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Primeur weekly 2013-07-01

Special

A decade of HPC in evolution - Thomas Sterling takes the stage as the Charles Darwin of supercomputing ...

The Cloud

Cloud Summer School 2013 - Final Call for Participation ...

EuroFlash

Atos wins contract for the second most powerful supercomputer in Spain ...

Eurotech, University of Regensburg and University of Wuppertal sign co-operation agreement for QPACE2 ...

Eurotech supercomputers Eurora and Aurora Tigon score first and second place in the Green500 list ...

Projectiondesign to amaze visitors to Kennedy Space Center Visitor Complex's newest attraction - Space Shuttle Atlantis ...

Towards a Second EUDAT Roadmap of common services ...

Grants available for Europeans to attend the 2nd RDA plenary meeting ...

Cray awarded supercomputer contract from the European Centre for Medium-Range Weather Forecasts (ECMWF) ...

Programming model for supercomputers of the future ...

Allinea tools to help Professor Stephen Hawking's Consortium get more Bang from COSMOS ...

Researchers unmask Janus-faced nature of mechanical forces with the Julich supercomputer ...

SPEX Group announces Scotland's fastest growing young company doubles turnover ...

IBM harnesses power of Big Data to improve Dutch flood control and water management systems ...

USFlash

13th edition of the Green500 List to make use of new energy measurement methodologies ...

GPU-accelerated SGI servers enable Department of Geosciences at Princeton University to simulate seismic activity in record time ...

Clemson supercomputer is 5th among U.S. universities ...

University of Florida lands $8 million federal award for supercomputing research ...

China shocks the supercomputer community again with HUST's HPL Championship at ISC'13 ...

Understanding a novel enzyme from a family of marine crustaceans may bolster biofuels development ...

NVIDIA Tesla GPU accelerators power world's most energy efficient supercomputer ...

Researchers use TACC supercomputers to simulate orbital debris impacts on spacecraft and fragment impacts on body armour ...

Purdue builds nation's fastest campus supercomputer - again ...

Sequoia tops Graph 500 list of 'Big Data' supercomputers ...

New project aims to make New York's Lake George the "smartest lake" in the world ...

Lawrence Livermore's Vulcan brings 5 petaflops computing power to collaborations with industry and academia to advance science and technology ...

SDSC GeoComputing Lab named Winner of HPC Innovation Excellence Award by IDC ...

Researchers unmask Janus-faced nature of mechanical forces with the Julich supercomputer


P. Dopieralski, D. Marx
17 Jun 2013 Bochum - The harder you pull, the quicker it goes. At least, that used to be the rule in mechanochemistry, a method that researchers apply to set chemical reactions in motion by means of mechanical forces. However, as chemists led by Professor Dominik Marx, Chair of Theoretical Chemistry at the Ruhr-Universität Bochum (RUB) now report in the journalNature Chemistry, more force cannot in fact be translated one to one into a faster reaction. With complex molecular dynamic simulations on the Jülich supercomputer "JUQUEEN" they unmasked the Janus-faced nature of mechanochemistry. Up to a certain force, the reaction rate increases in proportion to the force. If this threshold is exceeded, greater mechanical forces speed up the reaction to a much lesser extent.

In order to activate chemical reactions, an energy barrier first has to be overcome. This energy can, for example, be supplied in the form of mechanical forces that "distort" the molecules involved. In order to achieve that experimentally, two long polymer chains are attached to the molecule. These chains serve as ropes to stretch the molecule either using a force microscope or by radiating the solution with ultrasound. Until now it was assumed that the energy barrier decreases steadily, the more mechanical energy is put into the molecule. This hypothesis has now been refuted by the RUB-chemists. The key to success was a particularly complex form of computer simulation, the so-called ab initio molecular dynamics method, which they could only master on Europe's currently fastest computer at the Jülich Supercomputing Centre within the framework of a "Gauss Large Scale" project.

The RUB team was looking at a small molecule with a disulfide bond, i.e. two sulphur atoms bound to each other, as a computational model in the "virtual laboratory". "This molecule represents - in an extremely simplified fashion - the corresponding chemically reactive centre in proteins", stated Dominik Marx. In the course of the reaction, the sulphur bridge is cleaved. The harder the chemists pull on the molecule, i.e. the more they distort the molecular structure, the faster the cleavage happens - but only up to a mechanical force of approximately 0.5 nanonewtons. Forces above ca. 0.5 nanonewtons accelerate the reaction significantly less than forces below this threshold.

The Bochum team could explain this effect based on the relative position of the individual molecular building blocks to each other. During the reaction, a negatively charged hydroxide ion (OH-) from the surrounding water attacks the sulphur bridge of the virtual protein. At forces above approximately 0.5 nanonewtons, however, the protein is already distorted to such an extent that the hydroxide ion can no longer reach the sulphur bridge without difficulties. The application of the force thus blocks the access, which increases the energy barrier for the reaction. This can only be reduced again by an even greater mechanical force. In the next step, the researchers investigated the blockade mechanism on more complex models, including a large protein fragment, similar to previous experiments. "The Janus mechanism explains puzzling and controversial results of previous force-spectroscopy measurements on the protein titin, which is found in muscles", stated Prof. Marx.

"Around the world, several theory groups have already tried to explain this experimentally observed phenomenon", stated Prof. Marx. "It was crucial to correctly take into account the role of the solvent, which is water in the present case." The hydroxide ion that attacks the sulphur bridge is surrounded by a shell of water molecules, which changes over the course of the attack in a complex way. The experimentally observed effects can only be correctly treated in the "virtual lab" when these so-called de- and re-solvation effects are accounted for included in the simulation as the reaction goes on. However, theorists usually resort to methods that drastically simplify the effects of the surrounding water - microsolvation and continuum solvation models - in order to reduce the computational cost.

The German Research Foundation (DFG) funded the study through what is so far the only "Reinhart Koselleck" project in the field of chemistry. In addition, the Cluster of Excellence "Ruhr Explores Solvation" (RESOLV, EXC 1069) has supported these studies since approval of the DFG in 2012. The project was only possible due to allocated computing time on the IBM Blue Gene/Q parallel computer JUQUEEN at the Jülich Supercomputing Centre. There, the Gauss Centre for Supercomputing (GCS) provided a large part of the total computation time within the framework of a "GCS Large Scale" project.

The paper titled "The Janus-faced role of external forces in mechanochemical disulfide bond cleavage" is written by P. Dopieralski, J. Ribas-Arino, P. Anjukandi, M. Krupicka, J. Kiss, D. Marx. It appears inNature Chemistry, DOI: 10.1038/nchem.1676.

Source: Ruhr-Universität Bochum

Back to Table of contents

Primeur weekly 2013-07-01

Special

A decade of HPC in evolution - Thomas Sterling takes the stage as the Charles Darwin of supercomputing ...

The Cloud

Cloud Summer School 2013 - Final Call for Participation ...

EuroFlash

Atos wins contract for the second most powerful supercomputer in Spain ...

Eurotech, University of Regensburg and University of Wuppertal sign co-operation agreement for QPACE2 ...

Eurotech supercomputers Eurora and Aurora Tigon score first and second place in the Green500 list ...

Projectiondesign to amaze visitors to Kennedy Space Center Visitor Complex's newest attraction - Space Shuttle Atlantis ...

Towards a Second EUDAT Roadmap of common services ...

Grants available for Europeans to attend the 2nd RDA plenary meeting ...

Cray awarded supercomputer contract from the European Centre for Medium-Range Weather Forecasts (ECMWF) ...

Programming model for supercomputers of the future ...

Allinea tools to help Professor Stephen Hawking's Consortium get more Bang from COSMOS ...

Researchers unmask Janus-faced nature of mechanical forces with the Julich supercomputer ...

SPEX Group announces Scotland's fastest growing young company doubles turnover ...

IBM harnesses power of Big Data to improve Dutch flood control and water management systems ...

USFlash

13th edition of the Green500 List to make use of new energy measurement methodologies ...

GPU-accelerated SGI servers enable Department of Geosciences at Princeton University to simulate seismic activity in record time ...

Clemson supercomputer is 5th among U.S. universities ...

University of Florida lands $8 million federal award for supercomputing research ...

China shocks the supercomputer community again with HUST's HPL Championship at ISC'13 ...

Understanding a novel enzyme from a family of marine crustaceans may bolster biofuels development ...

NVIDIA Tesla GPU accelerators power world's most energy efficient supercomputer ...

Researchers use TACC supercomputers to simulate orbital debris impacts on spacecraft and fragment impacts on body armour ...

Purdue builds nation's fastest campus supercomputer - again ...

Sequoia tops Graph 500 list of 'Big Data' supercomputers ...

New project aims to make New York's Lake George the "smartest lake" in the world ...

Lawrence Livermore's Vulcan brings 5 petaflops computing power to collaborations with industry and academia to advance science and technology ...

SDSC GeoComputing Lab named Winner of HPC Innovation Excellence Award by IDC ...