A quantum of science

In physics we do things and afterwards worry about whether they worked

Andrei Geim Nobel lecture

I thought I would point out the excellent Nobel lecture by Andrei Geim which I found myself listening to while taking a break from something much less fascinating that I was doing this afternoon. It hardly needs mentioning that this is an example of how physics (and in fact all of science – I have fallen into the habit of talking about physics specifically when I mean science in general) can be done successfully. I haven’t listened to Novoselov’s lecture yet but I should imagine it is as worthy of my and your time as Geim’s.

While on the subject of video lectures, I would also like to recommend, as many on the blogosphere have done, Edward Witten’s lecture on knots. It’s a fascinating subject discussed by a fascinating physicist, and I like it to the extent that I have now begun reading about it. I have found it hard to locate the original link so I will refer you to the article on The Reference Frame (which is worth reading by the way) because there is an embedded video and a download link there.


2011 Announcements!

(This post was written on January 1st – I apologize for the delay.)

Happy New Year!

Last year was good, I hope this one will be even better! I would continue in the festive mood if it wasn’t for the pile of work I’m supposed to have done over the holidays and need to get through in the course of this weekend, luckily extended by the Bank Holiday on Moday.

2011 is the International Year of Chemistry, and I think it would be nice if I contributed in some way. I have therefore decided to blog about chemistry a little bit more than I would otherwise have done,  albeit with an interdisciplinary slant of the sort that I like. In particular I intend to discuss some of the exciting aspects of chemical physics such as DFT (which I am yet to learn about), quantum Monte Carlo simulations etc., and possibly some chemical biology which, although rather removed from my current academic course of study, I have found to be of interest.

I would like to think that these are New Year’s resolutions of some sort. Since I may just as well go on, I also intend to learn and blog about quantum foundations. From the papers I have been reading recently I am gradually becoming aware of the central problem of the field which has thus far eluded me, i.e. to find a set of physical principles from which quantum theory can be derived, rather than the axioms being a description of the mathematical formalism.

I also intend to learn some biology –  because of the fascination I have for the subject and the variety of problems to work on that it provides. From a more physical perspective, biology appears to me to provide interesting and accessible examples of physics that is not well understood, i.e. chaos, non-equilibirum statisitical mechanics, possibly even quantum mechanics (see earlier post).

I could go on… but I think this is a good place to stop. I’m now going away to do these things :P.

The Christmas post

I have been posting very little in the last few months. This was because I was busy learning “textbook physics” (or more correctly “textbook science&math”) which I assume to be of little interests to you, the reader of this blog. However, having learnt a lot I am now starting to read research papers which I will post about (hopefully) frequently.

I am hoping to get on a flight tomorrow which, given the current weather situation in Europe, is almost certain to lead to me and my family spending prolonged periods of time at the airport. I have therefore equipped myself with some reading material to keep myself busy and I thought that I might share it with you:


    The authors discuss the concept of information causality by first postulating it to be a physical principle: “the information gain that Bob can reach about a previously unknown to him data set from Alice, by using all his local resources and m classical bits communicated to him by Alice, is at most m bits.” According to the abstract, they then suggest information causality as a way to distinguish physical theories from the non-physical ones. Sounds like a fun read!


  • Multi-particle entanglement, J. Eisert, D. Gross This is part of a book (presumably) on quantum mechanics from a foundational/informational point-of-view.


Abstract: We review the theory of multi-particle entanglement. In this book chapter we aim at briefly “setting the coordinates” and guiding through the extensive literature in this field. Our coordinate system chosen for this chapter has the axes labelled pure and mixed states on the one hand, entanglement in single specimens and the asymptotic setting on the other hand. We very briefly mention ways to detect multi-particle entanglement, and introduce the concepts of stabilizer and graph states.


  • James Munkres’ “Topology”, 2nd edition. This is one of the great many gaps in my science education. If I am stuck in the waiting room of some airport, this should keep me busy for quite some time!


I would like to recommend a series of papers on novel methods of DNA sequencing (yes,I have been doing some biology!), see the references in the following Nature News piece:

I would also point the readers of this blog  to one of my favourite blogs, Condensed Concepts. The author is Ross McKenzie, a condensed matter physicist from the University of Queensland, Australia, and he is astonishingly good at pointing out fascinating pieces of condensed matter theory that can be great fun to explore!

Merry Christmas, a Happy New Year and see you then!

The Open Science Unjournal

I haven’t been posting for a while – I do apologize. I have been quite busy but I do have quite a few drafts that need to be finished and posted and I intend to do that as soon as I can.

For now, however, I would like to heartily support the Open Science unjournal. It is an initiative to rid scientific publishing of some of its biggest problems, such as the commercialisation (fees), loss of copyright by the author etc. I would urge anyone to whom this is relevant to become involved, it really IS something that needs to be enocuraged. I don’t think I can do any better at explaining the details than Jan Jensen in his post on Molecular Modelling Basics, so I am reblogging his post below:

What is an unjournal?
An unjournal is to journals what an unconference is to conferences.  To define what an unjournal is, take the first 2 sentences in the wikipedia entry on unconferences and substitute a few words:  “An unjournal is a facilitated, participant-driven journal centered on a theme or purpose. The term “unjournal” has been applied, or self-applied, to a wide range of publications that try to avoid one or more aspects of a conventional publishing, such as loss of copyright, high fees, [list your favorite pet-publishing-peeve here].”

Here are some frequently asked questions (FAQs) about Open Science:

How do I publish in Open Science?
The usual way is to deposit your manuscript on openscienceunjournal.org.  Once you have completed the submission process the paper is given a time and date stamp and the paper is published and open for review (see next question).  While there is a recommended template available for the paper, there is no fixed formatIt is possible to upload all your raw data or link to the data if it is hosted elsewhere.  Experience has shown that this tends to increase the scores (see below) of your papers significantly.

You can also choose to publish the paper on any of the unjournal sites whose contents are linked to openscienceunjournal.org.  These sites are often run by established publishers and offer more user-friendly interfaces, but may require a fee and may ask you to give up your copyright (though the content is open access by definition).

Is Open Science peer reviewed?
For a publication in an unjournal such as Open Science the question should be: is my article in Open Science peer reviewed?  That is in large part up to you.  The paper is open for online, non-anonymous, and completely transparent review and you have 2 months in which you can change the content of the article in response to the comments.  After the 2 month period you cannot change the content, but you can of course respond to new comments online.  For very serious criticisms you may want published a new Open Science article to respond.

It is up to you to solicit reviews, though any published author of a peer-reviewed paper (defined below) can review your paper during the 2 months review process.  Based on our experience only well-written and well-presented articles on scientifically interesting questions get reviewed.

An Open Science article is neither rejected nor accepted at the end of the review process.  Instead it receives an initial score (see next FAQ).  Obviously, any paper that does not generate a single review (or is reviewed but gets an initial score of 0) is not considered peer reviewed.

What is the impact factor of Open Science?
For a publication in an unjournal such as Open Science the question should be: what is the impact factor of my article in Open Science?  During the 2 months review process each reviewer gives the paper a score between 5 (good) and 0 (bad).  This score can be adjusted by the reviewers based on the changes you make within the first 2 months, after that it is fixed. The initial score for your paper is the average of all reviewers final scores.

If the paper is cited it receives an additional score (called the current score).  The score is determined by the number of citations, and if the citing paper is published in Open Science, the score is weighted by the initial and current score of that paper.  The authors of that paper can also choose to indicate how important your paper was to theirs.  If high scoring papers cite your paper in a positive manner, the current score of your paper increases. Self-citations are not included.

Why should I review for Open Science?
The work you put into reviewing is now documented for all to see.  Have you contributed greatly to science by identifying Open Science papers with high current scores?  Do the reviews you submit carry more weight with the author and other reviewers as a result?  Some sites now list Open Science reviewers with particularly high impact as a kind of editorial board for the journal.

How should I cite an Open Science paper?
One suggestion is: Author(s), Title, Open Science, date of submission, initial/current score.  If you publish in Open Science using the suggested template, the current score is updated automatically.

Why should I publish in Open Science?
There are many reasons:
(1) You retain the copyright and anyone can see the paper.
(2) Your paper is accessible upon submission. (Don’t rush to publish though: you only have 2 months to get a good initial score).
(3) The impact of your paper is evident in the citation, but disconnected from the conventional impact factor of the journal you managed to get it in to.  The initial score of your paper can help the paper off to a good start, but your truly important papers will ultimately be identified by its current score.
(4) You choose the publishing format you like.  What’s your pleasure? machine readable? interactive figures? link to raw data?
(5) Your paper is a living document: comments or questions continue to roll in on important papers and you can update links to your papers (related articles, a new data format) as you see fit.
(6) If you write a good paper, you will get more reviews (i.e. more suggestions and input) but the rantings of a single idiot reviewer will not prevent publication.  Isn’t this the place to publish daring and ground-breaking work?

So what brought this on?
The blogosphere: Egon Willighagen’s latest post got me thinking about this particular idea, but the general problems it is trying to address was brought to my attention by many other blogs such as Michael Nielsen‘s The Future of Science and Is Scientific Publishing About to be Disrupted? posts; most posts by Peter Murray-Rust; Henry Rzepa‘s long fight to include interactive figures in conventional journals; Mat Todd‘s excitement for an unconference and the discussion it generated at Derek Lowe’s blog.  Why can’t we have this in a journal?

Is the Open Science unjournal a good idea?
The blogosphere will decide: no comments on, and no re-blogging of, this post will mean this idea dies a quiet death (by receiving an initial and current score of 0).  But if you get enough smart people fired up about an important idea that can be solved by IT, good things can happen.

Home-made graphene

I have just come across a youtube video, pointed out at Asymptotia, which gives detailed instructions on how to make graphene at home using a pencil and some gecko tape. It is one of the coolest physics I’ve come across, although I will only be able to look at my graphene when I have access to a microscope which I won’t until next week! This makes the end of my holiday something to look forward to, I suppose…

Quantum effects in biology

Quantum mechanics is omnipresent – I wouldn’t go as far as calling it a theme of this blog because I don’t think I’ve been blogging for long enough to have established any themes.

The point still stands, though. Quantum mechanics is now accepted as a fundamental theory of nature and it is the basis of modern physics and chemistry. Biology, However, over its rapid development in the last 60 years or so has not manifested any inherently quantum mechanical effects beyond those that are part of the underlying chemistry.

That is changing. I have recently come across three papers on the arxiv which demonstrate quantum mechanics in avian navigation, photosynthesis and, however speculative it may be, the structure of the DNA.

Benoit Mandelbrot (1924-2010)

Benoit Mandelbrot died on last week, aged 85. He made a well-recognize contribution to the emerging science of chaos and nonlinear systems and in my opinion its significance will greatly increase in the coming years.

It is often said that the best way to celebrate an artist is through its work. I recommend the article on the Mandelbrot set over at n-Category cafe.

Quantum Optics and Quantum information at UCSB

As some of you might have realized from my earlier posts, I’ve been getting very excited about quantum information, quantum foundations and related fields.

The thing is, these are very new, albeit incredibly vibrant research fields and there is no tried and tested route into the subject in the way there is for some of the more traditional disciplines. I have therefore been spending quite a bit of time surfing the net to find the right resources and I thought I’d post some of the more interesting ones here. This is the first post in an informal series, if you like.

So today’s link is Dirk Bouwmeester Quantum Optics and Quantum information group and UCSB. The leader of the group, Dirk Bouwmeester was involved in the first experimental demonstrations of quantum teleportation, quantum cloning, 3-particle entanglement and stimulated emission on entangled photons. The group’s research is in four main areas:

  • entangled photons
  • quantum dots and microtubules and DNA
  • quantum dots and microcavities
  • macroscopic quantum superposition

For someone like me, a newbie to the field, it makes great reading!

As soon as I can I will write something about the details of this work.

Carbon is this year’s theme: Nobel Prize in Chemistry

Congratulations to Richard F. Heck, Ei-iechi Negishi and Akira Suzuki who were awarded this year’s Nobel Prize in Chemistry for “palladium catalysed cross couplings in organic synthesis”. It is a very well deserved prize: one of today’s articles mentioned that about 25% of all reactions in pharmaceutics uses the methods developed by the three professors, and with that in mind it is a surprise that they they did not receive the award earlier.

As has already been pointed out elsewhere, carbon seems to be the theme of this year’s Nobel Prizes, in science at least, given the graphene Physics Prize (see the post below) and today’s prize on carbon bonding. It is a testimony, I think, to the growing important of the emerging interdisciplinary field of Materials Science 🙂

For those interested in learning more about Heck, Negishi and Suzuki’s work, I would point to the Swedish Academy’s Scientific Background document for the prize (the link is directly to a reasonably-sized pdf file). If you are interested in theoretical approaches to the problem, I would suggest that you visit this article by Ross H. McKenzie who has found a study of the problem using DFT.

Nobel Prize in Physics 2010

Congratulations to Andre Geim and Konstantin Novoselov who received today’s Nobel Prize in Physics for their work on graphene.

Graphene, as some of you will no doubt know, has been a “hot” research topic since 2004 with an astonishing number of potential applications; however, how much of this potential is actually realized is to be seen, as Joerg Heber argues in his post Great, the physics Nobel prize for graphene! Now don’t overhype it… .

For those wishing to find out more, I recommend the post on Backreaction which contains some excellent links.

Finally, I would also like to congratulate the exceptionally well deserved yesterday’s Nobel Prize in Medicine laureate, Robert Edwards.