PC to Mac

Yup, I’ve caved. I’ve been a PC user all my life, but the one I’ve had for the past several years has been slowly and steadily grinding to a halt, while my digital work load has equally been consistently rising, so it was time for a change. While I get the impression that switching to Mac is the new ‘in’ thing these days - IP has noted that new converts often favor style over functionality (and Macs are pretty, without a doubt) - my main reason was much more simple: it’s true, Macs generally do tend to be more stable, secure, and easy to use, and now with Boot Camp, I’m running Windows as well. There’s nothing to lose and a whole lot to gain, and for people like me who treat life as one giant optimization problem, that’s a big deal. Indeed, making the transition, transferring data, getting comfortable with (mostly) everything, &c. took under a week. Here’s how I do my ‘basic’ tasks…

• Presentations/Word Processing: MS Powerpoint & MS Word 2004. while I’ve heard good things about iWork, I went with MS Office simply because, at the end of the day, most of the files I work with (e.g. in collaborations) are Office files, and I wanted to make sure that I was 100% compatible (even though from what I hear, there aren’t too many major compatibility issues). I’m slightly regretting this now on the Word front (Powerpoint I can live with) - it’s notoriously slow at times. I’m trying to wait it out until Office 2008 for Mac comes out, but I may end up shelling out some more and get Pages (or something free, like OpenOffice).

• E-mail/Calendar: Apple Mail/iCal. Like everything else that came along with this machine, these are wonderful. Plus I can sync the iCal to my iPod, which is great (although I really do hate all these ‘i-’ prefixes).

• RSS reader: Vienna. Open-source, freeware, sleek, built-in browser, and tons of functionality. Works great.

• Plotting data: OriginLab/Plot/Apple Grapher. I’ve always used OriginLab for data analysis, making figures, &c. so I decided to install it on my Windows partition (sadly, no Mac version). However, I recently discovered Plot (a freeware program) and the built-in Grapher app, both of which are wonderful for making high-quality figures, both 2d and 3d. They’re very bare bones, which is great for what I use them for (I fought with Origin for a half hour the other day trying to format a polar plot correctly, whereas Grapher took five minutes to do the same thing).

• General data analysis: OriginLab/Igor Pro. Our lab has a license for Origin, and it’s what I’ve always used, so I installed it - but I wanted something I could run on my Mac as well, without having to switch to the Windows partition. I’ve hear some good things about Igor, and their amazing student personal purchase deal made it economical enough to buy. Haven’t had much chance to play around with it, though.

• AFM/SPM image analysis: Gwyddion, sometimes Image SXM. I do a lot of AFM/SPM image processing and analysis, and have so far tended to use Veeco’s Nanoscope software (again, which isn’t supported on Mac). I’m happy about that though, because I don’t think I would’ve ever bothered to try out Gwyddion, which is a wonderful piece of software. It’s freeware, has just about every kind of functionality imaginable, and best of all: it tells you what it’s doing (with excellent supporting documentation). Installing it is somewhat involved, but not too difficult. (The only major point to note is that Gwyddion for Mac OS X needs X11, which comes on the Mac installer disk). Oh, and before I installed Gwyddion I played around with Image SXM a bit, too - pretty nice as well, but I’m far more impressed with Gwyddion.

• Graphics: GIMP (the GNU image manipulation program). I used to use Adobe Photoshop for all my graphics needs, but it’s ridiculously expensive. This program does, as far as I can tell, pretty much everything Photoshop does - for free. (Again, like Gwyddion, it uses X11, which is a tool OS X uses to run certain open source programs). The only issue is that it’s not that great with certain very simple tasks, like - of all things - drawing a circle.

• Lab Notebook: VoodooPad. Another great free program with a ton of functionality - basically like a personal wiki that I plan to use as a lab notebook, but I haven’t used it enough to pass judgement. Very easy to use, though.

• Organizing Papers: Zotero. I tried the much-raved about Papers for a bit, but soon quit, because they only supported PubMed (which only includes a fraction of the journals I read). Now that they include Web of Science I’d be more inclined to stick with them, but Zotero’s been serving me wonderfully. It’s a simple firefox plug-in that supports pretty much every publisher I’ve encountered. It downloads a paper’s metadata (author list, journal, abstract, etc.) with a click of a button, and lets you store the paper as an attachment, too. Only two issues are (i) integration with Word is poor, but I can easily export my Zotero citations as an endnote file and use endnote to put in citations, as I’ve done before; (ii) data is only stored on this computer, not on some central server somewhere (although they claim to be working on including this, which will be great).

• Windows-in-Mac: None at the moment. A number of programs exist that enable one to use the Windows partition while in conventional Mac mode. I tried CrossOver briefly, but it didn’t work all that great. I plan on giving Parallels Desktop a shot at some point, but frankly, I haven’t really needed Windows all that much. (Which is probably the take-home message from this experience…)

Of course, if anyone has suggestions for good software or simply personal favorites, I’d love to hear about them.

All in all, no complaints so far, except for one, which is a slightly big one that I’m not sure what I’ll do about: it turns out that my laptop doesn’t work with certain kinds of projectors, which sucks when I have to give a talk. Quick googling reveals that this is a problem with many MacBooks, and that not much has been done to acknowledge or fix the problem, which is ridiculous. Particularly since I have to give a talk at a conference in a week or so… I’ll probably have to pdf it and carry it on a USB drive just in case things don’t work out, which stinks (and is definitely not a long-term solution).

Talks Part 3: Biomaterials

Another talk that was particularly interesting was Angela Belcher’s Grace Hopper lecture on “Genetic Control of the Synthesis and Assembly of Materials for Electronics and Energy”. I’m not going to post much on it save for a number of references, because I’ve been aware of a lot of her group’s work for a good deal of time now. In general, what they do is try to combine man-made fabrication tools and the specificity inherent in living systems (via millions of years of evolution) to figure out easy, controllable, environmentally-friendly ways to make new materials for a variety of purposes. I was particularly struck by her emphasis on the simplicity of everything they do - if it can’t be transferred to industry or undergrad labs within several years, they won’t do it, which is an interesting philosophy. Anyway, one of the particularly cool things Prof. Belcher’s group has come up with recently is the use of viruses to direct the formation of nanowires, and they’ve been working to use them to make things like self-assembling, cheap and efficient Li-ion batteries. This kind of work definitely appeals to the part of me that likes science because of all the neat things that it enables us to make. Anyway, here are some of her publications that I’ve found most useful:

- B. D. Reiss et al., “Biological Routes to Metal Alloy Ferromagnetic Nanostructures“, Nano Lett. 4 1127 (2004).
- S. Jaffar et al., “Layer-by-Layer Surface Modification and Patterned Electrostatic Deposition of Quantum Dots“, Nano Lett. 4 1421 (2004).
- P. J. Yoo et al., “Spontaneous assembly of viruses on multilayered polymer surfaces“, Nature Materials 5 234 (2006).
- K. T. Nam et al., “Virus-Enabled Synthesis and Assembly of Nanowires for Lithium Ion Battery Electrodes“, Science 312 885 (2006).
- Y. Huang et al., “Programmable Assembly of Nanoarchitectures Using Genetically Engineered Viruses“, Nano Lett. 5 1429 (2005).
- C. Mao et al., “Viral assembly of oriented quantum dot nanowires“, PNAS 100 6946 (2003).

Philosophia Naturalis #8

This post was delayed by a number of ridiculous technical mishaps, but issue number eight of Philosophia Naturalis - the physics blogosphere’s very own blog carnival - is finally here. There were a number of very interesting submissions spanning pretty much everything that is involved in physics and the practice of it, and so I’ve split them up accordingly. Enjoy!

Cool Experiments
Motivated by some recent quantum optics work recording the birth and death of microwave photons in a superconducting resonant cavity by a French group, Chad Orzel has proclaimed this to be “the golden age of experimental quantum optics”. And indeed, it seems to be: two other such experiments include this study of the Hanbury-Brown-Twiss effect, and this more recent realization of the delayed-choice experiment first proposed by John Wheeler in 1978. A closely related experiment is that of the ‘quantum eraser’ proposed by Scully and Drühl in 1981, and this post does an excellent job of summarizing the general principles.

On the opposite end of the size spectrum, Cosmic Variance recently hosted a very interesting discussion on some analysis of cosmic microwave background radiation data from WMAP (NASA’s much-publicized effort to very accurately measure the temperature of the CMB).

Interesting Theory
As tends to be the case, most posts were of a more theoretical bent. The mapping of the E₈ Lie group recently received a good deal of press, including a rather vague article in the New York Times (the gist of which was something along the lines of “a bunch of mathematicians did something really complicated involving a pretty picture, and apparently it has profound implications but we’re not exactly sure what.”) Mark Chu-Carroll and John Baez have taken a different approach, recently posting about the actual math involved and the whole point of the project. And speaking of recent math-y work that has received a good deal of press, these two posts report on this paper by Peter Lu and Paul Steinhardt (who used to be at Penn!) on signatures of quasicrystalline Penrose tilings in medieval Islamic architecture.

Penrose is an excellent segway into two posts by Scott Aaronson. The first poses the question: “what’s the connection between a black hole having an event horizon and its having a singularity? In other words, once you’ve clumped enough stuff together that light can’t escape, why have you also clumped enough together to create a singularity?” (This is related to the Penrose-Hawking theorems of general relativity). The second (or rather, the subsequent comments) deals with possible connections between the brain and quantum computers, something Roger Penrose has discussed in a good deal of depth. (Matt Leifer has a similar post, asking the question: “if quantum computers are more efficient than classical ones then why didn’t our brains evolve to take advantage of quantum information processing?“)

There’s more out there, too: see, for example, this post discussing the much-storied Bayesian theorem and connections to Bell’s inequalities, or this post on ‘biophysical economics’, an economic theory rooted in biological and physical realities first put forth in the 20’s. Something that struck me as being particularly interesting was this post on the use of evolutionary algorithms in lattice QCD simulations. Meanwhile, Ponder Stibbons has been plowing through Huw Price’s book (Time’s Arrow and Archimedes’ Point) on some of the more philosophical questions of physics, with posts on Price’s objection to dynamical explanations of entropy increase (”they can never account for the asymmetry in our observations unless they themselves have asymmetric assumptions”) and a modern-day version of Olbers’ paradox.

And of course, a good deal of very interesting physics (albeit of a different sort) goes into fields of inquiry that some would consider unconventional, like geophysics. These two posts dealing with earthquakes and volcanoes touch on this to a certain extent. The latter is particularly interesting, looking into the various possible triggers for volcanoes (and drawing connections between large earthquakes and volcanic eruptions, motivated by a fictional account of Charles Darwin’s journey on The Beagle).

The Culture of Physics
Speaking of geophysics, Jennifer Oullette has written about a talk at the recent APS March Meeting on large-scale pattern formation in geological systems, citing some work by Meredith Betterton (who gave a talk here at Penn on an unrelated subject recently) on the creation of artificial spiky ice formations. (March Meeting is an event when thousands of physicists get together and tell each other about what they’re working on - held, incidentally enough, in March.) A number of people have posted about various events at March Meeting; see, for example, this other post by Jennifer Oullette, this post by Travis Hime, and this one by Doug Natelson - or see the PhysicsWeb blog.

Having huge meetings and partying like rock stars isn’t everything, though. Among other things, the physics community (just like any other) has its share of scandals, politics, marketplace tactics, things of that sort. Sabine Hossenfelder, for example, has recently blogged about the problems of treating the scientific community as a marketplace, while Julianne Dalcanton’s post on physics’ “cult of genius” definitely touched a nerve among readers. Meanwhile, Clifford Johnson has shared his views on recent events regarding an imprisoned theoretical physics grad student. (And of course, there’s the media aspect of things: John Conway recently picked up on his two previous posts on the search for the Higgs boson to blog about the unexpected media response.)

Communicating Physics
Tommaso Dorigo recently posted about some of the problems associated with the way physicists communicate things to laypeople, dealing specifically with an example from high energy physics (what is a lower limit at 95% confidence level, anyway?). At the end of the day, the physics blogosphere’s rather good with this kind of thing. For example, ‘basic concepts’ posts (like the ones mentioned in this excellent post, or this one - part of a series - on special relativity) do an excellent job. And hey, communicating physics is kind of the whole point of this blog carnival, in a sense. I think that’s where I’ll end things - hopefully it’s been interesting. Thanks to everyone who submitted either their posts or someone else’s.

Funny Journal Content

1. A candidate for the funniest journal title/paper graphic…
Here’s a cute paper: rolling a single molecular at the atomic scale. The authors look at C₄₄H₂₄, a molecule possessing two triptyene ‘wheels’ (with three ‘paddles’, each) and thus two intramolecular degrees of freedom when adsorbed on a metal surface (the independent rotation of each wheel), and push it along with an STM tip. Interestingly, the STM current is a good indicater of what kind of motion the molecule is undergoing (’rolling’ versus ‘hopping’). What I find most amusing is that the molecule was previously used to construct a ‘molecular wheelbarrow’, a result which was published in Tetrahedron Letters - probably the funniest journal title I’ve come across - and includes the following priceless graphic:

2. Can a biologist fix a radio? Or, what one scientist learned while studying apoptosis
Speaking of funny papers, this paper by Yuri Lazebnick (via Structure+Strangeness) is great. Here’s an excerpt, dealing with the question of how would a biologist fix a radio, knowing only that it is a box meant to play music?

How would we begin? First, we would secure funds to obtain a large supply of identical functioning radios in order to dissect and compare them to the one that is broken. We would eventually find how to open the radios and will find objects of various shape, color, and size. We would describe and classify them into families according to their appearance. We would describe a family of square metal objects, a family of round brightly colored objects with two legs, round-shaped objects with three legs and so on. Because the objects would vary in color, we will investigate whether changing the colors affects the radio’s performance. Although changing the colors would have only attenuating effects (the music is still playing but a trained ear of some people can discern some distortion), this approach will produce many publications and result in a lively debate.

3. Formation of a nematic fluid at high fields in Sr₃Ru₂O₇:
I had quite a lengthy post on electronic liquid crystals in 2-dimensional electron gases (e.g. GaAs/AlGaAs heterostructures) a while back, and briefly noted that:

Scientists in Europe have measured a large magnetoresistive anisotropy in the correlated electron oxide strontium ruthenate (Sr₃Ru₂O₇) near the ‘metamagnetic quantum critical point’, indicating the formation of a new quantum nematic phase. This is strikingly similar to the tranport anisotropy in 2DEGs I’ve been talking about… in particular, both show strong sensitivity to disorder - and the authors claim that the formation of this phase is tuned by the divergence in the quasiparticle effective mass near this critical point. One can only wonder what other kinds of systems could yield such behavior as well.

This European work is now one of the feature papers for the online Journal Club for Condensed Matter Physics, with a far more in-depth (yet very readable) commentary by Catherine Kallin of McMaster University in Canada.

Nano-coax cable

This was a good idea just waiting to happen:

“Subwavelength waveguide for visible light”: J. Rybczynski et al., Applied Physics Letters 90, 021104 (2006).

The authors demonstrate transmission of visible light through metallic coaxial nanostructures many wavelengths in length, with coaxial electrode spacing much less than a wavelength. Since the light frequency is well below the plasma resonance in the metal of the electrodes, the propagating mode reduces to the well-known transverse electromagnetic mode of a coaxial waveguide. They have thus achieved a faithful analog of the conventional coaxial cable for visible light.

Or, in simpler terms, a coaxial cable made from a carbon nanotube (CNT)! Here’s a picture that nicely summarizes the ‘device’:

The CNT is shown in (a) and is grown on the glass substrate using plasma-enhanced chemical vapor deposition (CVD); it is then coated with aluminum oxide (b) and chromium (c) by sputtering. To have an open end, the authors used a mechanical ‘polishing’ technique.

The end result? Nanoscale coaxial cables that are able to “strongly transmit light in the entire visible frequency range, without frequency cut-off… the propagation is essentially via the conventional TEM mode of a common coaxial cable.