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Department of Chemistry Aurora Clark Group

Dr. Mustafa Kucukkal

Ph.D., Physical Chemistry (Computational) Clemson University, Clemson, SC 2014
Master of Science degree in Analytical Chemistry Bilkent University, Ankara, Turkey, 2001
Bachelor of Science degree in Chemistry Bilkent University, Ankara, Turkey, 1998

Currently, I am studying the effect of porosity of MOF pore on the energetics and dynamics of solvent adsorption on the pore surface and solvent organization in the pore.

Research Experience 
Parametrization of AIREBO Potential to Simulate Hydrofluorocarbons

The Adaptive Interactive Empirical Bond Order Potential (AIREBO), a reactive MD potential, was entirely reparameterized to incorporate F atoms. The empirical parameters are fitted to properties obtained by experiments or high-level quantum mechanical calculations. In addition, the AIREBO was made fully polarizable, i.e. the charges change depending on the change in their environment.

Carbon Nanotube Welding by Ar Bombardment

Cross junction of two single wall carbon nanotubes (SWCNTs) placed on an imaginary Lennard-Jones surface perpendicular to each other was bombarded by Ar atoms. The successive bombardments were performed through MD using the AIREBO potential. The optimum experimental conditions such as CNT types, annealing time and temperature and impact energy of Ar atom.

Translocation of ssDNA through Nanopores
Translocation of single stranded (ss) DNA through nanopore under an electric potential has been studied by Monte Carlo simulation using Brownian Dynamics.

1. Kucukkal MU, Stuart SJ, “Single Walled Carbon Nanotube (SWNT) Welding through Ar Bombardment” to be sent to J Physical Chemistry (In submission)

2. Kucukkal MU, Stuart SJ, “Reparameterization and Fully Polarizable Model of AIREBO to Incorporate F Atom”, (In Preparation)

3. Kantcheva M, Kucukkal MU “Identification, Stability, and Reactivity of NOx Species Adsorbed on Titania-Supported Manganese Catalysts” J. Catal. 204 (2001) 479-494.

4. Kantcheva M, Kucukkal MU, Suzer S, “Spectroscopic Investigation of Species Arising from CO Chemisorption on Titania-Supported Manganese” J. Catal. 190 (2000) 144-156.

Conferences and Professional Experience 

1. Presenter, South East American Chemical Society Meeting (SERMACS), Nashville, TN, October 2014

2. Participant, Multiscale Theory and Simulation Workshop (Coarse graining, QM/MM Protein Design, Advanced Sampling), University of Chicago, June 2013

3. Participant, CAMS Summer School on Simulation of Complex Microstructure in Materials, Gainesville, FL, May 2012

4. Presenter, Modeling Advanced Materials, Systems Biology and Alternative Energy Sources Workshop, Knoxville, TN, October 2011

5. Participant, OTEI Workshop: For Graduate Students: Finding Research Funding Opportunities Tailored to Your Needs, Clemson, SC, March 2011

6. Presenter, Southeast Theoretical Chemistry Association (SETCA) Conference, Columbia, SC, May 2010

7. Participant, Modeling of Ion Channels Workshop, University of Pittsburgh, 2004

8. Presenter, 4th European Congress on Catalysis Catalysis and Chemical Technologies for a Sustainable Future, Rimini, Italy, 1999

9. Presenter, EUCMOS XXIV, Prague, Chezh Republic ,1998