Mark E. Tuckerman

Professor of Chemistry
B.S., University of California at Berkeley; Ph.D., Columbia University; Postdoctoral fellow, IBM Forschungs-laboratorium, Zürich, Switzerland; NSF Postdoctoral fellow, Department of Chemistry, University of Pennsylvania, Philadelphia, PA.

Email:
Phone: 212-998-8471
Office: Silver Center, 100 Washington Square East, Room 1001L
Personal Homepage

Areas of Research/Interest
Theoretical chemistry: ab initio molecular dynamic simulations and statistical mechanics

Research Description
Modern theoretical methods combined with advanced scientific computing have transformed our ability to perform modeling and simulation studies of key processes in chemistry, nanoscience, and biology that generate realistic results with full atomic resolution. The research efforts in my group are focused on advancing this emerging capability and applying it to chemically important problems. Currently, we are investigating how protons are transported through various hydrogen-bonded media (water, liquid and solid acids, acid hydrates, and doped salt crystals) with an eye toward understanding and designing materials for proton-exchange membranes in fuel cells. These studies employ the method of ab initio molecular dynamics, in which the finite-temperature dynamics of a system is generated via electronic structure calculations performed “on the fly”. Using this approach, we are also studying how organic molecules attach to semiconducting surfaces. Finally, we are developing ! new approaches for conformational sampling in complex systems such as biomolecules and crystalline polymorphs.

Publications
"On the connection between proton transport, structural diffusion, and reorientation of the hydrated hydroxide ion as a function of temperature", Z. Ma and M. E. Tuckerman , Chem. Phys. Lett. 511:117 (2011).

"On the Use of the SiC(100)-c(2 x 2) Surface as a Substrate for the Creation of Ordered Organic-Semiconductor Interfaces", Y. L. Zhang and M. E. Tuckerman, J. Phys. Chem. Lett. 2:1814 (2011).

"Temperature-Accelerated Method for Exploring Polymorphism in Molecular Crystals Based on Free Energy", T. Q. Yu and M. E. Tuckerman, Phys. Rev. Lett. 107:015701 (2011).

"Enhanced Conformational Sampling of Peptides via Reduced Side-Chain and Solvent Masses", I. -C. Lin and M. E. Tuckerman, J. Phys. Chem. B 114:15935 (2010).

"A statistical mechanical theory of proton transport kinetics in hydrogen-bonded networks based on population correlation functions with applications to acids and bases", M. E. Tuckerman, A. Chandra, and D. Marx, J. Chem. Phys. 133:124108 (2010).

"Enol Tautomers of Watson-Crick Base Pair Models Are Metastable Because of Nuclear Quantum Effects", A. Perez, M. E. Tuckerman, H, P. Hjalmarson, and O. A. von Lilienfeld, J. Am. Chem. Soc. 132:11510 (2010).

"Aqueous Basic Solutions: Hydroxide Solvation, Structural Diffusion, and Comparison to the Hydrated Proton", D. Marx, A. Chandra, and M. E. Tuckerman, Chem. Rev. 110:2174 (2010).

"Concerted Hydrogen-Bond Dynamics in the Transport Mechanism of the Hydrated Proton: A First-Principles Molecular Dynamics Study", T. C. Berkelbach, H. S. Lee, and M. E. Tuckerman, Phys. Rev. Lett. 103:238302 (2009).

"Hydroxide anion at the air-water interface", C. J. Mundy, I. F. W. Kuo, M. E. Tuckerman, H. S. Lee, and D. J. Tobias, Chem. Phys. Lett. 481:2 (2009).

"Ab Initio Molecular Dynamics Studies of the Liquid-Vapor Interface of an HCl Solution", H. S. Lee and M. E. Tuckerman, J. Phys. Chem. A 113:2144 (2009).

"Dynamical spatial warping: A novel method for the conformational sampling of biophysical structure", P. Minary, M. E. Tuckerman, and G. J. Martyna, SIAM J. Sci. Comput. 30:2055 (2008).

"Connecting solvation shell structure to proton transport kinetics in hydrogen-bonded networks via population correlation functions", A. Chandra, M. E. Tuckerman, and D. Marx, Phys. Rev. Lett. 99:145901 (2007).

“Structure of liquid water at ambient temperature from ab initio molecular dynamics performed in the complete basis set limit.” H. S. Lee and M. E. Tuckerman, J. Chem. Phys. 125:154507 (2006).

“Ab initio molecular dynamics with discrete variable representation basis sets: Techniques and application to liquid water.” H. S. Lee and M. E. Tuckerman, J. Phys. Chem. A 110:5549 (2006).

"Molecular grand-canonical ensemble density functional theory and exploration of chemical space", O. A. von Lilienfeld and M. E. Tuckerman, J. Chem. Phys. 125:154104 (2006).

“The molecular origin of the ‘continuous’ infrared absorption in aqueous solutions of acids: A computational approach”. R. Iftimie and M. E. Tuckerman, Angew. Chem. Intl. Ed. 45:1144 (2006).

"Mechanism of cis 1,3-butadiene addition reaction to the Si(100)-2x1 surface", P. Minary and M. E. Tuckerman, J. Am. Chem. Soc. 127:1110 (2005).

“Ab initio molecular dynamics: Concepts, recent developments, and future trends.” R. Iftimie, P. Minary, and M. E. Tuckerman, Proc. Natl. Acad. Sci. 102:6654 (2005).

"Molecular dynamics investigation of the connection between flap-closing and binding of fullerene-based inhibitors of the HIV-1 protease", Z. Zhu, D. I. Schuster and M. E. Tuckerman, Biochem. 42:1326 (2003).

"The nature and transport mechanism of hydrated hydroxide in aqueous solution", M. E. Tuckerman, D. Marx and M. Parrinello, Nature 417:925 (2002).

"Using novel variable transformations to enhance conformational sampling in molecular dynamics" Z. W. Zhu, M. E. Tuckerman, S. O. Samuelson and G. J. Martyna, Phys. Rev. Lett. 88:100201 (2002).

“On the use of the adiabatic molecular dynamics technique in the calculation of free energy profiles.” L. Rosso, P. Minary, Z. W. Zhu and M. E. Tuckerman, J. Chem. Phys. 116:4389 (2002).

Fellowships/Honors
NSF Postdoctoral Fellowship for Advanced Scientific Computing (1995-1996); NSF Career Award (1999); Golden Dozen Award for Excellence in Teaching (2000); Whitehead Fellowship in biomedical and biological sciences (2000-2001); Alexander von Humboldt Stiftung Research Award (Friedrich Wilhelm Bessel Award) (2005)

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