Infinite Strings and Imaginary Machines

Infinity Art

 

Strings of symbols dwell in so many realms of our lives; we use them to communicate the language and the stories we share with each other every day. For another example, look slightly deeper into the recesses of your computer and you’ll find streams upon streams of symbols from which emerge fascinating websites and programs which allow humans to come together and connect in new and exciting ways. But how far can we take this? These are examples of using symbols to communicate and store information – be it a fairytale or a photograph. By assigning constraints to the process of forming a sequence of symbols, which we call a string or word, we have what mathematicians call a code. These constrains allow us to interpret meaning, in the same way the constraints which we call grammar empower us to communicate through language. In general, this is a way of creating, capturing and communicating information in an abstract form.

However, we can make this even more enjoyable, because mathematics doesn’t like to live in the real world! So we try and expand these notions into the bizarre and the beautiful to see what things we can create if we take reality with a pinch, or more often a bucketful, of salt. For example, beautiful literature is communicated on paper through sequences of finite words, but what could we create if we delve into the worlds of infinite words, and how might we transform and interact with that which we have created?

So for three weeks I’ve been exploring the effect of some imaginary machines, called synchronising transducers, on bi-infinite strings – which are strings that extend infinitely in both directions. In particular I spent the first week finding isomorphisms between the “group” of such synchronising transducers and other objects such as “sliding block codes” and some “Automorphism groups”. It’s easiest to think of an “isomorphism” as a metaphor. In mathematics we create these ‘metaphors’ because an alternative perspective or representation of an object may be illuminating in some way.

I must be brief (so please forgive me!), but a group is essentially an object mathematicians created to abstractly capture and form a structure of the symmetries of an entity. The second isomorphism I created involved a group of sliding block codes, which are a way of encoding information by mapping ‘windows’ of information on to individual points – which intimately reflects the idea of synchronicity explained later. The last and final isomorphism I looked at concerns automorphism groups, which are a set of isomorphisms between an object and itself together with a notion of how they interact with each other. This last is of particular interest, because the particular automorphism group I looked at concerns the isomorphisms of a well known and extensively studied dynamical system. Thus the isomorphism I worked on will allow us to view this classic object in terms of transducers – an entirely new perspective to explore in future weeks.

I’ve since moved on to begin looking at the order question for these synchronising transducers. That is, trying to understand whether successively transforming a Cantor space with a given transducer will ever cause it to return to its original state.

Mathematicians have pondered similar questions before, but not for the transducers which we call synchronising. This beautiful property defines a structure on the machine, where reading certain words almost magically transports you to a certain state in the machine – regardless of what state you start in. This is analogous to a set of directions to Kings Cross Station which work whether you start in Johannesburg or on Jupiter!

And this is where I stand now! I’m really happy to have seven weeks left to explore this inspiring area and couldn’t be more excited to see where it will lead me.

Lapis Lazuli, Sacrebleu!

lapiselephant

My research so far has been somewhat hindered by the fact that my samples have not yet arrived from America! They were purchased in a physic/palm-reading shop in Los Angeles, where my supervisor learned that lapis lazuli is a ‘gateway-stone’ to palm reading… Clients are tempted in with the promise of pretty stones – no, really! So since the middle of June I’ve been gathering as much data as I can from the relatively limited amount of available literature, most of which dates from the 1970s. The lack of literature is slightly intimidating, but also exciting as I now have the opportunity to use modern instruments and techniques to answer many of the remaining questions surrounding this beautiful gemstone.

Since antiquity, the gemstone lapis lazuli has been admired for its remarkable blue colour. When ground into a powder it becomes the pigment ultramarine, most commonly used in Renaissance depictions of the Virgin Mary. Its principal source is located in the mountainous Badakhshan region of northern Afghanistan, although there are also important deposits in Russia and South America. I am mainly looking at material from Afghanistan.

Lapis lazuli is thought to form during contact metamorphism of limestones and meta-evaporites. The conditions of this metamorphism are almost entirely unknown and uncovering them is the main focus of my research. The formation of lapis lazuli likely involves hydrothermal fluids, and I should be able to deduce the temperature, chemistry and origin of these fluids by examining the ways different elements are partitioned between the minerals lazurite, pyrite and pyrrhotite.

So why does all this matter? Well the knowledge gained during my research could potentially be of use to economic geologists. The rock types that host lapis lazuli can contain valuable metal ores in deposits elsewhere in the world. It could also be used to determine the provenance of historical artefacts, perhaps shedding light on ancient trade routes. At least that’s what I’m hoping for!

My project involves a significant amount of self-leadership, and looking forward I know that the experience will prepare me well for my dissertation and all the challenges next year will bring.

A fermion walked into a bar…

Hello, everyone! Week 5 for me, and I am currently representing a Quantum Mechanical system using balls and springs – only in physics!

I began my project just a few days after my last exam. First I worked to reproduce the initial results obtained by Max, one of the PhD students in physics, thus familiarizing myself with the project so far, and reminding myself how to use Mathematica (the programming language that I would be working in). This involved modelling the “jump” of an optical harmonic trapping potential that contains a lattice of non-interacting fermions.

Instead of falling to the base of the potential gradient—like you would expect from balls rolling into a valley—some of the fermions become “Bragg Localised”. This means that the system acts as though there is an invisible barrier that kicks our figurative balls back up the side of the hill if they start to move too quickly— thus preventing them from rolling to the valley floor. Fortunately, my model also demonstrated this, so I then moved on to simplifying the problem using those balls and springs.

I modelled the centre of mass of the system as a ball on a spring, and a compression wave within the fermion gas as a secondary ball and spring. This reproduced the same centre of mass motion as that observed within the quenched fermionic cloud.

Capture

Introducing the Bragg localisation effect to this simple scenario has proved a little more challenging; however, I have it working now, and am working to match parameters in my simple model to those in the trap-jumped fermionic cloud system. My main problem is, of course, all the error messages while coding!

With half the people I know graduating this week, I am looking forward to graduation weekend to catch up with friends!

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What does Fritillarian even mean anyway?

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A few months ago I was sitting in front of my computer with a research proposal, a supporting letter from my supervisor, and a statement `about my leadership goals all pretty much complete. It was ready to convert to pdf, attach to an email, and send…apart from the title. Y’know, the bit that gets published on websites and stuff. Great.

Let’s backtrack a bit. My research is on the work of the Irish poet Paul Muldoon. He published his first collection when he was still in university, he’s won too many prizes to mention, he teaches at Princeton, and his poems are weird. I’m focusing on his 2010 collection. It’s called Maggot,  a word that has about five different definitions, all of which Muldoon plays with in the book’s 120 pages. This book has a lot in it: three famous elephants, a selection of helpful dolphins, ancient British history, less ancient American history, Irish myth, Classical myth, American foreign policy, forensic science, cannibalistic children, lots of car crashes, a Japanese murder scene, Samuel Beckett, etymological puns, and a whole poem about balls. And that’s just off the top of my head.

(Oh, I forgot to mention earlier, Muldoon was the Oxford Professor of Poetry between 1999 and 2004. The post required him to give a total of fifteen lectures, which he later published in his book The End of the Poem. These aren’t like regular literary criticism. He barely talks about what any of the poems ‘mean’. Instead, he looks at how they link up with other poems through sly intertextual reference, etymology, shared words, and he goes beyond other poems, looking at newspapers, translations, and biographies. About two thirds through the book he writes

I know this kind of reading may sometimes seem a little fritillarian (in the dicey sense which underlies both the butterfly and the flower)

invoking lilies, the butterflies fluttering between them, and the latin fritillus, or dice-box, which comes with its own sense of chancing it.)

Maggot is full of stuff, but is remarkably structured. There isn’t a poem in the book that doesn’t point to another one, and half the poems loop back on themselves too. I’m trying to read Maggot the way Muldoon reads everyone else, and that means making the Flitiralium Firltiralian Fritillarian Reading I eventually decided to mention in my project title.

For the past five weeks I’ve been grappling with the collection’s complex internal structure, and trawling Heaney, Yeats, Frost, Wilbur, Homer, Joyce and W. I. Kipedia to find the little phrases, images, and ideas that Muldoon invokes. I’m not going to come out of this internship being able to say quite what Maggot means. It doesn’t work in the ‘X is like Y so Z’ way, so I’m reading it according to its own rules: playful, surprising, and a little bit dicey. It’s proving difficult, but I’m learning a lot about my subject, the world, and just what it’s like to work on something of this scale. I’ve a lot still to do, and I wish all the other interns good luck for their projects – we’ll definitely need it because how we’re meant to concentrate when Greggs has stopped making macaroni pies, I don’t know.

Meet Staph the Superbug

Greetings from the lab

Greetings from the lab

Hello Laidlaw interns! Five weeks into my project and this is what it’s looking like:

The project: I have cultured 103 isolates of staphylococcus aureus that have been genetically characterised (genome sequenced) by Whole Genome Sequencing (WGS). WGS is very high resolution and accordingly expensive. I will sequence the isolates with a cheaper, rapid but lower resolution technique called MALDI-TOF (Matrix Assisted Light Desorption Ionization- Time Of Flight). I will then compare the two results to see if additional resolution can be extracted from the MALDI-TOF. The project has potential relevance to the diagnostics of  microbiological and infectious disease. The ultimate goal is to apply this to the rapid identification of MRSA (Methicillin Resistant Staphylococcus Aureus) outbreaks, a “superbug” much in the news today.

The problem: The biggest hurdle has been gaining access to the MALDI-TOF machine. I was meant to travel to Liverpool at the start of June to use the MALDI-TOF and collect data, but due to scheduling errors the first opportunity to use the machine is actually a week into July. Given that my project ends a week after this date, my advisor and I had to think of an alternative.

The new plan: In the lab there sits a blue orb-like machine. It was made by one of the PhD’s who created it using a 3D-printer. Essentially it shoots a laser beam onto a sample of isolates and records the pattern of light it reflects which gives information on sensitivity or resistance of an organism. It is typically used for tuberculosis but we will now try to use it for staph aureus. I will still travel to Liverpool at the later date to collect the MALDI-TOF data.

The other things: On Friday, I’ll travel to Kirkcaldy to shadow a diagnostic microbiologist to see the importance of rapid diagnostics first hand.  I’ve also seen the importance of leadership in the face of adversity. After hearing the news that the MALDI-TOF was unavailable, my advisor was immediately thinking of alternatives instead of giving up on the project. He encourages me to think as a scientist and develop my own leadership skills within the project. I feel lucky to be working with him and other bright minds in a research facility.

Good luck to all interns and happy researching!

 

 

 

Plasmons, Waveguides and Invisibility

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Multilayer film made up of PMMA, Silver, PMMA

The internship I am currently undertaking is making steady progress as we round up week 3. We have had a good start at getting to terms with the theory and have already built an analytical model of what we expect. Apart from some minor mishaps (e.g. laser breaking, forgetting how to do simple arithmetic, crashing computers using overly complicated code) it has been an exciting few weeks with lots of new experiences.

The project involves trying to characterise a multilayer film produced in the cleanroom (place where we make high quality samples, incidentally its pretty clean)  that displays some interesting effects when light is incident upon it. We have a few ideas as to what is going on, but still need to get a full set of experimental data from the sample and to have a look at some numerical models. This will hopefully get done in the coming weeks.

What we think is going on is light that is shone on the surface of the film becomes guided, this is a well-documented effect when looking at single layer films but is still a relatively new field when looking at several layers. If the light is guided then it will ‘stick’ to the film and propagate along it. The film’s we make are very thin and this makes them flexible, because of this we can bend them, effectively allowing us to control the direction the light travels. If this is what is going on with our sample, then we can control the light to go around some kind of object rendering the object ‘invisible’.

To get to this point will mean that there is still a huge amount of work to get through over the next 7 weeks and hopefully I’ll be up to the challenge.

I hope everyone else is enjoying their own projects as much as I am enjoying mine and good look for the rest of the summer

multilayerfilm output

Pretty (or not) graph of when we expect light will be guided, peaks correspond to guided light

Can classical music help you concentrate?

When thinking about the research in a neuroscience lab, many of you would imagine participants wearing caps with wires coming out in all directions from their heads. Often in close proximity to these tortured souls there will be an evil, most likely short, experimenter trying to read their brain impulses from a screen. Unfortunately, in this scenario, the short guy with big googles will have to be me.

In all honesty, I came to enjoy this role! Learning how to set up and use electroencephalogram (EEG) was initially challenging, but nevertheless fascinating. It still took me some time to learn how to arrange and connect all 72 electrodes and then clean each of them using a toothbrush! What I didn’t know before is that that the recordings from electrodes on the head (face/scalp/ behind ears) could code for a wide range of information. The latter might vary, for instance, from attention and error monitoring to whether the participant is chewing gum during the experiment.

So far, I’ve spent the last month trying to collect data to answer my main question, namely “Does background music influence one’s performance on a cognitive task?”. Since my work is entirely human-based, it helped me realize how crucial communication and trust could be for obtaining reliable results. For example, explaining the experiment and mentally preparing the participants for what is coming up next have been useful in making them relax and forget about the wires on their heads. At some point, many students even ask for a photo with the EEG cap on, so I’m expecting these pictures to replace the selfie trend very soon.

One last thing I’ve noticed during the internship is the importance of feedback for improving one’s performance. On the one hand, the feedback my advisor has been giving me allowed me not only to learn how to work with the EEG apparatus, but also how to interact with participants. Rule number one was that nobody likes when you try to fit on their head a small cap when their actual size was large.  More importantly, however, the feedback with which I provided students during their behavioral tests (everyone had to complete a cognitive task on a computer) significantly enhanced their performance. That is, explanations of the task together with general encouragement helped most people stay motivated during the experiment and score high on the tests.

If my research sounds good to you and you’d like to take part, feel free to get in touch! Otherwise, enjoy your internships.

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Thanks to Vanya, who was kind enough to let me publish this, you can see our testing conditions, EEG apparatus and genuinely happy participants.

 

Finishing exams, Flying home, and Females in Folk!

Joni Mitchell and Joan Baez in Berkeley, CA, 1980. Photo by Roger Ressmeyer, courtesty of jonimitchell.com.

Joni Mitchell and Joan Baez in Berkeley, CA, 1980.
Photo by Roger Ressmeyer, courtesty of jonimitchell.com.

“Standing on a hill in my mountain of dreams

Telling myself it’s not as hard, hard, hard as it seems…”

Three weeks into my research on the topic “Experiences of Women and Gender in the American Folk Music Revival, 1900-1980”, these lyrics from the song “Going to California” by Led Zeppelin accurately sum up my attitude towards the project. Having originally begun conceptualizing my research last December, months of anticipation came to a head in the last week of May when I was officially free to focus entirely on research of my own devising. It was surreal and overwhelming. Where to start? How to do it justice?

The topic is inspired by a module I took this last semester entitled “Making People’s Music: Folk Music Revival and Society in the United States, 1900 – 1970” with my supervisor Dr Gillian Mitchell, and so the month of May was consumed as usual by revision and exams until I began to re-read literature from that module with a new eye towards the inclusion and treatment of women and role of gender in the so-called “Revival” periods. The aforementioned lyrics are also topical, as the song was reportedly inspired by Joni Mitchell and is thought to refer to her 1967 song “I Had a King”. Mitchell’s musicianship, career, and work are of great interest to me in my research, in addition to individuals including but not limited to Aunt Molly Jackson, Bess Lomax, Sarah Ogan Gunning, Joan Baez, and Emmylou Harris.

Since leaving my beloved St Andrews behind for my native Washington, DC, I have been reading around the careers of those figures and digging into themes like membership and belonging in the Revival movement, image and performance, success, fame, political and protest dimensions, and notions of voice and agency. I decided being back stateside would be best for my internship as I can study sources at the American Folklife Center at the Library of Congress and the Rinzler Folklife Archives and Collections at the Smithsonian, both here in the nation’s capital. DC weather has been duly obliging, the sticky humidity making the inside of an air-conditioned library the best place to be in the city.

However as of now I am in the secondary literature phase of my research, looking at what has been written already with a critical eye, keenly aware of gender, genre, “folk”, and authenticity as social constructions needing to be contextualized. I have been asking questions in my research like: to what extent did folk music live up to its reputation as a genre where the confines of popular music did not apply in terms of its acceptance of women as artist and audience? In its continual search for authenticity, did the Revival incorporate the experiences of American women in its spaces: songs, festivals, venues, publications, and organisations?

The aspect of my internship that is both the most frustrating but also the very inspiration for my topic is that very little work has been done within the existing historiography of the Revival that focuses on women or gender. For me, this near-vacuum is a blessing of sorts because it allows me to combine my interests in gender and music history. Though both of those subschools within the discipline of history are too-often dismissed as not being serious or substantive enough, I firmly agree with what Joan Scott compellingly argued in 1986 (thank you to my second year Historiography module), gender is indeed a “useful category of historical analysis” and that studying cultural productions of a given period will serve to allow us a fuller picture of it. One drawback in being widely interested in so many aspects and offshoots of this seemingly specific topic is that approaching it in an restrained, chronological fashion and staying on task is tricky. I devoured Kim Gordon’s memoir Girl in a Band on the plane back to DC, which proved a fascinating read on gender in the music industry, but unfortunately falls outside the confines of my studies in terms of period and style. Similarly, the collections at American Folklife and Rinzler are both packed to the brim with fascinating material, but I have to keep in mind that I only have 10 weeks to be fortunate enough to climb this “mountain of dreams” looming in front of me- the rest will just have to wait.

A Thin-Film Sensor System for Dual-Phase Explosives Detection

 

Laidlaw3

Welcome to St Andrews! Welcome to the leadership weekend! Welcome to the school of physics and astronomy! Welcome Iain, I hope you enjoy your internship!  If it wasn’t for all of the kind people we meet I’m sure we would feel well out of our depths.  Last week was a week of welcomes, of induction and one of learning and research for me.

Above is shown an example of the sorts of things I’ve been looking at recently, this is the hardware and software design part of the project and I’ll be showing it to my supervisors on Monday to ask for some advice on these preliminary designs.

This is my shot at trying to build an inexpensive measurement instrument capable of recognising hazardous chemicals such as explosives amongst various distractants such as diesel and fertiliser.  Most current devices used in this type of detection require significant sample preparation before measurement but here we are trying to build something which can be used in the field.

There is an array of fluorescent films inside this device, these are excited to fluoresce by an LED (light emitting diode) array.  When the analyte is incident on these films their light emission is ‘quenched’, the camera shown above monitors the intensity of the film and transduces this signal into an electrical signal which is then processed in the Raspberry Pi device shown.  We have tested the instrument for gaseous sensing but now need to update the films and the instrument to work in an aqueous environment.

I have also spent some time in a clean room (where the films are made) which required me to dress up in a suit, mask, gloves, boots and hairnet!  It was a bit stuffy in there but is required to produce high quality work.  I’ll be paying close attention because after next weeks mentoring has finished I’ll be in there myself to fabricate these films!

Wishing you a’ the best,

Iain

 

Consider your origins: you were not made to live as brutes, but to follow virtue and knowledge.

William Blake - The Lovers Whirlwind. (Francesca da Rimini and Paolo Malatesta)

William Blake – The Lovers Whirlwind. (Francesca da Rimini and Paolo Malatesta)

 

A week into my research on the study of literal and visual translations of Dante’s Inferno, I find it hard to believe how much my perspective of this project has changed since I applied for the internship itself, developing as I developed over the months. Over the next nine weeks, I shall analyse two different textual renderings in English of six canti from the famous poem, together with a study of the ways in which those canti have been depicted in art. More than just being a pedantic attempt to repeat what dozens of scholars have already said on the matter, my aim will be to provide an exegetic study of two different types of translation of a text so rich its interpretation is, to this day, still subject to debates. I also hope to be able to interview a contemporary Scottish artist, with the aim of discussing his own way of depicting the Comedy and, with some luck, of convincing him to engage with the established Lectura Dantis Andreapolitana for a sort of multidisciplinary exhibition, later in the year. Fingers crossed.

The Leadership weekend and the online modules on Research Ethics and Methodology have been very useful in shaping the first stages of my research, giving me the tools to prepare myself for the work I was delving into and to make the most out of it. I have had to design a new schedule for my days, involving becoming an early riser (which I am still struggling with) and a balanced ratio of work and rest. As the Proctor had anticipated in her speech, refusing my friends’ invitations to join them at the beach in these torrid days in Italy (I am talking 35 degrees…) has been incredibly challenging. Nevertheless, I am quite satisfied with my work so far, as I have been able to establish the foundations for the following nine weeks of my research.

On June 3rd and 4th I have had the fortune of being able to attend the annual two-day seminar AlmaDante, held by the University of Bologna, which brought together some of the most interesting new takes on the Comedy, with a series of presentations by Phd students from Italian and international academic institutions. Being there as an undergraduate student with little knowledge of philology and linguistics, I found it both intimidating and incredibly motivating. The wide range of presentations made me even more aware of the importance that Dante’s Comedy still holds in literary research as a perennial source of inspiration for further studies in several different disciplines. Most importantly, though, the seminar gave me a lot of new material to think about and to consider for my own work, for which I am incredibly grateful.

To everyone I wish good luck on their research, and an enjoyable summer.