NSpill's blog: December 2009

Tuesday, December 29, 2009

New From Nassim Taleb

Site of the day: http://molecularstation.com/

http://www.fooledbyrandomness.com/notebook.htm

First Functional Molecular Transistor

Site of the day: http://molecularstation.com/

Nearly 62 years after researchers at Bell Labs demonstrated the first functional transistor, scientists say they have made another major breakthrough.

Researchers showed the first functional transistor made from a single molecule. The transistor, which has a benzene molecule attached to gold contacts, could behave just like a silicon transistor.

The molecule’s different energy states can be manipulated by varying the voltage applied to it through the contacts. And by manipulating the energy states, researchers were able to control the current passing through it.

The transistor, or semiconductor device that can amplify or switch electrical signals, was first developed to replace vacuum tubes. On Dec. 23, 1947, John Bardeen and Walter Brattain (who’d built on research by colleague William Shockley) showed a working transistor that was the culmination of more than a decade’s worth of effort.

Vacuum tubes were bulky and unreliable, and they consumed too much power. Silicon transistors addressed those problems and ushered in an era of compact, portable electronics.
Now molecular transistors could escalate the next step of developing nanomachines that would take just a few atoms to perform complex calculations, enabling massive parallel computers to be built.

The team, which includes researchers from Yale University and the Gwangju Institute of Science and Technology in South Korea, published their findings in the Dec. 24 issue of the journal Nature.

For about two decades — since Mark Reed, a professor of engineering and applied science at Yale, showed that individual molecules could be trapped between electrical contacts — researchers have been trying to create a functional molecular transistor.

Some of the challenges they have faced include being able to fabricate the electrical contacts on such small scales, identifying the molecules to use, and figuring out where to place them and how to connect them to the contacts.

“There were a lot of technological advances and understanding we built up over many years to make this happen,” says Reed.

Despite the significance of the latest breakthrough, practical applications such as smaller and faster molecular computers could be decades away, says Reed.

“We’re not about to create the next generation of integrated circuits,” he says. “But after many years of work gearing up to this, we have fulfilled a decade-long quest and shown that molecules can act as transistors.”

Photo: A benzene molecule can be manipulated to act as a traditional transistorCourtesy: Hyunwook Song and Takhee Lee

(http://www.wired.com/gadgetlab/2009/12/functional-molecular-transistor/)

Thursday, December 24, 2009

Scientists Take a Step Towards Uncovering the Histone Code

Site of the day: http://www.berkshirehathaway.com/

Researchers at Emory University School of Medicine have determined the structures of two enzymes that customize histones, the spool-like proteins around which DNA coils inside the cell.

The structures provide insight into how DNA's packaging is just as important and intricate as the information in the DNA itself, and how these enzymes are part of a system of inspectors making sure the packaging is in order.

The results are published online this week in the journal Nature Structural and Molecular Biology.

A team of scientists led by Xiaodong Cheng, PhD, professor of biochemistry at Emory and a Georgia Research Alliance eminent scholar, used X-rays to probe the architecture of two enzymes, PHF8 and KIAA1718. The enzymes are known as histone demethylases because they remove methyl groups (chemical modifications of a protein) from histones.

Mutations in the gene encoding one of the enzymes, PHF8, cause a type of inherited mental retardation. Understanding how PHF8 works may help doctors better understand or even prevent mental retardation.

Many biologists believe the modifications on histones are a code, analogous to the genetic code. Depending on the histones' structure, access to DNA in the nucleus can be restricted or relatively free. The idea is: the modifications tell enzymes that act on DNA valuable information about getting to the DNA itself.

"This work represents a step toward uncovering the molecular basis for how demethylases handle multiple signals on histones," says Paula Flicker, PhD, who oversees cell signaling grants at the National Institutes of Health's National Institute of General Medical Sciences. "Knowledge of how these complex signals help govern patterns of gene activity will bring us closer to understanding how cells determine their identity during development."

To understand histone demethylases' role in the cell, Cheng says, think of the cell as a library with thousands of books in it.

"To find a particular book in a library, you need some signs telling you how the stacks are organized," he says. "Similarly, the machinery that reads DNA needs some guidance to get to the right place."

Histones have a core that the DNA wraps around and flexible tails extending beyond the core. The cells' enzymes attach a variety of bells and whistles -- methyl groups are just one -- to the histone tails to remind the cell how to handle the associated DNA.

Methyl groups mean different things depending on where they are on the histone. In addition, the modifications vary from cell to cell. In the brain, for example, the modifications on a particular gene might signal "this gene should be read frequently," and in muscle, a different set of modifications will say "keep quiet."

"What these enzymes do is make sure all the signs are consistent with each other," Cheng says. "If a sign is out of place, they remove it."

PHF8 and KIAA1718 are each made up of two attached modules. One module (called PHD) grabs a histone tail with a methyl group on it, while the other module (Jumonji) removes a methyl group from somewhere else on the tail.

Scientists previously knew the structures of the methyl-binding and methyl-removing modules in isolation. What is new is seeing how the modules are connected and how one part regulates the other, Cheng says.

The research was supported by the National Institutes of Health and the Georgia Research Alliance.

(http://www.sciencedaily.com/releases/2009/12/091220143925.htm)

Friday, December 18, 2009

IDA Pro

Site of the day: http://diybio4beginners.blogspot.com/

If you reverse-engineer programs, search for bugs etc., IDA Pro is absolute must have:
http://www.hex-rays.com/idapro/