Crowdsourcing the phase problem

Jun 17, 2014 by Jonathan Agbenyega
This is an overlay of electron-density maps calculated from the final crowdsourced phase solutions and the true phases for the two test cases. Credit: Jorda et al./International Union of Crystallography

Compared with humans, computers have the capacity to solve problems at much greater speed. There are many problems, however, where computational speed alone is insufficient to find a correct or optimal solution, for example because the parameter "space" cannot be fully searched in a practical time. In contrast, the human mind can formulate expert knowledge specific for particular problems, providing a capacity to guide more efficient searches, although with more limited processing speed.

The power of the human contribution can be multiplied through the efforts of a greater number of individuals. The term `', which combines the two domains of human and electronic computing, was coined in 2006 and since then has seen its definition broadened to a wide range of activities involving a network of people.

A challenging problem that might benefit from crowdsourcing is the phase problem in X-ray crystallography. Retrieving the phase information has plagued many scientists for decades when trying to determine the crystal structure of a sample.

In a diffraction experiment, the observed diffraction pattern allows measurement of the amplitudes of the reflection structure factors (as the square root of the intensities) but not their phases. The amplitudes and phases are both needed to reconstruct an electron-density map (by Fourier synthesis) so that a model of the crystallized molecule can be obtained.

There are a number of ways currently scientists try to solve the phase problem, all with varying degrees of success.

Regardless of the particular approach, most attacks on the phase problem can be viewed as having two sub-problems. One concerns how a high-dimensional space (i.e. of phases) can be efficiently searched, while the other concerns how a good solution can be recognized.

Crowdsourcing may be a route to solving these sub-problems [Jorda et al. (2014), Acta Cryst. D70, 1538-1548; doi:10.1107/S1399004714006427 ], here scientists have developed a game based on a genetic algorithm (a powerful search-optimization technique), where players control the selection mechanism during the evolutionary process (by recognising the good solutions). The algorithm starts from a population of "individuals", in this case a map prepared from a random set of phases, and tries to cause the population to evolve towards individuals with better phases based on Darwinian survival of the fittest. Players apply their pattern-recognition capabilities to evaluate the electron-density maps generated from these sets of phases and to select the fittest individuals.

The game called CrowdPhase was applied to two synthetic low-resolution phasing puzzles and it was shown that players could successfully obtain phase sets in the 30 degree phase error range and corresponding molecular envelopes showing agreement with the low-resolution models.

Successful preliminary studies suggest that with further development the crowdsourcing approach could fill a gap in current crystallographic methods by making it possible to extract meaningful information in cases where limited resolution might otherwise prevent initial phasing.

Explore further: Melting an entire iceberg with a hot poker: Spotting phase changes triggered by impurities

Related Stories

A new approach for solving protein structures

Sep 06, 2012

(Phys.org)—Using synchrotron x-ray beams to solve the molecular structures of proteins and other large biological molecules has yielded many advances in medicine, such as drug therapies for cancer. Improvements ...

Thermotropic phase boundaries in classic ferroelectrics

Feb 04, 2014

(Phys.org) —Novel monoclinic subphases in ferroelectric BaTiO3 were observed by ANL's Center for Nanoscale Materials users from The Pennsylvania State University in collaboration with CNM's X-Ray Microscopy ...

Recommended for you

Pseudoparticles travel through photoactive material

Apr 23, 2015

Researchers of Karlsruhe Institute of Technology (KIT) have unveiled an important step in the conversion of light into storable energy: Together with scientists of the Fritz Haber Institute in Berlin and ...

From metal to insulator and back again

Apr 22, 2015

New work from Carnegie's Russell Hemley and Ivan Naumov hones in on the physics underlying the recently discovered fact that some metals stop being metallic under pressure. Their work is published in Physical Re ...

Electron spin brings order to high entropy alloys

Apr 22, 2015

Researchers from North Carolina State University have discovered that electron spin brings a previously unknown degree of order to the high entropy alloy nickel iron chromium cobalt (NiFeCrCo) - and may play ...

Expanding the reach of metallic glass

Apr 22, 2015

Metallic glass, a class of materials that offers both pliability and strength, is poised for a friendly takeover of the chemical landscape.

Electrons move like light in three-dimensional solid

Apr 22, 2015

Electrons were observed to travel in a solid at an unusually high velocity, which remained the same independent of the electron energy. This anomalous light-like behavior is found in special two-dimensional ...

Quantum model helps solve mysteries of water

Apr 20, 2015

Water is one of the most common and extensively studied substances on earth. It is vital for all known forms of life but its unique behaviour has yet to be explained in terms of the properties of individual ...

User comments : 0

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.