Computer Programming News and More: other

Sunday, July 1, 2012

Video games lead to new paths to treat cancer, other diseases

ScienceDaily (Feb. 16, 2012) — Anqi Zou never thought she would thank video gamers for showing her the way to exciting discoveries in molecular biology.

But here she is, acknowledging that the technology she uses to show the inner workings of cells was originally perfected to create realistic images on gaming screens worldwide.

No matter. Sam Cho and his students are using graphics processing units -- also called GPUs or graphics cards -- to explore the biomolecular processes in the cell and take on challenges, including a cure for cancer.

"We have hijacked the same technology that creates the detailed gaming scenes on your computer screen to perform molecular-dynamic simulations," Cho said.

Zou is helping Cho push the limits of GPU-optimized cell simulations. This Mathematical Business and Computational Science major is comparing the data provided by GPU and non-GPU simulations.

"Because of the powerful computational ability of these GPU devices that are usually used for gaming, I couldn't help registering for Dr. Cho's GPU programming course," she said. "Halfway through the semester, I was much impressed by the computational performance of the GPUs, and I approached Dr. Cho about working on a research project related to GPU programming."

For his most recent published study, Cho, an assistant professor of physics and computer science, simulated the folding and unfolding of a critical RNA molecule component of the human telomerase enzyme. This enzyme lengthens DNA strands during cell division. It's what makes tumors continue to grow.

Knowing how human telomerase works could lead to cancer therapies that essentially obliterate tumors, Cho said.

His research findings appear in the Journal of the American Chemical Society.

Now, Cho and his research assistants are looking at a much larger cell system -- the bacterial ribosome -- to see what they can uncover through GPU-optimized molecular dynamic simulations. The graphics cards were donated by Nvidia, the company that invented the GPU; Cho developed a new GPU programming course so he could teach Wake students how to use the cards.

The benefit of the GPU-optimized simulations is that they are much quicker to perform. The ribosome simulation, for example, would take more than 40 years on a standard computer. Using GPUs, Cho and his students will see results in a few months.

The end goal is to map the ribosome's functions so researchers can develop antibiotics to specifically kill bacteria.

And that would be an amazing accomplishment, thanks in large part to videogamers, Cho said.

"If it wasn't for gamers who kept buying these GPUs, the prices wouldn't have dropped, and we couldn't have used them for science," he said.

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Story Source:

The above story is reprinted from materials provided by Wake Forest University, via Newswise. The original article was written by Alicia Roberts.
Note: Materials may be edited for content and length. For further information, please contact the source cited above.

Journal Reference:

Shi Biyun, Samuel S. Cho, D. Thirumalai. Folding of Human Telomerase RNA Pseudoknot Using Ion-Jump and Temperature-Quench Simulations. Journal of the American Chemical Society, 2011; 133 (50): 20634 DOI: 10.1021/ja2092823

Note: If no author is given, the source is cited instead.

Disclaimer: This article is not intended to provide medical advice, diagnosis or treatment. Views expressed here do not necessarily reflect those of ScienceDaily or its staff.

View the original article here

Saturday, June 2, 2012

Zappos breach goes beyond credit cards: Consumers face identity theft if hackers correlate other penetrated databases

ScienceDaily (Jan. 18, 2012) — Stephen B. Wicker, Cornell professor of Electrical and Computer Engineering at Cornell University, comments on the Zappos web site breach by hackers.

Wicker conducts research in wireless information networks. He focuses on networking technology, law, and sociology, and how regulation can affect the privacy and speech rights. He is the author of the book "Cellular Convergence and the Death of Privacy," to be published by Oxford University Press at the end of 2012.

He says: "Though Zappos has not stated how security was breached, this event is a reminder that security is not a fix or an overlay, it is an ongoing process that must be intrinsic to the design and maintenance of an Internet presence.

"Zappos said that credit card information was not stolen, but acknowledged that email addresses, billing and shipping addresses, phone numbers, and the last four digits from credit cards may have been compromised. This is a lopsided outcome for the customer.

"The bigger problem Zappos faces is that large databases of consumer information can be used for identity theft. As Zappos acknowledged, users who use the same or similar passwords are at risk of theft through access to other sites such as Amazon or Ebay.

"More generally, information about a customer can be used to 'de-anonymize' other databases on other Web sites, further invading customer privacy. Correlation attacks enabled by such data have been shown to strip anonymity from NetFlix, AOL and other databases that were assumed safe. Thus, the information used can include customer preferences, beliefs and practices that are far harder to change than a credit card number.

"Zappos' response is admirable for its forthrightness and immediacy, but this is a reminder of the risk run when online service providers maintain databases of user data. This is a practice that many, many web site and service providers engage in for convenience and, in some cases, for profit. This is a practice that a networked society cannot afford for the long term if individual privacy is to be preserved."