As a young student, I was taught that mathematics is the language of physics. While largely true, one also cannot communicate in CMS at the CERN LHC without learning a plethora of acronyms. When we wrote the CMS Trigger and Data Acquistion System (TriDAS) Technical Design Report (TDR) in year 2000, we included an appendix that contained a dictionary of 203 acronyms from ADC to ZCD, quite necessary to digest this document.  In the next years, the list of acronyms would grow exponentially. We even have nested acronyms, LPC, for example standing for LHC Physics Center. In a talk of many years ago, one of my distinguished collaborators flashed a clever new creation and quipped “I believe this is the first use of a triply-nested acronym in CMS.” I do not know if since then we have reached  quads or quints. Somehow it would not surprise me.

One of the latest creations is YETS: Year End Technical Stop, referring to the period between the end of the heavy ion run on 7 December 2011 and the restart of LHC operations due to begin next week with hardware commissioning leading ultimately to pp collisions in April. So what to physicists do during YETS? A lot as it turns out!

One of the major activities is how to cope with the projected instantaneous luminosity of 7e33 (per cm**2 per s). This luminosity will likely come with a 50 nanosecond beam structure (the time between collisions) as was used in 2011. This means that the average number of pp interactions per triggered readout will be about 35, the one you tried to select with the trigger, plus many more piled on top of it. This affects trigger rates and thresholds, background conditions, and the algorithms used in the physics analysis. In addition, we shall likely run at 8 TeV total energy (compared to 7 last year). These new expected conditions are being simulated, a process requiring a huge amount of physicist manpower and computing resources. The results are carefully scrutinized in collaboration-wide meetings. That is the “glory” activity.

Besides the glory work, there is also a huge amount of technical service work, both hardware and software. At CMS in Point 5 (P5) we have observed beam-induced pressure spikes (rise and fall) in the vacuum. The pumping required for recovery is using up the supply of non evaporable getter (NEG) needed to achieve ultrahigh vacuum (UHV). The UHV in turn is needed to ensure that the beams do not abort which nearly happened last year. A huge effort was launched to radiograph the region in question to see if the same problems of drooping radio frequency (RF) fingers are present as has been observed in other sectors. An electrical discharge from the RF fingers can possibly cause the UHV spikes. Also at P5 work will be done on the zero degree calorimeter (ZDC), the Centauro And Strange Object Research (CASTOR) detector (not to be confused with CERN Advanced Storage Manager), the cathode strip chamber (CSC), the restive plate chamber (RPC) and the drift tube (DT) muon detectors which are accessible without opening the yoke of CMS. In addition, there is maintenance of the water cooling and rewiring of the magnet circuit breaker.

Each of the CMS subsystems has work to do as evident by a recent a trip into the P5 pit. The detailed activities of the pixel (PX), silicon tracker (TK), electromagnetic calorimeter (ECAL), and muon (MU) subdetectors are beyond the scope of this blog. I can give you some idea of what is going on with the hadron calorimeter (HCAL), where a bit of the details are fresh in my mind.

The HCAL activities are quite intense. Detector channel-by-channel gains, the numbers that are needed to convert electrical signals into absolute energy units can vary with time for a variety of reasons (e.g. radiation damage) and need periodic updating. This information has to go into the look up tables (LUTs) that are used by the electronics to provide TPGs (trigger primitive generation) which are in turn used by the level-1 hardware trigger to select events. If these numbers in the LUTs are slightly off, then the energy threshold that we think we are selecting is off target which is very bad because trigger rates vary exponentially with energy.

The HCAL uses 32 optical S-LINKs (where the S stands for simple, although I don’t remember anything simple about getting it to work) to send the data to DAQ computers. My group at Boston designed and built the front end driver (FED) electronics that collects and transmits the data on these links. The data transmission involves a complex buffering and feedback system so that the data flow can be throttled without crashing in case something goes wrong. The data flow reached its design value of 2 kBytes per link per event at the end of 2011 so we are going to reduce the payload by eliminating some redundant data bits which were previously useful for commissioning the detector but are no longer needed. This will allow us to comfortably handle the expected increase in event size due to increased pileup. Also 4 of our boards developed dynamic random access memory (DRAM) problems after a sudden power failure which took up two days of my time at CERN to inventory spares, isolate the affected DRAMS, and arrange for repairs.

The HCAL computers at P5 are running 32 bit Scientific Linux CERN (SLC4, another nested acronym). While we enjoyed the stability of this release over a number of years, it will no longer be supported by CERN after February 2012.  These computers are being upgraded (as I write this!) to 64 bit SLC5.

The HF calorimeters will have their photomultiplier tubes (PMTs) replaced in the LS1. We would like to do measurements with a few new PMTs in order to study performance stability and aging in the colliding beam environment. This activity requires building and testing new high-voltage (HV) distribution printed circuit boards (PCBs). The HV PCBs require testing and installation in the current HF read out boxes (ROBOXs) while there is still access to the detector.

Our group at Boston in also involved with designing electronics needed for the HCAL upgrade, the first part of which will take place in the first long shutdown (LS1). The new electronics is based on micro telecommunications computing architecture (uTCA). In Boston we have built a uTCA advanced mezzanine card for the unique slot number 13 (AMC13). This card will distribute the LHC clock signals needed for trigger timing and control (TTC) as well as serve as the FED. We plan to test these cards during the 2012 run. To prepare for these tests we have installed an AMC13 card in the central DAQ (cDAQ) lab which can transmit data on optical fibers to a multi optical link (MOL) card which exists in the form of a personal computer interface (PCI) card that can be readily attached to a computer. I addition, to be able to perform the readout tests with the new electronics without interrupting the physics data flow, we have installed optical splitters on the HCAL front end digital signals for a portion of the detector, parts of the HCAL barrel (HB), HCAL end cap (HE), and HCAL forward (HF), so that one path can be used for physics data and the other path for uTCA tests.

I can assure you that the activities in parts of CMS are (almost) as intense as during physics runs. There has been a lot to do!

I once met a secretary in California, the land of innovative thinkers, who was exposed to physics through typing exams, that could not understand why students thought physics was so hard. She thought each letter always stood for the same thing and once you learned them you were pretty much set. I am not sure she believed me when I told her there weren’t enough letters to go around. Same thing with acronyms. A quick search for CMS will include: Center for Medicare & Medicaid Services (a nested acronym), Content Management System, Chicago Manual of Style, Chronic Mountain Sickness, Central Middle School, City Montessori School, Charlotte Motor Speedway, Comparative Media Studies, Central Management Services, Convention on Migratory Species, Correctional Medical Services, College Music Society, Colorado Medical Society, Cytoplasmic Male Sterility, Certified Master Safecracker, Cryptographic Message Syntax, Code Morphing Software, Council for the Mathematical Sciences, Court of Master Sommeliers, and my own favorite, a neighborhood landscaper Chris Mark & Sons, of which am proud owner of one of their shirts.

And for those against acronym abuse, you can buy an AAAAA T-shirt (maybe I will too):

Thanks to Kathryn Grim for suggesting a blog about what goes on at an LHC experiment during shutdown.

Are you addicted to YouTube? No, I wouldn’t say that about myself, but gosh, it’s rather amazing what you can find on there. At home with the kids lately, we’ve been looking at classic bits of The Electric Company, the 1970′s Children’s Television Workshop educational show which spans the period of late Tom Lehrer to early Morgan Freeman. Part of what makes YouTube great is that it’s so easy to use. You put a phrase into the search window, and some computer somewhere (don’t ask me where) quickly finds the data that you are looking for. Then you just click a button and the videos come streaming onto your computer, without a whole lot of effort from you. You don’t have to know what computer disk the file resides on, or the directory structure of that computer. For all you know, the video might be coming from several different computers at once, with the source being adjusted in real time to give the best streaming performance.

Now, compare that to how we go about getting our data in particle physics experiments. Back in the day, you definitely had to know the exact directory and exact file names of the dataset that you wanted to analyze, and then carefully type that into your computer programs. A single typo could destroy hours or days of computing effort. We’ve largely gotten past that — we have better technology for file catalogues, such that you can just specify the name of a dataset, and all the file names will be looked up for you. But we are still largely constrained by “data locality,” the requirement that your analysis program must be running on a computer in the same room as the computer that has the disk with your data on it. This constraint leads to a variety of optimization problems. What if a dataset gets popular all of a sudden — are there enough processing resources in the right place to handle the demand? Can you get more copies out to the bigger processing centers quickly? Are you then under-using other centers and letting CPU cycles go idle? If you want to run on a given dataset, you might know which computing sites have that data, but how do you know which has the most available resources right now? And finally, what if data at a site gets corrupted? Will all the jobs running in that computer room start failing? Needless to say this doesn’t sound like YouTube at all.

I and some colleagues are working on a project that tries to change this. We’ve called it “Any Data, Anytime, Anywhere,” as our goal is to make it as easy to access LHC data as it is to access a YouTube video. At the heart of the system is a “redirector,” a system that serves as a giant index of files that reside at computing sites all over the country. A computer program asks the redirector for a file, the redirector finds an optimal source for the file, and the program then reads the file from that source, without the user having to know where the file actually is. That means that the source could be thousands of miles away, and the only way for the remote reading to be efficient is for it to be nearly as fast as reading from a computer in the same room, so some effort has gone into making that happen. Once you have removed the data locality requirement, all sorts of things are possible. If a file is corrupt at one site, it could introduce a fallback mechanism so that a read failure results in an attempt to get the same file through the redirector instead. If a particular site gets overloaded with jobs, we could start to migrate them to a less busy site, even if that site doesn’t actually have the data that the jobs want; they can be obtained through the redirector instead. That could lead to a better global balancing of supply and demand for resources. While we imagine that it’s computers at CMS institutions that will be reading the data, there’s nothing to stop any computer anywhere from reading the data, even if it is not part of CMS. That could really fulfill the promise of grid computing — if we can borrow a computer for a few hours, we can use it to analyze CMS data even if that computer starts out knowing nothing about CMS. It also gives us a straightforward way to use cloud-computing resources, if that were to turn out to be cost effective.

And on top of all that, what stops this from being limited to the LHC? Many disciplines have large datasets that need to be analyzed by distributed teams of scientists. In principle, they could use the same infrastructure. We’re hoping that this technology could eventually be used across the sciences and even into emerging fields like digital humanities. If that were to happen, then researchers from all sorts of disciplines could consider themselves Easy Readers, at least as far as their data is concerned.

On a past blog post I came across the most wonderful comment from Kelly, one of our readers:

Lay people are far smarter than it is supposed, they are also fickle and quick to get bored or offended if talked down to

This got me thinking about the last time I spoke to an expert in another field about their research, about the last time I got “layed”, if you’ll excuse the awful pun. I also hope you’ll excuse an excursion into biochemistry for one post.

Alex and Kia, relaxing in the sun

I was in Manchester for the weekend, spending the evening with Alex and Kia, a couple of friends from undergraduate and we had a lot of catching up to do! They’re both biochemistry graduate students and they work in the same lab, although in different areas. We stayed up all night over tea and biscuits (how British), discussing our research, using analogies, looking at diagrams, and coming up with all sorts of thought experiments to try to understand what was happening. They had a lot of questions about how the detector works, how we reconstruct particles (including the Higgs!) and why it takes so long to find it.

Having a discussion about something technical with an expert is not only lots of fun, but it also tells you a lot about your own skills when it comes to explaining concepts. As Kelly mentioned in her comment, there’s a temptation to talk down to people, but I find it’s more rewarding for all involved if we match our discussion to the intelligence of the audience. I’d like to think that most people who read Quantum Diaries and US LHC Blogs are here because they’re intelligent, they’re not scared of nuance, they want to read more than what a press release will tell them, and they may even be a scientist too. Once we find the right level of discussion for a given audience things get much more rewarding!

From the outside biochemistry is such a wonderful field of research. Their work is instantly relevant to the fight against disease and cancer, the field is expanding so rapidly that what students learn one year may be out of date a couple of years later, and there’s no end to the range of different topics you can research. It’s about as fast paced as you can get! It must have its frustrations, like any area of research, but being a layperson I got a chance to appreciate the concepts without the hard work, and that made it sound amazing.

The watered down version of what they told me went something like this:

HIV and T cells

What HIV looks like (Telegraph)

The HIV virus is extremely dangerous for one reason- it infects the white blood cells (T cells) that fight disease in the body. This in itself isn’t a huge problem, but when a person with HIV have some infection then things become very serious. It’s not so much that the white blood cells don’t function anymore, it’s more that they use so many of their resources building more copies of the virus. The virus attaches itself via a protein, and a small percentage of the population have a different form of the protein, which has a different shape. In principle, if a person could get a complete blood transfusion then they could be given the white blood cells with the other protein and may become immune to HIV. An easier way to do this would be to have a bone marrow transplant from another person, as the bone marrow creates the white blood cells. Naturally there are dangers associated with any procedure like this, so it’s not something to be taken lightly. Still, in the course of an hour or so my friends gave me a wonderful insight into how HIV works and some of the discoveries in the fight against the disease.

Genetic diseases

While on the topic of diseases with risky treatments we also discussed a family of genetic diseases (known as mucopolysaccharide diseases, a name I could not remember) which cause premature aging or degradation of the body. The diseases are associated with the failure of the body to break down certain sugars, so the cells get clogged up, do not function as well and then part of the body ages. The exact type of disease manifests in different ways, and sometimes they can only be identified once the disease has progressed. So I asked why children aren’t just screened for this at birth, as they are for many other diseases. It turns out that the cost of the test isn’t low enough and rate of incidence of the disease isn’t high enough for that to become a realistic option yet. Putting groundbreaking, life saving research in that kind of context is rather chilling. I’m glad physicists don’t have to deal with those kinds of choices!

Kia was kind enough to link to one of the charities, so I could find out more about the disease and how it affects us: The MPS Society.

The immune system

But we weren’t done yet! We also talked about the immune system and cancer. Having heard so much about T cells, I was curious about where they came from and why they only attacked foreign objects in the body. It turns out that T cells spend much of their time in the thymus where they are trained to learn what cells in the body look like. When the T cells are produced there is some shuffling of genes and each T cell ends up a little different. If a T cell latches onto part of the thymus it gets destroyed and isn’t allowed into the rest of the body. Otherwise the T cell is let out into the bloodstream. If it finds a cell it “thinks” is attractive, it latches on and releases chemicals into the blood stream. Other T cells respond to the chemical gradient and they too latch on. After a short while the foreign body is overwhelmed and dies.

A red blood cell, a platelet and a T-cell, side by side (Wikipedia)

Well that’s how it works in principle, and there are many ways in which it can go wrong. Some viruses are adept at mutating so that their appearance changes. (On the subject of mutations, my friends also treated me to a discussion of “frame shifts” and how you can get two proteins from one gene!) If one of these viruses gets identified and overwhelmed, one copy may mutate into another form, and the T cells are back to square one again. Another “nightmare scenario” is when a cancerous growth releases a different kind of chemical which essentially says “All fine over here! Carry on!” to the T cells. If that happens then things can go quite seriously wrong quite quickly. If all that wasn’t complicated enough, T cells can also get “confused” and latch on cells from their host body, giving rise to auto immune diseases. The immune system is so amazingly intricate that you could easily spend a whole evening just scratching the surface of the subject. At the same time it also seems immensely fragile and wonderfully robust. Although the apparatus for making an immune system is inherited, the good work it does fighting disease isn’t. If those ideas doesn’t blow your mind then I don’t know what will!

The PhD problem

To round off the evening we also discussed how our PhDs had progressed. Biochemistry seems less forgiving than physics, and they told me that between them and two other mutual friends, two of them had to find new topics, new funding and new institutions. Sometimes, when a research idea doesn’t work out and the funding disappears, even if it’s through no fault of the student, the student has no choice but to start again. I faced a similar situation with my own PhD, as funding for the experiment was cut short and I suddenly found myself with 18 months left, no research topic and no service task. My colleagues rallied round, asked questions, contacted people and helped me find a new topic and a new service task on the same experiment. I finished about 9 months later than expected (but still within four years!) with a decent thesis and some glowing letters of recommendation. Once again, I was glad to be in the cozy realm of physics! It’s differences like these that aren’t at all obvious, and make us realize just how much we have to learn from each other. (My friends were also amazed to find I had about a hundred papers with my name on!)

PhDs are elastic... (PhD Comics)

When did you last get layed?

So for a few hours I was a layperson with two experts at my disposal, and it was one of the most entertaining evenings I’ve had in a long time. So to the lay people reading this blog, if you don’t find the term “layperson” pejorative, it would be great to hear about your experiences. What discussions particularly excited you? How you deal with being patronized or, perhaps worse, overwhelmed with ideas? Or for that matter, if you’re an expert in another area, what are your experiences telling other people about your work? In short, tell us happened last time you got “layed”.

Over the Christmas Holiday the ATLAS Collaboration submitted an article to Physical Review Letters, a peer-review journal.  The article titled, “Observation of a New χ_b State in Radiative Transitions to Υ(1S) and Υ(2S) at ATLAS,” can be found on arXiv.

The processes under study in this paper are the following:

χ_b(nP)→ Υ(1S) γ → μ⁺μ^- γ

χ_b(nP)→ Υ(2S) γ → μ⁺μ^- γ

Where n = 1,2 or 3.

The focus of this paper was on finding a meson known as the χ_b(nP). Mesons are a class of particles formed by a bound state of a quark and an anti-quark; the χ_b(nP) happens to be a bound state of a b-quark (termed b, for beauty) and an anti-b-quark (termed b).  The (nP) part means that quark/anti-quark are bound together in a P-orbital of energy level n. As a consequence of the relativistic energy-momentum relation, different energy levels correspond to bound states with different rest masses.  So basically for each value of n you have a unique particle! The n = 3 particle has only ever been theoretically predicted, so in this paper a new particle was discovered!

Now the χ_b(nP) particles are very short lived and usually can’t be observed directly.  So to find them the ATLAS Collaboration has to infer their presence by summing up the energy of their decay products.  In the above two equations, the χ_b(nP) is decaying into another meson known as the Upsilon, Υ(kS), and in the process a photon is also emitted (hence the “radiative transition” in the title). Now the Upsilon is also made up by a bb pair.  The (kS) part means that the quark/anti-quark pair are bound together in an S-Orbital of energy level k = 1 or 2.

The Υ(kS) is also a very short lived particle (mean lifetime of approximately 10^-20 seconds).  To identify the Upsilons needed for this study the ATLAS Collaboration had to look for two oppositely charged muons, called a di-muon or μ⁺μ^- pair, having a summed rest mass (termed “invariant mass”) near the published mass values for the Υ(kS).  A plot of the di-muon invariant mass can be see at right [1].  From left to right the peaks in the graph represents di-muons originating from decays of the Υ(1S),  Υ(2S), and the Υ(3S), respectively. The muons in the shaded regions from the Υ(1S) and Υ(2S) decays were used in the search for the χ_b(nP) particles.

Then to find the χ_b(nP) particles, ATLAS researchers looked for a point in the detector from which a di-muon and a photon originated from.  This point is known as a vertex.

Charged particles, such as muons, leave tracks in the ATLAS Detector’s inner tracking detector (which consists of a silicon pixel detector, a silicon microstrip detector, and a transition radiation tracker).  The inner tracking detector is like a giant CCD camera, and is based on the same technology.

However, neutral particles, like photons, do not leave a track in the tracker.  Photons are detected by energy depositions in the ATLAS Detector’s electro-magnetic calorimeter.  To see if an energy deposition marked as a photon comes from this di-muon vertex, you take every di-muon vertex, and you try and match it with one of your photon energy depositions.  If the match is “good enough” you call this di-muon plus photon a χ_b(nP) candidate.

Before we show you these χ_b(nP) candidates I want to talk about the di-muon invariant mass plot one more time.  Notice how the peaks in this plot have some width to them.  This has to do with the resolution of the ATLAS Detector.  The narrower the peaks are the better the resolution.  However, there is a limit to how thin these peaks can be.  For example, the Υ(1S) has its own natural width of  about 54 keV or 0.000054 GeV.  So suppose you had the perfect particle detector and made the measurement shown in the di-muon invariant mass plot.  Even using your perfect detector your Υ(1S) peak would still have a width of exactly 0.000054 GeV.  As you can see the peaks are no where near this, and as I said this is due to the finite resolution of the ATLAS Detector.  To account for this resolution, researchers at ATLAS worked with a variable defined as:

Δm = m(μ⁺μ^-γ) - m(μ⁺μ^-)

This takes the invariant mass (e.g. rest mass) of the di-muon and the photon, the χ_b(nP) candidates, and subtracts the di-muon mass.  Then the ATLAS researchers add the world average values of the Upsilon masses back to Δm.

m _k = Δm + m_Υ(kS) = m(μ⁺μ^-γ) - m(μ⁺μ^-) + m_Υ(kS)

Note, for your perfect detector measuring the Υ(1S) this quantity: m(μ⁺μ^-) – m_Υ(1S) is approximately zero, but has a maximum value of 0.000027 GeV, e.g. this would be half the width of the Υ(1S)!  This is how the use of Δm and the world average value of the Upsilon minimizes the affect of the ATLAS detector’s resolution.

A little side note about world average values in particle physics.  They are a single value for some experimental observation, produced by the Particle Data Group [2], and take into account every experimental result that has ever been published.

A plot of m_k is shown at left [1] for the χ_b(nP) candidates in which the photon was measured directly (as opposed to an indirect measurement from the photon splitting into an e⁺e^- pair).  The first two peaks are the previously observed χ_b(1P) and χ_b(2P) particles.  The third peak is the first ever observation of the χ_b(3P)!

In case you all remember the golden rule of particle physics, the ATLAS Collaboration reports that:

“the significance of the χ_b(3P) signal is found to be in excess of six standard deviations in each of the unconverted and converted photon selections independently” [1]

Or put plainly, the probability that this third peak could have happened by coincidence is about 2 in one billion.  You literally have a higher probability of winning the lottery at 1 in approximately 16 million [3] or being struck by lightning this year at 1 in 775,000 [4].

So how about that? Not everyday a new particle is discovered!

Until Next Time,

-Brian

References

[1] The ATLAS Collaboration, “Observation of a New State in Radiative Transitions to and at ATLAS,” arXiv:1112.5154v1 [hep-ex].

[2] K. Nakamura et al. (Particle Data Group), J. Phys. G 37, 075021 (2010). Note this may be found online here: http://pdg.lbl.gov/2011/tables/contents_tables.html

[3] wikiHow, “How to Calculate Lotto Odds,” http://www.wikihow.com/Calculate-Lotto-Odds, Jan 10^th 2012.

[4] NOAA, “Medical Aspects of Lightning,” http://www.lightningsafety.noaa.gov/medical.htm, Jan 10^th 2012.

Lincoln, Nebraska, where I live, is on the western end of the Central time zone, and as a result, the sun goes down pretty late on the clock here. Even at this time of year, sundown isn’t until 5 PM, and it’s not really dark until at least six. We usually get home with the kids around five, and then we do dinner and playtime inside until bed. That means that the children, who are five and three, are rarely outside when it is really dark out, and they don’t get to see the stars, beyond the bright planets, very often.

The past weekend was an exception; it was Chanukah and there were many evening celebrations, as you are supposed to light the candles at sundown, so we were out past bedtime. On Friday night, as we went out to our car to drive home, my daughter, the older kid, looked up at the cloudless sky and marveled at the number of stars that she could see. I looked up too, and took the opportunity to point out one of the few constellations that I can identify, Orion. (Whenever I think about Orion, I think about John Guare’s “The House of Blue Leaves” — sorry.) “See, it looks like a person, with a top part and a bottom part, and those three stars are a belt,” I explained. My daughter looked at this a little more, and then asked, “Does the world want it to be like that?”

Interesting question — what she meant was whether the stars were intentionally arranged in the shape of a person, or whether it was just something that people made up when they looked at the stars. The answer is the latter, of course, although perhaps the ancients thought differently. Our conversation for the evening went on to other topics in astronomy (“Planets are round,” she said, “so it’s very hard to stand on them.”), but I kept thinking about what she had asked me.

As scientists, we collect data from the world around us, and try to make patterns out of it that we can understand. These patterns are theories, really, and as more data come in, we re-evaluate the theories to see if they are still consistent with the data. Do all the stars make shapes that look like familiar things? Are all of the measurements from the LHC consistent with a Higgs boson at 125 GeV? Are we humans just imposing an anthropic view onto the world? Measurements throughout particle physics, not just at the LHC, seem to support the idea of the Higgs mechanism. Is that consistency just a pattern that we have invented? Or does the world actually want it to be like that?

A year from now, we hope to have an answer to this question. As we head into 2012, a potentially decisive year for particle physics, I hope that all of our Quantum Diaries readers have the opportunity to ask, and answer, their own questions about what the world wants it to be like.