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.