Visit additional Tabor Communication Publications
November 07, 2012
Carcinogens seem to be everywhere, from automobile exhaust to secondhand smoke. With cancer the second leading cause of death in the US, research into various carcinogens may be the first step in preventing cancer from developing. Now, with the help of researchers at NYU, HPC may give us the necessary tools to curb cancer development.
High performance computing resources help researchers model those airborne cancerous chemicals, known as polycyclic aromatic hydrocarbon (PAH), and their effect on DNA strands in human cells. Carcinogens, or chemicals that manipulate the DNA of cells in such a way that the cells replicate uncontrollably leading to tumors, can be broken into two categories. Some of these chemicals destabilize the actual DNA strands, making them easier to defend against. Others, however, actually create stronger bonds between the strands than there exists between normal DNA, making them particularly effective at propagating themselves.
As Suse Broyde, professor of biology at NYU, said, "Some lesions cause DNA to be locally destabilized, but there are lesions that actually stabilize the DNA so that the two strands come apart with great difficulty. Sometimes they're even more stable than undamaged DNA."
High performance computing facilitated the process of determining which carcinogens manipulated the DNA so effectively. Broyde's lab used the Longhorn, Lonestar, and Ranger systems at the Texas Advanced Computing Center (TACC) to perform these simulations, along with resources in the Extreme Science and Engineering Discovery Environment.
The key was figuring out the Van der Waals forces, forces in chemistry which dictate how chemicals interact with each other at an atomic level. Modeling those forces would give the group insight on how a particular carcinogen moved about a strand of DNA as well as the energy involved.
"You can make movies of the dynamic trajectory which allow you to see the real mobility of the entire system," Broyde said. This amount of resolution helps to indicate how well the particular chemical reacts with the DNA. "You can watch the DNA flexing and the backbone moving dynamically and the carcinogen moving in and out. It's not rigid – you can see its aliveness."
Modeling those complex forces and interactions is no small feat, as it was necessary to garner the coordinates of the structures over a period of time. Broyde's team needed to determine the molecular dynamics. This is where TACC came in.
Using TACC's resources, Yuqin Cai, a post-doctoral research scientist in Broyde's lab, developed a series of computer simulations. Cai's work combined with the HPC allowed each simulation to be properly visualized and analyzed. "The computer simulations revealed the structural, energetic and dynamic properties of the DNA containing the PAH-derived lesions," said Broyde.
After simulating three different carcinogens in two different configurations each, Broyde's team determined that dibenzo[a,l]pyrene was most likely to cause tumors. According to Broyde, that particular carcinogen contains a five-ring structure that lends itself to easy "stacking," which artificially stabilizes the DNA and disarms its repair mechanism.
Determining which carcinogens pose the greatest risk is important to preventative medicine, as doctors can warn patients which chemicals they should be more cautious around, especially, as Broyde noted, in the case of smokers. The research could also lead to the development of more effective chemotherapeutic drugs.
In quieter times, sounding the bell of funding big science with big systems tends to resonate further than when ears are already burning with sour economic and national security news. For exascale's future, however, the time could be ripe to instill some sense of urgency....
In a recent solicitation, the NSF laid out needs for furthering its scientific and engineering infrastructure with new tools to go beyond top performance, Having already delivered systems like Stampede and Blue Waters, they're turning an eye to solving data-intensive challenges. We spoke with the agency's Irene Qualters and Barry Schneider about..
Large-scale, worldwide scientific initiatives rely on some cloud-based system to both coordinate efforts and manage computational efforts at peak times that cannot be contained within the combined in-house HPC resources. Last week at Google I/O, Brookhaven National Lab’s Sergey Panitkin discussed the role of the Google Compute Engine in providing computational support to ATLAS, a detector of high-energy particles at the Large Hadron Collider (LHC).
05/10/2013 | Cleversafe, Cray, DDN, NetApp, & Panasas | From Wall Street to Hollywood, drug discovery to homeland security, companies and organizations of all sizes and stripes are coming face to face with the challenges – and opportunities – afforded by Big Data. Before anyone can utilize these extraordinary data repositories, however, they must first harness and manage their data stores, and do so utilizing technologies that underscore affordability, security, and scalability.
04/15/2013 | Bull | “50% of HPC users say their largest jobs scale to 120 cores or less.” How about yours? Are your codes ready to take advantage of today’s and tomorrow’s ultra-parallel HPC systems? Download this White Paper by Analysts Intersect360 Research to see what Bull and Intel’s Center for Excellence in Parallel Programming can do for your codes.
In this demonstration of SGI DMF ZeroWatt disk solution, Dr. Eng Lim Goh, SGI CTO, discusses a function of SGI DMF software to reduce costs and power consumption in an exascale (Big Data) storage datacenter.
The Cray CS300-AC cluster supercomputer offers energy efficient, air-cooled design based on modular, industry-standard platforms featuring the latest processor and network technologies and a wide range of datacenter cooling requirements.