ORNL's Jeremy Smith collaborated on devising a method -- dynamical fingerprints --that reconciles the different signals between experiments and computer simulations to strengthen analyses of molecules in motion. The research will be published in the Proceedings of the National Academy of Sciences.
"Experiments tend to produce relatively simple and smooth-looking signals, as they only 'see' a molecule's motions at low resolution," said Smith, who directs ORNL's Center for Molecular Biophysics and holds a Governor's Chair at the University of Tennessee. "In contrast, data from a supercomputer simulation are complex and difficult to analyze, as the atoms move around in the simulation in a multitude of jumps, wiggles and jiggles. How to reconcile these different views of the same phenomenon has been a long-standing problem."
The new method solves the problem by calculating peaks within the simulated and experimental data, creating distinct "dynamical fingerprints." The technique, conceived by Smith's former graduate student Frank Noe, now at the Free University of Berlin, can then link the two datasets.
Supercomputer simulations and modeling capabilities can add a layer of complexity missing from many types of molecular experiments.
"When we started the research, we had hoped to find a way to use computer simulation to tell us which molecular motions the experiment actually sees," Smith said. "When we were finished we got much more - a method that could also tell us which other experiments should be done to see all the other motions present in the simulation. This method should allow major facilities like the ORNL's Spallation Neutron Source to be used more efficiently."
Combining the power of simulations and experiments will help researchers tackle scientific challenges in areas like biofuels, drug development, materials design and fundamental biological processes, which require a thorough understanding of how molecules move and interact.
"Many important things in science depend on atoms and molecules moving," Smith said. "We want to create movies of molecules in motion and check experimentally if these motions are actually happening."
View a supercomputer simulation of a protein in motion here: http://www.ornl.gov/ornlhome/hg_mer.htm
"The aim is to seamlessly integrate supercomputing with the Spallation Neutron Source so as to make full use of the major facilities we have here at ORNL for bioenergy and materials science development," Smith said.
The collaborative work included researchers from L'Aquila, Italy, Wuerzburg and Bielefeld, Germany, and the University of California at Berkeley. The research was funded in part by a Scientific Discovery through Advanced Computing grant from the DOE Office of Science.
ORNL is managed by UT-Battelle for the Department of Energy's Office of Science.
Morgan McCorkle | EurekAlert!
Cutting edge research for the industries of tomorrow – DFKI and NICT expand cooperation
21.03.2017 | Deutsches Forschungszentrum für Künstliche Intelligenz GmbH, DFKI
Molecular motor-powered biocomputers
20.03.2017 | Technische Universität Dresden
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...
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...
In the eternal search for next generation high-efficiency solar cells and LEDs, scientists at Los Alamos National Laboratory and their partners are creating...
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...
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...
20.03.2017 | Event News
14.03.2017 | Event News
07.03.2017 | Event News
24.03.2017 | Materials Sciences
24.03.2017 | Physics and Astronomy
24.03.2017 | Physics and Astronomy