January 07, 2010 Thursday 15:30
Uğur Akgün, University of Iowa
Tale of Two Kingdoms: Subatomic and Molecular

This presentation targets general audience and aims to give highlights from recent studies of the speaker on two different research areas; Experimental High Energy Physics and Computational Biophysics. Part 1: CMS Hadronic Calorimeter Upgrade Studies for SuperLHC The Large Hadron Collider (LHC) performed observed its long waited first collisions on Nov 23, 2009. Now the world is waiting for the data that will open the doors of new physics, and the four LHC experiments are getting ready for 14 TeV collisions. This unprecedented quest for discovery requires constant upgrade studies on the detectors of each experiment. The Compact Muon Solenoid (CMS) is a general-purpose detector designed to run at the highest luminosity provided by the CERN LHC. The CMS Hadronic Endcap and Hadronic Forward calorimeters cover the pseudorapidity range of from 1.4 to 5 on both sides of the CMS detector, contributing to superior jet and missing transverse energy resolutions. However these hadronic calorimeters are far from being perfect. HF calorimeters require short term upgrade plan to eliminate abnormally high amplitude signals due to punch through charged particles, mostly muons, producing Cherenkov photons at the PMT window. We also need to address the radiation damage problems of HE calorimeters as the LHC increases peak luminosity to 1035cm-2s-1 in near future. Here we present the results from the R&D studies as well as discussing the proposed and long term upgrade scenarios for both calorimeters. Part 2: Molecular Dynamic Simulations on Membrane Proteins As the computational capabilities increase, the mechanisms of biologically important membrane proteins increasingly become more popular research topics. The fact that more than 50% of drug designs are based on membrane proteins is enough to emphasize their importance. The transport of ammonia, fundamental to the nitrogen metabolism in all domains of life, is regulated by the Rh/Amt/MEP membrane protein superfamily. The first structure of this family, AmtB from E.Coli shows a pathway for ammonia that includes two vestibules connected by a long and narrow hydrophobic lumen. The proposed mechanism for AmtB is to recruit NH4+ and conduct neutral NH3 by deprotonation of NH4+ at the end of periplasmic vestibule. Here we present the results of more than 500 ns of Molecular Dynamic (MD) simulations, utilizing various computational biophysics techniques, to determine the mechanism of substrate selectivity and conduction in the ammonia channels. Our detailed study reveals that the AmtB periplasmic vestibule prefers NH4+ over NH3 and CO2, and the rate of ammonia conduction is regulated by the motion of the phenyl rings at the bottom of the vestibule. We also report that the conserved D160 is essential for substrate conduction by stabilizing the NH4+ at the recruitment site through charge interactions.