Bench Press

What can you do with a 110 foot wide, nine story tall radio telescope that weighs almost a million pounds? Not a question the average person or even educational institution asks themselves. Yet, this was a question Lewis Center founder Rick Piercy contemplated when he convinced NASA to donate a radio telescope being decommissioned that had once been used to communicate with Apollo spacecraft.

Thanks to Rick Piercy’s efforts K-12 students around the world have access to the Goldstone Apple Valley Radio Telescope through the Lewis Center’s GAVRT program which is a partnership with NASA offering a variety of programs exposing students to radio astronomy and cutting edge scientific work. Teachers from all institutions are welcome to join the program and are given a training seminar and visit to the telescope in order to familiarize themselves with the curriculum currently designed around the GAVRT as well as learn how to control the telescope via the internet.

In one of the ongoing projects students have been giving NASA scientists a helping hand track the Lunar CRater Observation and Sensing Satellite (LCROSS) spacecraft with the GAVRT. The LCROSS mission is ongoing and the satellite is scheduled to make impact with the moon in order to look for water on October 9, 2009. One of the beauties of this program is that not only is this a unique learning opportunity for the students, but they also help provide additional data gathering time for NASA scientists as explained by Brian Day of the NASA Ames Research Center,

Because LCROSS has a very steeply inclined orbit, we have only a 2-hour window once every 3 days when we can check out the spacecraft using the Deep Space Network. So we decided to ask GAVRT for help. These kids help us get extra listening time for our spacecraft, and they get an incredible educational experience in return.

Thanks to the internet and some enterprising individuals some lucky students will have a front row seat to some exciting scientific exploration of our nearest celestial neighbor. I look forward to hearing about the results of the LCROSS mission. Congratulations guys!

Read more about GAVRT and the LCROSS mission.

We’ve talked before about researchers using PlayStation game consoles and gaming graphics cards to perform scientific computing, but we hadn’t heard too much about Microsoft’s XBox. Until now, that is, when University of Warwick researcher Dr. Simon Scarle demonstrated the use of the graphical horsepower on an XBox360 in high performance computing. By taking advantage of the parallel processing power of the on-board GPU, Dr. Scarle was able to use an Xbox360 to aid in his research and sidestepped the need to reserve time on a dedicated parallel processing computer or shell out thousands for a parallel network of PC’s.

Armed with his gaming console, Dr. Scarle used the Xbox’s GPU computing power to calculate and even predict cardiac arrhythmias based on his model of electric excitations of the heart. The result? A paper titled Implications of the Turing completeness of reaction-diffusion models, informed by GPGPU simulations on an XBox 360: Cardiac arrhythmias, re-entry and the Halting problem.

This is a highly effective way of carrying out high end parallel computing on “domestic” hardware for cardiac simulations. Although major reworking of any previous code framework is required, the Xbox 360 is a very easy platform to develop for and this cost can easily be outweighed by the benefits in gained computational power and speed, as well as the relative ease of visualization of the system.

So much attention thus far has focused on using the PlayStation 3 in distributed computing projects like Folding@Home — maybe its time that Microsoft release some sort of software to let the legions of XBox360 owners out there show the PS3 users that their machines are good for more than just gaming?

I have a great deal of respect for the early pioneers of chemistry — not just because they were intelligent and inquisitive and spawned entire fields of research, but mainly because they were able to do this while never having the ability to see what they were studying. So, although the early experimenters could conduct experiments to indirectly validate or invalidate their hypotheses on a macro-scale (like shaking a tree to see what fruit fell out rather than actually looking up at the tree to see the individual fruit), the fact that they could never see or manipulate or count molecules meant that most of their work resided in the domain of thought experiments.

And, although the scientific community now take the existence of atoms and molecules for granted, I think the early Avogadros of chemistry would have been especially gratified by the recent work at IBM’s research facility in Zurich to use atomic force microscopy to actually see molecules of pentacene (five fused aromatic 6-carbon rings, pictured below)

The results are detailed both on IBM’s press page as well as in the Aug 28 issue of Science. But, in graphical terms, this is the scientific community’s current best picture of pentacene:

Amazing isn’t it? More of the technical details are presented in the video IBM put together in conjunction with the press release (below), but in a nutshell, atomic force microscopy uses a well-defined atomic tip to “feel” out the electronic surface of a molecule. The ability to do this and even be able to resolve the respective hydrogen atoms is a testament to IBM’s ability to put together an incredibly stable (both to mechanical and thermal fluctuations) and precise setup.

From IBM’s perspective, this breakthrough allows them to continue to push ahead on the advanced nanotechnology and semiconductor research which they depend on to churn out next-generation electronics, but for the scientific community, these advances could result not only in better atomic force microscopy experimental techniques, but potentially also a new way to understand and study the chemical reactions and structures which have such great influence over our lives.

Publication: Science 28 August 2009: Vol. 325. no. 5944, pp. 1110 – 1114; DOI: 10.1126/science.1176210

(Image credit – Pentacene chemical diagram) (Image credit – AFM picture)

One of my favorite bands is They Might Be Giants, famous for quirky songs including one of my science-related favorites “Why Does the Sun Shine?” with the amazing line which caught my interest immediately when I first heard it:

“The sun is a mass of incandescent gas, a gigantic nuclear furnace! Where hydrogen is built into helium at a temperature of millions of degrees”

It is with great pleasure that I stumbled on (courtesy of Mr. Gunn’s FriendFeed) one of their latest creations, “Meet the Elements” which I have embedded below for your enjoyment:

Awesome!

If you’d like to follow the Bench Press authors on Friendfeed you can follow me at http://www.friendfeed.com/benjamintseng, Kevin at http://friendfeed.com/ktseng, Eric at http://friendfeed.com/ericsuh, and Anthony at http://friendfeed.com/atphan.

An impressive demonstration of the power of graphics cards is the use of graphics processing units (GPUs) in ray tracing. For those of you not in the know, ray tracing refers to a technique for rendering graphics by tracking how rays of light behave as they reflect from surface to surface, allowing you to create photorealistic images that have complicated reflections and shadows which traditional graphics methods fail to deliver. The flip side of this photorealism is that these techniques are incredibly taxing on computational systems, and it has been something of a “holy grail” for GPU and CPU makers to demonstrate so-called “real time” ray tracing on their systems.

Of course, while ray tracing is an impressive computational feat, most of these demonstrations only show off the aesthetic benefits of being able to implement ray tracing quickly. There are much more real-world impacts in the scientific and medical domains, such as in the field of radiotherapy.

In a nutshell, the idea behind radiotherapy as a cancer therapy is that you use strong bursts of radiation to kill off a tumor while minimizing the side effects of radiation exposure to the surrounding tissue. This balance is extremely difficult to manage as the calculations necessary to understand the effect of applying radiation from an external source on a complex three-dimensional maze of organs and liquids like the human body are highly sophisticated. Interestingly, these calculations actually resemble a ray tracing problem, as the problem of understanding radiotherapy dosage is one of understanding how individual “beams” of radiation travel and interact with the human body.

The result is that computer models which have been used to do dosage calculations are slow (making it impractical for physicians to consider multiple regimens or use more sophisticated “adaptive”/modulated radiation therapies), error-prone from the introduction of assumptions to “gloss over” some of the more sophisticated calculations, and very expensive given the need for large clusters of computational power.

What researchers at the University of Amsterdam have demonstrated is an implementation of a ray tracing algorithm targeted at the radiotherapy dosage question using GPU maker NVIDIA’s CUDA toolkit for performing mathematical calculations using the power of a graphics processor. The researchers used the fact that the power of a GPU rests in its ability to split up complicated math problems into many simpler problems to have the GPU calculate the paths of multiple “rays” of radiation simultaneously, resulting in a performance increase over a non-GPU accelerated technique ranging from 50% faster to 6 times faster! Amazingly, because of the way the GPU does its calculations (mainly that it avoids using a look-up table the CPU-driven algorithm needs), the GPU’s results are also more accurate, despite a single GPU implementation being both faster and cheaper than traditional techniques.

The implications to medicine? To quote the paper:

“The developed GPU algorithm now enables dose calculations at a speed that will be experienced as real time for conventional forward planning based on clinically relevant datasets. this can lead to a major reduction in the workload of radiotherapy treatment planning. Moreover, the presented GPU algorithm can be used to accelerate more advanced treatment planning optimization techniques.”

Paper: M. de Greef et al, “Accelerated Ray Tracing for Radiotherapy Dose Calculations on a GPU.” Medical Physics, Vol 36, Issue 9 (link: http://dx.doi.org/10.1118/1.3190156)

Presentation: http://www.amc.nl/upload/teksten/radiotherapie/hyperthermie/RayForDose-NVIDIA.pdf

(Image credit – Ray tracing schema) (Image from presentation)

Two weeks ago a large wildfire broke out north of Los Angeles within the Angeles National Forest. It grew quickly becoming the largest wildfire in Los Angeles County’s history. A suspected case of arson, it has burned over 160,000 acres as of today and is only 62 percent contained. The immediate impact of the Station Fire is illustrated dramatically by this image produced by NASA’s Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) instrument on the Terra satellite.

Even having lived in San Diego during the 2007 wildfires, images like that one are just incredible. In addition to this image NASA’s Aqua satellite monitored carbon monoxide concentration within the atmosphere over the first seven days of the fire. Click through for the full animation.Thanks to NASA’s satellites some potentially useful scientific data can be gleaned from this disaster. Too bad they don’t have a satellite to help us catch those responsible.

(Station Fire Image)(Carbon monoxide measurements)

We’ve previously covered the computer modeling solutions being used to model and track the paths of near-earth asteroids (especially those which might treat Earth like a dartboard), but for those of you not content to just sit at home while NASA scientists do all the tracking, the asteroid trackers at NASA’s Jet Propulsion Laboratory have made it now easier to follow what’s going on in the world of near-earth asteroids from the comfort of your own home.

The first little gadget they’ve developed is a computer widget (pictured on the left) which is compatible with the Mac OS and Yahoo widget engines.

What it will show is a list of the next five near-earth asteroid approaches (within ~20x the distance of the moon) and an estimate of their size (including a pictogram depiction of what that size means) as well as their distance. The widget will also make it easy to find more information about the particular asteroids it is identifying (an example is linked here) which will show off a dynamic Java applet map of the asteroid’s orbit through the inner solar system (which you can manipulate so you can see how the orbit looks in 3D) as well as a wide range of data on the asteroid such as the eccentricity of an asteroid’s orbit (in layman’s terms, how oval-like versus how circular), the orbital period (the time it takes for an asteroid to complete one rotation around the sun).

The second thing the brains at NASA’s JPL have put together for researchers and amateur astronomers is a Twitter account (@AsteroidWatch), which accompanies NASA JPL’s main Asteroid Watch site. The feed went live on July 29, 2009 and, although not written in the cutesy voice of the MarsPhoenix twitter account (which followed the exploits of the Phoenix Mars probe NASA launched a while back), the AsteroidWatch feed so far has reported on near-earth asteroids and new reports and articles issued by NASA’s official asteroid tracking team.

You can follow the BenchPress team on Twitter! You can follow us at Anthony (@AnthonyPhan), Ben (@BenjaminTseng), Eric (@EricSuh), and Kevin (@Kevin_Tseng).