Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Protein simulation can be done three times as fast

24.06.2002


Protein movement can be simulated three times as fast than had been thought possible up to now. Researchers from Groningen achieved the gain in speed by leaving out the calculations concerning hydrogen atoms. Meanwhile research groups around the world are adapting their simulation programs.



Up until now researchers calculated all of the positions of atoms in a protein molecule after two femtoseconds. A femtosecond is one millionth of a billionth of a second. The research from Groningen reveals that steps of 7 femtoseconds are also good enough. With this the simulation is three times as fast. A number of research groups are already using the results from the Groningen study.

Steps of 7 femtseconds ignore the forces which occur between hydrogen atoms. The researchers have demonstrated that these forces are not relevant for the simulation. Indeed, taking into account how the forces were always described up until now, they are best left out of the calculations.


PhD student Anton Feenstra: "The forces around hydrogen atoms are so small that they cannot really be calculated according to the standard billiard ball description. However, up until now we did do this. If you really want to include hydrogen, although I have shown that does not really need to be done, you should describe it using quantum mechanics."

The researchers expect that the intervals will not become much greater than 7 femtoseconds. Even greater intervals result in unrealistic situations. For example, particles come so close together that it is no longer natural and during the next interval they are further apart than is actually possible.

Biologically interesting processes such as the folding of proteins, occur in a matter of milliseconds. For this the fastest Pentium has to calculate day and night for 200 years. Supercomputers can perform these calculations about 100 times faster. Researchers expect that supercomputers will be so fast in ten years time that they will be able to perform these calculations in one week.

Michel Philippens | alfa

More articles from Life Sciences:

nachricht Cryo-electron microscopy achieves unprecedented resolution using new computational methods
24.03.2017 | DOE/Lawrence Berkeley National Laboratory

nachricht How cheetahs stay fit and healthy
24.03.2017 | Forschungsverbund Berlin e.V.

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Giant Magnetic Fields in the Universe

Astronomers from Bonn and Tautenburg in Thuringia (Germany) used the 100-m radio telescope at Effelsberg to observe several galaxy clusters. At the edges of these large accumulations of dark matter, stellar systems (galaxies), hot gas, and charged particles, they found magnetic fields that are exceptionally ordered over distances of many million light years. This makes them the most extended magnetic fields in the universe known so far.

The results will be published on March 22 in the journal „Astronomy & Astrophysics“.

Galaxy clusters are the largest gravitationally bound structures in the universe. With a typical extent of about 10 million light years, i.e. 100 times the...

Im Focus: Tracing down linear ubiquitination

Researchers at the Goethe University Frankfurt, together with partners from the University of Tübingen in Germany and Queen Mary University as well as Francis Crick Institute from London (UK) have developed a novel technology to decipher the secret ubiquitin code.

Ubiquitin is a small protein that can be linked to other cellular proteins, thereby controlling and modulating their functions. The attachment occurs in many...

Im Focus: Perovskite edges can be tuned for optoelectronic performance

Layered 2D material improves efficiency for solar cells and LEDs

In the eternal search for next generation high-efficiency solar cells and LEDs, scientists at Los Alamos National Laboratory and their partners are creating...

Im Focus: Polymer-coated silicon nanosheets as alternative to graphene: A perfect team for nanoelectronics

Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are less stable. Now researchers at the Technical University of Munich (TUM) have, for the first time ever, produced a composite material combining silicon nanosheets and a polymer that is both UV-resistant and easy to process. This brings the scientists a significant step closer to industrial applications like flexible displays and photosensors.

Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are...

Im Focus: Researchers Imitate Molecular Crowding in Cells

Enzymes behave differently in a test tube compared with the molecular scrum of a living cell. Chemists from the University of Basel have now been able to simulate these confined natural conditions in artificial vesicles for the first time. As reported in the academic journal Small, the results are offering better insight into the development of nanoreactors and artificial organelles.

Enzymes behave differently in a test tube compared with the molecular scrum of a living cell. Chemists from the University of Basel have now been able to...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

International Land Use Symposium ILUS 2017: Call for Abstracts and Registration open

20.03.2017 | Event News

CONNECT 2017: International congress on connective tissue

14.03.2017 | Event News

ICTM Conference: Turbine Construction between Big Data and Additive Manufacturing

07.03.2017 | Event News

 
Latest News

Argon is not the 'dope' for metallic hydrogen

24.03.2017 | Materials Sciences

Astronomers find unexpected, dust-obscured star formation in distant galaxy

24.03.2017 | Physics and Astronomy

Gravitational wave kicks monster black hole out of galactic core

24.03.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>