Welcome back for yet another installment of "beamrun at the APS."

Our first day has been rather frustrating thus far. The day crew suffered from some alignment and equipment issues. Those have, we think, been solved, but we're still not to the point of actually taking data yet.

We've got one of the titanium-dioxide samples prepared and mounted in the hutch ready to go. But we're having a little trouble on two fronts. The confined geometry that we're forced to work with is keeping us from being able to orient everything easily. This is something that we can eventually overcome, but it takes lots of little checks until we're confident that it's all going to be ok.

The other problem may be more serious. The sample, quite small in size, is held in position by a small suction pump. So it's on a flat surface with a tiny hole. There's a pump trying to pull air through that hole and so, in principle, the sample should be stuck there. I'm not entirely convinced that it is. While the sample does not appear to move to our eyes, I'm beginning to think that it's still moving by huge leaps on the atomic scale (which is deadly to our experiment).
Or it could be that it's deforming... I'm not quite sure.

There seems to be another issue... we're getting too many photons at this point. My guess is that either they use a different (ie lower) set of filters on this beamline, or that one of the filters in series just isn't installed. Regardless we are having to take pains not to saturate the detector. We know it's not simply that we have more photons as the device making them has a much lower output than what we've used previously. So either it's a difference of filters or a difference in the electronics of the detector.

Well, at this point we have many banal questions and are rather frustrated trying to figure them out instead of doing real science. The truth of the matter is however, that this is exactly what real science involves. It's a long road to get to the point where you've got a system doing something interesting. Much of the work along the way isn't nearly as glamorous as we might like.

I did have an interesting thought today though. Scientists "love" to make posters. and what better place to put up your posters than around a facility like the APS. So we have probably a few thousand of them scattered around the ring talking about all the science that goes on here. Much like people's ability to give talks, the posters can vary from actually quite exciting and interesting to complete obfuscation and opacity.

Anyhow... nearby is a poster with several names on it for an xray scattering experiment. One of the names on there is my advisor from graduate school. This was long before I began working for Larry (about two students before my time). The person who made this poster was trying to convey their work, their results, etc... but the thing I went away with was what can only be described as a feeling of home. Here in this far off land (well, is Chicago really that far from Seattle?), in this far off place (again, is there really that much difference between hard and soft x-ray work?), one of the most important people in my life had been here doing science. It's probably not the intended "take home" message that the author of the poster intended.


Ok, enough procrastination. I need to get back to this blasted sample. We're still not sure what's wrong with our setup.

So we've done some good experiments, analyzed data, and found some interesting results. What now? It's time to write everything up and submit it to a journal for publication. If only it was that easy...

Writing up work for publication is not exactly an easy task and not something to be done lightly. Once it's out there and published, it will be there as a permanent indication of your work. If everything is done well, interesting, and correct to within your error, then it's great news. If you mess up, that mistake is there forever with your name stuck on it. That's certainly exacerbated if you're the primary author on the paper. This is of course assuming that it actually gets published.

We're aiming rather high with this publication and, principally, writing a second longer paper in tandem. The first paper will be submitted to Physical Review Letters, with the second to a journal that accepts more lengthy publications. Physical Review Letters (PRL) is the top physics journal (aside from the much broader Nature or Science journals) and publishing in it is no easy feat. As an experimental paper, we've got to present either a new novel technique, unique system, or widely interesting result with a fair amount of reliable interpretation and analysis. Merely showing a "cool" result without qualification doesn't work. Nor does trying to publish something that is too small or incremental an increase to public knowledge. It has to be good enough to be interesting to physicists (and other scientists) that are not in the same field. True that if you've got a Nobel prize you can publish twadle, but most of the community has a pretty high bar to meet (and not too many Nobel physicists attempt to publish idle prattle either).

So we're in the middle ground right now. We've got a very interesting phenomena, in a new system. What we've seen is a nice effect, but has been seen in other materials. In and of itself, this wouldn't cut it. However, the material of interest, where it's been seen and studied before is extremely interesting (Platinum) and the results and conclusions of those studies are not yet final (ie, there is inconsistency between different models and experiments). So, what we're offering is in some ways a new system that is close enough to the old to be compared, but different enough that it might provide significant insight into the underlying mechanisms. ie, can this new system be used as a benchmark to settle which of the previous theories for platinum are correct?

We've got a new (though not novel) system with an interesting behavior (though previously observed). Still... that might not cut it. Thankfully we've got a good deal of data from our experiments that provides several different clues as to what is happening. Plus, we've done the experiment in two very different and complementary ways. So, if we put it all together, observations, comparisons, interpretations, and contrast it with one of the most interesting (and unsettled) metal surfaces, then we've got a strong case for PRL. Undoubtedly the referees will respond with comments and criticism which we will need to address. Potentially we will need some significant improvements in our work before it's deemed acceptable. But, I think we've got a strong case and are in good shape.

Today went very well! I'm pretty well exhausted at this point, between the recent beamrun experiments and multiple talks. This was my first chance to publicly present our new work since starting my post-doc. It's a rather big step in that (aside from the nice science in it) I'm really trying to say, "look my thesis project wasn't just a fluke. I really can do good work in a variety of areas."

It's nice because now I can also talk more freely about this subject. We'll submit our first paper in a week or two and will continue our supplementary experiments in the lab (which frankly is where I'm really anxious to be back at). We've got a little more work left to do before we can wrap it all up, but we're really close. People seemed generally receptive and interested in the material. I had a few good questions, but they're things we've thought about considerably beforehand. I think the preparation for the talk did a great deal to help me get all my ducks in a row for the paper. There are two more days of presentations which should be interesting.




Sum

Howdy!

Today we're in Madison Wisconsin for a workshop on a possible Free-Electron-Laser to be built with the University of Wisconsin. There is already a synchrotron here that is operated by U of Wisc., the Synchrotron Radiation Center. I've never done any work at the SRC personally, but this is an interesting conference on a potential future machine. There's a strong team being led by U of Wisc. and MIT that wish to have such a facility built here. The conference has been to invite scientists that would likely use such a machine to discuss ideas for science that could only be done at such a machine. The cost will be expensive (by science standards), but hardly a blip compared to other things on which the government spends money.

So we're here to help them develope a strong proposal. Strong means many things. It has to be exciting work that's not possible elsewhere. It also must be feasible and realistic enough to actually be realized and not fizzle. On the whole I feel as though my personal contribution to the conference was a bit lacking. I'm very glad I came and I learned a great deal, but it was difficult for me to find my own voice or own opinions. Alot of that is that I've changed areas of focus since leaving graduate school. Had I continued down a very similar track, then I would have been more useful to that subject. But still... I'm pretty new and still very much in the learning phase. I got to hear some very interesting "think big" talks and even got to interject my own questions a few times. My own "think big" ideas turned out to be either totally unrelated to x-ray study or potentially feasible at current light-sources(and that's not a bad thing, it means we've got a nice idea to try in the next few months.... maybe).

I'm glad that we made the trip for another reason. It's been great to be in a university town and setting once again. It really makes me feel as though that's where I'd really like to spend a great deal of time. There's a vibrance and exuberance to a university that I miss at the lab. I also miss the luxury of being able to walk everywhere, having the library, lab, office, coffeeshop, restaurants, and potentially home, all within walking distance, all with a community feel. I think Kerri does as well. The suburbs of Chicago are a bit lacking in that respect. It's certainly something to keep in mind for the future. It's also an interesting carrot to have in front of me during my time as a post-doc.

Madison itself, at least the parts we've seen, is really a beautiful city. It sits between two large lakes, surrounded by others. It's relatively small and built largely around the university. It reminds me of Austin or Seattle(that's a good thing).

We're headed to Urbana-Champaign this afternoon. I've got my first presentation of the gold surface physics we've been observing. I'm certainly a bit nervous about presenting it, but not too much so. I'm comfortable talking about magnetism and coherent x-ray scattering as it's what I've been doing for a number of years. But this will be my first chance to speak before other scientists (potentially not receptive to my message!) about what I've seen at Argonne. It's also an incomplete story at the moment as we don't know everything about what's going on. On the one hand it means there are a large number of questions I can't answer yet. But it also means that I'll have the chance to ask various experts about what they think is happening.

Not much time to write at the moment. We're working hard to get some result for the other postdoc's experiment.

We're trying some energy dependent scattering experiments on Pt nano-particles. Unfortunately we spend much of the evening with the experiment not working. We only began taking data around 3am. Since we lose beam privledges at 8am, that doesn't really leave us much time to do work and collect data.

Wish us luck.

This seems like quite a long night as nothing terrible has happened. Thankfully!

I'm taking the last of our scattering data for the TiO2 samples, at least the last of it for this beamrun. We lose our photons at 8am, so I've only got a few hours remaining. I hope it's enough to get what we need.

In the intervening minutes I've got time to work on my talk for next week. I must admit to being a little nervous about it. This will be the first time I really get to present my work on gold surfaces to a general audience of other scientists and it's a big step for me. I remember what it was like the first time I presented my thesis work and this isn't nearly as bad. However, there's still some pressure.



and speaking of that talk (a pun Kerri would be proud of)...

I've been digging up pictures for use in it. I pulled up more of our microscopy images from a few months back and decided to post this one here as well. The little white blobs in the picture are actually individual gold atoms on the surface of a gold crystal. There's quite a bit of noise in the picture and it's actually not the greatest quality. However, I've been primarily an x-ray scattering person and so for my first foray into direct imaging of atoms that's not too bad. The whole image is about 4 nanometers on each side. The atoms are arranged in a hexagonal pattern which is actually different from at more square arrangement below them (technically "more square" means face-centered-cubic or cubic-close-packed).

The cicadas have invaded the APS. Last night there were hundreds right by the door I use. This morning there were more out on one of the trees. I managed to actually find a white one. I think they're supposed to be fairly uncommon (at least this is the only white one I've seen). By the time I came back and had a camera he had been smushed by a passing car or person. While trying to take a picture of the tree, many of the little guys decided I made a good tree and attempted to perch on me. I did not agree with their assessment and quickly dispatched

ugh.... It's been no fun this evening. Much of our earlier optimism is gone. We're continuing for the time being, but it's with "lowered expectations." We learned, tragically, that the sample we were hoping to see such great things from had been ill-prepared. So despite all our efforts, there was never anything there to see in the first place.

With little time remaining we're doing what we can. We've got our best bet sample reprepared and back in the beamline. We still have 2 more full days (48 hours) of beamtime, plus a day break in between the last two days. But we really need to move past this project and to the other postdoc's experiment. Each hour we spend trying to finish this experiment is one less hour on his project. It's not an ideal situation and makes it hard on everyone.



I'm not quite sure why I'm inspired to include the above picture, but there it is. It's nothing that we're studying this time, but rather a picture of my gold atoms arranged on a surface. The atoms are regularly arrayed in long rows that follow the step edge/terraces of the bulk crystal. You can't see the individual atoms in this picture, but you can see the "bumpiness" in the surface from their rows. Each row is about 5 atoms wide and 40 atoms long. The blobby things at the top are, for the moment just blobby things and will not be identified by their real names.

All aboard the midnight express.... Destination unknown!

Bear with me... I'm beginning to get a bit loopy these nights.

The picture above is with our sample being illuminated by UV light. We've got a rather hot (like perma-tan-cancer-maker-roast-your-face-real-bad hot) UV light source to trigger some effects in our sample (the sample likes it). Because much of the sample stage is made of white teflon, the whole thing just lights up brilliantly. It's quite a sight(from a safe place). And no, of course I'm not in the hutch while taking this picture.

Shortly after we turned on the UV light source this morning, our optical filters exploded. The UV source produces a great deal of other wavelengths that we don't want and don't need hitting our sample. So we have a setup to filter the light before it reaches the sample. My guess is that someone at some-point touched the surface of a filter with their hands. Even a light touch could have left enough grease on the filter to cause its destruction once it was under full power. It's not that the filter will combust or catch fire, it just shatters. But not to worry... we have several more filters.

It's been another hard evening and I think it was a particularly difficult time for the day shift. A large number of things simply broke during the day. One of our motors, one of the stages, and more. It's been a real struggle this time to get to the point of data collection. My solace is that we are (I think) reliably taking good, useful data. Reliable, good, useful... those have been difficult conditions to satisfy. But I think we've got it going well enough finally.

We're back to our old "data pipeline," and while this does mean that things won't look quite as glamorous, they will be both correct and finished on time.... I hope.

In the periods during long minutes of data collection I've managed some useful calibration of our new detector. So while we're not going to use it further this time, we will know quite a bit more about it the next time we show up. Quite surprising to me was that the "dark noise" in the camera didn't respond when I increased the gain (sensitivity) of the detector. I figured it would increase, but wasn't quite sure how much. It turns out that the dark noise is the same regardless of gain setting and only depends upon time. Look, I made a graph of it. Haha... no I won't bore you with it.

I'm reminded of a "Simpson's" episode where Lisa is explaining what it's like to be smart to her farther: "It's sad but often intelligence and happiness are inversely related. Look, I made a graph of it. sigh..."

I've also been working on a presentation for the week after next. I'm going to talk at a conference at University of Illinois Urbana-Champaign about or results on the gold surface experiments. It will be our first presentation of the results and my first chance to present my new work as a post-doc for Hoydoo. We've got some really nice results from it and so I'm rather excited to hear what some other surface science people have to think about it.



I saw this little guy and took pictures of him for Kerri. He's got quite a loud call and seems to be fat and happy with all the cicadas to eat. From all his talking I would assume he's either looking for a mate or already has one and is enforcing his territory. He's always outside near our parking lot eating the insects.

That's about it for now. Another scan has finished running and I need to start working again.

Thankfully things seem to have worked well enough through the day. We are taking at this very moment the data set that will tell us whether or not the experiment will ultimately be a success or whether we will be limited to merely having confirmation results of experiments by other scientists. It's going to be a nervous hour as we collect the data.

Pretty much regardless of what we see while we're taking the data, we've got another sample prepared and ready to go in. As soon as this one is done I will swap samples and begin taking the same data on a second sample. If we do see anything of interest, it needs to be seen at least twice on different samples. And truth be told, the effect may be subtle enough that we miss it with our quick "in situ" analysis at the beamline. And that's the other reason to repeat everything regardless of what we learn in the next hour. The effect could be quite small and subtle enough to require real effort to tease out correctly from the data. We just won't know until we've done it all. So... more data and more data.

While the scan is running there's not anything pressing left to do. So I'll turn my attention back to preparing my carbon-monoxide and gold presentation for the upcoming conference. That and I have some reading to get done. I recently got what I think will be a very fun book, "Entropy, Order Parameters, and Complexity" by Jim Sethna. I'm anxious to get into it a bit more than just my previous cursory glances. Sethna is a really sharp guy and I've always been entertained by his work.

I've also been vexed by a recent question concerning magnetic linear dichroism and my own scattering experiments. It's possible to argue, quite convincingly, from two different directions that it should or should not work for unmagnetized materials such as the films I studied in graduate school. I think I've finally figured out all the little steps to get to the answer (there's a couple of subtle points), but I want to make sure I'm not missing anything. I did this several years ago and convinced myself of the correct answer, but merely saying "I figured it a while back (but don't quite remember at the moment)" isn't very satisfying conversation.

more soon. I hope....

Things are somewhat better today. It's still at the somewhat frustrating stage, but it has improved past the "please make it stop" phase that we spent much of yesterday in.

The day shift had little luck it would seem. When we left we requested a new sample because we'd found sufficient evidence that the current sample was trash. Once they installed the new sample they had trouble getting the geometry back on the experiment, basically only restoring the experiment by about 8pm. A rough day indeed.

We've been doing something a bit dangerous today, at least in my opinion. No, not physically dangerous..... Instead of taking the data in the way we've done in previous experiments, we're using a new CCD detector. While this will certainly give, in the long run, better quality data, I'm not convinced that we're taking an unnecessary risk by using it right now. We did not use the new camera very much and we're not set up to easily do the data reduction and analysis for it yet. Necessity is often the mother of invention and so we're working hard to get the routines moved over to the new detector. The necessity in this case is so that we can interpret our results while we take data. Without it we're flying blind.

So long as we've got a grasp on what the data is telling us, we are usually more sensitive to mistakes and interesting twists. If we're unable to read the results while the experiment is in progress, then we've got to just proceed and hope everything is working as intended.

For instance, the image at the top of this post is one of our scattering peaks. This IS a picture in reciprocalspace, though I'll have to explain that in a later place. In the center is a blob/blur that is an example of the scattering we observe. The intensity, shape, and position all tell us important information. Unfortunately it is often difficult to find such a nice looking peak. This is especially true when the peak is smaller than any background noise.

We though this was indeed the case for our set up today. The data looks very, very noisy and the scattering peak doesn't look very strong compared to the background. Very often with counting type experiments (and our detectors simply just do that, count photons), you have a statistical random variation. The simplest way to get around this is to simply count longer.

Our images appeared to have just this kind of noise in them, but after a few attempts at counting longer, nothing really improved. The signal did get stronger, but the background also appeared to get stronger. So I pulled up two different images from very different places and put them side by side. Zoomed in you get something like the picture below. Indeed, it looks like noise.




but what I hope you can notice is that the two pictures are almost identical. The noise is almost perfectly correlated even though the sample and the experimental geometry have both changed quite a bit between the two. The only thing that is the same is the exposure time....

So what you see is that our exposures are dominated by a "dark current" in the detector. The longer you wait, the more current is accumulated in each pixel. It's not really "bad" news because it means that (so long as things behave) we can simply subtract some "background" images and the result should be a nice exposure. And that's what you get at the top of the post(though not from subtracting the two frames in the second image).

Anyhow, all this is fine, but I sure wish we were not figuring it out while the data collection is in progress. Ideally we would have known this coming in. But then again, it's better that we know it now rather than figuring it out much later after the run is over. I suppose part of it is that I'm just a little concerned about changing the "data pipeline" when we already had it flowing and just needed a little more to finish the experiments we'd been doing. But perhaps this will improve our data sufficiently and ease things in the future.

We're taking reasonably good data (we think) at this point. Everything seems to be working. We are a little concerned that the sample may be trashed again, but that's only a mild suspicion at the moment. We'll know soon enough. Very, very soon we'll begin to illuminate our sample with UV radiation and the effects should be quite clear.

Today is my last day before our upcoming experiments at the Advanced Photon Source. We're again running at a BESSRC beamline, however this time it is 12-BM. I don't think it will make too much difference in our work. Most of the software and hardware is similar to where we've worked before. I think I'm more or less ready, but have not heard from the other post-docs since shifting over to nights.

I'm continuing to work on a manuscript for our gold surface experiments. My advisor has the manuscript during the day and I work on it at night. This will be my first paper with Hoydoo You and it's been a little different from my graduate school publications. Not to say better or worse, just different. Part of it of course is working with different people and having a different advisor (I still call Hoydoo an advisor or mentor and not boss). And certainly part of it is writing about new work that is quite separate from my graduate school experience. But I think part of it is also my own voice maturing a bit more(at least I hope so).

I'll be on the night shift for the coming beamrun. I've begun trying to stay up late in order to make the shift early. Usually it's not too difficult for me if done over several days, a few hours at a time. But for the moment I'm really dragging.

Working nights is a mixed bag. It's actually not so difficult aside from the unpleasant shift in sleep and being away from Kerri so much. Depending on how you're feeling it can also dull your wits off and on. But in terms of working, things are often very quiet on the night shift and it can be a great time to get things done. With so few interruptions it's easy to concentrate on the job at hand.

One odd thing about working nights (for me at least) is that inevitably within a few days I will lose track of which day is which. I can count the number of times I've been at work and can count from there to figure out which morning it is. But in terms of intuitively knowing which day of the week it is, I no longer know. It's a little disconcerting and unnatural. However, all this does give me the chance to see a few of the original Star Trek episodes that only seem to come on TV between 4am and 6am.

Well, it happens occasionally: someone else beats you to the punchline. We've been working on titanium-dioxide surfaces and their properties for a little while now. We're almost at the point of submitting our results but just got a large blow to our egos today. On friday a very similar paper was published by a different group of x-ray scattering experimenters.

It happens. They're studying the same system under very similar conditions and finished up before we did. It was quite surprising actually. I had no idea they were doing similar work as well.

There is still potentially a positive for us. While our starting systems are the same, what they do (studying the sites where ad-atoms bind in wet TiO2) is different from the direction we've been heading. What it means is that if we're really successful and things work as we intend, then we'll still have a new result(forgive me being a bit vague at this moment). We've got a reasonably good indication that the TiO2 surface will behave as we want from previous experiments. But to really be definitive and clear, we need one more set of data. And hence that's what we've been planning for our beam-run later in the week.

If things don't work out as we hope.... well, we can still write up what we've got. It won't be very exciting to say, "our results are the same as..." but at least we can add confirmation of another experimental result. We've worked on this for quite a while independently of the other group and it would be a shame to not write up anything at all about it.

But that's part of the endeavor and it's part of what keeps me up some times. My own main projects are still relatively safe and progressing. We've got a paper almost ready for publication and I will be publicly presenting the results (for the first time) at a conference later in the month. Plus we've already got the set of experiments that build on this work in progress and underway.

Still.... it can put your stomach in knots, especially as a young (ie not established) researcher. The last thing you want is for someone else to figure out your baby before you do.

In other news....

I'm still happily working away on my nano-faceting project. I've got the AFM(atomic force microscope) going down the hall. With two mostly identical samples I'm able to have one being prepared while the other is being imaged. It just requires lots of walking between rooms! For the first time, I think I'm getting a good handle on the faceting and its trigger. I'm annealing for the last time today and, if it works as I hope, then the trend will be established. Once I've got a good "hook," then it's possible to really move forward. The first step was establishing a stable (and reproducible) starting point. Now that's done and I'm in the process of trying to get my surface to facet "spontaneously."

I suppose tonight's faceting experiments will be a good stopping point and my last for a week or two. Things are a bit tense as we try to finish the last of the preparations before beam-time on Thursday. We're constantly uncovering things that need doing and doubtlessly we will be working hard in the coming days. I've already begun the process of shifting my sleep schedule over to nights (which is where I'll be during the experiments later in the week).

In the meantime I'm also continuing to run magnetic domain simulations on my workstation. I'll try to post some pictures of the domains and (hopefully) facets soon.

As a first step I've enabled comments through Halo-scan.com. While it does allow for a controlled commenting system, and doesn't clutter the actual content of the website with ads, it does have the small flaw of putting a few ads in the comments (which only show up separately). If it gets annoying, or I just get the whim, then I'll attempt to change the system over. However, this was the easiest solution and doesn't make a terrible mess of the website.

Moreover, the webpage software I'm using also is getting an upgrade soon. Once that happens I should have a bit more freedom over things like this and ability to edit the content of the site. So things are still in a state of rapid flux and the site will remain in the nascent stage for a while longer.

I finally broke down and got a real webservice to host the site. In doing so I got to formalize the domain and site names. That brought up an interesting question: should I actually keep the name as The Second Law? In fact, there already is a website with the name of secondlaw.com in use. It's actually an established site with a great deal of content. While I could use "thesecondlaw," it really would just be an attempt to get around what's already there and not very fair to Frank L. Lambert.

So off to choose a new name. I had a few in mind already, but when I went to check them they were already taken. "Reciprocalspace.com" is alreayd registered, though there's no content. So, while not my first choice, I'm happy with this as a name.

I found a few other interesting things (well, probably only interesting to me in this particular time) . The name reciprocalspace.net was actually previously owned by someone previously. However, about 1 year ago they stopped paying

However, does this mean that I now need to stick to scattering experiments?