairly well determined, need to be planned and where possible, a time schedule and checkpoints set out. Remember you have limited time. Planning what you are going to do will help to keep a project on schedule and ensure that you do not run out of time at the end. It is important for your other studies that you do not let a project drag on beyond its allotted time. Students should produce a one-page project outline with a time schedule.

Laboratory Note Book

During all experimental or computational work you must keep a Laboratory Note Book which is to be submitted with the Report. This book should be used to record the project plan, day to day experiments, list of results, graphs, short notes from references, and any other information you think may be helpful when it comes to writing your report. If you produce graphs on a computer, attach a copy of the graph into the Note Book to ensure you have a record. The Note Book must be written during the laboratory time; it is not useful if it is “written-up”' afterwards.

The Note Book must be a book, not a loose leaf folder from which things tend to get lost or out of order. Suitable books are available for approximately £2.

Supervision

The role of the project supervisor is to aid and guide you in your project and not to stand over you and tell you what do. For most projects the supervisor has a fairly clear idea of where the project should go and what the outcomes should be. Almost all projects are closely related to the supervisor's research interests and expertise, and they will be able to help you in all aspects of the project. If you think of a way that the project could be improved, then say so.

All staff have other teaching duties and will not be available at all times during laboratory days. Additionally many staff have external commitments that take them away from the School. Discuss suitable times for meetings with your supervisor and periods when they will not be available. There are no fixed rules about how often meetings are required. Some projects which require the learning of a specialised technique will involve frequent and extended meetings, while some projects require only occasional contact. You must meet with your supervisor at least once a week, and inform him/her of any periods of absence. Remember, ultimately, it is your project, and if you do not seek advice and discuss problems with the supervisor, or ignore advice given, then don't be surprised if the project runs into trouble.

Most projects go smoothly, and most students enjoy their project work. However problems can occur. If, for some reason the project work is going badly, see your supervisor at the earliest opportunity and discuss what should be done. If you feel that there is still a problem, or would just like to discuss your project with somebody else, see the Senior Honours Project Organiser.

If, for any reason, you decide to abandon a project and start another one, you must inform the Senior Honours Project Organiser, and complete a new Project Start Form.

Laboratory Times

The standard laboratory times for experimental projects are Mondays and Thursdays from 10.00 am to 5.00 pm, in Weeks 2-11 of Semester 1 and Weeks 1-11 of Semester 2. Access outwith these times may be available with agreement from the supervisor or technician in charge of the laboratory, provided that there is safety supervision available. Such access must be arranged in advance.

Undergraduate student access to any experimental laboratory is strictly limited to Monday to Friday 9.00 am to 5.00 pm.

School or University public access computing areas, such as the CP Lab, JCMB PC-Labs etc. are available at times posted on the appropriate notice boards.

Safety

Senior Honours students are expected to work with a considerable degree of independence and be familiar with the contents of the School Safety Leaflet and Keynote Guide. You should have a copy from the Junior Honours (Third Year) laboratory; additional copies can be obtained from Mr George Hughes, Room 4207. It is vitally important to consult the project supervisor about any hazards associated with the project and to follow the recommended working practices. This is of particular importance when working with hazardous chemicals, radioactive materials, X-rays or lasers. Some projects involve experimental procedures that require training or close supervision to be carried out safely: these procedures must be carried out as recommended by your supervisor. Remember also that one of the greatest dangers in the laboratory is the 230/240 Volt mains supply. A copy of the School procedures for supervisors, Safety Procedures for Honours Projects is posted on the Senior Honours Notice Board, and any variation in this procedure should be notified to the Project Organiser.

If you are in any doubt about the safety of any procedure, ask before you do it. You can obtain advice from your project supervisor, the technician in charge of the laboratory where you are working, the Project Organiser or the Senior Honours Year Laboratory technician, Mr George Hughes (Physics) or Mr Jim Boulter (Astrophysics).

Report any accidents, however minor, immediately to your supervisor, to George Hughes or, in the case of research laboratories, to the technician in the laboratory.

Report

You are required to submit a separate report for each project. If you are working with a partner, this report must make it clear which parts of the project were your work, and which parts were carried out by your partner. The report must contain a signed declaration; details of this will be available on-line in due course.

Report Preparation

A guide to assist in the preparation of Senior Honours project reports will be available on-line in due course. The style suggested is that of the formal laboratory report. Clearly one report style is not appropriate for all possible laboratory projects, but the basic layout is common. If you find this style does not fit your particular project feel free to modify it, but major variations should be discussed with your supervisor.

When planning and writing a report, be selective about what you include. There are no fixed rules regarding how long, or short a report should be, but remember you are writing a concise technical document, not a diary or novel, so you don't get any marks for size. Good reports are typically 15 to 20 pages; reports significantly longer than this are frequently too wordy. Technical documents are traditionally written in the third person and in the rather impersonal passive voice. This is no longer considered mandatory. While the first person active voice (I/we) is still considered somewhat radical (in scientific circles), it is gaining respectability. However an arbitrary mixture is not acceptable.

The Poster has been added as an exercise in presenting your work to a non-specialist.

It is expected that reports are typed or word processed. The \LaTeX\ template for the guide referred to above will be made available on the CP lab machines, once finalised.

Workshops on Literature Review, and Report and Poster Preparation

There will be two one hour workshops on literature review and report and poster writing. These will be held on the afternoons of 7th and 28st October 2009 at 2pm in 6301 JCMB.

Report Submission

Physics, Computational Physics, Physics with Meteorology and Musical Acoustic project reports must be submitted to the Teaching Office in JCMB. Astrophysics project reports must be submitted to the Teaching Office in the ROE.

The submission deadline for Semester 1 Projects and Posters is 4th December 2009 – 12:00 NOON

The submission deadline for Semester 2 Projects and Posters is 19th March 2010 – 12:00 NOON

Deadlines for laboratory reports must be adhered to. If you submit your report after the deadline, your project mark out of 100 will be reduced by 5 marks for each weekday by which the deadline is exceeded. If, for good reason, you are unable to meet a deadline you, or your supervisor, should contact the Project Organiser and the Teaching Office immediately. Note that only the Senior Honours Project Organiser can grant extensions to the deadline, not your supervisor.

Poster Presentation

Most national and international scientific conferences have a poster session. This provides an efficient means to communicate results to other interested scientists. As part of the project, a poster session will be held in Semester 2 at 3pm on Thursday 25th March 2010 and will be attended by the project supervisor and second marker for each project. The aim of a poster is to provide enough information to understand the basic sense of the project (the reason for doing the work, the method used and the principal results) which can then be amplified by discussion in front of the poster. A workshop on preparing posters will be held in Semester 1.

Project Assessment

The work done during the project, the poster presentation, the logbook, and the report itself will be assessed according to the criteria specified on the Project Mark Sheet, a copy of which will be available on-line in due course. The final Senior Honours Project mark will be formed from a weighted average of the project work, your poster presentation and report marks.

Contents

1. Physics

1.1 Optics 1.2 Nuclear Physics 1.3 High Energy Physics 1.4 Colloid Physics 1.5 Condensed Matter 1.6 Fluid Dynamics 1.7 Acoustics 1.8 Physics Education

2. Computational Physics

2.1 Computer Simulations

3. Musical Acoustics

3.1 Fluid Dynamics 3.2 Acoustics

4. Physics with Meteorology

4.1 Meteorology

This section contains a list of Honours Projects. Each project has a short description, typically one or two references and the name of the supervisor. It should be noted that because some projects share common equipment, it is not possible to offer all projects at once. Also some projects may be withdrawn, substituted, or added to at short notice. Additional projects will be posted on the Senior Honours Notice Board.

1. Physics

1.1 Optics

Propagation of holographically generated laser modes Contact: Jochen Arlt (Room 2606, extn. 51 7066, email: [email protected])

Laser beams with unusual spatial profiles such as doughnut shaped Laguerre-Gaussian beams have recently emerged as a useful tool for manipulating microscopic particles (‘optical tweezers’), cold atoms and Bose-Einstein Condensates. Such special laser beams are typically generated by modifying a standard beam using spatial light modulators. However, this does not generate pure modes but a superposition of many different modes, giving rise to a complex evolution of beam shape during propagation. Aim of this project is to set up a computer controlled spatial light modulator to generate hollow beams and study their propagation characteristics, especially in the vicinity of a focus.

1.2 Nuclear Physics

Quantum physics: illusion or reality? Contact: P Woods (Room 8203, extn. 50 5283, email: [email protected]) or: Tom Davinson (Room 8205, extn. 50 5250, email: [email protected])

In 1935 Albert Einstein, Boris Podolski and Nathan Rosen published a paper (referred to now as the EPR paper) which brought into question the completeness of quantum mechanics. Their main concern was associated with the predictions that quantum mechanics made concerning the influence that two particles had on each other once they were physically separated outside their interaction range. This called into question the whole concept of external reality in the physical world. In an effort to make quantum theory more complete, the idea of hidden variables was investigated. In 1969, Bell showed that it was possible to identify an experimental test for deciding between conventional quantum mechanics, with its holistic view of reality, or a theory that was based on a more localised concept of reality.

The idea behind the project is to undertake such an experimental test for two correlated gamma rays from the annihilation of a positron emission of Na22 radioactive source.

1.3 High Energy Physics

Muon Lifetime Measurement Contact: Franz Muheim (Room 5422, extn. 50 5235, email: [email protected]) or: Peter Clarke (Room 5421, extn. 50 6798, email: [email protected])

The muon is one of the elementary particles and a very clean probe to study the weak interaction. Cosmic ray muons are produced in the upper atmosphere. Some of these muons reach sea level such that their properties can be measured in the laboratory. The aim of this project is to measure the lifetime and/or the mass of the muon. Muons are stopped in a large block of scintillator, where they subsequently decay into an electron or positron and two neutrinos. A short light pulse is produced by the stopping muon which is detected and amplified by a photomultiplier tube. When the muon decays a second light pulse is produced by the emitted electron or positron. The scintillation light is detected by a the photo multiplier which converts it into an electronic signal. These signals are fed into an electronic circuit which determines the time delay between the two pulses. The circuit is connected to a PC which is used to read out the data. The experiment involves the set-up of the equipment, performing the actual measurement and the subsequent data analysis. You can also determine the mass of the muon by measuring the energy of the electron or positron emitted in the decay of the muon. This can be achieved by recording the pulse height of the photo multiplier signals.

References: http://www.ph.ed.ac.uk/~muheim/teaching/projects/index.html • T.K. Gaisser & T. Stanev, Cosmic rays, in Particle Data Group, Reviews, Astrophysics and Cosmology, http://durpdg.dur.ac.uk/lbl/2007/reviews/contents_sports.html#astroetc • W.R. Leo, Techniques for Nuclear and Particle Physics Experiments, 2nd edition, Springer Verlag (1994) Berlin, Heidelberg • P.R. Bevington & D.K. Robinson, Data Reduction and Error Analysis for the Physical Sciences, 3rd edition, McGraw-Hill (2003)

1.4 Colloid Physics

Modelling polymers using a vibrating chain Contact: Wilson Poon (Room 2620, extn. 50 5297, email: [email protected])

The behaviour of chain-like molecules, polymers, is an intense area of current theoretical and experimental research. Apart from its practical utility, understanding polymers is also a fascinating challenge to fundamental physics. It turns out, for example, that an elegant way of formulating the statistical mechanics of polymers maps the problem onto the Schrödinger equation. One of the first physicists to do this, P-G. de Gennes, was awarded the 1991 Nobel Prize partly for this contribution.

The foundational problem in polymer physics is the statistical behaviour of a long wiggly chain. In reality, of course, this is made up of many molecules (each one known as a ‘monomer’) covalently bonded together to form a giant molecule (macromolecule) of very high molecular weight; the ‘wiggling’ comes from Brownian (thermal) motion. Typically, experimental information has come from X ray or neutron diffraction, which yield information in Fourier space. Direct imaging is usually impossible, because even with tens of thousands of monomers, the whole polymer molecule is still below optical resolution. This problem can be circumvented by resorting to the very large (~ micron) DNA molecules in living cells. By making one of these giant DNA molecules fluorescent, physicists have been able to study the behaviour of a single wiggly chain in real time using optical microscopy.

Another way to access the behaviour of a single chain in real space is by simulating it. Typically this is done using computers. But in 2001, an American team has shown another way [1]: by studying a macroscopic chain on a vibrating table! By analysing video pictures, they showed that the behaviour of a knot in their vibrated chain conformed to the predictions of polymer theory. In particular, they studied experimentally how long a knot took to ‘unknot’ itself as a function of chain length (see figure, taken from [1]). Interestingly, such information is of relevance to understanding the behaviour of DNA in cells.

The vibrated chain can be used to model many aspects of polymer behaviour. You are invited to do just that in this open-ended project. The apparatus provided is very similar to that used by Ben-Naim et al. [1]. We suggest that you first seek to reproduce some of their data to familiarise yourself with the equipment, and to figure out its limitations (and maybe even improve it). Then, in consultation with your supervisors and from your own directed reading of the polymer physics literature, you can take the project in many different directions. Apart from being an opportunity to hone your laboratory skills, this project offers the chance to learn something about a new area of physics (which forms part of the Macromolecular Physics module).

References: [1] E. Ben-Naim et al., Phys. Rev. Letts. 86 (2001) 1414-1417, ‘Knots and random walks in vibrated granular chains’.

The Physics of Colloids Contact: Wilson Poon (Room 2620, extn. 50 5297, email: [email protected]) or: Paul Clegg (Room 2614, extn. 50 5295, email: [email protected])

About a century ago, Albert Einstein and Jean Perrin studied the Brownian motion of particles suspended in water and managed to convince their peers of the reality of atoms. The suspensions they studied were dilute – there weren’t many particles per unit volume of liquid. Today, the tradition they started – studying colloidal suspensions to throw light on fundamental physics – lives on, but the attention has moved on to concentrated systems. One way to measure the concentration is by quoting the volume fraction,  , the fraction of a sample that is made up of solid particles. Einstein’s theories and Perrin’s experiments pertained to suspensions with  << 0.1, while today, colloid physics mainly deals with systems with 0.1 <  < 0.6.

The School of Physics in Edinburgh is home to one of the world’s leading colloid physics groups. For many years, we have studied the behaviour of an extremely well characterized simple system – a suspension of nearly single-sized plastic spheres that interact with each other as nearly-perfect hard spheres (i.e. microscopic ping pong balls). From such a seemingly simple system, we have obtained new insights into issues as diverse as the process of crystallization and the nature of glasses, the latter widely agreed to be one of the ‘grand challenges’ facing twenty-first century physics. We have also used the insights obtained to make sense of more complex systems, such as protein solutions. Interestingly, because our particles are in the micron size range, our main experimental technique is real-space optical microscopy – this is one of the few areas of physics where we actually see what we study (see image of a colloidal crystal, each sphere is 1 μm).

Recently, the group is moving in two directions. First, we are now studying our favourite colloid under external perturbation, most importantly under shear. How a dense colloidal suspension actually flows is a very big mystery; our real-space imaging experiments are proving to be a unique source of information on this hard problem. The data obtained has relevance as far afield as geology (in particular, extreme deformation of rocks). Secondly, we are studying more complex suspensions; in particular, we study the same particles suspended in complicated solvents, such as a mixture of two liquids that don’t like each other. In the latter case, the particles have a tendency to move to the interface between the two liquids. This can be used to create a whole new class of soft materials (we hold a patent on this stuff!).

The group can offer one or more rather open-ended projects in the areas described above. Because research moves rather fast, it is not useful to say in advance what projects you may get involved in. The best thing to do, if you are interested, is to come and talk to one or both of us, and we will give you some ideas of what the up-to-the-moment hot topics are that you may get involved in. Since this is a relatively new area of physics, there are opportunities to make genuinely new discoveries even in the duration of an undergraduate project; indeed, many of our projects end up being published (usually as a part of larger investigations).

Flavour physics - in a Pickering emulsion Contact: Paul Clegg (Room 2614, extn. 50 5295, email: [email protected]) or: Joe Tavacoli (Room 2621, extn. 50 5883, email: [email protected])

Emulsions occur in many food stuffs and drinks as well as in a variety of other personal care and household products. In an emulsion there are droplets of one liquid, called the dispersed phase, surrounded by a second liquid, called the continuous phase. In a food or drink it is normally assumed that it is the flavour of the continuous phase which will be the flavour tasted by the person consuming it. An emulsion where the dispersed phase and continuous phase could easily switch roles would have a switch-able flavour.

Over recent years we have been studying emulsions stabilized by colloidal particles. The micrometer sized particles we use sit at the interface between the two liquids and stabilize the droplets of the dispersed phase. Particle-stabilized emulsions are generally known as Pickering emulsions. They have the property that the dispersed and continuous phases can be switched by changing the proportions of the two liquids alone.

In this project you will work with emulsions made of water and olive oil. To stabilize the droplets you will employ particles which are made of modified rice starch. The aim of the project is to find the range of conditions under which the emulsion can be switched from olive oil droplets in water to water droplets in olive oil. Tasting of samples won’t be required…

Factors affecting colloidal aggregation Contact: John Cosgrove (Room 4306, extn. 662 3344, email: [email protected])

Colloid science is a truly interdisciplinary subject and an area of great current interest. The aggregation of colloidal dispersions is a widely observed phenomenon and a thorough understanding of the factors affecting aggregation is very important to the study of numerous industrial, biological and environmental processes. Numerous system parameters such as salt concentration, pH, temperature, colloid concentration, density etc, have effects on colloidal dispersions and great care is often taken to ensure colloidal particles stay in suspension.

You may investigate the various factors which affect the aggregation of colloidal systems, and: compare experimental results to theoretical predictions, investigate the use of peptization to stabilize colloidal dispersions,

1.5 Condensed Matter

Phonons in 1D Periodic, Aperiodic and Quasicrystal Systems Contact: Malcolm McMahon (Room 3804 (CSEC), extn. 50 5956, email: [email protected])

Phonons are the quantised modes of vibration of a crystalline lattice, and play an important role in the physical properties of materials, such as their thermal conductivity and the speed of sound. In this project, a taut steel wire loaded with carefully positioned small masses is used to model a 1D crystal. A digital lock-in amplifier is then used to measure the normal modes (eigenvalues) of the system. After investigating the acoustic and optical phonons in a monatomic and diatomic system (which repeats the experiment of Luerssen, below), one can then choose to investigate the properties of either a 1D aperiodic system, a 1D random system, a Fibonacci chain (a 1D quasicrystal), or look at the effects of an impurity on the behaviour of phonons.

References: S. He and J.D. Maynard, Detailed Measurements of Inelastic Scattering in Anderson Localisation, Phys. Rev. Lett. 57, 3171 (1986). D. Luerssen et al, A Demonstration of Phonons that Implements Linear Theory, Am. J. Phys. 72, 197 (2004).

Looking for the Devil’s staircase: magnets with singlet ground states Contact: Andrew Huxley (Room 2619, extn. 51 7053, email: [email protected])

It may appear surprising that ferromagnetism can occur at all in metals with magnetic ions having a singlet ground state. The exchange interaction can, however, stimulate a mixing of the singlet states with higher orbits giving rise to a net magnetic moment, realised in several Praseodymium compounds. The project is to synthesise a very pure sample of one of these compounds and characterise its properties by low-temperature magnetisation (and if time permits heat capacity) measurements. Particular attention will be paid to accurately measuring the transition to the ferromagnetic state in low magnetic field. In the one material of this type we have studied to date the transition from paramagnetism to ferromagnetism passes by two intermediate incommensurate magnetic structures, suggesting that it is close to forming a Devil’s staircase; an infinite chain of transitions brought about by competing interactions. The project will help select the best material for future investigation aiming to study quantum critical phenomena around such transitions. The student undertaking it should be a careful experimentalist with a keen interest in theory.

Metamagnets and superconductivity Contact: Andrew Huxley (Room 2619, extn. 51 7053, email: [email protected])

In meta-magnetism a magnetic phase transition is crossed at a temperature that depends on the magnetic field. The transition can be thought as analogous to a liquid vapour transition. For the latter, application of pressure typically weakens the jump in properties at the first-order transition and the transition eventually 'disappears' at a critical point (at the critical pressure and temperature). At this point the phenomena of critical opalescence (large density fluctuations at all length scales) is observed. For meta-magnets, application of magnetic field can also tune a first order transition to a critical point. The critical fulcutations are now those of magnetism rather than density. If the critical point occurs at low temperature, the fluctuations can cause new states of electronic matter to form, some of which are manifest as special forms of superconductivity (see further reading). The project is to prepare crystals of a new material for study. The magnetic properties and heat capactiy of the crystals grown would then be investigated around a magnetic critical point at low temperatures, down to below 0.5K if necessary. The work would make use of low temperature apparatus, crystal growth equipment and X-ray diffraction facilities in the Centre for Science at Extreme Conditions located in the JCMB.

References: F. Lévy, I. Sheikin, B. Grenier, and A. Huxley, Magnetic Field-Induced Superconductivity in the Ferromagnet URhGe, Science 309 (2005), 1343-1346. F. Lévy, I. Sheikin, and A. Huxley, Acute enhancement of the upper critical field for superconductivity approaching a quantum critical point in URhGe. Nature Physics, 3 (2007) 460.

Nucleation of self-assembly in peptide systems Contact: Cait MacPhee (Room 5417, extn. 50 5291, email: [email protected])

Aberrant self-assembly of proteins and polypeptides into nanoscale fibrils is linked to diseases like Alzheimer’s Disease and adult-onset diabetes. Outside the body, it appears that fibrillar self- assembly is a fundamental property of the polypeptide chain, possibly representing the lowest energy state of all proteins. Although we understand increasing amounts about how these structures are formed and what they look like, the initial events that trigger self-assembly remain beyond our grasp. We know that fibril assembly is a nucleated process, and that addition of pre-formed nuclei dramatically accelerates aggregation. This project will use analytical mass spectrometry and light scattering techniques to explore the nucleation event(s) underlying self-assembly of fibrils in a well- characterised model polypeptide system. (With Dr Perdita Barran, Department of Chemistry).

Nucleation of novel morphological forms of calcium phosphate in organic gels Contact: Cait MacPhee (Room 5417, extn. 50 5291, email: [email protected])

Calcium phosphates are the most important inorganic constituents of biological hard tissues, present in bone, teeth, and tendons. In contrast to large geological calcium phosphate crystals which grow over many years under extreme conditions of pressure and temperature, biological calcium phosphates are typically nanocrystals that are precipitated under mild conditions of ambient pressure and room temperature to form complex 3-D architectures. This project will explore the nucleation of novel calcium phosphate structures using simple organic gels, and will use scanning electron microscopy, X-ray diffraction and rheological measurements to explore the influence of gel strength and composition on morphology.

The Physics of DNA-mimic proteins Contact: Wilson Poon (Room 2620, extn. 50 5297, email: [email protected])

A number of proteins in nature are known whose function is to mimic DNA. Viruses use these to 'fool' the defence system of host cells. Like DNA, these proteins carry a very high negative charge density. This is an experimental project, jointly supervised with Dr. David Dryden in the Chemistry Department, on the properties of such proteins. In particular, we want to investigate how these proteins aggregate when salts are added to their solutions. Most proteins precipitate, because the salt screens out the repulsion between the electrostatic charges on nearby protein molecules. In the case of the first of these DNA-mimic proteins we have studied (a protein called 'ocr'), such aggregation is not observed. Instead, for one particular salt (ammonium sulphate), ocr formed a transparent 'gel' at high salt concentration - a unique and unusual behaviour. This project seeks to understand this behaviour better, both by studying mutants of ocr with lower charges, and, possibly, by investigating a newly isolated DNA mimic with even higher charges than ocr.

The Physics of bacterial propulsion in polymer solutions Contact: Wilson Poon (Room 2620, extn. 50 5297, email: [email protected])

The E-coli moves through water is well understood. Each cell is propelled by a bundle of helical 'flagella'. The way this bacterium moves through polymer solutions, however, is very poorly understood. Such understanding is important because in nature, bacteria often find themselves having to negotiate their way through polymeric solutions, e.g. the mucosal lining of mamammlian guts. Polymer solutions are not just more viscous than water. Under the right circumstances, they can be viscoelastic, i.e. have 'bouncy' as well as viscous properties. As a first step towards understanding bacterial propulsion in polymer solutions, we want to do macroscopic 'model' experiments by dropping helical coils of wire (modelling the flagella) through polymer solutions prepared with well-defined properties, and study their motion using video recording. (Such experiments played a cruical role in the original understanding of E.coli motion in water; they were performed by Nobel-Prize-winning physicist, Ed Purcell.)

Measuring the optical properties of homegrown ruby and sapphire Contact: Robin Perry (Room 2604, extn. 51 7234, email: [email protected])

Synthetic gemstones are of enormous use in both the industrial and research sectors. Typical applications include ruby lasers, infra-red optics and insulating wafers in the semiconductor industry. The colour in these gemstones originates from crystal field transitions between d-electron states in impurities ions on the crystal lattice. The parent compound of both Ruby and Sapphire is Al2O3 (trigonal R-3c or Corundum). The structure is three dimensional with six negatively charged oxygen ions surround each triply charged Al. This non-spherical electrical field lifts the energy degeneracy of the d-orbitals on the aluminium ion, splitting them into a triplet and doublet states separated by energy 0. The red colour in Ruby is created by adding small amounts of Chromium impurities into the Al site; the CrO6 octahedron is further distorted to create two atomic transitions at 414nm (purple) and 560nm (green). The photon absorption at these frequencies gives the ruby the red with slight blue colour. The project will involve growing single crystals of ruby and sapphire using an infra-red image furnace; a state-of-the-art device that uses focused radiation to melt material from which a single crystal can be pulled. Crystals of up to several grams can be grown using this technique. Once made, the optical absorption spectra will be measured to understand how the atomic transitions of the transition metal ion control the colour observed in the gemstone. The project is quite open-ended with the several paths available for the curious scientist. For example, chromium is not the only dopant that could be added to the corundum structure, other possibilities include iron and titanium. Successful students might also be permitted to keep the gemstones at the end of the project.

Thermoelectric materials for the 21st century Contact: Robin Perry (Room 2604, extn. 51 7234, email: [email protected]) or: Graeme Ackland (Room 2502, extn. 50 5299, email: [email protected])

Thermoelectric power cells offer the potential of clean electricity generation from waste heat production. The concept of thermoelectric power generation is not new but its full realization has been hampered by a lack of suitable materials. Indeed, one of the best known materials Bismuth Telluride Bi2Te3 was discovered in the 1960’s and there has been little improvement since. Good thermoelectric materials have large thermopower or Seebeck coefficients. The Seebeck effect is the voltage drop across a material when it is placed in a temperature gradient and the polarity depends on the charge of electric carrier; hole or electron. The magnitude of the Seebeck coefficient is extreme sensitive to the electronic band structure and it turns out that there are quite specific predictions for the form of the band structure which will generate a large thermopower. This project will involve modeling the band structure of Bi2Te3 using sophisticated computer code to understand why it has a large Seebeck coefficient. This knowledge will be crucial for developing algorithms to search for new thermoelectric materials. This project is suitable for theoretical students and those interested in modeling and programming.

Crystal structure studies using x-ray diffraction Contact: John Loveday (Room 3801 (CSEC), extn. 51 7233, email: [email protected])

The application of relatively modest pressures makes large changes to the density of a solid. For example, at 100,000 atmospheres the density of ice is double that at ambient pressure. Such large changes in density provide a powerful means to explore the interactions within solid matter. The school has a long established programme of research in studies of the high-pressure structures of elements and simple compounds and state of the art facilities for high-pressure structural studies.

The project provides an introduction to x-ray single crystal structural studies. Initially, ambient pressure studies of simple compounds like iron pyrites (FeS2) and Calcite (CaCO3) will be used to explore techniques for structure solution. Following this, high pressure studies of ice and ammonia monohydrate will be attempted.

1.6 Fluid Dynamics

Breaking Waves Contact: Clive Greated (Room 7306A, extn. 50 5232, email: [email protected])

Wave breaking is one of the most important mechanisms in environmental ocean dynamics. It plays a key role in ocean mixing, sediment transport and coastal erosion. In this project, different breaking mechanisms will be examined using a computer-controlled wave maker in a water channel. Breakers will be generated by both superposition and bed interaction and will be studied by still and video photography. The mixing of surface pollutants by breaking will also be examined.

References: Measured internal kinematics for shoaling waves with theoretical comparisons Griffiths MW, Easson WJ, Greated CA Journal of waterway port coastal and ocean engineering-ASCE 118 (3): 280-299 May-Jun 1992 Geometry and Kinematics of Breaking Waves Lader PF PhD thesis 2002 Trondheim Technical University

Flow measurement using Laser Doppler Anemometry Contact: Clive Greated (Room 7306A, extn. 50 5232, email: [email protected])

Laser Doppler Anemometry (LDA) is one of the most powerful and widely-used techniques for measuring flow in both fluid dynamics research and industrial applications. In this technique, a laser beam is split and the two components focused down to the measuring point. Light scattered by tiny particles in the fluid is then collected and analysed, the spectrum of the signal being related to the mean flow and turbulence characteristics. In this experiment, the flow in a small channel will be analysed using LDA. Of particular interest will be the transition of turbulence.

References: Laser Systems in Flow Measurement T S Durrani and C A Greated , Plenum 1977 Cardiovascular Fluid Dynamics Bergel. DH (1972).. Academic Press, New York, vols.1, 2. S H Douglas, C A Greated, R Royles, et al. Analysis of non-stationary Doppler signals ACTA ACUST UNITED AC 89(3):430-434 May-Jun 2003.

1.7 Acoustics

Electronic Music Synthesis Contact: Clive Greated (Room 7306A, extn. 50 5232, email: [email protected])

The project will investigate the use of two techniques (a) frequency modulation and (b) wave shaping, for the generation of musical tones. The first part of the project will involve investigating the temporal and spectral characteristics of sounds from at least one chosen instrument e.g. a trumpet, a clarinet, a drum or a tubular bell. A simulation program will then be written in CSOUND, a programming language specially designed for sound synthesis. The final submission should include a CD of selected synthesized sound fragments.

It is recommended that students opting for this project should attend lectures for the course Sound Synthesis, taken by Music Technology students but they will NOT sit the examination. The lectures are given in JCMB and include instruction of CSOUND programming.

References: Curtis Roads 'The computer music tutorial' MIT Press 1996 Charles Dodge and Thomas A Jerse 'Computer Music' Schirmer 1997 Richard Boulanger (Ed) 'The CSOUND book' MIT Press 2000 Murray Campbell, Clive Greated and Arnold Myers 'Musical Instruments' OUP 2004

Stereoscopic sound localization Contact: Clive Greated (Room 7306A, extn. 50 5232, email: [email protected])

This project investigates the ability of humans to localize auditory events on the horizontal plane using two ears. Rayleigh’s duplex theory of inter-aural time and intensity differences will be investigated through a series of experiments on a dummy head in the anechoic room and the limitations of the theory examined. Spectral position cues will be analyzed using head-related transfer functions. A stereoscopic loudspeaker configuration will be used to implement different ways of panning virtual sound images.

References: J Blauert "Spatial Hearing: The Psychophysics of Human Sound Localistion" MIT Press 1997 F Rumsey "Spatial Audio" Focal Press, Elsevier 2001 F R Moore "Elements of Computer music" Prentice Hall 1990 W Hartmann "Signals, Sound and Sensation" Springer 1997

The Singing Bubble Contact: Clive Greated (Room 7306A, extn. 50 5232, email: [email protected])

When a bubble is formed in water it will oscillate and emit acoustic energy. The frequency of the sound produced depends on its size and other parameters. This process is of great importance in a number of industrial problems but also in the environment e.g. the sound produced by breaking waves in the ocean and the effect of rain on the surface of water.

The aim of this project is to study the fundamental mechanism by which sound is produced by bubbles. Tiny bubbles will be release in a water tank and the sound measured using a hydrophone. The sound files will be analysed by spectral analysis and comparisons made with theoretical predictions. Finally the more complex situation of a stream of bubbles from a tube will be studied. Theory for this is not well understood.

References: Leighton, T. and Walton, A. ‘An experimental study of the sound emitted by gas bubbles in a liquid.’ Eur J Phys 8 pp 98-104 (1987). Leighton, T. The Acoustic Bubble. Academic Press 1994.

Acoustic pulse reflectometry Contact: Murray Campbell (Room 7306, extn. 50 5262, email: [email protected])

Acoustic pulse reflectometry is a non-invasive technique for measuring the internal dimensions of musical wind instruments and other ducts. A sequence of sound pulses is injected into the duct under investigation, and the reflections returning from the duct are recorded. Suitable computer analysis yields information about the internal bore profile. In this project the accuracy of the technique will be investigated through measurements on simple tubes whose dimensions are known. A number of musical instruments will also be studied, with a view to exploring the relationship between an instrument’s physical shape and its playing characteristics.

References: D.B. Sharp and D.M. Campbell, Leak detection in pipes using acoustic pulse reflectometry, Acustica- Acta Acustica 83, 560-566, 1997. J.M. Buick, J. Kemp, D.B. Sharp, M. van Walstijn, D.M. Campbell and R.A. Smith, Distinguishing between similar tubular objects using pulse reflectometry, Meas.Sci.Technol. 13, 750-757, 2002.

Influence of key movement on the sound of a pipe organ Contact: Murray Campbell (Room 7306, extn. 50 5262, email: [email protected]) or: Alan Woolley (Room 4306, extn. 50 5259, email: [email protected])

Many players of mechanical action pipe organs believe that they can significantly influence the sound of the organ by the way in which the keys are pressed down. Recent research has suggested that in many cases this belief is erroneous. In this project an experimental pipe organ will be used to investigate the physics of the key mechanism in the mechanical action organ. Small laser sensors will be used to track the motion of different parts of the action in synchronism with the recording of the sound from the pipe, in an attempt to gain a clearer understanding of the way in which the starting and stopping transients in the sound are related to the motion of the key.

References: A.G.Woolley, The Physical Characteristics of Mechanical Pipe Organ Actions and How They Affect Musical Performance, PhD Thesis, University of Edinburgh, 2006. N.H. Fletcher and T.D. Rossing, Physics of Musical Instruments, 2nd ed., Springer, 1998. M. Campbell and C. Greated, The Musician’s Guide to Acoustics, Oxford University Press, 1987.

Input impedance of musical wind instruments Contact: Murray Campbell (Room 7306, extn. 50 5262, email: [email protected])

The Physics Department's anechoic chamber houses an experimental apparatus for measuring the response of musical wind instruments. Projects this session will include development of the PC interface, and studies of a variety of brass instruments.

Optical techniques for the study of vibrating objects Contact: Murray Campbell (Room 7306, extn. 50 5262, email: [email protected]) or: David Skulina (Room 4306, extn. 50 5259, email: [email protected])

Optical techniques can provide valuable information about the normal modes of vibrating objects such as musical percussion instruments and loudspeaker cones. In this project three techniques can be explored. The simplest is the study of the Chladni patterns formed when sand is sprinkled on the vibration object. More detailed information can be obtained using a laser vibrometer, which derives the velocity of a vibrating object from measurement of the Doppler shift in a reflected laser beam. Finally an electronic speckle pattern interferometer can be used to visualise in real time the operating deflection shapes of the vibrating object.

References: N.H. Fletcher and T.D. Rossing, Physics of Musical Instruments, 2nd ed., Springer, 1998. M. Campbell and C. Greated, The Musician’s Guide to Acoustics, Oxford University Press, 1987. T.R. Moore, A simple design for an electronic speckle pattern interferometer, Am.J.Phys. 72, 1380- 1384, 2004.

The vibration of piano strings Contact: Murray Campbell (Room 7306, extn. 50 5262, email: [email protected])

On a well tuned piano, the fundamental frequencies of two strings an octave apart have a frequency ratio slightly greater than 2. This “stretched tuning” is related to the fact that the normal mode frequencies of a stiff string depart in a systematic way from the harmonic series which characterises an ideal flexible string. In this experiment the inharmonicity of real strings on grand and upright pianos is compared with theoretical predictions. The decay rates of single and multiple strings can also be investigated.

References: H. Fletcher, Normal vibration frequencies of a stiff piano string, J.Acoust.Soc.Am. 36, 203-209, 1964. G. Weinreich, Coupled piano strings, J.Acoust.Soc.Am. 62, 1474-1483, 1977. N.H. Fletcher and T.D. Rossing, Physics of Musical Instruments, 2nd ed., Springer, 1998. M. Campbell and C. Greated, The Musician’s Guide to Acoustics, Oxford University Press, 1987.

Vibrations of bars and plates Contact: Murray Campbell (Room 7306, extn. 50 5262, email: [email protected])

Impulsively excited long thin bars have natural mode frequencies which are far from harmonic. For a uniform bar, the theory is straightforward; for non-uniform bars, numerical predictions can be made. Glockenspiels, xylophones and tubular bells provide musical examples. Two dimensional plates have more complicated sets of natural modes than bars. Square and circular plates can be investigated; the small tuned cymbals known as crotales would make an interesting study.

1.8 Physics Education

Over-assessment and 'live marking' in undergraduate pre-Honours Physics Contact: Simon Bates (Room 5416, extn. 50 5285, email: [email protected])

A huge amount of staff time and effort is invested in marking weekly assignments throughout undergraduate Physics. If the feedback provided is not acted upon by students (or even worse if scripts are left uncollected) then we should ask if this volume and method of assessment and feedback is as effective and efficient as it could be. If it is not, then we should investigate alternatives.

This project has two main aims, and two distinct parts to the investigation: (i) To investigate (via Monte Carlo simulation) what the critical volume of marked assessment is per student on a given course to ensure preservation of broad grade similarities (to within a certain tolerance). (ii) To evaluate the effectiveness of an alternative assessment and feedback methodology that we term 'live marking': the student's work is marked in real-time, in the presence of the student, and the dialogue audio recorded and emailed to the student for further reflection. The first of these is a computing and data analysis exercise making use of historical course mark data in various pre-Hon courses. The second aspect of the project is an action-research investigation which requires the design and execution of the evaluation protocol (but not the marking!) The project is ideally suited to a reasonably computer-literate student with a keen interest in how the subject is taught, and will be supervised by members of staff / PG students with an interest in Physics Education Research.

Expertise in Physics Contact: Simon Bates (Room 5416, extn. 50 5285, email: [email protected]) or: Ross Galloway (Room 5414, extn. 50 8614, email: [email protected])

One of the main aims of a physics degree is to progress undergraduate students from a novice view of physics towards a more expert view. But is this a gradual progression for students, or something more akin to a phase change, with a step change in expertise at some critical moment? And what is an 'expert view' of the subject and how physics is 'done'? Is there a concensus amongst 'expert' practictioners about what expert views actually are?

This project will attempt to answer questions such as these. It will build on on-going work in Physics Education Research in the school, specifically looking at the delivery and analysis of the Colorado Learning Attitudes about Science Survey (CLASS). This instrument measures attitudes and beliefs towards physics, rather than content knowledge, and has been widely used in North America, but has not been applied within the UK undergraduate system. Last year, we gave this survey to first year students on entry and also at the end of their first year of study. Our results show that there are some interesting differences between our data and that previously published, particularly when the data are split according to degree intention and gender. This has prompted us to consider how expertness develops during the undergraduate programme and also to question if the 'expert view' of the survey, derived from faculty responses at the University of Colorado, is shared by staff in the UK.

The project will involve quantitative analysis of previously-obtained CLASS data, together with collection and and analysis of new data, supported by an appropriately devised qualitative analysis program. It will be of interest to students who are considering a career in education or science communication, and those with an interest in Physics education at undergraduate level.

Deployment and evaluation of a concept test for pre-honours quantum mechanics Contact: Judy Hardy (Room 3403, extn. 50 6716, email: [email protected])

Concept tests are being used increasingly in science education, both to gauge students’ understanding of the concepts underpinning a particular subject area and to evaluate the effectiveness of the teaching approaches used. One of the best-known examples is the Force Concept Inventory (Hestenes et al, 1992), which is widely deployed in physics undergraduate teaching to check students’ conceptual understanding of Newtonian mechanics. More recently, a quantum mechanics concept test has been developed (Archer, 2009). Many of the concepts and ideas associated with quantum mechanics are non-intuitive and difficult, and this test is aimed at uncovering misconceptions at the introductory (pre-Hons) level. Addressing misconceptions at this early stage should, in turn, help students with the more advanced treatment of the subject that they will encounter in higher-level (Hons) courses.

In this project, the quantum mechanics concept test will be administered to students taking the semester 2 course Physics 2B, both pre- and post-instruction. It is also planned to administer the test to students taking equivalent courses at Glasgow University and the University of St Andrews. The results will be analysed in terms of the following research questions:

• To what extent does performance improve pre- to post-instruction? • What are the common misconceptions, and how successfully have these been addressed? • Do direct entry students perform significantly differently compared to students who have encountered quantum mechanics previously? • How does the performance of students from different universities compare?

Time permitting, and depending on the interests of the student, there will be scope for refining questions and / or feedback in the test, or for a wider investigation into student views of quantum mechanics learning and teaching.

References: Hestenes, D., Wells, M., & Swackhammer, G., Force Concept Inventory, The Physics Teacher, 30, 141 (1992). Archer, R.S.K., Towards a Quantum Mechanical Concept Inventory, MSc Dissertation, University of Edinburgh (2009). 2. Computational Physics

2.1 Computer Simulations

Lotka-Volterra waves Contact: Graeme Ackland (Room 2502, extn. 50 5299, email: [email protected])

The Lotka-Volterra (LV) equations describe the coevolution of a predator prey system. They cannot be solved analytically, but numerically give oscillations. When implemented on a grid as a cellular automaton equivalent to the differential equation form, with an added spatial dimension, the LV equations produce not only oscillations in time, but also waves. This project involves studying these waves. You will need good programming skills (the main code and graphics can be provided) and creative thinking for making measurements from data. More details at… http://www.ph.ed.ac.uk/nania/lv/lv.html

Skills: This project requires creativity, imagination and java coding skills. No special skills at a Junior or Senior Honours level needed.

Explosives and armour: Molecular dynamics of shock waves Contact: Graeme Ackland (Room 2502, extn. 50 5299, email: [email protected])

In this project you will simulate a shock wave travelling along a 1D chain.

The chain comprises masses connected by anharmonic springs, which have two "natural" lengths (energy minima). You will write a computer program to simulate their motion as one end of the chain is displaced at constant velocity, straining the medium. The shock wave will induce transitions between the two lengths.

There are three cases. If the two spring minima are the same, we are simulating Twinning Induced Plasticity (TWIP), where the strain is accommodated by formation of crystal twins. If we start in the lower energy state, the transformation absorbs energy: this is Transformation Induced Plasticity (TRIP). TRIP and TWIP are new types of damage resistant steel. Finally, if we start in the higher energy state, the shock wave releases energy: this models an explosive.

Chaos in a two particle system Contact: Graeme Ackland (Room 2502, extn. 50 5299, email: [email protected])

This project involves writing a computer programme to simulate two elastic particles falling under gravity and colliding with a hard surface. The programme will follow the equations of motion of the particles, finding the chaotic and non-chaotic regions. A comparison between random and chaotic phase space sampling will be made. By the end of the project you should obtain a complete solution of a 2007 Physics Skills paper question. An extension to relativistic particles and/or non-constant gravitational field is possible.

Skills The project involves developing a short computer code from scratch, and developing some visualisation software to examine the results. You will need some elementary dynamics, programming skills and some ideas from JH Statistical Mechanics will be introduced.

References: A rather similar project can be seen in "How efficiently do hard rods sample phase space?" S.G.Cox and G.J.Ackland, Phys.Rev.Letters, 84, 2362 (2000)

The motion of asteroid 3753 Cruithne -- Earth's second Moon? Contact: Arjun Berera (Room 4411, extn. 50 5246, email: [email protected])

The near-Earth asteroid 3753 Cruithne is now known to be a companion, and an unusual one, of the Earth. This asteroid shares the Earth's orbit, its motion 'choreographed' in such a way as to remain stable and avoid colliding with our planet. This relationship was revealed in a paper by Paul Wiegert, Kim Innanen and Seppo Mikkola, and published in Nature on June 12, 1997. However, Cruithne's path is much more complicated than simple satellite motion. The aim of this project is to write a program (probably in C) to simulate the orbit of Cruithne and to investigate its stability.

Relevant Physics: Computer Programming, orbital dynamics.

Multi-shift iterative solution of QCD Dirac Equation Contact: Peter Boyle (Room 4407, extn. 50 5233, email: [email protected])

The Lattice QCD simulation approach solves non-perturbative hadronic field theory using Monte Carlo methods. A critical component of this is the solution of the quark Dirac equation in a background vector gauge potential that the Monte Carlo has selected.

This project will develop generalised version of the conjugate gradient algorithm for solving the Dirac equation simultaneously for multiple quark masses.

The starting point will be from an implementation of the single mass conjugate gradient algorithm.

Solving the QCD Dirac equation with Graphics Cards Contact: Peter Boyle (Room 4407, extn. 50 5233, email: [email protected])

This project is appropriate for computer literate students, perhaps with some experience of assembler programming a bonus.

The Lattice QCD quark Dirac equation will be implemented and solved using graphics cards. These current provide up to 1 TFlop/s theoretical performance, and can be exploited to accelerate scientific computation. Once implemented, a numerical analysis component may be involved to limit the effects of reduced numerical precision on the accuracy of results.

Computational studies of proteins and protein-ligand interactions Contact: Lindsay Sawyer (Room 3.29, Swann Building, extn. 50 7062, email: [email protected])

There will be at least one project available looking at the interaction of small molecule ligands with proteins. The field of molecular recognition is one that is currently of great interest and importance to, inter alia, the pharmaceutical industry. There are also possible projects in molecular dynamics simulation of modelled protein structures, in the electrostatics of protein molecules, and in the detailed analysis of existing protein structures including protein metal interactions. A flavour of the field can be found in the references below, all of which are available in the Darwin Library or on-line. One possible project is to investigate the trajectory of a substrate as it is converted to a product by an enzyme and to see if there is an essential rotation of part of the molecule relative to the rest of it, during the reaction. Another might be to investigate the relationship between the length of the saturated fatty acid ligand, its conformation (twist around the C-C bonds) and the binding constant. We have X-ray crystallographic data on some of these compounds so that the theory and the experiment can be compared. Most of the software is written but its application will require both understanding and ingenuity. Some knowledge of chemical structure would be an advantage. Interested students might like to contact L Sawyer for a preliminary discussion.

References: Overviews Dinner, AR; Sali, A; Smith, LJ; Dobson, CM; Karplus, M (2000) Understanding protein folding via free- energy surfaces from theory and experiment Trends Biochem.Sci. 25,331-339 Daniel, RM, Dunn, RV, Finney, JL, Smith, JC (2003) The role of dynamics in enzyme activity Ann.Rev.Biophys. Biomol.Struct. 32, 69-92 Jorgensen, WL (2004) The many roles of computation in drug discovery. Science 303,1813-1818 Alberts, IL, Todorov, NP, Dean, PM (2005) Receptor flexibility in de novo ligand design and docking. J.Med.Chem. 48,6585-6596 Karplus, M, Kuriyan, J (2005) Molecular dynamics and protein function. Proc.Natl.Acad.Sci.USA 102,6679-6685

More specific Daura, X; Haaksma, E; van Gunsteren, WF (2000) Factor Xa: Simulation studies with an eye to inhibitor design. J. Comput.-Aided Mol. Des. 14,507-529 Mordasini, T, Curioni, A, Andreoni, W (2003) Why do divalent metal ions either promote or inhibit enzymatic reactions? - The case of BamHI restriction endonuclease from combined quantum- classical simulations J.Biol.Chem. 278, 4381-4384 Wu, SY et al. (2003) Discovery of a novel family of CDK inhibitors with the program LIDAEUS: Structural basis for ligand-induced disordering of the activation loop Structure 11, 399-410 Gumbart, J, Wang, Y, Aksimentiev, A, Tajkhorshid, E, Schulten, K (2005) Molecular dynamics simulations of proteins in lipid bilayers. Curr.Opin.Struct.Biol. 15,423-431 Freddolino, PL, Arkhipov, AS, Larson, SB, McPherson, A, Schulten, K (2006) Molecular dynamics simulations of the complete satellite tobacco mosaic virus. Structure 14, 437-449 Jain, T, Jayaram, B (2005) An all atom energy based computational protocol for predicting binding affinities of protein-ligand complexes. FEBS Lett. 579, 6659-6666 Glattli, A, Chandrasekhar, I, van Gunsteren, WF (2006) A molecular dynamics study of the bee venom melittin in aqueous solution, in methanol, and inserted in a phospholipid bilayer Eur.Biophys.J.Biophys.Lett. 35,255-267 3. Musical Acoustics

3.1 Fluid Dynamics

Breaking Waves Contact: Clive Greated (Room 7306A, extn. 50 5232, email: [email protected])

Flow measurement using Laser Doppler Anemometry Contact: Clive Greated (Room 7306A, extn. 50 5232, email: [email protected])

3.2 Acoustics

Electronic Music Synthesis Contact: Clive Greated (Room 7306A, extn. 50 5232, email: [email protected])

Stereoscopic sound localization Contact: Clive Greated (Room 7306A, extn. 50 5232, email: [email protected])

The Singing Bubble Contact: Clive Greated (Room 7306A, extn. 50 5232, email: [email protected])

Acoustic pulse reflectometry Contact: Murray Campbell (Room 7306, extn. 50 5262, email: [email protected])

Input impedance of musical wind instruments Contact: Murray Campbell (Room 7306, extn. 50 5262, email: [email protected])

The vibration of piano strings Contact: Murray Campbell (Room 7306, extn. 50 5262, email: [email protected])

Vibrations of bars and plates Contact: Murray Campbell (Room 7306, extn. 50 5262, email: [email protected])

4.1 Meteorology

Evolving River Networks (Semester 2 only) Contact: Mark Naylor (Room 317, Grant Institute, extn. 50 4918, email: [email protected]) or: Mikael Attal (Room Room 1.05b, Geography Building, extn. 50 8533, email: [email protected])

Fluvial landscapes are draped by river networks that provide a pathway for water to drain off the landscape. These river networks self organise in response to changes in uplift distribution, base level and climate but potential new networks are also constrained by the inherited (antecedent) drainage network and the local erosion mechanism (either transport or detachment limited erosion). Transport limited erosion occurs in rivers where there is an excess of loose material such that the rate of erosion and deposition is controlled by the amount of water that can mobilise that material, and is characterised by a diffusive response. Detachment limited erosion occurs by the abrasion of bedrock; in contrast to the diffusive transport limited process, discontinuities in the profile advect upstream rather than diffusing away. The difference between these erosional algorithms has been investigated analytically for 1D stream profiles [1], but a computational approach is required to investigate network evolution [2]. You will use an existing computational coupled tectonic-erosion landscape evolution model (CHILD) to investigate the system scale differences in river networks that emerge from these different local erosional processes [3]. You require a working knowledge of C++ (the language CHILD is written in), graphing or statistical software and an interest in learning about fluvial geomorphology.

References: [1] Whipple, K. X., and G. E. Tucker (2002), Implications of sediment-flux-dependent river incision models for landscape evolution, Journal Of Geophysical Research-Solid Earth, 107. [2] Hergarten, S., and H. J. Neugebauer (2001), Self-Organized Critical Drainage Networks, Physical Review Letters, 86, 2689. [3] Tucker, G.E., S.T. Lancaster, N.M. Gasparini, and R.L. Bras (2001), The Channel-Hillslope Integrated Landscape Development Model (CHILD) http://www.geo.oregonstate.edu/~lancasts/TuckerEtAl_CHILD_2001_nofigs.pdf

Markov Chain Monte Carlo (MCMC) Inversion of a Hillslope Evolution Model Contact: Mark Naylor (Room 317, Grant Institute, extn. 50 4918, email: [email protected]) or: Simon Mudd (Room 1.05d, Geography Building, extn. 50 2535, email: [email protected])

Hillslope profiles and soil thickness distributions respond to changes in base level (i.e. the level of the river at the bottom of the hill) [1]. For example, if the river cuts down faster, a transient signal of that lowering will propagate up the hillslope and potentially mobilise soils. Therefore the distributions can be used to invert for the base level history. In this case, MCMC methods [2] involve (i) taking some assumed base level history, (ii) perturbing a point in that history (iii) running a forward model to estimate new hillslope profiles (iv) choosing whether to accept the new history by a Metropolis-Hastings Algorithm [3] (v) storing the favoured history and repeating. In this way we iterate towards the best solution whilst exploring parameter space in such a way that confidence intervals can be bootstrapped. The project is therefore to take an existing hillslope evolution simulation code [1] and write an MCMC inversion scheme [2] to invert modern, measured hillslope and soil thickness data for some erosional baselevel history. You will require an interest in statistical inversion by simulation, coding skills in Python, R and preferably C++.

References: [1] Mudd, S.M., and D.J. Furbish (2007), Responses of soil mantled hillslopes to transient channel incision rates, Journal of Geophysical Research-Earth Surface, 112, F03S18, doi:10.1029/2006JF000516 [2] K. Gallagher, K. Charvin, S. Nielsen, M. Sambridge and J. Stephenson (2009) Markov chain Monte Carlo (MCMC) sampling methods to determine optimal models, model resolution and model choice for Earth Science problems Marine and Petroleum Geology 26(4) pages 525-535 [3] See Web. e.g Wikipedia or http://kossi.physics.hmc.edu/courses/p170/Metropolis.pdf

Climate predictions for the nearterm: Effect of volcanic eruptions Contact: Gabi Hegerl (Room 353 Grant Institute, extn. 51 9092, email: [email protected]) or: Tom Crowley (Room 343 Grant Institute, extn. 50 5339, email: [email protected])

Predictions of climate within the next 30 years assume increases in greenhouse gases and other anthropogenic forcing in the next few decades, but do not account for the possibility of volcanic eruptions. This project analyzes a record of volcanism in the last millennium to estimate the likelihood of no, one minor, one major, or several volcanic eruptions in the next decade. An analysis with European mean temperatures can yield an estimate of what kinds of seasonal temperature changes each of these cases would trigger compared to the predictions that are being performed. The tools involve analysis of a reconstruction of volcanic forcing over the past few centuries and of a temperature timeseries, ideally with an interpreted language such as matlab.

References: Meehl, G.A., L Goddard, J Murphy, R.J. Stouffer, G Boer, G Danabasoglu, K Dixon, MA Gorgetta, AM Greene, E. Hawkins, G Hegerl, D Karoly, N Keenlyside, M Kimoto, B Kirtman, A Navarra, R Pulwarty, D Smith, D Stammer and T Stockdale (2009): Decadal Prediction: Can it be skillful? BAMS, in press. Hyde, W and Crowley, TJ (2000): Probability of future climatically significant volcanic eruptions. J Climate 13, 1445-1450

Is Arctic sea-ice thinning connected to UK summer weather and precipitation? Conact: Ruth Doherty (Room 308 Crew Building, extn. 50 6759, email: [email protected]) or: Chris Merchant (Room 305 Crew Building, extn. 50 5097, email: [email protected]) or: Gabi Hegerl (Room 353 Grant Institute, extn. 51 9092, email: [email protected])

Summer sea-ice extent around Greenland is reducing, with 2007 and 2008 the lowest and second- lowest on record (at time of writing) and both markedly below the trend over previous decades. These same two years were characterized by wet cool summers in the UK, with low pressure systems persistently tracking south of the climatological path for summer.

Is there a relationship between these observations? While we can deduce little from two summers, an analysis of data over a few decades may reveal whether such features tend to go hand. The idea is not implausible: Arctic summer sea-ice melting may be enhanced by higher pressure in the Arctic, associated with a tendency for Atlantic low pressure systems to track less northeastwards – and more eastwards towards the UK.

This project will investigate this speculations by analysing satellite datasets of Arctic summer sea-ice extent in combination with meteorological station rainfall datasets over the UK and summer surface pressure patterns. A possible extension to the project would be to run a storm track detector over historical weather analyses to count the number of low pressure systems (or low pressure days) over the UK for the last 30 summers or so.

Mapped data and summary data on sea ice extent are readily available, based on microwave sensors on satellites and other observations. UK summer rainfall data will be provided. In the extended project, datasets of daily sea-level pressure will be used to drive the TRACK model in order to estimate count and track Atlantic low pressure systems, and their central pressure. The student will analyse the trends in these datasets, will look for correlations to determine if any relationships exists, and will begin to explore the nature of any correlations found. Help will be given with setting up and running the TRACK model. Data analysis for pairs of time series could be done in Excel. For working with mapped data (e.g., looking at pressure patterns) familiarity with or willingness to learn R, IDL, Matlab or equivalent would be required.

Statistical analysis of lightning and earthquakes – is there evidence of a link? (Semester 1 only) Contact: David Stevenson (Room 314 Crew Building, extn. 50 6750, email: [email protected]) or: Ian Main (Room 314 Grant Institute, extn. 50 4911, email: [email protected]) or: Paul Odams

This project will test the highly controversial hypothesis that some earthquakes are near-coincident in time and space with lightning. Clearly, if unusual lightning activity precedes seismicity, this offers potential for earthquake forecasting. The student will need to have, or rapidly learn, good skills in data analysis and a high level computer language (e.g., IDL, Matlab, R).

Lightning locations (latitude, longitude, time) for the last 1-2 years are available from the Met Office detection system. Lightning flashes generate electromagnetic waves that are detected at a network of VLF (Very Long Frequency) receiving stations. If waves from the same event are detected at three or more stations, the lightning can be located, generally to within an uncertainty of a few km. The Met Office network detects lightning over much of Europe, and in some instances as far afield as North Africa and Central Asia; the detection region is limited by amounts of atmospheric water vapour. Most lightning occurs in clusters, associated with weather systems dominated by strong convection, but some events are more isolated.

Earthquake locations (latitude, longitude, depth, magnitude, time, and focal mechanism) can be downloaded for a region of interest from global earthquake catalogues available on the web (e.g. www.globalcmt.org/CMTsearch.html). Correlations between the two datasets will then be probed, and various statistical tests carried out to determine if there is any link between the two. Literature on the subject will also be critically reviewed.

Statistical analysis of altitudinal gradients in mountain climate and the free atmosphere Contact: Richard Essery (Room 353b Grant Institute, extn. 51 9093, email: [email protected])

Mountain environments are characterized by high spatial variability and are expected to be particularly sensitive to climate change, but observational networks are sparse in mountainous regions and climate models operate on scales that are coarse in comparison with important scales of mountain climate variability. Temperatures generally decrease with height in the free atmosphere, but vertical temperature gradients on mountain slopes are modified by energy exchanges at the surface. Together with orographic variations in precipitation, this has important influences on mountain vegetation zones, snowcover and glaciation. Prediction of these influences requires methods for interpolating observations and downscaling climate model outputs over mountain landscapes.

This project will make use of air temperature and other environmental variables measured by automatic weather stations at varying elevations in a mountainous area and measured in the free atmosphere by radiosondes. Several questions could be explored. How do near-surface and free- atmosphere lapse rates differ? How do these differences vary with time of day and time of year? Can physical explanations be found for these variations? How accurately can upland conditions be predicted if only lowland observations are available? Questions such as these could be addressed with Excel, although the use of a statistical package (e.g. R, S-Plus or SPSS) would be more appropriate.

Background reading: Barry, RG (1992). Mountain weather and climate. Routledge, London, 402 pp. (JCM Library shelfmark QC993.6 Bar)

Forecasting maximum and minimum temperatures Contact: Richard Essery (Room 353b Grant Institute, extn. 51 9093, email: [email protected])

Long before the widespread use of numerical weather forecasting, empirical techniques were developed to allow short-term forecasts of meteorological variables. For example, simple graphical methods of forecasting surface air temperatures for the following day can be used with midnight radiosonde temperature profiles (which are freely available on the internet). Your mission, should you choose to accept it, is to produce maximum and minimum temperature forecasts for Edinburgh and compare them with observations at the KB weather station. Forecasts should be made for as many days as possible to calculate verification statistics and to identify synoptic situations for which the forecasts can be expected to perform well or poorly. The Met Office produces 5-day forecasts of daytime and minimum temperatures for UK towns; can your daily forecasts beat the professionals at any of these lead times?

Background reading: Johnston, DW, 1958. The estimation of maximum daily temperatures from the tephigram. Meteorological Magazine, 79, 33 – 41. (available on request form the JCM library)

Impacts of possible future emissions of CO2 and other greenhouse gases using a simple climate model (20 Credit project) Contact: Simon Tett (Room 351 Grant Institute, extn. 50 5341, email: [email protected]) or: Dave Reay (Room G.06 Drummond Library, extn. 50 7723, email: [email protected])

The Copenhagen conference happens in December 2009. It aims to reach agreement on reductions in emissions of carbon dioxide and other greenhouse gases to avoid dangerous climate change. Avoiding dangerous climate change is thought to require that global-mean warming is kept to less than 2 degrees centigrade relative to pre-industrial conditions.

The aim of this project is to use a simple climate model to quantify the climatic consequences (e.g., surface temperature changes) of possible future emission pathways and to see which could lead to a warming of less than 2 degrees relative to pre-industrial. It could also be used to assess the consequences of different possible negotiating positions. Recent research (e.g. Allen, et al, 2009) suggest that warming is more sensitive to total emissions of carbon dioxide than to the emissions pathway and the model will also be used to explore this. The model that would be used is the “Model for the Assessment of Greenhouse-gas Induced Climate Change” (MAGICC) (http://www.cgd.ucar.edu/cas/wigley/magicc/) includes simple representations of the climate system, including the carbon cycle, atmosphere, ocean and the cryosphere and can be run on a desktop machine. It has been used to explore the impacts of many possible future emission scenarios.

References: Allen, M et al: “Warming caused by cumulative carbon emissions towards the trillionth tonne” Doi: 10.1038/nature08019

Climate Analysis: Are recent Scottish Temperatures unusual? Contact: Simon Tett (Room 351 Grant Institute, extn. 50 5341, email: [email protected]) or: Gabi Hegerl (Room 353 Grant Institute, extn. 51 9092, email: [email protected])

One of the longest instrumental records of temperature is the Central England Temperature time series (Parker and Horton, 2005). This record extends back to the 18th century. Jones and Lister, 2004 generated a record of Scottish monthly-mean temperatures which, with some uncertainty, extend back to 1800. The aim of the project is to explore how changes and variability in the Scottish record compare with CET and other records. The focus would be on recent 30-40 year trends in temperature partitioned by season or month and how these compare with trends from the earlier part of the record.

An extended version of the project would be to explore, using model results, the relative contribution of human and natural drivers to recent Scottish changes.

References: Jones, PD and Lister, D “The development of monthly temperature series for Scotland and Northern Ireland” Parker, DE and Horton, B “Uncertainties in central England temperature 1878-2003 and some improvements to the maximum and minimum series”. DOI 10.1002/joc.1190

Antarctic temperature variability and change Contact: G. Hegerl (Room 353 Grant Institute, extn. 51 9092, email: [email protected])

Antarctica has a unique climate, and high temperature variability that varies with the seasonal cycle. This project aims at analyzing daily station data from Antarctica, and analyzing changes in its seasonal cycle over time (from the 1950s to the present) and between locations (McMurdo station to stations more inland). It has been demonstrated that Antarctic temperature patterns have been influenced by changes in the composition of the atmosphere, including increases in greenhouse gases and the depletion of stratospheric ozone. However, how have these influenced temperature variability, which varies strongly between circulation stages? How unusual compared to the present records are the temperatures that Scott’s ill fated expedition faced in march 1911? The student will investigate this question by analyzing daily data from several Antarctic sites for their mean temperature distribution, frequency of cold air outbreaks and seasonal cycle as well as for changes in this temperature distribution. The project requires data analysis, which would work best using an interpreted language such as matlab, R or IDL.

Background reading: Gillett, N., D. Stone, P. Stott and G. Hegerl (2008): Attribution of polar warming to human influences. Nature GeoSciences, 1, 750 - 754 (2008) . Solomon, S. 2001: The coldest March. Yale University press, 383pp.

Numerical experiments with a lake stratification model Contact: Chris Merchant (Room 305 Crew Building, extn. 50 5097, email: [email protected]) or: Stuart MacCallum (Room 311 Crew Building, extn. 50 5096, email: [email protected])

In this project we will use a "simple" lake model which calculates the profile of temperature of lakes through seasonal variations, and includes the creation and destruction of lake ice cover. This is an off- the-shelf model designed to be incorporated as a subroutine for representing lakes in full scale numerical weather prediction. It calculates a temperature profile for a lake as a whole, as well as freeze and thaw events.

The objective is to run the model in comparison with observations for selected large lakes in the US, Canada and Sweden, and to draw detailed conclusions about the model's performance when applied to such water bodies.

Lakes exhibit some interesting physics and are of great importance to the societies nearby. Doing this project will give a good insight into how lakes "work" thermodynamically.

Has global warming stopped? Contact: Chris Merchant (Room 305 Crew Building, extn. 50 5097, email: [email protected])

The blogosphere is stuffed with self-appointed sages who declare that global warming has stopped (because the warmest year on record was over a decade ago). Is this a sensible interpretation of the data? This project is essentially to consider recent annual global mean temperatures and answer that question. But don't be fooled by the apparent simplicity of the question and the simple form of the data. Coming up with a well-reasoned analysis will require subtle statistical thinking.