PhysMath Central Blog
LaTeX is something of a misnomer in publishing in the 21st century. On the one hand a language to render and position text on a printed page is solving a problem which is largely solved today - but the markup of equations and mathematical symbols is rarely bettered.
Given a large corpus of existing material is already in LaTeX, then this development from Springer [disclaimer: Springer own BioMed Central and PhysMath Central] could be potentially enlightening for those whose work can be expressed in equations. A LaTeX search engine finds equations or part-equations across all of Springer's published articles. Very useful for finding a particular approach to solving some engineering problem, say, has already been described in the mathematical literature.
Check the example searches and give your own a whirl.
Posted by Chris Leonard at 12:34 Comments (0)
PhysMath Central will be at ICPEAC 2009 this week. The International Conference on Photonic, Electronic and Atomic Collisions is being held in Kalamazoo this year and Associate Publisher Chris Leonard will be there, with Dane Brookes, to talk about open access publishing in atomic and molecular physics - and to give away some of our special Rubik's cubes. There will be a few days to practice before a 'cube-off' on Friday to see who can win an iPod nano.
Come and visit us on stand #7 to find out more.
Posted by Chris Leonard at 17:32 Comments (0)
PMC Biophysics paper review - Hsu and Hsu
You may have seen on our RSS feed of latest articles the publication of a very interesting paper in PMC Biophysics by Hsu and Hsu. Prof. John Straub gives us a bit of background, and highlights the work's particular merits.
Zwanzig-Mori projection operators and EEG dynamics: deriving a simple equation of motion
David Hsu and Murielle Hsu
PMC Biophysics 2009, 2:6 (13 July 2009)
Sometimes it pays to borrow. A problem frequently encountered in science is to describe the behavior of a few experimental variables when these are coupled to many other variables about which we know very little. How does one infer relationships between the experimental variables in a rigorous way, with minimal ad hoc assumptions?
In the 1960’s, Robert Zwanzig and Hazime Mori independently addressed exactly this problem in describing the motion of large, slower moving particles in a “bath” of many smaller particles (the Brownian particle problem). Using “projection operators”, they showed that the equation of motion for the larger particles has the form of a generalized Langevin equation. This equation breaks down the forces acting on the larger (“Brownian”) particles into three contributions: one due to direct interactions between Brownian particles, a second due to frictional drag on the Brownian particles due to the bath, and a third which causes random fluctuations in Brownian particle trajectories due to collisions with bath particles.
Over time, Zwanzig-Mori projection operators have proven extremely useful in nonequilibrium statistical mechanics. Now David and Murielle Hsu have adapted projection operators to the analysis of electroencephalograms (EEG). In “Zwanzig-Mori projection operators and EEG dynamics: deriving a simple equation of motion”, they show that EEG dynamics also obeys a generalized Langevin equation. They point out that the parameters of this equation represent macroscopic properties, and then, most ingeniously, they identify two variational principles that allow these parameters to be extracted from experimental data. The variational principles of Hsu and Hsu open the way for practical application of the generalized Langevin equation to a wide array of real life problems, not just EEG dynamics. We can look forward to interesting results.
Posted by Morag Hickman at 11:52 Comments (0)
Eagle-eyed readers (or those with an RSS feed of latest articles) will have noticed that we have recently published a very interesting paper in PMC Biophysics by Tan and Luo. Handling editor Wei Yang explains below what makes this paper special.
Structural and functional implications of p53 missense cancer mutations
Yuhong Tan, Ray Luo
PMC Biophysics 2009, 2:5 (26 June 2009)
The transcription factor p53 is a central tumor suppressor protein that exerts its functions by relaying upstream stress signals, such as DNA damage, to downstream target genes that control DNA repair, cell cycle arrest, and apoptosis.
Close to 50% of all human cancers have p53 mutations, and 75% of those are missense mutations affecting the p53 DNA-binding core domain of approximately 200 amino acids.
These mutations inactivate the central p53 pathway leading to apoptosis, and allow cancerous cells to proliferate unchecked. Therefore, a long-held goal for anti-cancer therapy is to restore native function to p53 cancer mutants through pharmaceutical interventions, thereby activating apoptosis in cancerous cells and shrinking or killing the tumor.
However, without detailed analysis of the inactivation mechanisms in the cancer mutations, it is difficult to develop therapies targeting p53 cancer mutations.
Tan and Luo conducted a comprehensive computational analysis on all p53 core domain missense mutations to infer their likely inactivation mechanisms. They found that overall, 47.0% non-PRO/GLY mutants are stable and 36.3% mutants are unstable, 12.2% mutants are with 1.0kT < ΔΔG < 3.0kT. Only 4.5% mutants are with no conclusive predictions.
They correlated predicted stability with sequence, structure, and molecular contacts and found that the loss of protein-protein contacts may be an alternative cause for p53 inactivation, in addition to the loss of protein stability and loss of DNA contacts.
Nevertheless, their correlation analysis with clinical data shows that loss of stability and loss of DNA contacts are the two main inactivation mechanisms. Their correlation with functional data also shows that most mutations that retain functions are stable, and most mutations that gain functions are unstable, indicating destabilized and deformed p53 proteins are more likely to find new binding partners.
Posted by Chris Leonard at 14:36 Comments (0)
Brian Cox on what went wrong with the LHC
PMC Physics A board member Brian Cox on what went wrong with the LHC last September, how it was fixed and what they are looking forward to now. Originally presented at Ted U in February 2009.
Posted by Chris Leonard at 16:21 Comments (0)
PMC Physics A publishes first review article
PMC Physics A is proud to announce the publication of its first review article. The review, entitled "B meson decays" was written by Elisabetta Barberio of the University of Melbourne and Marina Artuso & Sheldon Stone of Syracuse University, New York.
They discuss the most important physics thus far extracted from studies of B meson decays. Measurements of the four CP violating angles accessible in B decay are reviewed as well as direct CP violation. A detailed discussion of the measurements of the CKM elements Vcb and Vub from semileptonic decays is given, and the differences between resulting values using inclusive decays versus exclusive decays is discussed.
Measurements of rare decays are also reviewed.
They point out where CP violating and rare decays could lead to observations of physics beyond that of the Standard Model in future experiments. If such physics is found by directly observation of new particles, e.g. in LHC experiments, B decays can play a decisive role in interpreting the nature of these particles.
We hope you enjoy the review and look forward to receiving your proposals for future reviews at pmcphysa@physmathcentral.com
Posted by Chris Leonard at 14:40 Comments (0)
We have just published an excellent editorial by PMC Physics A editor-in-chief, Ken Peach. In it, he outlines what we might discover with the LHC apart from the Higgs. In particular, given some of the more outlandish reporting of the LHC start-up, it explains why open access to the original reseach is important for all kinds of science:
The LHC machine has been built as a global collaboration, led by and from CERN. The four large experiments have also been built as global collaborations. We at PMC Physics A welcome the commitment by CERN and by the experiments to make the results freely available through publication in open access journals. The media coverage of the start-up of LHC demonstrates that there is interest in the general public in fundamental science, and in the structure and origins of our Universe. We should ensure that those who wish can see the results directly for themselves, and not only as viewed through the prism of the media.
Posted by Chris Leonard at 16:52 Comments (0)
We're with Brian Cox on this one. Although it should be taken with a pinch of salt. See Brian's explanation of his use of this entertaining and underused term in science.
Anyway, we're here to celebrate the most publically anticipated event in physics and probably science for quite some time. On Wednesday the LHC should be switched on and - should we not get swallowed up in a black hole - one of the biggest, most complex pieces of scientifice apparatus ever will hopefully, slowly start to reveal hitherto unknown secrets of the universe.
Everyone's talking about it and as a result, the radio and TV schedules are filled with programmes about the LHC (or maybe it's the other way round?). The BBC Radio 4 in particular is calling 10th September 'Big Bang Day'. A full ist of programmes is here, and will be availble to UK-based readers for 7 days afterwards on the BBC's iPlayer. Also see their interactive guide to the 4 main experiments and audio archive on particle physics.
Posted by Chris Leonard at 16:17 Comments (2)
Travis Brooks, posting on the new symmetry breaking blog, has analysed the titles of all 51 2007 Topcites from SPIRES (as well as abstracts from 37 of them and keywords from DESY for 27 of them) and thrown them at the TagCrowd.com generator to see what came out. Click on the image above, or here, to find out and get a flavour of HEP in 2007.
Posted by Chris Leonard at 12:18 Comments (0)
Looking and laughing at the LHC
Listening to comedian Bill Bailey on my iPod on the way to work isn't something which would usually warrant a mention on the blog here, but today was different. Today he was talking about the Large Hadron Collider and that the fact that the experiment has such a wide spectrum of success:
"The spectrum of success for this scientific experiment ranges from 'nothing will happen' when they switch it on...
- Turn it off, turn it on again.
...or, it will create a black hole under Switzerland. That seems to me to be huge margin of error. Nothing or Apocolypse."
He goes on to speculate that if it doesn't work, scientists will get bored and put other things in it, like Maltesers and satsumas.
And to complement that thought, some great photos from the latest issue of National Geographic of the LHC. Although they refer to the Higgs as 'The God Particle', something which annoys every physicist I know.
Posted by Chris Leonard at 10:56 Comments (2)
The title refers not to some ethereal thought experiment with antimatter, but rather to the existence of 'physics' outside of the realms of high-energy physics. The Incoherent Ponderer was upset with the recent Scientific American special report on The Future of Physics which seemed to focus exclusively on terascale/LHC physics:
I guess I am tired of arrogant statements like "physics" = "high energy physics", which is how a lot of popular media characterizes it. The irony, however, is that with ILC construction in serious peril, and with LHC not even operational yet (unclear what, if anything, they will find) - the REAL "future of physics" is arguably with biophysics, condensed matter or "materials" physics and AMO. I would expect that large particle collider experiments being phased out, with more useful data coming from cosmology (=astronomy).
At the same time, experiments in low-energy physics (condensed matter, optical, molecular, biophysics, materials and chemical physics) will continue to ramp up at an increasing rate.
It will be interesting to see how the proportion of students opting for a career in high-energy physics changes with the LHC switch-on and the potential non-appearance of the ILC over the coming 10 years.
Posted by Chris Leonard at 14:34 Comments (1)
Sign-up to fight the physics cutbacks
An email from Francisco Diego of the University College London Observatory is a call to action for UK-based scientists (or indeed anyone) to register their unhappiness with the current funding situation for physics & astronomy, which has lead to - amongst other things - the UK backing out of funding for the ILC.
There is now an approved (e)-petition online to collect signatures regarding the funding situation for physics and astronomy. Petitions with sufficient number of signees are forwarded to the government who then needs to come back with a response.
Its quick and easy;
http://petitions.pm.gov.uk/Physics-Funding/
Please sign it and then forward this on so that it might reach critical
mass.
You must be a British citizen or resident to sign the petition.
Also see this blog post from Imperial College for some more background to the story.
Posted by Chris Leonard at 13:58 Comments (2)
UK Physics Funding under pressure
Bad news for physics funding in the UK yesterday as the Science and Technology Facilities Council had its budget slashed by the somewhat bizarre-sounding Department for Innovation, Universities and Skills. Due to higher than planned operating costs and a frozen budget, money is being redirected from other projects to cover this shortfall. As a result, the UK has backed out of funding the ILC, which was announced in 2 curt sentences, as follows:
"We will cease investment in the International Linear Collider. We do not see a practicable path towards the realisation of this facility as currently conceived on a reasonable timescale."
Much more on this story below:
UK Physics Investment Decimated
UK Physics on the chopping block
Ministers review physics funding - including a quote from PMC Physics A ed board memeber, Brian Cox.
Boffins slashed in big-science budget blunder bloodbath - comments are also worth reading.
Posted by Chris Leonard at 13:36 Comments (1)
API opens up arXiv to new apps
Good news from the people at arXiv as they announced at the recent e-sciences conference that they have released an arXiv API. From their new blog:
The arXiv API is an HTTP/Atom-based application programming interface that exposes the search and retrieval functionality of arXiv.org to application developers.
... You can visit the official arXiv API homepage for documentation, tutorials, and information on how to participate in the developer community, including our discussion list. Or you can follow this blog to find out the latest news concerning the API.
Details about the arXiv API developer's list, and an extended entry to the capabilities of the current API is available on a new dedicated section of the arXiv website.
Posted by Chris Leonard at 13:59 Comments (0)
Although the Large Hadron Collider is often portrayed in the press as a 'European' facility, particle physicists are close-knit, international community and the reality is that scientists from many different countries and continents have collaborated on this unique accelerator.
To highlight the USA's involvement in the LHC, the US Department of Energy and the National Science Foundation have launched a new website called US/LHC. To quote from their homepage:
More than 1200 physicists from 90 American universities and laboratories have joined with scientific colleagues from around the world to collaborate in LHC experiments at the horizon of discovery.
You can follow LHC start-up from a US-perspective courtesy of 4 blogs on the site written by Monica Dunford, Pamela Klabbers, Steve Nahn and Peter Steinberg. A combined blog listing and RSS feed is available from here.
Incidentally, the LHC is still on schedule for producing its first results in 2008, according to Robert Aymar.
Posted by Chris Leonard at 11:05 Comments (1)