Principal Investigator
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Project Title
| Linear-scaling Ab-Initio Computations of Model Protein Systems the Potassium Channel and Citrate Synthase |
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Brief Description for General Publications
Over the last few years significant advances have been made to develop quantum chemical methods for which the computational time scales linearly with the number of atoms in the system. This project attempts to use these new algorithms in the study of two biologically significant systems, namely the potassium ion channel and the enzyme citrate synthase. Ion channels are responsible for the selective transport of ions across cell membranes, and our aim is to investigate the electrostatic potential inside this system. Citrate synthase catalyzes the condensation of oxaloacetate and an acetyl group attached to the acetyl-coenzyme A. This reaction is an essential step in the Kreb cycle for oxidation of fuel molecules. Use of the APAC National Facility is required since although the basic algorithms are linear scaling the threshold for on set of linear scaling is large. That is to reach systems of a size where linear scaling algorithms become applicable still requires substantial computational effort. Moreover computations on systems of this size require the large memory and disk available on the APAC National Facility. Our work, as well as improving the basic understanding of two biologically important systems, will also involve substantial further development and parallelization of the basic linear scaling electronic structure codes. This is expected to be of widespread benefit beyond this immediate project. |