Category Archives: science

Education in synchrotron

A new year is always a good time to try something new, and because we’re all stuck home because of the pandemic, it’s also a good occasion to learn more about some topics in science. I’ve consolidated here some resources that I have enjoyed over the years, or that are not easily accessible (the information about x-rays tend to be scattered, which is something x-ray do very well)

To get started, I recommend going through the free course by Philip Wilmott from PSI on EdX: Synchrotrons and X-Ray Free Electron Lasers. It is pretty comprehensive and covers a lot of the basis of x-ray science; it’s basically a boiled down version of the companion book “An Introduction to Synchrotron Radiation: Techniques and Applications” he wrote in 2011. This would take probably a week full-time, but you can probably stretch them over a few month if you’re not into binge watch (but it is probably as captivating as the Queen’s Gambit.)

The blue glow of the synchrotron radiation (AW 2020)

To mention also: if you’re a grad student working with synchrotrons, I would recommend applying for the three-week National School on Neutron and X-ray Scattering, generally at Argonne National Lab in the summer, but online this time around. I’m not sure if they will increase their cap of 60 participants.

Light source 101

For the ALS User Meeting this year (held remotely), Fanny Rodolakis and Monika Blum organized a new edition of the Light Source 101 workshop, where beamline scientists from the Advanced Light Source explain their science. Luckily, these talks where recorded (they are available as bulk here), and I have edited them in sizeable, 30-min chunks about most of the cool techniques we offer.

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The value of coffee in research

The past nine months have been spent working from home, and it has now become clear that what I miss the most is the casual interactions with colleagues in the coffee room.

It is a place where ideas sparks, and where information flows from one scientist to the other. The importance of this liminal space should not be understated. It provides a safe space where ideas can be freely challenged and developed, owing to the generally low number of participants, the low stakes and the general mood.

Over the years, I’ve developed several coffee clubs in my buildings (I’ve changed buildings three times), adding an espresso machine wherever I could (often on my own funds, though coffee beans where purchased collectively.)

Elementary Table of Coffee (Berkeley Lab building 2 coffee room, 2013-2016) (@awojdyla, Feb 4 2018)

The importance of the mood component became apparent as we switched to online meetings and we started to lack this kind of space (thankfully my colleague Diane B. organized regular coffee zooms!), though nothing replaces the in-person interaction, with a white board where people can share their thoughts.

Saul Perlmutter casting a definitive vote on the planet-ness of Pluto in our coffee room (Berkeley Lab building 2)

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Ecole Normale Inferior

In France, the Ecole Normale Supérieure (ENS) is a legendary institution, from which the vast majority of Nobel prize laureates emanates from. There are about 50 students admitted per section per year, making it much more selective than its international counterparts.

It sits in the very center of Paris, and the atmosphere within its wall is almost monastic. I spent a many nights of great intellectual excitement within its wall, visiting friends while in Paris.

Yet, this jewel of French educations seems deeply flawed – and because of the current pandemic situation, the crack shows through. Whereas in normal times, only 40% of graduates are women, this number jumps to 80% when the oral exam is removed.

This potentially shows how extreme the (unconscious) bias can be in such institutions.

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The scientist as public intellectual

Lately, I’ve been talking with a few early career scientists among my friends, trying to convince them to set up a website, and perhaps have some kind of open social media presence (e.g. Twitter.)

It’s not only about dressing things up, even if you may feel like it is

The primary reason is that since they’re going to have jobs where they will be judged on their past accomplishment, their names will necessarily be googled, and random results will appear; perhaps linkedin, google scholar, researchgate or a github account will show up on the first result page (try googling your name in private mode!) Having a website would allow to take control of the information about you, and highlight what you think is relevant.

The second reason, and perhaps the most important, is that as scientists we are public intellectual. We are paid to produce research and communicate around it. You are entitled to use your expertise on topics in your field and make it clear, through a webpage or a blog, and maybe share tools and resources you found useful. The scientific publication ecosystem is pretty bad, far from open access, and articles themselves are so terse they cannot be understood by anyone outside your field. You can use your website to make your research publicly available (it’s legal, you still own the rights, see here) and also give some context to it, by surrounding it with other relevant pieces or break it down to make it digestible.

Don’t be afraid of the light

However, the typical reaction of my fellow researcher is that “it’s not my style”, “I don’t want to self-promote.” I tend to think it’s oftentimes and extension of the impostor syndrome (great piece by my friend Maria Żurek)

It was about one year ago when I received an email: “Dear Dr. Żurek, We are happy to offer you a postdoctoral position at Berkeley Lab”. And what was my first reaction? “They probably think I’m nice, so they didn’t realize I’m inadequate”. Yes, this was my first thought, even if I had objectively good research experience, even if I was very well prepared for the application, even if I was fully aware that what I had been dealing with was the monster called impostor syndrome.

Since you spend your time doubting about the depth of your knowledge, you can never find the right time to talk about it.

But in truth I believe a big part of it is laziness – or just knowing where to start: it’s not easy to set up a website, though there are helpful guides for those who are interested (e.g. Dan Quintana.)

The visibility of scientists

Another important aspect of the scientist as a public individual is to lead by example. Academia is rapidly evolving, and we need to be visible to make everyone welcome. While historically it’s been pretty white, pretty male and pretty old, with a heavy dose of reproduction among elites, it is important to share your own story, as younger scientists may not know how academia works, because their parents or nobody around them were not academics themselves. (alternatively, writing wikipedia pages for others is a good occasion to document such stories, and for you to learn from other people trajectory and pass it on.)

It also became increasingly important that the scientist engages the public sphere. Not only to counter false messages, but also because influential (read: established) scientist also happen to be out of touch.

Twitter presence is also good in your pursuit — it’s a good hook if you don’t have the time for a full blog/website and you’re looking for interaction. Here’s a piece on how to get started: Threads. It’s also important to understand the Science Twitter ecosystem; here’s a few account I enjoy which to me represent various aspects of the question

Science communication

Let me insist here once again that papers aren’t written to be read, but to be evaluated (eventually, if you land Nature, you’ve scored an A+) and actually very few people will do the promotion of your research (there’s no money to make out of it.) Write a paper is like getting a great, it’s your role to make it accessible. Plus doing this effort at the start will compound — later on you can more easily share research and *its context* with others.

It is good to have some experience with writing non-scientific articles: it pushes you to conduct interviews to substantiate your claims. Asking colleagues is sometimes… anathema in science, for fear of competition. But this is rarely the true excuse: people are often just too lazy to reach out. Teach yourself and your colleagues to do it!

In “Between the World and Me”, Ta-Nehisi Coates characterize journalists as seekers, and scientists should also seek to be seekers, and not only through producing new results but also by synthesizing information which is already there or summarizing opinions on a given topic. And that’s an acquired skill you learn by doing, and may help you create fruitful collaborations: the most interesting results often come from serendipitous interactions, and that’s something to cultivate.


Politics is a very sensitive topic in science. People like to think science is neutral, because scientists are seeking some kind of grand objective truth, and that politics has nothing to do with it. In truth, they are afraid (and reasonably so) to get their funding cut. Actually, scientists love to talk about politics, but it barely transpires outside the coffee room.

The current period, where the current pandemic of covid-19, and the looming threat of climate change has never made clearer that scientists are under assault and need to speak up. You are entitled to your opinion, and as long as you don’t speak in the name of your institution (and make it clear), things should be fine.

Just look at the most prominent scientist of the current era, Anthony Fauci. He doesn’t hesitate to reach out, and he’s perfectly comfortable with that:

A very public intellectual

If he can do it at age 80, why couldn’t you?

Some thoughts about gender gaps in STEM

Liminary note: I am not a social scientist, but I try to educate myself about some issues facing academia, and this is the result of my inquiries. If you think some elements are incorrect or if you have good resources to share, please let me know!

In this short Life
that only merely lasts an hour
How much – how
little – is
within our

Emily Dickinson

Gender gaps in academia are pretty dire, and while it seems to get acknowledged and addressed, it’s not clear whether the root causes – especially social norms – are fully understood and can be solved. The paper Understanding persistent gender gaps in STEM (Science 368, 6497; June 2020, pdf) offers interesting statistics and insights.

Gender gap in physical science majors

The problem does not seem to be a difference in achievement, but social factors rather.

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Scientific mentoring of interns – covid edition

(I owe this piece to a conversation with Laleh Coté – she’s doing an incredible job on STEM mentorship, and even in these difficult times, she documents her observations on how it impacts these efforts.)

I’m always happy to mentor students, for it gives you a change to light a candle, but also forces you to explain things in a legible way – and if you can’t perhaps you don’t really understand things yourself.

Berkeley Lab has a great program for interns, and it comes with some resources: WD&E Mentor Handbook (pdf)

Because of the pandemic, all the summer internships have morphed into virtual internship. While everyone is still trying to figure out how to make it work best, some initial best practices where collected here:  Virtual Remote Mentor Guide -DOE-SC-WDTS Programs- May 2020 (pdf)

Virtual summer internship

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It’s the units, stupid

Whenever I see scientific code without units I scream inside my heart.

Everytime you write simulations of physical phenomena (often using numpy or matlab), make sure to always have variables where the units are clear, e.g. :

lambda_m = 633e-9 #wavelentgh in meters
c_mps = 3e8 #speed of light in meters per seconds
freq_Hz = c_mps/lambda_m

Failure to keep good track of the units has led to disasters. Yet complete lack of clarity  happens more often than not – just look at the code of a random scientist on github to witness the extent of the damage.

The reason why I am adamant about this is because a lot of time is wasted trying to debug code where it there’s a silly unit mismatch, and because we are doing physics.

Math versus physics

Why is coding without units such a terrible practice? It all boils down to the fact that computing is mostly about math and logic, and therefore not geared towards physical quantities. There is beauty in mathematical abstraction, but sometimes it doesn’t mean anything.

Take a mathematical statement that should be true:


Now ask yourself: what does it mean? If I add one orange to one apple:

1 orange + 1 apple = ?

It might sound silly but it’s actually pretty deep. You cannot add quantities which are not congruent. Yes, you may say that by adding one fruit with another fruit you get two fruits, but you’re cheating then.

This is somehow why object-oriented programming was invented: with the notion of “classes”, you can add entities which are compatible, through the game of function overloading and other niceties. In an ideal world, physical quantities in simulations should all have their own class, where the units would be defined.

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Effective online presentations

Thomas Danthony

respect the flow

Nowadays, many conferences and workshops are going online because of the pandemic, and we all are ill-prepared for this kind of shift forced upon us. Delivering an online presentation is very different from delivering an in-person presentation, for a few reasons, and we need cognizant of the nuances.

While many talks are indeed disastrous (people lack proper training), going to a conference is often not only about the content of the talks (you could just read the papers), but about visual and vocal cues which are often absent from literature. These cues help you figure out what are the important points and make clear what what other people are interested in.

Therefore, it is important to establish and maintain contact with the audience. For this, there are many things we can learn from news anchor: they also talk to the camera, they have dedicated studios and they alternate between speaking and news content.

I attended an online workshop by Jean-Luc Doumont on delivering an online presentation, and I found it useful. Here are some of my takeaways.

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It’s getting pretty crammed at the bottom

Let us represent a dot by a small spot of one metal, the next dash by an adjacent spot of another metal, and so on. Suppose, to be conservative, that a bit of information is going to require a little cube of atoms 5 x 5 x 5 – that is 125 atoms. Perhaps we need a hundred and some odd atoms to make sure that the information is not lost through diffusion, or through some other process.
– Richard Feynman

Spoiler alert: we are nearly there!

* *

These very old line (1959) fro Feynman’s famous speech “There’s Plenty of Room at the Bottom” is still valid, though nowadays are getting very close to the bottom!

With my colleague Gautam Gunjala, we published an article in Berkeley Science Review on the ongoing contributions of UC Berkeley and Berkeley Lab to photolithography, the process of making microchips: Room to Shrink.

Photolithography is how you make tiny circuits

It was supposed to be part of the BSR Issue 38 (Spring 2020) but I guess it got covided.

Here are other pieces from yours truly on the topic:


The topic is getting red hot politically:
Lawmakers Propose Multibillion Dollar Semiconductor R&D Push  (American Institute of Physics, June 24, 2020)

if not down right nasty:
Trump administration pressed Dutch hard to cancel China chip-equipment sale: sources (Reuters, January 2, 2020)

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