Interesting article studying writing journal articles

Last fall I looked at methods for improving the efficiency of MC simulations, and was pointed to the article, Efficient Monte Carlo methods for the computer simulation of biological molecules by Djamal Bouzida, Shankar Kumar, and Robert Swendsen.

A search of the author's names on Yahoo turned up a fascinating article by Ann Beakeslee, who studied the process of writing this paper. The article examines the interaction of the graduate student (Bouzida) and the advisor (Swendsen), covers the process of learning to write scientific papers, and looks at difficulties Bouzida faced as a novice.

Search for chemicals

Check out chmoogle, the search engine for chemicals. Many of the results are for suppliers (not so useful for theoreticians), but some of the results contain more information about the chemical.

The "details" link by the chemical structure picture also has alternate names, along with links to search Google or Yahoo.

[APS] First Principles Molecular Dynamics on Blue Gene

Francois Gygi gave a talk about scaling a first principles molecular dynamics code to 65,536 processors on the Blue Gene/L at LLNL.
The core numerical algorithms that need to scale are the FFT and dense linear algebra. The FFT is limited in scalability to 512 processors per k-point. Fortunately, there are many k-points and they can be computed independently.

Modifying the assignment of tasks to processors increased the performance by 64%! FLOPS are free, it's the communication patterns that are determine performance.

One research problem is improving the scalability of computations for small systems (ie, 32 water molecules), so they can be simulated for longer times.

[APS] Solar Power

David Carlson (from BP Solar) gave a talk titled, The Status and Outlook for the Photovoltaics Industry. His presentation slides are also available online.

Some random facts I found interesting

• The photovoltaic industry has been growing at 35% per year.


• This year, the PV industry will use as much or more silicon than the semiconductor industry. This may cause problems with the growth curve, as suppliers ramp up to supply the PV industry.


• The current cost per kWh is $0.18. Less than half of the cost is due to the PV module. (Slide 30)


• Given the cost of PV electricity, the cost of conventional electricity, and the availability of sun, Spain is almost to the point of cost-competetive PV electricity. (Slide 31)

[APS] QC for QC

Intersting point from Alan's talk about using Quantum Computing to solve Quantum Chemistry problems: computing cholestrol is about as hard as breaking encryption algorithms.

The quantum computing approach takes quite a bit of setup - an actual Hartree-Fock calculation or more. The advantage of QC is that the exact answer (Full CI) can be obtained easily[1] by the QC from that starting point. (But going from HF to FCI is the hard part classically - I think Full CI scales exponentially in the system size)

[1] as much as anything with quantum computers can be called _easy_

[APS] Hydrogen storage

I went to a few talks in a session about Simulations of hydrogen storage. It appears that compressed gaseous hydrogen has about 10 times less energy density than gasoline. (Some quick googling found this explanation. It really matters if you're using volume or weight density - by weight hydrogen has a much higher energy density.)

John Tse talked about hydrate clathrates (there's lots of methane at the bottom of the ocean, and it may be a way to store hydrogen ).

One point I found interesting - the potential bewteen a hydrogen molecule and a graphene sheet fits a Lennard-Jones potential quite well (for one particular site or orientation).

Technical note - Doing simulations with DFT is not quite sufficient to get good energies, they used MP2 level theory. (Seems this was repeated in another talk). Question - are MP2 energies good enough, or is doing better just too expensive?

William Goddard presented theoretical evaluations of several approaches to hydrogen storage.

• Metallo-Organic Frameworks
  
• Mg nanoparticles
  
• Metal hydrides
  
• Carbon materials (nanotubes, some doped with Li)
  

In the Mg nanoparticle section, he talked about solving the inversion problem - designed the material to specifications. Their approach was find the potential (I think?) of a desirable atom, and find reals atoms to match.
(There was a similar idea presented by Alex Zunger, trying to find materials that matched specific band-related properties)

Monte Carlo methods in CISE

Monte Carlo methods are the theme for the March issue of Computing in Science and Engineering. There's a broad overview article, an article covering the geometric cluster method (contains descriptions of the lattice-based cluster algorithms as well), an article examining Markov chains arising from computer science, and an article on sequential importance sampling.