This page contains a Flash digital edition of a book.

This content requires Macromedia Flash Player version 8 or later. Get Flash.

If you believe you do have Macromedia Flash Player version 8 or later installed, there is a problem with your Flash installation and we were unable to detect it. Please follow the solution in Adobe TechNote 7d1862a to resolve this issue.

Attempt to view the Digital Edition anyway.
Always attempt to Digital Edition content anyway (sets a cookie)

HPC APPLICATIONS: BIOMEDICINE


Simulating biology


Greg Blackman looks at some of the applications using HPC in the field of biomedicine


Images of the retina acquired with an OCT scanner and displayed inside Weill Cornell Medical College’s high-definition visualisation Cave. Image courtesy of Dr Luis Gracia, assistant imaging technology engineer at Weill Cornell


T


he complexity of biological systems means more researchers are turning to computing to better understand the


processes involved in biological pathways. Conducting experiments in silico will in no way replace hard actual biological research, whether that’s at the level of the cell or the organism, but it does guide researchers in the direction their work should take. At the University of London, the Cancer Research UK Protein-Protein Interactions Drug Discovery Research Group and the Biomolecular Structure Group within the School of Pharmacy are involved in a project modelling STAT transcription factors, believed to be instrumental in cancer signalling pathways.


The work revolves around molecular dynamic simulations of protein-protein and protein-DNA interactions, for which the National Grid Service (NGS) provides


22


computational time. Jarmila Husby, a researcher working on the project, explains: ‘We are hoping to see some conformational changes in the protein-DNA complex – how the transcription factor interacts with the DNA, what the nature of the conformational changes is, if there are any changes, and how it affects the function. Based on those simulations, the group will try and design potential small molecule inhibitors for these interactions to stop or limit the signalling process leading to cancer development.’ The transcription factors are important for cell development processes, but studies show that the proteins are overproduced in many types of cancer. Both proteins and DNA are large molecules and cannot be investigated as rigid bodies. Molecular dynamics allow these molecules to be understood better. Molecular dynamic simulations can be used to understand the physical basis of the


SCIENTIFIC COMPUTING WORLD OCTOBER/NOVEMBER 2010


structure and function of biomolecules, such as proteins and nucleic acids. Within an MD simulation, molecules and atoms are allowed to interact according to known laws of physics, thereby giving an indication of the motion of the molecules over time. An important part of the simulation is the ‘force field’, which describes the interactions between the atoms within the molecules. A large protein or DNA molecule consists of many atoms and the computer simulation has to be able to describe the relationships and interactions between individual atoms. The simulation applies this force field to model the dynamics of the biomolecules and their conformational changes at the full atomistic scale of the complete biomolecular complex. ‘The biomolecular systems are very large,’


comments Husby, adding that the complex has 250,000 atoms and, in order to make the simulation as realistic as possible, the


www.scientific-computing.com


Page 1  |  Page 2  |  Page 3  |  Page 4  |  Page 5  |  Page 6  |  Page 7  |  Page 8  |  Page 9  |  Page 10  |  Page 11  |  Page 12  |  Page 13  |  Page 14  |  Page 15  |  Page 16  |  Page 17  |  Page 18  |  Page 19  |  Page 20  |  Page 21  |  Page 22  |  Page 23  |  Page 24  |  Page 25  |  Page 26  |  Page 27  |  Page 28  |  Page 29  |  Page 30  |  Page 31  |  Page 32  |  Page 33  |  Page 34  |  Page 35  |  Page 36  |  Page 37  |  Page 38  |  Page 39  |  Page 40  |  Page 41  |  Page 42  |  Page 43  |  Page 44  |  Page 45  |  Page 46  |  Page 47  |  Page 48  |  Page 49  |  Page 50  |  Page 51  |  Page 52  |  Page 53  |  Page 54  |  Page 55  |  Page 56
Produced with Yudu - www.yudu.com