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HPC APPLICATIONS: BIOMEDICINE


molecule is modelled in solution. ‘The relationships between the atoms are described within the force field and to simulate this requires a large number of computational hours. NGS provides the computational resources, without which it would be impossible to simulate these molecules over the timescale we’re looking at.’ Currently, simulations are 40ns in length – which, according to Husby, equates to several months of computation. To simulate one nanosecond of the dynamics takes around 48 hours on 16 CPUs using the NGS system. The project has been using NGS resources


for about a year and, up until now, the group has described the interactions over the course of the simulation. ‘The results from molecular dynamics provide much more information compared to a crystal structure obtained from X-ray crystallography, which is a static model,’ says Husby. ‘We obtained a number of structures over the course of the simulation and describe the interactions between them – therefore identifying which of the interactions are crucial, whether they occur over the entire simulation, their nature, whether the amino acid residues remain at a certain distance from each other or whether they are mobile. Based on these observations, because we know the important DNA residues involved in the interactions, we can develop a small molecule inhibitor that would target these interactions and weaken the interaction between the transcription factor and the DNA.’


Working in the Cave Researchers at Weill Cornell Medical College are also using molecular dynamic simulations, in this case to study the structure and mechanisms of action of neurotransmitter- transporter proteins. The simulations are calculated using supercomputers, and the resultant information is displayed in a 3D high definition Cave, powered by eight Christie three-chip Mirage DLP projectors. The Cave is housed in the David A. Cofrin Center for Biomedical Information facility at the HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine (ICB), Weill Cornell Medical College. It provides a resolution of 1,920 x 1,920 pixels per wall, allowing researchers to visualise their research in an immersive 3D environment.


Researchers are using the Cave for three general problems: volumetric reconstruction


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of sliced-based data including MRI, OCT, and confocal microscopy images; visualisation of protein structures and dynamics; and gene network visualisation.


‘One of the more interesting projects we’re doing now is creating interactive molecular dynamic simulations within the Cave,’ explains Vanessa Borcherding, systems administrator at the ICB. ‘This is a work in progress, but essentially what we’d be doing is taking protein and a small molecule or peptide that it is known to interact with, and trying to figure out the atomic level details of the interaction. This is done interactively, with a supercomputer working in the background to compute the effects of changes in geometry and orientation imposed by the researcher as he or she manipulates the system.’


In other projects, researchers are using the Cave to reconstruct scans of portions of the brain, looking specifically at MRI scans of children’s brains exposed to drug abuse while in utero. The aim is to determine the effects of such exposure on the development of specific structures in the brain, and what the behavioural and clinical effects of those changes are. The scans are put through a software pipeline developed by Dr Luis Gracia, assistant imaging technology engineer at the ICB, using an application called Free Surfer to automatically segment out the various structures in the brain. These


segmented images are transferred to the Cave for visualisation.


‘The data is comprised of a number of slices,’ explains Borcherding. ‘Radiologists used to handling the images can look through slices of MRI or CT data and are able to, thanks to their training, reconstruct these models in their heads. What this technology is allowing us to do is to give people that don’t have that training the ability to see and interact with the thing they’re studying, and to quantify its geometry in a consistent manner.’


It is hoped that the study will lead to objective assessments of the risk of developmental issues that are associated with prenatal drug exposure, which can act along with medical histories taken from the mother. The Cave is also being used to visualise 2D confocal microscope images to investigate iron trafficking within the cell, as well as reconstructions of retinal tissues from images acquired using Optical Coherence Tomography (OCT). Dr Szilard Kiss of the Department of Ophthalmology is looking at visualising various dismorphologies of the retina, particularly those that result in the formation of cystic spaces in the tissue. This is the first time some of these morphologies have been visualised from living tissues and quantified using immersive 3D technologies. ‘You can try to build these models in a 2D display and you can even do 3D modelling





Weill Cornell Medical College staff inside its 3D HD Cave, which is powered by eight Christie projectors. From left to right: Jason Banfelder, assistant professor and technology engineer; Vanessa Borcherding, systems administrator; and Dr Luis Gracia, assistant imaging technology engineer. Image courtesy of Dr Luis Gracia


SCIENTIFIC COMPUTING WORLD OCTOBER/NOVEMBER 2010


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