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Miroslav Hodak

Research Assistant Professor


Miroslav Hodak received his PhD from the University of Pennsylvania in 2002. He then came to North Carolina State University for his postdoctoral research and in 2008 he became a Research Assistant Professor.

His current research involves using large-scale computer simulations to understand behavior of biological systems. This includes metal-protein interactions, enzymatic mechanisms, bio-sensing and transport properties of biomolecules. He is also one of the main developers of RMG, a high performance density functional (DFT) code available at

He has developed a new DFT-based method for simulation of fully solvated biomolecules, which has been selected for the 2001-2009 Breakthrough Report of DoE's SciDAC program. An application to copper binding to prion protein (PrP), a protein playing the key role in “mad cow disease”, predicted roles of the metal in diseased and normal forms of the protein. Another application investigated interaction between copper and α-synuclein (aS), the protein implicated in Parkinson’s disease. It was found that copper causes structural changes in the protein, leading to development of β-sheets, which are the hallmark of Parkinson’s. Based on this, a mechanism for copper-induced onset of the disease was proposed. Current projects include transport properties of DNA and sensing of biomolecules and enzymes using nanotube-based nanocircuits.

Select Publications

Y. Li, M. Hodak, W. Lu, J Bernholc, Nanoscale 9, 1687-1698 (2017),
"Selective sensing of ethylene and glucose using carbon-nanotube-based sensors: an ab initio investigation"

Y. Li, M. Hodak, W. Lu, J Bernholc, Carbon 101, 177-183 (2016),
"Mechanisms of NH 3 and NO 2 detection in carbon-nanotube-based sensors: An ab initio investigation"

Y. Li, M. Hodak, J. Bernholc, ACS Biochemistry54, 1233 (2015),
"Enzymatic Mechanism of Copper-Containing Nitrite Reductase"

S. Moore, E. L. Briggs, M. Hodak, W. Lu, J. Bernholc, and C. W. Lee, Proceedings of the Extreme Scaling Workshop (2011),
"Scaling the RMG Quantum Mechanics Code"

F. Rose, M. Hodak, and J. Bernholc, Nature Scientific Reports 1, 11 (2011),
"Mechanism of copper(II)-induced misfolding of Parkinson's disease protein"

M. Hodak and J. Bernholc, Prion4, 13 (2010),
"Insights into prion protein function from atomistic simulations" (invited perspective and cover)

M. Hodak, R. Chisnell, W. Lu, and J. Bernholc, Proc. Nat. Acad. Sci. 106, 11576 (2009),
"Functional implications of multistage copper binding to the prion protein."

J. Bernholc, M. Hodak and W. Lu, J. Phys. Cond. Matt20, 294205 (2008),
"Recent developments and applications of the real-space multigrid method"

M. Hodak, W. Lu, and J. Bernholc, J. Chem. Phys.128, 014101 (2008),
"Hybrid ab initio Kohn-Sham DFT/frozen-density orbital-free DFT simulation method suitable for biological systems"

M. Hodak, S. Wang, W. Lu and J. Bernholc, Phys. Rev. B, 76, 085108 (2007),
"Implementation of ultrasoft pseudopotentials in large-scale grid-based electronic structure calculations"

L.A. Girifalco, M. Hodak and R.S. Lee, Phys. Rev. B, 62, 13104 (2000),
"Carbon nanotubes, buckyballs, ropes, and a universal graphitic potential"