Congratulations of Sarah and Rebecca, both graduating from the MPhy course. It was a pleasure to have you in the lab. Will you be back?
It appears that there is a rumps in the Quantum world. At a major scientific conference (15th ICQC: conference website) the first round of invited speakers, chairs and honorary chairs were all men. Three leading women academics in the field decided to boycott the event. The conference organisers have responded and amended their list. See http://iopenshell.usc.edu/wtc/ICQC/icqc_story.html for further details.
Whatever the ins and outs of this case, it does highlight the inbuilt gender bias in science. But it also shows that there is now a fight to redress this bias. What we have to ask ourselves is, in 2014 is it really acceptable to be happy with such small steps taken to begin addressing the issues? Really by now we should expect equality and not have to strive for it. But strive we all must (unless one really is sexist in which case you may wish to rage against the dying of the light).
I will be signing the petition born from the ICQC incident here
Here is a "class photo" of an invitation only conference taken some time ago:
So we've used up all the storage space in our last post, but here is the rest of the story...
Week 8: Oh what a lovely crumble!
So this week we needed to sort out the jolting in our images resulting from the chairs of the caffeine fueled drinkers in the cafe upstairs. To do this high density rubber pads were placed under the feet of the STM to dampen the vibrations. But nothing is ever that simple, and so we needed to re-align the STM again so ensure the microscope could hang freely on its springs. As the centre of mass is not in the middle of this set-up, this led to a fun game of turning each leg a quarter of a turn in various combinations until we could see the bubble of the spirit level move.
As we are getting closer to starting our experiment and now we have more of a handle on all the terminology, it was time for us to look into understanding how the tunneling actually works and causes the Toluene on our surface to float away. So there were lots and lots of diagrams going on!Then it was time to start dosing the surface with Toluene. To do this, another LabVIEW program is used to control the opening of the test tube's value and measure the amount of the chemical dosed. Only the stepper motor doesn't seem to want to talk to LabVIEW at the moment so Duncan had to open the value manually. We dosed 5 langmuirs onto the surface which saturated the Silicon so it can no longer bond with more. The maximum coverage is actually 50% of the surface, because the Toluene needs to form 2 bonds, so a maximum of 6 Toluene molecules per unit cell are seen. Scanning the surface now looks like it is really dirty, but this is because the Toluene appears as dark blobs. This is why it was so important to get a clean sample in the first place, so now we know the dark blobs are actually Toluene and not some other dirt like we had been seeing previously.
We took lots of images with this set-up and tried to check our thermal drift still works... you guessed it... we made another movie!! Yippeeee!
With the Toluene splattered all over our sample, we had a go at some non-local desorbing. Peter fished out his old program to do this, and walked us through how it runs. We had a few goes at different injection voltages, trying to find the threshold. Here's one example of how things come and go over time.
The final excitement for the week was getting to try out Peters local LabVIEW program, where we can click an Toluene molecule to desorb and the tip is automatically moved to this selected position to carry out an injection! Snazzy!
Week 9: Tuesday's Trauma
Monday brought along more playing around with the injection program, but more practicing than taking actual data. It's cool to be able to see how much more comfortable we are with 'playing' with things in the lab now. When we first got here, watching Peter and Duncan fiddle with buttons and voltages and programs looked totally out of our depth! It's funny how happy we are now with things such as perfecting the tip by digging up silicon from the surface with a high negative bias, or shaking it off with a high positive bias. In fact we're now left alone to move the sample here and there, and still haven't dropped it!
On Tuesday evening just before we left we were retracting the tip and about to pluck the sample plate out of its enclosure (casually), when we looked a little closer and noticed things weren't quite as happy as they normally are. The tip seemed to be at an odd angle to the sample, and we knew enough to know that misalignment could be a big deal! As happy as we are with things, we still know when it's best for us to just walk away. We left the skewed microscope be, and hastily rang up to Peter. He confirmed our hesitancy, and told us to leave it to him. We spent Wednesday in emotional turmoil...after all these weeks of set up had we gone and broken it?! (We'd barely touched it so we weren't sure how we could have!). We hid in the lab reading, until Thursday morning, when Peter and Duncan came and reassured us that everything was fine. Something had just slipped off its track, but was easily fixable without having to open everything up (YIPPEE!!!).
With things back on track (!) we got back to the job in hand: physics. The point and click injection program was now ready to go, so our questions about local desorption could finally be investigated. On Friday we toyed with this a little, ready to take proper measurements next week.
Also this week: we dabbled in LabVIEW a little more, proof-read an Athena SWAN (encouraging woman in physics) application (causing much debate among our peers), and yet more paper reading.
Week 10: The Final Countdown
With only 10 days to go it's time for some serious data collection. Now the multiple-point-'n'-shoot program works we can collect 5 current injections within one scan making everything so much quicker! In the time it took us to take 30 injection last week was now have around 150! We accidentally learned how OCD we can be about things, when without meaning to noticed just how beautifully ordered the data was recorded in the log book! Although it's just the not too important recording of what each file saved contains, everyone is very aware of the importance of keeping to the right coloured pens when. So much so that if someone dares to make a mistake, it is soon corrected as best as can. It's just a shame we're not as fussed about keeping it in straight lines...
So you can see we are recording the experiment number, and then the parameters set for each. We are alternating between the values the bias is rammed to: a choice of 1.5, 1.8, and 2 V, all below the threshold for non-local desorptions. Current values are picked accordingly. At first for all voltages, a current of 200 pA was used, but we were seeing so few desorptions for 1.5 V and 1.8 V it was decided to increase the number of electrons so events were more likely to happen. All the injections last 15s. At first we played around with the number of injections to do for each data set, so kept a note of this, but even since deciding to stick to five every time we have insisted on keeping our pretty pattern with writing it down. We also just keep a note of which ones of those 5 we think actually did desorb. The program saves the tip height as a function of time, so desorptions can be seen. Because the toluene molecule does not have empty states below the scanning voltage, they are 'seen' by the tip as reason to move closer to the surface in order to maintain the tunneling current. So when a molecule flies away, the tip is now exposed to the juicy p-orbital of the Silicon atom underneath, which much more readily accepts the electrons. This causes the tunneling current to go up, so the tip pulls away to balance the feedback loop again. So watching the tip height as a function of time, we can tell exactly when the desorption occurs. Clever, ay?
I have just walked up the hill to the University of Bath listening to my radio. On the Today program there was an interview with the head of Ofqual explaining the new GCSE (or whatever they are) exams. Instead of 8 grades as we presently have they will have 9 and so there will be more “differentiation” between candidates. I am due to write ½ an exam paper today for my bit of Quantum and Atomic Physics (PH20013/60) and that got me thinking.
Many moons ago Universities judged students by asking them questions in one-two-one interviews, or vivas as we call them. But these are time consuming and open to the whim of the examiner. So written exams were introduced. We still have them. I have sat countless exam papers during my school and undergraduate life. Apart from my very last exam as an UG, I always did well, hence why I’m now lecturer. I have to say I always enjoyed them, the 1-2-1 combat of pitting myself against the cunning and sly lecturer.
But exams are not really about the top end showing off. They are about giving a grade to a student that can be entered into a spread-sheet so that upon graduation a student can be given the correct piece of paper which tells the world something about them. But what does it tell? What are these elusive marks that is at the core of the game we play at University? These are grand ideas and questions that will have little bearing on how I in practice compile my exam paper.
Here’s roughly how I do it:
(1) Read through the lecture notes and the unit outline to get a feel for what I said the students should be able to do.
(2) Split the total number of marks roughly equally between the main section of the course.
(3) Write out questions for 40 % of my marks that allow conscientious and studious students (who will know more about the subject than those who didn’t sit through the lectures) but yet who are really not very bright, to pass. These will be typically “state the principle of…” style questions showing a bit of knowledge. And perhaps a few repeat questions already covered in problem sheets.
(4) Write a few more questions for say 20 % on number crunching.
(5) The next 20 % go on more extended questions on the physics of the course, which gets at understanding and may well include unseen questions.
(6) Finally the last 20 % bit. These will include physics from outside the course, typically from an earlier year, to see if the candidate can see the bigger picture and how things fit together.
OK, but the candidate has a set time for this and in this time we try and ensure we ask questions on as much of the course as possible, and we try to see if the candidate can think. This is hard.
I look through past papers, look at the course work problems, in books and on line for good ideas for questions. I bung them together. I then sit the exam myself and if I can’t physically write out all the answers in the half the allotted time, the exam is too long. I then revise the questions and, if I am feeling really diligent, I sit the exam again. Phew.
Marking? Well, I write out mark scheme for each of my questions. I divvy the marks up based on the length of the question and the degree of toughness, which usually reflects the number of “physics” steps required to get the answers.
I’m finished! I had in my exam and answers to the University and relax. How do we ensure my questions are fair? Peer review. One of my colleagues reads my paper and makes comment. Then we send it off to an external colleague and they also make comments. Once all these QA process have been ticked off I have it, a document that will tell me if you are worth 58 %, or 61 % or perhaps 36 % or even 97 % (well done). But wait, my exam is out of 60 marks, so the smallest % quantum is 1. 7%. But wait, the University explicitly bans certain % totals, the examiner is asked to review certain percentages and think again. But only for these cases, and with the understanding (or at least my understanding) that I’ll just bump the % up out of these forbidden zones. But we don’t do this for all, so the % scale is not only quantised but is also non-linear. These are the obvious sources of uncertainty on a final mark, what about the over sources?
What if a question or exam paper is just too easy or too hard. What then? Now we get into the world of normalization, mark scaling and other schnanagins so that the average mark looks OK. Last year I set an exciting and interesting exam. It was excellent. It really tested the understanding of the students and allowed many to shine and really show they are excellent physicists and scientists with broad grasp of the subject and a good understanding of how it all fits together. Well done me (and them).
However, what also happened was that the middling students, who are contentious and worked hard were shafted. I had slightly changed the rules on them. I had somehow abandoned my scheme outlined above and tried to get at understanding a bit more. Or it could have been just a slightly badly worded questions, or slightly too much in the paper, or a bit that I taught badly and the students just didn’t get. The upshot was a lot of post-processing to make the outcome fair for the students, fair that is in terms of the overall game that we play at University.
There is a lot of room for error, there is a lot of subjectivity, there is a lot of cross-correlation, there is a lot of reliance on the setter (me!) knowing the difference between a 56 % student and a 58 % student. These grades are important, but perhaps should come with a standard deviation.
Will the new GCSE exams, with their 9 grades, really have a standard deviation of less than 2 %?
Recommended listening for this post:
Sometimes, life can feel like you're stuck in the part of the training montage where nothing is going right. No matter how much you "wax on, wax off", the finish on Mr. Miyagi's car remains lacklustre. While Rocky Balboa can magically improve once the inspirational music gets to the chorus, we have to deal with, and learn from our mistakes in real time. This can be frustrating.
However, with enough time and perseverance, you can reach the end of the montage.
The Silicon lab is reopened.
During the fourth year of an MPhys degree at Bath, students are required to pick a research project to join for semester one. Our names are Rebecca and Sarah and we selected to join the atomic manipulation group. After completing the STM lab in 3rd year, and being given a tour of Peter's 4W lab, we were excited to begin. This weekly blog is a lighthearted view of the trials and tribulations of our Masters Project. Week One: Tent, Tips, and Tension
So we arrive in the lab on Monday morning, filled with anticipation and excitement at the challenges ahead of us. The first thing we notice is the heat...then the tent...then the frustrated look on Duncan's face. Turns out the poor little STM isn't quite ready for our arrival, and we soon learn the term 'baking'. (Not the cupcake kind we are familiar with unfortunately). Thankfully, being at this stage worked in our favour, as it meant we got to follow step by step how to set up all the equipment. Once the tent was off and we could finally see the STM in all it's chrome glory, we had a whistle-stop tour of how it all works. To clarify to ourselves what does what, we invented a game called "Vacuum or no Vacuum", where we imagined various valves being opened or closed and had to work out what situation would be occurring. (Don't worry Peter, we didn't really touch anything!). One of the first things we got to be part of was cooling the system down with liquid nitrogen to improve the vacuum. After the simple signing of a health and safety form, and the addition to our outfits of a garish yellow glove, we were finally able to help...even though lifting the Dewar flask was quite a task in itself. The day we get bored of liquid nitrogen is a day we don't want to see. After learning a bit about flashing the pumps, we were ready to move onto our next challenge: tip etching.
To obtain a sharp enough tip, electrolysis is used to etch away at some Tungsten wire. With the help of a cleverly adapted microscope stand to keep the cathode in place, and a lot of wires, we set it up ready to watch the magic happen. Ten minutes later we were still waiting and finding it hugely less exciting than we first thought. However the joy came back when through the microscope we could see this...
Unfortunately it didn't last long as the tips began to get progressively worse in quality; some were too long, most were 'jaggerdy', all were below par. During our one last attempt to redeem ourselves...it stopped working completely. After various attempts to rectify the problem (none of which worked), it was home time.
With Friday came the next stage of equipment preparation: getting the tip in. We crept quietly round the lab as Duncan mounted it, watched expectantly for the orange glow during annealing, and held our breaths as Peter attempted to transfer the tip to the microscope... Having had a play with the wobble stick ourselves, we understood the tense atmosphere (it's not called wobble for nothing!). Unfortunately this tip was not the one, and as it fell onto the mesh below the preparation chamber, Peter and Duncan sighed and groaned. We however we just glad we weren't the first ones to drop something!
Week Two: The Waiting Game
5 tips down and no more spares: we had a problem. The tip etching station was still not playing ball so it was time to act the detective. The usual tactic of 'turn-it-off-and-on-again' wasn't helping, and changing the sodium hydroxide electrolyte made no difference, so we used our trusty friend the multimeter to look for any shorts in the circuit. This narrowed the issue down to the trip box, where Peter discovered the problem...10 Volts in...2 Volts out... Uh Oh!
After opening up the box we were greeted with this:
The little burnt resistor hiding in the centre of the image was the culprit! After Peter's re-soldering we were back up and running. Using the last of the Tungstan we cautiously made 3 last tips, being very careful at every stage not to cause any vibrations.
But our tips need something to scan, so next on the preparation list was the Silicon sample. Once it was mounted and placed under vacuum, it needed to be cleaned of any invisible muck, that would prevent good pictures being achieved at atomic scale. Said muck is blasted off by passing high current through the Silicon, causing it to reach temperatures of 960-1200 degrees (and glowing a beautiful orangey-yellow). The temperature is measured using an infrared detector gun, while balancing precariously on top of a step ladder. Keeping an eye on the temperate is necessary in working out what current is needed to achieve the temperature of gunk-blasting. This particular view point also enabled us to spot an unexpected extra glow near the sample. At first it was thought to be a mere reflection of the sample's shininess, but when we realised the temperature of this 'reflection' was actually hotter than the sample itself we decided maybe there was more to it! In fact it was a ceramic plate that was accidentally part of the circuit. So more rewiring.
However even then all was not quite well. As we tried to increase the current to raise the temperature, the power supply got stuck at 2.6A regardless of what was asked of it. Many suggestions later Peter again came to the rescue by debugging the program. This done we were finally finished with sample flashing, and ready to move on.
So: we had our tip (hoping it was sharp enough) and we had our sample (hoping it was clean enough), now time to put both together and try out the microscope! After learning how to approach and withdraw the tip so the two are a few nanometers apart, we finally got to do some imaging. Unfortunately the images were quite noisy and we've decided to change both the sample and the tip for better ones...
Week 3: LabVIEW for beginners
This week involved a lot more waiting...trying to get a good tip and a clean sample at the same time was proving difficult. After trying various combinations of our tips with different samples we were still only getting sausage shaped 'atoms' and a noisey picture. As we're still getting to grips with the 'tricks of the trade' to get a clear picture, we weren't very much help with the nanonis software. So we largely left it to Peter and Duncan to play with the settings and try to get a clear image whilst we watched closely to take in all their sneaky cheats.
We tried to make ourselves useful by mounting another sample, something Duncan had shown us twice before so we were feeling confident to have a go... Apart from the massive increase in time for us to complete the same task, we successfully managed to attach the sample within the holder and didn't even lose any of the tiny nuts and bolts! Testing the resistance to make sure there were no shorts and that the current would flow across the sample correctly stumped us for an embarrassing amount of time! But we got there in the end! Here's a picture of Sarah struggling with the fiddly job...
While Peter and Duncan were tinkering away at the microscope we were set a mission (should we choose to accept it...) of programming. We're trying to use LabVIEW to create a code that performs cross-correlation on the images obtained from the STM. Once it's written this will compensate for the shifts seen in the images due to the expansion and contraction of the sample set-up (due to temperature changes). We have so far worked on this for a few days (mostly borrowing other people's code and pasting it together), and here's what we've got to:
Having never heard of LabVIEW before, to begin with the progress was very slow (mostly spent looking up terms on Wikipedia). However we are getting more of a handle of it now, and it's exciting to be learning a new skill.
Week 4: Plane pain
This week was spent buried in the depths of LabVIEW. We had so far managed to take the two images and cross-correlate them, but could not make head or tail of the result. This was apparently because the original images were too wonky and so to make it happy we should take a global plane (like a line of best fit but in 3D...not an aeroplane like Google thought!) off. After getting stuck on our own for a bit, we headed over to ask Philippe Blondel if he could spare us a moment to help. It's so lovely that our department is small and friendly enough to have lecturers know who you are and go out of their way to help with any problems! Philippe taught us all about Kernels, although after implementing this we were still left with the same problem. So back to the global plane idea...
Even after trying many different directions of thought we still ended up with a wonky background...it seemed like we just couldn't win! We would arrive in the morning and Peter would have come up with a new idea for how to fix it. Finally on Thursday he presented us with a printed booklet containing a scary looking matrix equation for creating a global plane to fit your data. Would we be able to work it out? Would LabVIEW like it? Was it even correct?? We set off to find out! By breaking it down into simpler steps we saw it wasn't nearly as bad as we thought, and after a while (and a LOT more wires) we had a picture. Still a wonky picture. AHHHHHHH!!! Flustered and confused we sent an SOS email to Peter who came down to help. The three of us spent the next 3ish hours labouring over the code. We rearranged, and added things, and took others away. We tried separate sections, and different numbers. We got the program to print out the results of every step of its calculations just to pin point the faulty section. Eventually we found the source: we were giving an array to an input box, but what the box received was crazily different!!! Much head bashing went on. The issue was with the memory of the program because of the size of the data going in. So in the end all it took was changing the way we stored some data...and hey presto a flat result with a peak in the middle! Just what we were hoping for!
Much excitement followed.
Week 5: We played around with Excel a bit. Then we read. Then we highlighted. Then atoms.
Moving on from our successful end to last week, we next needed to check we really could use the LabVIEW program to predict and alter for the drift. So we checked all the data we had and plotted various graphs to look for trends. It took us a while to get our heads round what we were even trying to test, and even after deciding on a strategy we couldn't seem to find a convincing answer. Data points seemed all over the place! We needed more data...but the microscope was still out of action.
So instead we spent a fair bit of time reading up on what we were trying to do. Google, print, read, highlight, repeat. Some papers went way over our heads, but others were exciting to read as they were discussing very similar things to what we were doing. Hooray for relevant literature!
And then everything seem to happen so quickly. We had learnt not to get our hopes too high up when the suggestion of testing the microscope came up, so when Peter came and found us to say they could see atoms it didn't really sink in for a bit. But sure enough once we had made our way down to the lab...there they were!!
Aren't they beautiful!
Our final job for the week was to make them less squishy. (Also known as calibrating the dimensions, so the size the computer thought it was matched the known unit cells size from literature.) This involved a lot of head bashing, drowning in a sea of simultaneous equations, and much typing into Wolfram (since Rebecca got so mad at the whole thing she 'threw' her calculator on the floor and it broke). We thought our simple way worked, but Duncan's complicated trig proved the victor in the end. Then all that was left to round the week off was a spectacular smash of Duncan's dinosaur coffee mug (Sarah's clumsiness 1, coffee cup 0), a visiting speaker at the nanoscience seminar, and a drink in Plug with Peter and his tutees. Hello weekend.
Week 6: Meet me halfway
50% through the project...
Progress is steadily being made to get the stm back to full working order. Eventually the whole set-up needs to be clean and stable enough to perform experiments on and collect data for several hours at a time. Since the main issue stopping that right now is just tweaking the sample and tip to get them as clean as possible, so our images are nice and noise free, this week we were introduced to the next stage of preparation for actual experiments: chemicals. The group's experimental focus at the moment is studying the manipulation of benzene and toluene on the surface of the Silicon sample. For this, they need these chemicals in pure gaseous form, ready to inject on a nice flat Silicon sample (when we eventually find one we're happy with!).
Enter the freeze-pump-thaw method. The name does a pretty good job of explaining what this is. First the test tube containing liquid benzene is bolted onto the bottom of the stm. Then it is frozen solid using liquid nitrogen, and the valve which connects it to the pump is opened to suck out any air left in the tube. Then we thaw it. The oxygen melts first, so is sucked out while the benzene is still a solid, and once the benzene has itself melted, we repeat the process. This is done until we see no more bubbles of oxygen escaping, and no change in pressure (so we know nothing more is being sucked out). This leaves us with a sample of pure benzene. (We will eventually check this with a mass spectrometer to check we really just have the good stuff.) Here's a picture of Rebecca doing this...
The remainder of the week was spent back in the world of LabVIEW. (Slightly more exciting these days, as we have learnt how to change the background colour of our windows. So much nicer staring helplessly at a sky blue screen than dull grey!) Putting some of the new images taken through our cross-correlation program illustrated noise was an issue that stopped us from being able to correctly evaluate the shifts. Boo. Peter pointed out that what we wanted was a low-pass filter, to get rid of all the yucky uber-high data (from the tip regurgitating all over the sample), and leave us with just the bits we wanted to look at. But we couldn't work out how to connect the pre-made vi to our current program...so we decided to make our own from scratch. This involved lots of histograms, averaging, and a return to the dreaded plane game! We're still working on it.
Week 7: Movie Makers in the Making
This week was very exciting. We're nearly there with the drift LabVIEW program, but we gave up on the low pass filter, as this was deemed unnecessary and takes experts ages...let alone us! Meanwhile Peter has managed to get us some very stable images, so good in fact the thermal drift was pretty negligible! So for us to test our program on it he shifted images randomly to mimic drift. However when we came to cross correlating them, it turned out they were so big that they induced some x-direction drift, causing a parabolic dip in our data (a.k.a it looked like a bowl). Hmm, how do we get rid of this one?! Our global plane fitting didn't fix it, so we thought maybe we needed to fit something else. We pointlessly implemented a rather disgusting matrix to the program, before deciding this didn't help. Then we learnt all about case structures, and put a load of them in the program to let us choose which fit to try. When none worked on their own, we just started trying different combinations. Funnily enough this didn't work either! Then Duncan came to the rescue and told us not to bother...we'd never be using images this big for real data (as this was way too big to actually see the atoms). So we went back to the original. All that was now needed (we hoped) was to bolt it onto the scanning software.
While we were fiddling with all our case structures, Peter had been on the microscope. He had just been scanning a tiny section, and pointed out what appeared to be an atom (or dirt) moving between adjacent sites. It bopped backwards and forwards quite happily for quite a number of images. The next day, when everyone else was busy we decided to have a little fun with these pictures. After a lot of converting individual files to jpgs, changing the colours, and importing to Windows Movie Maker, we produced this...
We like to think of it as an atom, but truth is it's quite possible that the black blob is a bit of 'dirt' that can't make it's mind up where to settle. Although we did it just for fun, it's been really cool having something like this to show people when trying to explain what we're doing. It also illustrates the thermal drift well, and so shows why it needs correcting. It also proves how awesome physics is. We showed off this video at the Physics Department Welcome Evening to all our friends (yes, we're that chuffed with it), but it didn't manage to eclipse the enjoyment of seeing and hearing lecturers hit the karaoke machine!
This week we've again been trying to learn bits of chemistry so we can understand better exactly what we're seeing and what is going on. As we get ready for the next stage (adding the chemicals) we have been reading papers (and googling lots) on the electron configuration of silicon and benzene, and how they bond. While we were struggling with doughnut electron clouds, Peter was putting the finishing touches to the drift correction program. Finally this was done, and it's goodbye thermal drift.
Next on the to do list:
* Fix the x/y calibration (again)
* Stop the vibrations from people in the cafe upstairs mucking up our scans.
Here are the slides I used at today's brief overview of the Physics Department's draft application for a Bronze Athena SWAN award. Any comments of suggestions to email@example.com
Some attempts to toss a penguin over an ancient, ~ 4000 years old, Standing Stone of Stenness (Link). Well when you're in Orkney one really should try new things.
I like Prezi, I like Latex. Here is how to get nice Latex equations into Prezi.