Category Archives: resources

Units, please

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:

1+1=2

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 https://thomasdanthony.com/

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:

Also:

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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The Lessons Of The Pandemic, May 1919

It’s like a war
Except the enemy is monumental incompetence

We’ve been there, we know what to do – yet, we don’t.
doi.org/10.1126/science.49.1274.501

Graph alignment chart

There are many ways to document research, and some are better than others.

Make beautiful graphs : only start to write when you have the best data our group can get.
Paul Alivisatos

Here’s my graph alignment chart, curated from personal experience.

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Brutalism in Berkeley

One silver lining of the shelter-in-place is that you get to go out with no other goal than going out, and you discover new things about your city. I was always intrigued by the Brutalist architecture in the Bay Area – the first time I encountered it was at the Berkeley Art Museum during the Uncharted Festival in 2013. This kind of architecture, promoted by Mario Ciampi in the Bay Area, is often maligned, and while I can’t say I like, I definitely recognize its esthetic impact.
The name brutalism comes not from the word “brute” (though it could!), but from the French word “brut,” where it signifies “raw” as in raw concrete. Here are a few buildings I stumbled upon who may qualify for the category. Enjoy!

Woo Hon Fai Hall, in Berkeley, CA (former Berkeley Art Museum, BAMPFA)

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Antoine’s insider guide to Paris

Because we’re in time of covid, it’s good to look back at the beauty of a vibrant city and all the things we miss. Here’s guide I made for a friend, and shared with a few others when they asked me what should the absolutely not miss in Paris. Enjoy!

Here are a few addresses you might want to look up during your stay in Paris, that will not be in tourist guides:)

Centre Pompidou

Breakfast at Ladurée

Christmas lights

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Earth Day

Today is Earth Day, a celebration of Earth and the environment started fifty years ago. This year, as the covid-19 pandemic upends the regular unfolding of the world, we can step back and ask how what we learn from the current crisis can help us scientists make science better and more efficient to curb climate change and its consequences.

 

Here’s a set of eight question to ponder about this, and some preliminary thoughts gleaned during a forum@ESA.

1. The interdependence of the supply chain has become very apparent. Can we make the case for renewable energy in terms of resilience of systems?

Solar energy is the only form of energy available everywhere on the planet: all others need to be transported and transferred. Geothermal energy should also be tapped (it is essentially low grade solar energy!)

2. The dramatic reduction of activity in urban centers has brought back clean air in some cities for the first time in decades. Can we envision a world without emission, from energy production to energy use?

Cars on the road have the most impact – we need to switch to switch transportation modes. We could have electrical energy on tracks, some flavor of autonomous driving could quickly provide modular transportation schemes. We also need to change how some cities are built, to make it easier to have common transportation (relative location of schools, business and housing)

3. The current covid-19 crisis is global, and scientists have broken paywalls and started new collaborations with their peers around the globe. What can we learn from this, and promote meaningful collaborations?

Open Access is on the rise (Project DEAL, Plan S,  White House Open Access plan.) Wikipedia is a great resource, completely under-used; it seems that it stems from the issue of ownership (who gets to write on who? and who gets the credit for this work?) We can also rethink research tools, to make them more efficient and more collaborative. The way academia is organized (race to tenure, etc.) may hamper collaboration and therefore innovation.

4. The global economy has been hit severely, and it will be important to promote new economic activity when the outbreak will be over. How can energy technologies inform policies and shape capital projects?

We could build mass transportation system, with initiatives similar to the New Deal (infrastructure is manual labor intensive.) Science can help to find which are the most effective or efficient ways (data science and machine learning.) Scientists could work in tandem with civil engineers, maybe using their school network to reconnect. There should be incentives for scientists to do so.

5. The disruption school year has taken a toll on kids and parents alike. How can scientists engage with students, when the distance is measured in bits per seconds rather than miles?

It would be good to reuse and repurpose older devices. There could be an open OS for discarded devices that would provide minimal functions (video conferencing, calculator, etc.) Scientists should also learn to mentor without physical presence (though one-on-one interaction is important), and therefore allow more frequent interactions, over larger distances.

6. When resources are lacking – masks, ventilators,– engineers and scientists devise creative ways to fill the need using available resources and altering them. How could we repurpose existing facilities to help with climate change?

7. The shelter-in-place is difficult to negotiate, but as anthropogenic emission of CO2 affects the environment, it may become routine. How can we fix the harm done using science and technology?

8. There is a lot of contradictory information being circulated around the epidemic. How can scientists help disseminate information and prevent the spread of alternative facts?

 

In addition, here are some historical and current resources on Climate Change:

I also made a thread about Berkeley Lab Art Rosenfeld on his Art of Energy Efficiency.

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Know your Burning Man art

The world is burning with fear, and the best thing we can do is the burn the fear with arts – and that’s the central appeal of Burning Man.

Burning Man is a ten-day long arts festival in the desert, in Black Rock City, NV (a 4 hours drive from San Fransisco) and usually held at the end of August, where people come for the peculiar experience, littered with real life arts. This event is among the only in the world where people do art for the sake of art, without galleries or commissioning needed, thanks to its sheer scale and captive audience (70,000 people over a week.) There are many groups of artists preparing arts year long, in the hope to touch the heart of others; some even get commissioned and get to build real big stuff. Some of them may be ephemeral, but their legacy lives on.

Associated acts

The influence of Burning man runs deep, especially in the Bay Area. For example, the lights blinking on the Bay Bridge (Bay lights) where partly an offshoot of a Burning Man project by Leo Villareal, whereas the “Day For Night” built on Jim Campbell’s experience. The latter recently had an exhibition at the Hosfelt gallery in San Francisco which was… illuminating.

The sculptor Marco Cochrane is also famous for the Bliss series, his large sculptures of iron mesh of dancing characters, found on Treasure Island and at festival in California.

A piece for No Spectator, at The Oakland Museum of California (2020) – HYBYCOZO, Trocto, 2014

There was recently a very tiny retrospective of Burning Man arts at the Oakland Museum of California, No Spectator: The Art of Burning Man. It didn’t render the scale of the event, but it allowed people to get a sense of what’s happening there, and tell the history of the event. Continue reading

Hikes in the East Bay and the Bay Area

Because wee need to socially distance, perhaps most interesting right now are the nice places to hike nearby (East Bay/regional parks; stay away from state parks as they tend to be crowded and closed subsequently.)

Hikes in the East Bay

They’re all less than 30 min drive from Berkeley. Some can be reached by walking or cycling.
  • Cesar Chavez park (Berkeley Marina, 30min hike), stunning at sunset, great walks
  • Fire Trail (Berkeley), entrance a little before Botanical garden (3h hike)
  • Tilden Park (Berkeley hills): wild cat canyon hike, inspiration point (1h20 hike)
  • Lake Anza (Berkeley hills): 30 min hike; It is gorgeous, and a place of quiet; excellent if you want to bring a book
  • Huckleberry preserve (Berkeley/Oakland skyline boulevard, 1h hike)
  • Mountain View cemetery (Oakland, 1h): great views of the bay, solemn setting but not spooky.
  • Pinole Point (Richmond, 1h30 hike), wonderful at sunset
  • Redwood regional park (1–2 hours) many trails, very varied landscapes
  • Pinehurst East Ridge (start from Pinehurst Staging area – map)
  • Briones Crest trail loop (Orinda, 4 hours, or Lafayette Ridge staging area is open. It’s a very long hike, and portions can be steep. Plan at least 3h!)
  • Mt Diablo (Walnut Creek): stunning view of the highest peak in the Bay
  • Angel island (daylong hike, you need to take the ferry from Tiburon) might be closed

East Bay hikes

Hikes in the greater Bay Area

You’ll need to drive a littlemore, but these are splendid hikes:

  • Mt Tamalpais (Marin county, 1h30): beautiful hikes to the top.
  • Cataract Falls (one of the best hikes, map, on the dipsea trail, seems closed too)
  • Dipsea trail (from Mill Valley to Stinson Beach, 4h. beware: it seems closed, because it is too popular)
  • Pt. Reyes & Pt. Reyes Lighthouse (seems closed)
  • Russian River (usually you can rent canoes from late May to October, to go down the 10 mile stretch from Forestville to Gerneville. Maybe they’ll open. I LOVE this one. In the meantime, you may be able to enjoy wading in the river in a few locations; the drive is also quite nice)
  • Bodega Bay Trailhead (1h from Berkeley, gorgeous sights of the ocean. A fav!)
  • Mount St Helena (North of Napa, map, it seems closed for the time being:-/)
  • Half Moon Bay (South bay, 45min from Berkeley – nice beaches, and the boardwalk is very beautiful. Start from Miramar and head South)

and here’s a few more: Best beginner hikes in the Bay Area!

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Additional suggestions:

  • Walking around lake Chabot.
  • Tilden Park at full moon. Get the code for EBMUD lock for $5!
  • Pt Reyes has 7 distinct ecosystems — totally great!
  • Don’t miss Indian Rock in Berkeley, and the Mountain View Cemetery in Oakland
  • Castle Rock in the southbay is a great place for hike
  • if you happen to be on Highway 92 near Half-Moon Bay, don’t forget to stop at Sam’s Chowder
  • Lake Almaden has nice, easy walks great for kids

You can also discover a lot of crazy place in Berkeley by just walking around in the streets:

https://www.berkeleyside.com/tag/quirky-berkeley

https://www.newyorker.com/business/currency/things-quirky-berkeley

Your favorite places, inspired by Berkeley Rep’s Place/Settings

Part 2: Your favorite places, inspired by Berkeley Rep’s Place/Settings