Simulating the cell, one molecule at a time
A novel technique for ultrahigh-precision simulation of cellular dynamics has enabled researchers to uncover a mechanism underlying a ubiquitous response process in eukaryotic cells.
The findings, to appear in the upcoming issue of the Proceedings of the National Academy of Sciences (PNAS), mark a first step toward the full-scale molecular-level simulation of biological cells.
Signaling processes in cells depend on a complex web of interactions whose macro-level behavior arises from micro-level dynamics of molecules. In mitogen-activated protein kinase (MAPK) cascades, a key pathway for signaling, such dynamics have been shown to generate rich phenomena such as ultrasensitivity and bistability that are critical to biological function. Conventional techniques for modeling MAPK, however, ignore such micro-scale dynamics to reduce computational time.
With their latest work, researchers at RIKEN and the FOM Institute for Atomic and Molecular Physics (AMOLF), Holland, have sidestepped this problem. The group applied a technique they developed, enhanced Green Function Reaction Dynamics (eGFRD), to simulate particle-level dynamics of the MAPK system, dramatically reducing computation time. Their results reveal that micro-level details of the interaction between enzyme and substrate molecules, overlooked in earlier models, can have a dramatic impact on the nature of response.
While challenging conventional theory, the findings also prelude an era of cellular simulations on a level of molecular detail never before possible. By exploiting the power of RIKEN's Next- Generation Supercomputer, currently under construction in Kobe, the new technique opens the door to the full-scale simulation of living cells, with key applications to cancer and stem cell research.
For more information, please contact:
Dr. Koichi Takahashi
Biochemical Simulation Research Team, Computational Systems Biology Research Group
Advanced Computational Sciences Department
RIKEN Advanced Science Institute
Tel: +81-(0)45-503-9430 / Fax: +81-(0)45-503-9429
Ms. Saeko Okada (PI officer)
Global Relations Office
Tel: +81-(0)48-462-1225 / Fax: +81-(0)48-462-4715
Saeko Okada | Research asia research news
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...