SPARC (the Scholarly Publishing and Academic Resources Coalition), the Public Library of Science (PLoS), and Students for FreeCulture have jointly announced the first international Open Access Day. Building on the worldwide momentum toward Open Access (OA) to publicly funded research, Open Access Day will create a key opportunity for the higher education community and the general public to understand more clearly the opportunities of wider access and use of content. Open Access Day will help to broaden awareness and understanding of OA, including recent mandates and emerging policies, within the international higher education community and the general public.

OA is a growing international movement that uses the Internet to throw open the locked doors that once hid knowledge. It encourages the unrestricted sharing of research results with everyone, everywhere, for the advancement and enjoyment of science and society. For example, this issue has been especially highlighted for the field of biomedical research and health care.¹ OA is the principle that publicly funded research should be freely accessible online, immediately after publication, and it’s gaining ever more momentum around the world as research funders and policy makers put their weight behind it.

Why OA matters? First, I was really fascinated by the personal perspective by Jonathan Eisen published in PLoS Biology.² Second, perhaps it signals a fundamental change in the way that information is flowed from writers to readers and an admission that the traditional publishing process is obsolete in the digital age. We live in a world where people expect instant information in the top 20 hits from a Google and that expectation is transferring the science too. It doesn’t matter how prestigious your journal is. People want information, they want it now! And if you can’t deliver, they are going somewhere else.

C’mon, I am just a postdoc (poor assistant professor, grad, undergrad, etc)… What can I do? It’s very simple, try to submit articles to OA journals and review papers for them. Next, spread the world. There are plany of stuff the faculty, librarians, Universities, administrators and even Research Funders can do to promote OA.

1. Heather A. Piwowar, Michael J. Becich, Howard Bilofsky, Rebecca S. Crowley (2008). Towards a Data Sharing Culture: Recommendations for Leadership from Academic Health Centers PLoS Medicine, 5 (9) DOI: 10.1371/journal.pmed.0050183
2. Jonathan A. Eisen (2008). PLoS Biology 2.0 PLoS Biology, 6 (2) DOI: 10.1371/journal.pbio.0060048

Not all publishers have embraced it, some have tried to exact exorbitant fees for allowing manuscripts to be transferred to PMC. Others have engaged in aggressive lobbying against open access efforts. Those efforts may be paying off. The House of Representatives has seen the introduction of legislation, HR 6845 that, depending on its final format, may significantly curtail or eliminate the NIH’s ability to continue its open access policy. The current bill would prevent any arm of the federal government from making research funding contingent upon “the transfer or license to or for a Federal agency of… any right provided under paragraph (1) or (2) of section 106 in an extrinsic work, to the extent that, solely for purposes of this subsection, such right involves the availability to the public of that work.” Those Section 106 rights include the reproduction of the work.

Although that would seem to rule out the existing NIH policy, there is a certain amount of legal wiggle room there. For example, the NIH could fund a private entity to maintain PMC, and thus have the right to reproduction transferred to an independent entity. Nevertheless, the bill would appear to directly target the prior legislation that put the NIH in the business of mandating public access in the first place.

[via http://arstechnica.com]

Our work on AIMD simulation of CL-20 thermal decomposition just get published in the J. Phys. Chem. B!

CL-20 (2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane or HNIW) is a high-energy nitramine explosive. To improve atomistic understanding of the thermal decomposition of CL-20 gas and solid phases, we performed a series of ab initio molecular dynamics simulations. We found that during unimolecular decomposition, unlike other nitramines (e.g., RDX, HMX), CL-20 has only one distinct initial reaction channel—homolysis of the N—NO₂ bond. We did not observe any HONO elimination reaction during unimolecular decomposition, whereas the ring-breaking reaction was followed by NO₂ fission. Therefore, in spite of limited sampling, that provides a mostly qualitative picture, we proposed here a scheme of unimolecular decomposition of CL-20. The averaged product population over all trajectories was estimated at four HCN, two to four NO₂, two to four NO, one CO, and one OH molecule per one CL-20 molecule. Our simulations provide a detailed description of the chemical processes in the initial stages of thermal decomposition of condensed CL-20, allowing elucidation of key features of such processes as composition of primary reaction products, reaction timing, and Arrhenius behavior of the system. The primary reactions leading to NO₂, NO, N₂O, and N₂ occur at very early stages. We also estimated potential activation barriers for the formation of NO₂, which essentially determines overall decomposition kinetics and effective rate constants for NO₂ and N₂. The calculated solid-phase decomposition pathways correlate with available condensed-phase experimental data.

Isayev, O., Gorb, L., Qasim, M., Leszczynski, J. (2008). Ab Initio Molecular Dynamics Study on the Initial Chemical Events in Nitramines: Thermal Decomposition of CL-20. Journal of Physical Chemistry B, 112(35), 11005-11013. DOI: 10.1021/jp804765m

Q: What do you get when you cross an elephant and a grape?
A: Elephant x Grape x sin(alpha)
Q: What do you get when you cross an Elephant and a mountain climber?
A: You can’t cross a vector and a scaler!

Q: What is the difference between a Quantum Theorist and a Beauty Therapist?
A: The Quantum Theorist uses Planck’s Constant as a foundation, whereas the Beauty Therapist uses Max Factor.

Q: Why does e^x hate going to parties?
A: Because no matter how hard he tries, he always fails to integrate.

Q: Why don’t catholics pray for forgiveness when sitting down?
A: Because there’s no syn elimination in the chair conformation!

Q: Why does hamburger have lower energy than steak?
A: Because it’s in the ground state.

Q: What weapon can you make from the elements potassium, nickel and iron?
A: A KNiFe.

Q: How many theoretical physicists does it take to change a light bulb?
A: They can’t change light bulbs but they can run expensive computer simulations which predict the lifetime of the bulb with order of magnitude accuracy.

Q: Why did the chicken cross the road?
Issac Newton: Chickens at rest tend to stay at rest, chickens in motion tend to cross roads.
Albert Einstein: Whether the chicken crossed the road or the road crossed the chicken depends on your frame of reference.

Even more jokes

Did you hear about the biologist who had twins? She baptized one and kept the other as a control!

A small furry animal walks into a bar, orders a drink. Bartender looks at him, says “Sorry, the occupancy is 6.023×10²³. We cannot serve a mole.”

Heisenberg is pulled over for speeding:
“Do you know how fast you were going?” the police officer asks, incredulously.
“No,” replies Heisenberg, “but I know exactly where I am!”

Two atoms are walking down the street.
Says one atom to the other, “Hey! I think I lost an electron!”
The other says, “Are you sure??”
“Yes, I’m positive!”

I wish I was Adenine so I can be paired with U!

Famous last words

Nuclear physicist: See, cold fusion does not work.
Nuclear physisist: What was the critical mass, exactly?
Physisist: And now we reach absolute zero.
Astronomer: That asteroid won’t hit the Earth.
Chemist: And now the tasting test.
Chemist: And now a little bit from this…
Chemist: And now shake it a bit.
Chemist: Why is there no label on this bottle?
Chemist: In which glass was my mineral water?
Chemist: Why does that stuff burn with a green flame?!?
Chemist: First the acid, then the water…
Chemist: Oh no, wrong beaker…
Microbiologist: These bacteria cannot live outside the substrate.
Field biologist: They never attack humans.

Question: What is “IT”?

Geologists do IT on the ground.
Astronomers do IT all night.
Chemists do IT by bonding.
Chemists also do IT on a table, periodically.
Newton did IT with force.
Eighteenth century physicists did IT with rigid bodies.
Maxwell did IT with magnetism.
Analytical Chemists do it with precision and accuracy.
Volta did IT with a jolt.
Watt did IT with power.
Joule did IT with energy.
Ohm did IT with resistance.
Pascal did IT under pressure.
Hooke did IT using springs.
Coulomb got all charged up about IT.
Hertz did IT frequently.
Boltzmann did IT in heat.
Ampere let IT flow.
For Franklin, IT was an electrifying experience.
Edison claims to have invented IT.
When Richter did IT, the Earth shook.
For Darwin, IT was natural.
Freud did IT in his sleep.
Mendel studied the consequences of IT.
When Wegener did IT, continents moved.
Classical physicists do IT in perfectly uniform harmonic motion.
Heisenberg was never sure whether he even did IT.
Bohr did IT in an excited state.
Pauli did IT but excluded his friends.
Schrödinger did IT in waves.
Bose did IT with partners.
Einstein did IT on a curved surface.
Oort did IT in a cloud.
Hubble did IT in the dark.
Watson and Crick got all wound up about IT.
Cosmologists do IT in a big bang.
Theorists do IT on paper.
Wigner did IT in a group.
Richter and Ting did IT with charm.
Astrophysicists do IT with young starlets.
Planetary scientists do IT with Uranus.
Electron microscopists do IT 100,000 times.
Feynman did IT in fields.
Hawking wrote a brief history of IT.
Soil chemists do IT dirty.

Answer: IT = science, of course

Roadrunner supercomputer, built by IBM with funding from the National Nuclear Security Administration (NNSA) for Los Alamos National Laboratory, achieved a long-sought supercomputing goal: performing more than a thousand trillion operations per second, or petaflop/s. Roadrunner is the first supercomputer to use a hybrid processor architecture, which is based on 6,912 dual-core Opteron X64 processors from Advanced Micro Devices (AMD) and 12,960 IBM Cell Broadband Engine™ (Cell BE) processing elements. The Roadrunner system has 98 terabytes of memory, and is housed in 278 refrigerator-sized, IBM BladeCenter® racks occupying 5,200 square feet. Its 10,000 connections – both Infiniband and Gigabit Ethernet — require 55 miles of fiber optic cable. Roadrunner weighs 500,000 lbs. At the end of May, the system posted a peak performance of 1.026 petaflop/s running the Linpack benchmark. This test consisted of solving linear equations involving more than 2 million equations and an equal number of unknowns. Roadrunner is also rated as very energy (performance/watt) efficient (green).

For me, breaking the petaflop/s barrier is the equivalent of a runner finally running the 100-meter race in 9.5 seconds — a level of performance everyone hopes for but proves elusive to actually achieve. This will be the third time at ISC that we will have a presentation about the almost magical surpassing of a thousand-fold increase in HPC performance. Twenty-two years ago, in 1986, the legendary Cray 2 passed the 1 gigaflop/s level, and in June of that year we held the first ISC. Eleven years later, when the Intel ASCI Red system landed atop the 9^th TOP500 list presented at the conference, this was the first time a system reached the teraflop/s level. And now RoadRunner has cracked the next magical barrier and will be number one on the 31^st edition of the TOP500 list.

said Prof. Hans Meuer, general chair of ISC and founder of the TOP500 list.

On the Web, vertical rhythm — the spacing and arrangement of text as the reader descends the page — is contributed to by three factors: font size, line height and margin or padding. All of these factors must calculated with care in order that the rhythm is maintained. The basic unit of vertical space is line height. Establishing a suitable line height that can be applied to all text on the page is the key to a solid dependable vertical rhythm. It will engage and guide the reader down the page.

Unfortunately, many sites using the sup or sub tags do not instruct the browser how to display them. Frankly, the default display is limp. A vertical rhythm in text with these tags can be ruined since sup or sub tag can throw off the line-spacing of a text block:

Disappointedly, even Wikipedia did not style them as well! Look on picture below, awkward white spaces marked with red arrows, that is especially visible on selected text (blue field).

The solution of this issue is easy and elegant:

Using vertical-align we are fixing line heights and slightly shifting blocks using relative position. Please, note the value 0.4em should be adjusted to the particular site. Lat’s magic work:

Certainly, I have added this hack to the CSS on this site as well. Please visit my research projects for the real life example.

Example files and enchanced pdf copy of this article are coming. Stay tuned!

May 9 — Victory Day all over Eastern European countries, a national holiday which remembers the Victory over Nazi Germany in World War II and honors 20 million Soviets who died in the war.

Victory Day marks the capitulation of Nazi forces to the Allies (the Soviet Union, the United Kingdom, the United States and other principal Allied nations) in Berlin on May 8, 1945. It is celebrated in the successor states to the Soviet Union on May 9, because when the German Instrument of Surrender was signed (in the midnight), it was already May 9 in the USSR and Eastern Europe. The US, UK and most western European countries mark Victory in Europe Day on May 8.

The main reason for the celebration of Victory Day was to remember the people who died in the war. On that day, flowers are laid on their graves and veterans that are still alive go out on the streets wearing their medals and orders. There are few of them left now days and the number is getting smaller every year. Russia mainly fought a war to defend itself, which is called a “Great Patriotic War”. That is what most Russians call WWII. In Russia almost all the families have at least one person who took part in the war. The other old citizens who did not fight during the war had to work in factories to make guns and preparations, which wasn’t easier than fighting. They too are honored on Victory Day.

I’ve lost my Great Grand Father to the battle of Stalingrad.  Although he was komdiv or divisional commander (corresponds to present day lieutenant-general), he was reported MIA.  On this day, I take time to remember him and be thankful for everything that I have. Because I live in a better age and place.

Unfortunately several ugly bugs pup-up during the upgrade process. Mysteriously, all “pi” letters disappeared in pi-day news. Permanlink structure collapsed, and I was not able to restore it in the old shape. It causes multiple 404 errors:( Several features are still off. I hope to work on these issues over the weekend.

Last night, I programmed new quick-n-dirty implementation for “Colophon” and photo gallery. Next, “Design” part will be completely re-aligned and updated too. So, a lot of new and excited stuff is coming. Stay tuned!

Last, but not least, I successfully defend my Ph.D. thesis on May 2nd, 2008:) I am pretty excited about that. I hope to put some pictures from these events. In the mean time, a friend of mine, Dmytro Kosenkov highlighted some of these events in his notes.

Coincidentally, ?-Day is also the birthday of Albert Einstein, who no doubt knew more than a little about ? :-)