# Category Archives: Education

## DIY Garage Work

Recently, I heard about a string of YouTube videos where Ben Krasnow of the Applied Sciences YouTube Channel makes a series of scientific instruments in his garage. One of the particularly impressive achievements is his homemade Scanning Electron Microscope, where he constructs a pretty decent instrument with approximately $1500. This is definitely outstanding from an educational viewpoint —$1500 will probably be affordable for many high schools and will enable students to see how to image objects with electrons.

Here are a couple videos showing this and another one of his projects where he uses a laser and a couple optical elements to construct a Raman spectroscopy setup:

Lastly, I’d like to point out that Christina Lee has put together an excellent set of Jupyter code (i.e. IPython Notebook code) to solve various condensed matter physics problems. It’s definitely worth having a look.

## An Undergraduate Optics Problem – The Brewster Angle

Recently, a lab-mate of mine asked me if there was an intuitive way to understand Brewster’s angle. After trying to remember how Brewster’s angle was explained to me from Griffiths’ E&M book, I realized that I did not have a simple picture in my mind at all! Griffiths’ E&M book uses the rather opaque Fresnel equations to obtain the Brewster angle. So I did a little bit of thinking and came up with a picture I think is quite easy to grasp.

First, let me briefly remind you what Brewster’s angle is, since many of you have probably not thought of the concept for a long time! Suppose my incident light beam has both components, s– and p-polarization. (In case you don’t remember, p-polarization is parallel to the plane of incidence, while s-polarization is perpendicular to the plane of incidence, as shown below.) If unpolarized light is incident on a medium, say water or glass, there is an angle, the Brewster angle, at which the light comes out perfectly s-polarized.

An addendum to this statement is that if the incident beam was perfectly p-polarized to begin with, there is no reflection at the Brewster angle at all! A quick example of this is shown in this YouTube video:

So after that little introduction, let me give you the “intuitive explanation” as to why these weird polarization effects happen at the Brewster angle. First of all, it is important to note one important fact: at the Brewster angle, the refracted beam and the reflected beam are at 90 degrees with respect to each other. This is shown in the image below:

Why is this important? Well, you can think of the reflected beam as light arising from the electrons jiggling in the medium (i.e. the incident light comes in, strikes the electrons in the medium and these electrons re-radiate the light).

However, radiation from an oscillating charge only gets emitted in directions perpendicular to the axis of motion. Therefore, when the light is purely p-polarized, there is no light to reflect when the reflected and refracted rays are orthogonal — the reflected beam can’t have the polarization in the same direction as the light ray! This is shown in the right image above and is what gives rise to the reflectionless beam in the YouTube video.

This visual aid enables one to use Snell’s law to obtain the celebrated Brewster angle equation:

$n_1 \textrm{sin}(\theta_B) = n_2 \textrm{sin}(\theta_2)$

and

$\theta_B + \theta_2 = 90^o$

to obtain:

$\textrm{tan}(\theta_B) = n_2/n_1$.

The equations also suggest one more thing: when the incident light has an s-polarization component, the reflected beam must come out perfectly polarized at the Brewster angle. This is because only the s-polarized light jiggles the electrons in a way that they can re-radiate in the direction of the outgoing beam. The image below shows the effect a polarizing filter can therefore have when looking at water near the Brewster angle, which is around 53 degrees for water.

To me, this is a much simpler way to think about the Brewster angle than dealing with the Fresnel equations.

## Book Review – The Gene

Following the March Meeting, I took a vacation for a couple weeks, returning home to Bangkok, Thailand. During my holiday, I was able to get a hold of and read Siddhartha Mukherjee’s new book entitled The Gene: An Intimate History.

I have to preface any commentary by saying that prior to reading the book, my knowledge of biology embarrassingly languished at the middle-school level. With that confession aside, The Gene was probably one of the best (and for me, most enlightening) popular science books I have ever read. This is definitely aided by Mukherjee’s fluid and beautiful writing style from which scientists in all fields can learn a few lessons about scientific communication. The Gene is also touched with a humanity that is not usually associated with the popular science genre, which is usually rather dry in recounting scientific and intellectual endeavors. This humanity is the book’s most powerful feature.

Since there are many glowing reviews of the book published elsewhere, I will just list here a few nuggets I took away from The Gene, which hopefully will serve to entice rather than spoil the book for you:

• Mukherjee compares the gene to an atom or a bit, evolution’s “indivisible” particle. Obviously, the gene is physically divisible in the sense that it is made of atoms, but what he means here is that the lower levels can be abstracted away and the gene is the relevant level at which geneticists work.
• It is worth thinking of what the parallel carriers of information are in condensed matter problems — my hunch is that most condensed matter physicists would contend that these are the quasiparticles in the relevant phase of matter.
• Gregor Mendel, whose work nowadays is recognized as giving birth to the entire field of genetics, was not recognized for his work while he was alive. It took another 40-50 years for scientists to rediscover his experiments and to see that he had localized, in those pea plants, the indivisible gene. One gets the feeling that his work was not celebrated while he was alive because his work was far ahead of its time.
• The history of genetics is harrowing and ugly. While the second World War was probably the pinnacle of obscene crimes committed in the name of genetics, humans seem unable to shake off ideas associated with eugenics even into the modern day.
• Through a large part of its history, the field of genetics has had to deal with a range of ethical questions. There is no sign of this trend abating in light of the recent discovery of CRISPR/Cas-9 technology. If you’re interested in learning more about this, RadioLab has a pretty good podcast about it.
• Schrodinger’s book What is Life? has inspired so much follow-up work that it is hard to overestimate the influence it has had on a generation of physicists that transitioned to studying biology in the middle of the twentieth century, including both Watson and Crick.

While I could go on and on with this list, I’ll stop ruining the book for you. I would just like to say that at the end of the book I got the feeling that humans are still just starting to scratch the surface of understanding what’s going on in a cell. There is much more to learn, and that’s an exciting feeling in any field of science.

Aside: In case you missed March Meeting, the APS has posted the lectures from the Kavli Symposium on YouTube, which includes lectures from Duncan Haldane and Michael Kosterlitz among others.

## Disorganized Reflections

Recently, this blog has been concentrating on topics that have lacked a personal touch. A couple months ago, I started a postdoc position and it has gotten me thinking about a few questions related to my situation and some that are more general. I thought it would be a good time to share some of my thoughts and experiences. Here is just a list of some miscellaneous questions and introspections.

1. In a new role, doing new work, people often make mistakes while getting accustomed to their new surroundings. Since starting at my new position, I’ve been lucky enough to have patient colleagues who have forgiven my rather embarrassing blunders and guided me through uncharted territory. It’s sometimes deflating admitting your (usually) daft errors, but it’s a part of the learning process (at least it is for me).
2. There are a lot of reasons why people are drawn to doing science. One of them is perpetually doing something new, scary and challenging. I hope that, at least for me, science never gets monotonous and there is consistently some “fear” of the unknown at work.
3. In general, I am wary of working too much. It is important to take time to exercise and take care of one’s mental and emotional health. One of the things I have noticed is that sometimes the most driven and most intelligent graduate students suffered from burnout due to their intense work schedules at the beginning of graduate school.
4. Along with the previous point, I am also wary of spending too much time in the lab because it is important to have  time to reflect. It is necessary to think about what you’ve done, what can be done tomorrow and conjure up experiments that one can possibly try, even if they may be lofty. It’s not a bad idea to set aside a little time each day or week to think about these kinds of things.
5. It is necessary to be resilient, not take things personally and know your limits. I know that I am not going to be the greatest physicist of my generation or anything like that, but what keeps me going is the hope that I can make a small contribution to the literature that some physicists and other scientists will appreciate. Maybe they might even say “Huh, that’s pretty cool” with some raised eyebrows.
6. Is physics my “passion”? I would say that I really like it, but I could have just as easily studied a host of other topics (such as literature, philosophy, economics, etc.), and I’m sure I would have enjoyed them just as much. I’ve always been more of a generalist in contrast to being focused on physics since I was a kid or teenager. There are too many interesting things out there in the world to feel satiated just studying condensed matter physics. This is sometimes a drawback and sometimes an asset (i.e. I am sometimes less technically competent than my lab-mates, but I can probably write with less trouble).
7. For me, reading widely is valuable, but I need to be careful that it does not impede or become a substitute for active thought.
8. Overall, science can be intimidating and it can feel unrewarding. This can be particularly true if you measure your success using a publication rate or some so-called “objective” measure. I would venture to say that a much better measure of success is whether you have grown during graduate school or during a postdoc by being able to think more independently, by picking up some valuable skills (both hard and soft) and have brought a  multi-year project into fruition.

Please feel free to share thoughts from your own experiences! I am always eager to learn about people whose experiences and attitudes differ from mine.

A few nuggets on the internet this week:

1. For football/soccer fans:
http://www.espnfc.us/blog/the-toe-poke/65/post/3036987/bayern-munichs-thomas-muller-has-ingenious-way-of-dodging-journalists

2. Barack Obama’s piece in Science Magazine:
http://tinyurl.com/jmeoyz5

3. An interesting read on the history of physics education reform (Thanks to Rodrigo Soto-Garrido for sharing this with me):
http://aapt.scitation.org/doi/full/10.1119/1.4967888

4. I wonder if an experimentalist can get this to work:
http://www.bbc.com/news/uk-england-bristol-38573364

## Diffraction, Babinet and Optical Transforms

In an elementary wave mechanics course, the subject of Fraunhofer diffraction is usually addressed within the context of single-slit and double-slit interference. This is usually followed up with a discussion of diffraction from a grating. In these discussions, one usually has the picture that light is “coming through the slits” like in the image below:

Now, if you take a look at Ashcroft and Mermin or a book like Elements of Modern X-ray Physics by Als-Nielsen and McMorrow, one gets a somewhat different picture. These books make it seem like X-ray diffraction occurs when the “scattered radiation from the atoms add in phase”, as in the image below (from Ashcroft and Mermin):

So in one case it seems like the light is emanating from the free space between obstacles, whereas in the other case it seems like the obstacles are scattering the radiation. I remember being quite confused about this point when first learning X-ray diffraction in a solid-state physics class, because I had already learned Fraunhofer diffraction in a wave mechanics course. The two phenomena seemed different somehow. In their mathematical treatments, it almost seemed as if for optics, light “goes through the holes” but for X-rays “light bounces off the atoms”.

Of course, these two phenomena are indeed the same, so the question arises: which picture is correct? Well, they both give correct answers, so actually they are both correct. The answer as to why they are both correct has to do with Babinet’s principle. Wikipedia summarizes Babinet’s principle, colloquially, as so:

the diffraction pattern from an opaque body is identical to that from a hole of the same size and shape except for the overall forward beam intensity.

To get an idea of what this means, let’s look at an example. In the images below, consider the white space as openings (or slits) and the black space as obstacles in the following optical masks:

What would the diffraction pattern from these masks look like? Well, below are the results (taken from here):

Apart from minute differences close to the center, the two patterns are basically the same! If one looks closely enough at the two images, there are some other small differences, most of which are explained in this paper.

Hold on a second, you say. They can’t be the exact same thing! If I take the open space in the optical mask on the left and add it to the open space on the mask to the right, I just have “free space”. And in this case there is no diffraction! You don’t get the diffraction pattern with twice the intensity. This is of course correct. I have glossed over one small discrepancy. First, one needs to realize that intensity is related to amplitude as so:

$I \propto |A|^2$

This implies that the optical mask on the left and the one on the right give the same diffraction intensity, but that the amplitudes are 180 degrees out of phase. This phase doesn’t affect the intensity, though, as in the formula above intensity is only related to the magnitude of the amplitude. Therefore the masks, while giving the same intensity, are actually slightly different. The diffraction pattern will then cancel when the optically transparent parts of the two masks are added together. It’s strange to think that “free space” is just a bunch of diffraction patterns cancelling each other out!

With this all in mind, the main message is pretty clear though: optical diffraction through slits and the Ashcroft and Mermin picture of “bouncing off atoms” are complementary pictures of basically the same diffraction phenomenon. The diffraction pattern obtained will be the same in both cases because of Babinet’s principle.

This idea has been exploited to generate the excellent Atlas of Optical Transforms, where subtleties in crystal structures can be manipulated at the optical scale. Below is an example of such an exercise (taken from here). The two images in the first row are the optical masks, while the bottom row gives the respective diffraction patterns. In the first row, the white dots were obtained by poking holes in the optical masks.

Basically, what they are doing here is using Babinet’s principle to image the diffraction from a crystal with stacking faults along the vertical direction. The positions of the atoms are replaced with holes. One can clearly see that the effect of these stacking faults is to smear out and broaden some of the peaks in the diffraction pattern along the vertical direction. This actually turns out to gives one a good intuition of how stacking faults in a crystal can distort a diffraction pattern.

In summary, the Ashcroft and Mermin picture and the Fraunhofer diffraction picture are really two ways to describe the same phenomenon. The link between the two explanations is Babinet’s principle.

## Is it really as bad as they say?

It’s been a little while since I attended A.J. Leggett’s March Meeting talk (see my review of it here), and some part of that talk still irks me. It is the portion where he referred to “the scourge of bibliometrics”, and how it prevents one from thinking about long-term problems.

I am not old enough to know what science was like when he was a graduate student or a young lecturer, but it seems like something was fundamentally different back then. The only evidence that I can present is the word of other scientists who lived through the same time period and witnessed the transformation (there seems to be a dearth of historical work on this issue).

It was easy for me to find articles corroborating Leggett’s views, unsurprisingly I suppose. In addition to the article I linked last week by P. Nozieres, I found interviews with Sydney Brenner and Peter Higgs, and a damning article by P.W. Anderson in his book More and Different entitled Could Modern America Have Invented Wave Mechanics? In his opinion piece, Anderson also refers to an article by L. Kadanoff expressing a similar sentiment, which I was not able to find online (please let me know if you find it, and I’ll link it here!). The conditions described at Bell Labs in David Gertner’s book The Idea Factory also paint a rather stark contrast to the present status of condensed matter physics.

Since I wasn’t alive back then, I really cannot know with any great certainty whether the current state of affairs has impeded me from pursuing a longer-term project or thinking about more fundamental problems in physics. I can only speak for myself, and at present I can openly admit that I am incentivized to work on problems that I can solve in 2-3 years. I do have some concrete ideas for longer-term projects in mind, but I cannot pursue these at the present time because, as an experimentalist and postdoc, I do not have the resources nor the permanent setting in which to complete this work.

While the above anecdote is personal and it may corroborate the viewpoints of the aforementioned scientists, I don’t necessarily perceive all these items as purely negative. I think it is important to publish a paper based on one’s graduate work. It should be something, however small, that no one has done before. It is important to be able to communicate with the scientific community through a technical paper — writing is an important part of science. I also don’t mind spending a few years (not more than four, hopefully!) as a postdoc, where I will pick up a few more tools to add to my current arsenal. This is something that Sydney Brenner, in particular, decried in his interview. However, it is likely that most of what was said in these articles was aimed at junior faculty.

Ultimately, the opinions expressed by these authors is concerning. However, I am uncertain as to the extent to which what is said is exaggeration and the extent to which it is true. Reading these articles has made me ask how the scientific environment I was trained in (US universities) has shaped my attitude and scientific outlook.

One thing is undoubtedly true, though. If one chooses to resist the publish-or-perish trend by working on long-term problems and not publishing, the likelihood of landing an academic job is close to null. Perhaps this is the most damning consequence. Nevertheless, there is still some outstanding experimental and theoretical science done today, some of it very fundamental, so one should not lose all hope.

Again, I haven’t lived through this academic transformation, so if anyone has any insight concerning these issues, please feel free to comment.