Name: Rebeca Garcia Fandino
Institution: University of Oxford
Research: Simulating carbon nanotubules on the NGS
Carbon nanotubes (CNTs) are considered unique materials with very promising future applications especially in the field of nanotechnology, nanoelectronics, and composite materials. However they have poor solubility therefore limiting their application within these fields. For example, to be used in the pharmaceutical industry they need to be able to be ingested and absorbed by the human body, and to do so, they need to be soluble.
One of the most efficient ways of improving CNTs’ solubility has been by adding a functional group to their surface. These modifications can alter the inherent properties of the tube, which opens the possibility to explore new materials made from CNT’s with latent and new characteristics. These can be very different from those of unmodified CNTs facilitating the development of novel biotechnology, biomedicine, and bioengineering advances.
Rebeca’s research aims to gain insight into how adding functional groups to CNTs affects the inherent properties of the tube and how it changes their dynamical behaviour and transport properties, studying their interaction with water, ions and a lipid bilayer through Molecular Dynamics simulations.
The studied systems consist of different (14, 14) carbon nanotubes with several different chemical groups attached to the inner cavity of the pore at different positions (the central part and the edge of the channel), inserted separately in a bilayer and immersed into solvated with different aqueous solutions. Rebeca simulated these systems using all-atom molecular dynamic simulations (MD) using the Gromacs package and the Amber parameters on the NGS.
Besides the equilibrium MD simulations, Rebeca is also carrying Potential of Mean Force (PMF) to qualitatively and quantitatively measure how the adding a functional group to the internal cavity of the pore affects the energy necessary for an ion to cross it.
Representation of one of the CNTs studied inserted into a lipid bilayer and solvated with NaCl 1M (a) and representation of the region of the channel explored with the PMF calculations (b).
The size of each simulated system is about 138.000 atoms, which requires a great amount of computational time. The PMF calculations require MD simulations for 100 subsequent points in the z axis of the channel, which multiplied by each one of the systems and each one of the ions led to 1600 calculations using 2 processors for each one of them, which would translate to more than 300.000 hours needed for the simulation of only 1 ns for each one of the 100 points explored in each system.
Rebeca explained that “The large amount of calculations required constitute a very obvious reason for the necessity of high supercomputing capabilities for carrying out this project. The NGS can provide these facilities, and we are very satisfied from the benefit we are obtaining from these resources to make this project real”.
The NGS was essential for Rebeca’s research as “Carrying all these calculations on local computers would collapse the queues, since the number of jobs to run is really high (1600 calculations using 2 processors for each one of them). Local clusters are usually used by several users, and each user has a limit of jobs to be executed at the same time. So, the time for running jobs and waiting queues in a local cluster would transform this investigation into a practically inaccessible project”.
Project funding - BBSRC and the Spanish Government (Programa José Castillejo)
Project PI - Prof. Mark Sansom
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