Skip to content

LHC proton dump

How to stop a beam of protons traveling at 99.99 % of the speed of light and able to melt 500 kg of copper in less than a second ?

I’ve found this interesting article about how to dispose of the proton beam from the Large Hadron Collider. The amount of energy and the focus of the beam is so strong that any metal would melt. So they use graphite, a solid block of it, 8 meters long and almost one meter large, weighting almost 10 tons. Graphite has a very high melting temperature, making it a good choice for the task. Any other solution would either melt or instantly vaporize, leading to a catastrophic explosion.

As a consequence, the human head is not supposed to be used for the task. Despite this, a dramatic accident happened to Anatoli Bugorski, who happened to stick his head into a particle accelerator beam in 1978, and survived to tell the tale.

Share This

Error 1044 in MySQL: Access denied when using LOCK TABLES

I got an error while using mysqldump

mysqldump: Got error: 1044: Access denied for user x@y to database z when using LOCK TABLES

To solve this problem, either ask you administrator to grant you the lock privileges, or use the following command instead.

mysqldump -u username -p database –single-transaction >dump.sql

Share This

Proofreading!

Proofreading is fun.

You proofread something with three pair of eyes for a bunch of months. When you believe your manuscript is perfect, you send the stuff to the editor, which after a while returns you the formatted proofs.

Then you take the proofs and print them out, and again the three pair of eyes start again reading them. The result is that you still find a bunch of errors! And… there’s more. Each pair of eyes find errors than the other two pairs did not spot.

But the most funny part is when you send a document containing the cumulated corrections to the editor, and reviewing this document you spot errors in it.

You just have to live with it. A book will never be without errors.

Share This

Moving to ETH Zürich

I am starting a postdoc at ETH Zürich the 1st of October. I will work on data management and high throughput calculations in quantum chemistry, and I will probably be involved in a standardization process (as I already took part earlier) for communication and data sharing. The experience I did in sequence analysis was precious, as they already worked on standardization issues before quantum chemists. The experience I did outside academia was important to develop a method and a rigorous approach to programming.

I am very excited of the project and the opportunity. It will be fun and intriguing, and it is a project that can really create new perspectives in computational sciences.

Share This

Chestnut Package Manager 2.0.0 released

I just released a program I developed: Chestnut Package Manager, a utility to handle executables and resource files in a transparent, platform independent and relocatable way. Its concept is similar to Apple bundles and Java archives. It is implemented in Python.

I also provide a nice tutorial about how to use it and how to deploy your packages. It has been very useful to me, and I guess it will be for other people out there.

Share This

Computing for Comparative Microbial Genomics

I am proud to announce that Springer has finally released on the web (and Amazon as well) the descriptive information of the textbook I took part on: Computing for Comparative Microbial Genomics. It was a fantastic and incredible experience, for which I will always be grateful to Dave Ussery, my supervisor at Technical University of Denmark, and to Trudy Wassenaar, an independent professional and Associate Professor at the same institute.

Together with the book, I deployed a supplemental information website, comparativemicrobial.com. At the moment, it does not contain much information, apart of some biographies and a couple of links. We expect to enrich it with simple tutorial code and up-to-date news as time passes, following the feedback we obtain from the readers.

EDIT: specified that only the description is available on the web, not the textbook itself ;)

Share This

Long time no write

I am cooking a lot of stuff in the pot. Soon I will post about all of them, one after another, but I prefer to post about new things when they are ready and officially out. So, stay tuned, because there’s really a lot of good stuff.

Share This

Is SVN slow?

I am using SVN to manage my current development repository. As the project grew, the operations became slower and slower. Things like updating or committing could require minutes.

I ran some strace, and apparently SVN takes a lot of time in walking through the repository tree, probably checking for differences between the previous copy (in .svn) and the current copy. Also, it walks through the tree to remove all the lock files it created. These operations grow with the number of subdirectories involved during the operation, so if you don’t want to spend your time staring at the ceiling while committing or updating, either you keep the number of subdirs to an acceptable low amount, or you invoke operations involving a low amount of directories (like, committing only a subtree).

My situation is maybe quite extreme, as my repository has 2000 directories (I have lots of small applications to keep track of). I could check out a part of the repository, or split the repository into smaller, independent ones, but I don’t want to risk: it could prove potentially dangerous right now, where I have to work on other issues with a quite tight schedule.

Despite this, I like SVN, but I am considering taking a look at git.

Share This

Where are they?

I found a very interesting commentary by Nick Bostrom, about the existence of extraterrestrial life and the so-called Fermi Paradox.
The point Nick Bostrom presents is sensible: the current evidence is that life is apparently not very frequent in the Universe. Despite all efforts we did toward finding life, intelligent or not, we failed. Moreover, the human progression went from very low technology to space exploration in 10.000 years, a blink of an eye on the Universe time scale. There are pieces of our civilization travelling out there: the Pioneer 10, the two Voyager and much more. In two or three hundreds years, we could be able to manipulate matter so to create self-assembling space probes to scout the galaxy, the Von Neumann probes. If an intelligent civilization exists or existed in the galaxy, we would be surrounded by Von Neumann probes, or at least we would be able to receive some kind of signal, but this does not happen. Apparently, there has to be a filtering event that prevents human-intelligent life to reach a status where galaxy colonization could be started and self maintained without further intervention.

This filtering event could be before our time, or in front of us. If the filtering is before our time, it must act as a showstopper for the development of life forms, meaning that life is rare, potentially unique even on a universe scale.

However, if we happen to find extraterrestrial life, for example on Mars, it would mean that the conditions to form life are rather loose. Life formation is not at all uncommon, and we could expect to find it on any exoplanet with the right conditions, potentially a huge amount in the galaxy. Therefore, to address the experimental evidence of no space colonization despite the billion of years of time passed since the boot-up of the Universe, we are forced to theorize that in this case the filtering event is in front of us: mass extinctions already happened in the past. Could it happen for humanity as well? Under this perspective, Nick Bostrom states that finding no evidence of life on Mars is a good news, as this means that the Great Filter was behind of us, and there’s hope (not certainty) for a bright future, but what if we find something?

Are we the creators of the filter event we have in front of us? Very soon, we will be able to manipulate DNA in its small details, design and create nanomachines from scratch, or fully understand the processes governing our brain and body. Despite the groundbreaking nature of these discoveries, a single accident could wipe out our civilization entirely. It takes a match to start a fire.

Do we need, as Stephen Hawking says, to start colonizing other planetary systems right now, or face the consequences of the “all the eggs in one basket” situation we currently have? Should we accept the fact that our current technology, knowledge of closed biospheres and control of human psychology do not allow us to send a crew on Mars and bring them back? Should we just start sending people there with no chance of coming back? And in any case, once humanity gets there and a colony is started, how can people survive on a planet where water is apparently scarce and there is no breathable air?

Share This

So you want to write a book?

So you want to start writing a book? cool. Here is a suggestion I give you: renounce.

Still wanting to start writing a book? Second suggestion: renounce.

Are you still convinced that you really want to start writing a book? Third suggestion: I’ll give you more suggestion, but remember that start writing a book is not the same as writing a book. Between the two, there’s a book!

Continue reading ›

Share This
Close
E-mail It