Iconocast Logo

Welcome To Iconocast

How to add a URL link from your web site to the Iconocast web sites

Virtual tour of Southern California

 

Recent News and Articles on the Keywords: unfolding + code + web  Related to the article below (Last Update: 8/4/2008)

Between editors and editors
Vanguard, Nigeria - Aug 2, 2008
It needs no debate, therefore, to demand that the professionals in the media adopt a code of conduct and collectively ensure its enforcement. ...
Preacher to begin 12-day crusade in Alerus
Grand Forks Herald, ND - Jul 31, 2008
The ad bills the crusade as ?Unfolding Revelation,? referring to the last book in the Bible, John?s vision of what Christians have widely ? if disparately ...
Full Text
Science Magazine (subscription) - Jul 24, 2008
He also discusses a partnership between Google and StopBadware that identifies Web sites that have malicious code hidden in them and provides a warning to ...

The Tech Herald
AT&T first reported victim of DNS attack ? HD Moore was NOT ?Pwned?
The Tech Herald, IN - Jul 30, 2008
The drama is still unfolding, as Matasano is taking criticism for the details being leaked, with charges that it was intentional, not an accident. ...
Top 5 Reasons To Attend SMX Local & Mobile
Search Engine Land, CT - Jul 7, 2008
SMX Local & Mobile features sessions that dive deep into the crucial differences, from cracking the code of algorithms to exploring the unique opportunities ...
Will the Real Theory of Evolution Please Stand Up?
Scoop.co.nz, New Zealand - Jul 6, 2008
"He?sa one to watch in the unfolding evolution discourse," I was advised regarding New York Medical College cell biologist Stuart Newman. ...
Saving the South Central Farm: Listening to the Land
Dissident Voice, CA - Jul 19, 2008
Mayan Indians in a Zapatista community prayed for the land and for the life unfolding there. Native elders came and shared the lessons of their peoples. ...
Source: Google News

Measurement of energy and direction distribution of neutron and photon fluences in workplace fields -
M Luszik-Bhadra, M Reginatto, V Lacoste - Radiation Protection Dosimetry, 2004 - NTP
... The MAXED program is an unfolding code that applies the maximum entropy principle
to data analysis in the standard way, and allows for the use of pre ...

MITOM: a new unfolding code based on a spectra model method applied to neutron spectrometry -
M Tomas, F Fernandez, M Bakali, H Muller - Radiation Protection Dosimetry, 2004 - NTP
... MITOM: a new unfolding code based on a spectra model method applied to neutron
spectrometry. M. Tom?s 1 , F. Fern?ndez 1 ,* , M. Bakali 1 and H. Muller 2 ...

Characterisation of the IRSN CANEL/T400 facility producing realistic neutron fields for calibration … -
V Gressier, V Lacoste, L Lebreton, H Muller, G … - Radiation Protection Dosimetry, 2004 - NTP
... 7) performed with several other codes have shown that the derived energy distribution
is almost independent of the unfolding code and of the prior information. ...

Bayesian Prior Probability Distributions for Internal Dosimetry -
G Miller, WC Inkret, TT Little, HF Martz, ME … - Radiation Protection Dosimetry, 2001 - NTP
... internal dosi- metry code (the Bayes II software package, download- able from our
web site, www.lanl.gov bayesian). The Bayesian unfolding algorithm is ...

Bonner sphere neutron spectrometry at nuclear workplaces in the framework of the EVIDOS project -
V Lacoste, M Reginatto, B Asselineau, H Muller - Radiation Protection Dosimetry, 2007 - NTP
... The data were processed by means of two unfolding codes, NUBAY and GRAVEL,
both provided by the Physikalisch-Technische Bundesanstalt. ...

Haystack: A Platform for Authoring End User Semantic Web Applications -
D Quan, D Huynh, DR Karger - International Semantic Web Conference, 2003 - Springer
... ubiquity of Web browsers, we believe that the unfolding of the ... Adenine, for instance,
can code information processing algorithms on Web servers that ...

BUMS?Bonner sphere Unfolding Made Simple: an HTML based multisphere neutron spectrometer unfolding … -
J Sweezy, N Hertel, K Veinot - Nuclear Inst. and Methods in Physics Research, A, 2002 - Elsevier
... This package, Bonner sphere Unfolding Made Simple (BUMS) is built on the framework
of the BUNKI code developed by ... is designed to run on a web server, and ...

[PDF]  -
A Sahai, S Graupner, W Kim - in Internet Encyclopedia, J. Wiley, also HP Labs Technical …, 2002 - ce.sejong.ac.kr
... The past decade has seen the unfolding of the web services paradigm as a logical ...
With Microsoft .NET, web services? application code is built in ...

Direction distributions of neutrons and reference values of the personal dose equivalent in … -
M Luszik-Bhadra, T Bolognese-Milsztajn, M Boschung … - Radiation Protection Dosimetry, 2007 - NTP
... 10)/H DS * (10) using the four unfolding codes resulted in ... Bhadra M., d'Errico F.
An unfolding method for ... Published on web: http:irpa11.irpa.net/pdfs/3b12.pdf. ...

Neutron spectrometry at high mountain observatories -
A Zanini, M Storini, L Visca, EAM Durisi, F Fasolo … - Journal of Atmospheric and Solar-Terrestrial Physics, 2005 - Elsevier
... higher solar activity period (monthly mean sunspot number=61.1, from the web site
of ... passive systems (wide and short energy range) and the unfolding code BUNTO ...

Source: Google Scholar
 
 

Unfolding The Genetic Code

Article Date: 12 Dec 2006 - 6:00am (PST)
It turns out that sequencing the human genome - determining the order of DNA building blocks -- has not completely cracked the code of how DNA directs various cellular processes. In addition to the sequence of the base pairs, the instructions are in the packaging - how DNA is folded within a cell.

Virginia Tech researchers used novel methodology and the university's System X supercomputer to carry out what is probably the first simulation that explores full range of motions of a DNA strand of 147 base pairs, the length that is required to form the fundamental unit of DNA packing in the living cells -- the nucleosome. Contrary to a long-held belief that DNA is hard to bend, the simulation shows in crisp atomic detail that DNA is considerably more flexible than commonly thought.

The research is published in the December issue of the Biophysical Journal, in the article "A Computational Study of Nucleosomal DNA Flexibility," by Jory Zmuda Ruscio of Leesburg, Va., a Ph.D. student in the Genetics, Bioinformatics and Computational Biology Program at Virginia Tech, and Alexey Onufriev of Blacksburg, assistant professor of computer sciences and physics at Virginia Tech. They have been invited to do a platform presentation at the 51st Biophysical Society Annual Meeting in Baltimore in March.

Article continues below and (thank you)
 
There is about 12 feet of DNA in a human cell but it is packaged into nucleosomes - lengths of 147 base pairs each wrapped around eight special proteins. A nucleosome looks kind of like the lumpy beginning of a rubber-band ball. Or maybe more like a lumpy worm coil. Uncoiled, the worm wiggles, flexes, and even kinks, according to a simulation performed on System X.

As we know from watching forensic detective shows on TV, the DNA in all of an individual's cells is identical. The DNA in fingernail cells is exactly the same as in muscle. Yet the cells are different. "This is because, roughly speaking, the DNA in different cell types is packed differently and the complexes it forms with the surrounding proteins are in different positions, so only the relevant part of the code can be read at a time," said Onufriev. "Although nobody knows exactly how it happens, you can imagine reading only what you can see on a part of a crumpled newspaper."

The traditional view is that DNA is relatively rigid and that considerable energy is required when it needs to be bent to form protein-DNA complexes. However, recent experiments (Nature, Aug. 17, 2006) have begun to challenge that view. "The famous double-helix may be much more flexible than previously thought," said Onufriev.

The Virginia Tech research responded to this debate. Using 128 of System X's 1,100 processors, the research resulted in a System X movie revealing DNA wiggling like a worm, showing greater flexibility than expected from the traditional view. The DNA packing in the nucleosome is also found to be surprisingly loose. "The implication is that it may not cost much energy to bend the DNA - even to bend sharply," said Onufriev.

The methodology that is making it possible is based on the so-called "implicit solvent" approach being developed by Onufriev. "Biology does not happen in a vacuum," he said. "We are 75 percent water, and the effect of the water environment must be taken into account when studying biomolecules."

Previous simulations were often slowed because they accounted for the water that is present in living systems. For instance, in early studies of protein folding, only a few percent of the computing effort was being spent on the activity of the protein while the rest accounted for the activity of the surrounding fluids. The "implicit solvent" approach accounts for the role of water on average, but the movements of individual water molecules are not predicted, freeing computation capacity for simulation of whatever protein is being studied.

"Experiment cannot always probe atomic detail of living molecules because they are too small and often move too fast, said Onufriev. "But we can combine computational power with good algorithms to simulate these motions at high (atom-scale) resolution.

"It is an exciting time to do molecular modeling," he said. "The computing power and the methodology have come to the point that we can begin to fully probe biology on timescales very relevant to living things - such as DNA packing."

Virginia Tech's System X supercomputer was critical to this research, he said. "It was the combination of its sheer compute power with the algorithmic advantages that made it possible to run molecular simulations on that scale."

So far, the Virginia Tech research team addressed the question of how flexible the DNA is, which is only a small piece of the "second part of the genetic code" puzzle, Onufriev said. "However, this small piece should pave the way to addressing bigger questions, such as 'Exactly how is the tightly packed genetic content read by cellular machines"'"

"Atomic level simulations can complement experimentation and narrow competing theories," said Onufriev. "For systems as large as the nucleosome, simulations using virtual water may be the only practical way to estimate the stability of various confirmations," he said.

How DNA bends and flexes is critical for many cellular processes including cell differentiation and DNA replication. Although also observed in recent experiments, this unusual DNA flexibility is still unexplained. "Now seeing that DNA is not as hard to bend may lead to radical changes in our perspective," said Onufriev. "We are using these detailed pictures to see exactly how DNA bends and to understand the details of the mechanism behind it, something that is very hard or impossible to do experimentally."

Onufriev and his group of biochemistry, physics, biology, and other computer science researchers received a $1.1 million grant from the National Institutes of Health to develop high performance computing methodology to create molecular models and to probe in atomic detail the mechanisms of biology.

The purpose of the NIH award is to develop the methodology for computer simulations of complex biological processes and address the question of the atomic mechanism of DNA flexibility, Onufriev said. "This research may not only provide fundamental insights into how life works at the molecular level, but also has applications in drug discovery and in particular for rational drug design, which is an important consideration for the NIH."

###

Contact: Susan Trulove
Virginia Tech
 
 
 
Google
Web www.iconocast.com
 
 
 

 

Continue News With: News5 ; News6 ; News7 ; News8 ; News9 ; News9A


ADVERTISEMENT

Iconocast is about learning and teaching without borders; we offer eMarketing, Internet Advertising, Internet Marketing, Search Engine Optimization, Search Engine Marketing, Online Branding, and eMarketing News Services. Home

 
 © 2002-2006

Keywords::

Contact Iconocast

Home Page