Perspectives on computational biology methods
There have been impressive advances in computational methods, allowing researchers to better understand biological and physiological systems at the atomic level.
In its latest Perspectives in General Physiology series, the Journal of General Physiology (JGP) offers an in-depth look at several of these methods and the advantages of each as applied to membrane proteins, with special focus on ion channels. The Perspectives appear in the June issue (www.jgp.org).
The main focus of computational biology is to develop mathematical modeling and computational techniques to better analyze biological systems. As guest editor Benoit Roux (University of Chicago) explains, no single method can provide researchers with all the levels of description needed to fully examine every relevant lengthscale and timescale of a particular physiological process. However, the four Perspectives presented in this issue illustrate how various methods can be used to achieve different goals.
The Perspectives include: Denis Bucher and Ursula Rothlisberger (Ecole Polytechnique Fédérale de Lausanne) present ab initio (first-principles) simulations; David Shaw and colleagues (Columbia University) examine the all-atom molecular dynamics (MD) method; Ivet Bahar (University of Pittsburgh) shows how important insights can be obtained from "course-grained" (CG) models; and Jonathan Silva and Yoram Rudy (University of Chicago) examine a strategy using a small number of simplified "states" to represent a complex system.
The purpose of the Perspectives in General Physiology series is to provide an ongoing forum where scientific questions or controversies can be discussed by experts in an open manner.
About The Journal of General Physiology
Founded in 1918, The Journal of General Physiology (JGP) is published by The Rockefeller University Press. All editorial decisions on manuscripts submitted are made by active scientists. JGP content is posted to PubMed Central, where it is available to the public for free six months after publication. Authors retain copyright of their published works and third parties may reuse the content for non-commercial purposes under a creative commons license. For more information, please visit www.jgp.org.
Bahar, I. 2010. J. Gen. Physiol. doi:10.1085/jgp.200910368.
Bucher, D., and U. Rothlisberger. 2010. J. Gen. Physiol. doi:10.1085/jgp.201010404.
Dror, R.O., et al. 2010. J. Gen. Physiol. doi:10.1085/jgp.200910373.
Roux, B. 2010. J. Gen. Physiol. doi:10.1085/jgp.201010456.
Silva, J.R., and Y. Rudy. 2010. J. Gen. Physiol. doi:10.1085/jgp.200910358
Rita Sullivan | EurekAlert!
The most recent press releases about innovation >>>
Die letzten 5 Focus-News des innovations-reports im Überblick:
Whether you call it effervescent, fizzy, or sparkling, carbonated water is making a comeback as a beverage. Aside from quenching thirst, researchers at the University of Illinois at Urbana-Champaign have discovered a new use for these "bubbly" concoctions that will have major impact on the manufacturer of the world's thinnest, flattest, and one most useful materials -- graphene.
As graphene's popularity grows as an advanced "wonder" material, the speed and quality at which it can be manufactured will be paramount. With that in mind,...
Physicists at the University of Bonn have managed to create optical hollows and more complex patterns into which the light of a Bose-Einstein condensate flows. The creation of such highly low-loss structures for light is a prerequisite for complex light circuits, such as for quantum information processing for a new generation of computers. The researchers are now presenting their results in the journal Nature Photonics.
Light particles (photons) occur as tiny, indivisible portions. Many thousands of these light portions can be merged to form a single super-photon if they are...
For the first time, scientists have shown that circular RNA is linked to brain function. When a RNA molecule called Cdr1as was deleted from the genome of mice, the animals had problems filtering out unnecessary information – like patients suffering from neuropsychiatric disorders.
While hundreds of circular RNAs (circRNAs) are abundant in mammalian brains, one big question has remained unanswered: What are they actually good for? In the...
An experimental small satellite has successfully collected and delivered data on a key measurement for predicting changes in Earth's climate.
The Radiometer Assessment using Vertically Aligned Nanotubes (RAVAN) CubeSat was launched into low-Earth orbit on Nov. 11, 2016, in order to test new...
A study led by scientists of the Max Planck Institute for the Structure and Dynamics of Matter (MPSD) at the Center for Free-Electron Laser Science in Hamburg presents evidence of the coexistence of superconductivity and “charge-density-waves” in compounds of the poorly-studied family of bismuthates. This observation opens up new perspectives for a deeper understanding of the phenomenon of high-temperature superconductivity, a topic which is at the core of condensed matter research since more than 30 years. The paper by Nicoletti et al has been published in the PNAS.
Since the beginning of the 20th century, superconductivity had been observed in some metals at temperatures only a few degrees above the absolute zero (minus...