List of recent and prior publications

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Recent...



Improving the convergence of closed and open path integral molecular dynamics via higher order Trotter factorization schemes
A. Perez and M. E. Tuckerman J. Chem. Phys.135, 064104 (2011).
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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, 177 (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).
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Proton Transport in Triflic Acid Pentahydrate Studied via Ab Initio Path Integral Molecular Dynamics
R. L. Hayes, S. J. Paddison, and M. E. Tuckerman J. Phys. Chem. A 115, 6112 (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).

Path Integral Molecular Dynamics Study of Small H(2) Clusters in the Large Cage of Structure II Clathrate Hydrate: Temperature Dependence of Quantum Spatial Distributions
A. Witt, F. Sebastianelli, M. E. Tuckerman, and Z. Bacic J. Phys. Chem. C 114, 20775 (2010).

Constant pressure ab initio molecular dynamics with discrete variable representation basis sets
Z. Ma and M. E. Tuckerman J. Chem. Phys. 133, 184110 (2010).
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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).
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Failure of Perturbative DFT-Derived STM Images of Organic Molecules on Semiconductor Surfaces
R. L. Hayes and M. E. Tuckerman J. Phys. Chem. C 114, 15102 (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).

Concerted Proton-Electron Transfer to Dioxygen in Water
O. Snir, Y. F. Wang, M. E. Tuckerman, Y. V. Geletii, and I. A. Weinstock J. Am. Chem. Soc. 132, 11678 (2010).

Measure-preserving integrators for molecular dynamics in the isothermal-isobaric ensemble derived from the Liouville operator
T. Q. Yu, J. Alejandre, R. Lopez-Rendon, G. J. Martyna, and M. E. Tuckerman Chem. Phys. 370, 294 (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).

The effects of the hydrophobic environment on proton mobility in perfluorosulfonic acid systems: an ab initio molecular dynamics study
B. F. Habenicht, S. J. Paddison, and M. E. Tuckerman J. Mat. Chem. 20, 6342 (2010).

Ab initio molecular dynamics simulations investigating proton transfer in perfluorosulfonic acid functionalized carbon nanotubes
B. F. Habenicht, S. J. Paddison, and M. E. Tuckerman Phys. Chem. Chem. Phys. 12, 8728 (2010).

Proton Transport in Triflic Acid Hydrates Studied via Path Integral Car-Parrinello Molecular Dynamics
R. L. Hayes, S. J. Paddison, and M. E. Tuckerman J. Phys. Chem. B 113, 16574 (2009).

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).
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Hydroxide ions 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).

A comparative study of the centroid and ring-polymer molecular dynamics methods for approximating quantum time correlation functions from path integrals.
A. Perez, M. E. Tuckerman, and M. H. Mueser J. Chem. Phys. 130, 184105 (2009).
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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).

Efficient solution of Poisson's equation using discrete variable representation basis sets for Car-Parrinello ab initio molecular dynamics simulations with cluster boundary conditions.
H. S. Lee and M. E. Tuckerman J. Chem. Phys. 129, 224108 (2008).
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Efficient and Direct Generation of Multidimensional Free Energy Surfaces via Adiabatic Dynamics without Coordinate Transformations.
J. B. Abrams and M. E. Tuckerman J. Phys. Chem. B 112, 15742 (2008).

The structure and proton transport mechanisms in the superprotonic phase of CsH2PO4: An ab initio molecular dynamics study.
H. S. Lee and M. E. Tuckerman J. Phys. Chem. C 112, 9917 (2008).

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 (2007).
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Kinetic effects on the cycloaddition of 1,3-cyclohexadiene to the 3C-SiC(001)-3 x 2 surface studied via ab initio molecular dynamics.
R. L. Hayes and M. E. Tuckerman J. Phys. Chem. C 112, 5880 (2008).

Fine-grained parallelization of the Car-Parrinello ab initio molecular dynamics method on the IBM Blue Gene/L supercomputer.
E. Bohm, A. Bhatele, L. V. Kale, M. E. Tuckerman, S. Kumar, J. A. Gunnels, and G. J. Martyna IBM J. Res. Devel. 52, 159 (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).
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Role of surface dimer dynamics in creating ordered organic-semiconductor interfaces.
R. L. Hayes and M. E. Tuckerman J. Am. Chem. Soc. 129, 12172 (2007).

Alchemical variations of intermolecular energies according to molecular grand-canonical ensemble density functional theory.
O. A. von Lilienfeld and M. E. Tuckerman J. Chem. Theor. Comput. 3, 1083 (2007).

Dynamical properties of liquid water from ab initio molecular dynamics performed in the complete basis set limit.
H. S. Lee and M. E. Tuckerman J. Chem. Phys. 126, 164501 (2007).
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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).
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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).
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Efficient and precise solvation free energies via alchemical adiabatic molecular dynamics.
J. B. Abrams, L. Rosso, and M. E. Tuckerman J. Chem. Phys. 125, 074115 (2006).
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Molecular dynamics simulations of aqueous solutions of ethanolamines.
R. Lopez-Rendon, M. A. Mora, J. Alejandre, and M. E. Tuckerman J. Phys. Chem. B 110, 14652 (2006).

A Liouville-operator derived. measure-preserving integrator for molecular dynamics simulations in the isothermal-isobaric ensemble.
M. E. Tuckerman, J. Alejandre, R. Lopez-Rendon, A. L. Jochim, and G. J. Martyna J. Phys. A 39, 5629 (2006).
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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).

Unexpected deacetylation mechanism suggested by a density functional theory QM/MM study of histone-deacetylase-like protein.
C. Corminboeuf, P. Hu, M. E. Tuckerman and Y. K. Zhang J. Am. Chem. Soc. 128, 4530 (2006).

Revisiting the structure of (LiCH3)(n) aggregates using Car-Parrinello molecular dynamics.
H. Gerard, A. de la Lande, J. Maddaluno, O. Parisel, and M. E. Tuckerman J. Phys. Chem. A 110, 4787 (2006).

Ab initio molecular dynamics simulation of the structure and proton transport dynamics of methanol-water solutions.
J. A. Morrone, K. E. Haslinger, and M. E. Tuckerman J. Phys. Chem. B 110, 3712 (2006).

Structure and dynamics of OH-(aq).
M. E. Tuckerman, A. Chandra and D. Marx Acc. Chem. Res. 39, 151 (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).



Selected Previous...



Efficient evaluation of nonlocal pseudopotentials via Euler exponential spline interpolation.
H. S. Lee, M. E. Tuckerman, and G. J. Martyna ChemPhysChem 6, 1827 (2005).
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A polarizable multistate empirical valence bond model for proton transport in aqueous solution.
G. Brancato and M. E. Tuckerman J. Chem. Phys. 122, 224507 (2005).
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Decomposing total IR spectra of aqueous systems into solute and solvent contributions: A computational approach using maximally localized Wannier orbitals.
R. Iftimie and M. E. Tuckerman J. Chem. Phys. 122, 214508 (2005).
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Ab initio molecular dynamics: Concepts, recent developments, and future trends.
R. Iftimie, P. Minary, and M. E. Tuckerman Proc. Natl. Acad. Sci. USA 102, 6654 (2005).

First-principles calculation of the O-17 NMR parameters of a calcium aluminosilicate glass.
M. Benoit, M. Profeta, F. Mauri, C. J. Pickard, and M. E. Tuckerman J. Phys. Chem. B 109, 6052 (2005).

Mapping the backbone dihedral angle free energy surfaces of small peptides using adiabatic free energy dynamics.
L. Rosso, J. B. Abrams and M. E. Tuckerman J. Phys. Chem. B 109, 4162 (2005).

Reaction mechanism of cis-1,3-butadiene addition to the Si(100)-2x1 surface.
P. Minary and M. E. Tuckerman J. Am. Chem. Soc. 121, 11949 (2004).

Long range interactions on wires: A reciprocal space based formalism .
P. Minary, J. A. Morrone, D. A. Yarne, G. J. Martyna, and M. E. Tuckerman J. Chem. Phys. 121, 11949 (2004).
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Scalable fine-grained parallelization of plane-wave-based ab initio molecular dynamics for large supercomputers.
R. V. Vadali, Y. Shi, S. Kumar, L. V. Kale, M. E. Tuckerman and G. J. Martyna J. Comp. Chem. 25, 2006 (2004).

Reaction Pathway of the [4+2] Diels-Alder adduct formation on Si(100)-2x1.
P. Minary and M. E. Tuckerman, J. Am. Chem. Soc. 126, 13920 (2004).

Long time molecular dynamics for enhanced conformational sampling in biomolecular systems .
P. Minary, G. J. Martyna and M. E. Tuckerman, Phys. Rev. Lett. 93, 150201 (2004).
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Field theoretic approach to dynamical orbital localization in ab initio molecular dynamics .
J. W. Thomas, R. Iftimie and M. E. Tuckerman, Phys. Rev. B 69, 125105 (2004).
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On-the-fly localization of electronic orbitals in Car-Parrinello molecular dynamics .
R. Iftimie, J. W. Thomas and M. E. Tuckerman, J. Chem. Phys. 120, 2169 (2004).
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Ab initio molecular dynamics calculations with simple, localized, orthonormal real-space basis sets.
Y. Liu, D. A. Yarne and M. E. Tuckerman, Phys. Rev. B 68, 125110 (2003).
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Direct evidence of an anomalous charge transport mechanism in ammonium perchlorate crystal in an ammonia-rich atmosphere from first-principles molecular dynamics.
L. Rosso and M. E. Tuckerman, Solid State Ionics 161, 219 (2003).

A simple quantum mechanical/molecular mechanical (QM/MM) model for methanol.
J. A. Morrone and M. E. Tuckerman, Chem. Phys. Lett. 370, 406 (2003).

Algorithms and novel applications based on the isokinetic ensemble. I. Biophysical and path integral molecular dynamics.
P. Minary, G. J. Martyna and M. E. Tuckerman, J. Chem. Phys. 118, 2510 (2003).
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Algorithms and novel applications based on the isokinetic ensemble. II. Ab initio molecular dynamics.
P. Minary, G. J. Martyna and M. E. Tuckerman, J. Chem. Phys. 118, 2527 (2003).

Molecular dynamics study 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).

Ab initio molecular dynamics: Basic concepts, current trends and novel applications.
M. E. Tuckerman, J. Phys. Condens. Matt. 14, R1297 (2002).

Ab initio molecular dynamics investigation of the concentration dependence of charged defect transport in basic solutions via calculation of the infrared spectrum.
Z. Zhu and M. E. Tuckerman, J. Phys. Chem. B 106, 8009 (2002).

Ab initio molecular dynamics study of proton mobility in liquid methanol.
J. A. Morrone and M. E. Tuckerman, J. Chem. Phys. 117, 4403 (2002).
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The nature and transport mechanism of hydrated hydroxide ions in solution.
M. E. Tuckerman, D. Marx and M. Parrinello, Nature 417, 925 (2002).

On the use of adiabatic molecular dynamics to calculate free energy profiles.
L. Rosso, P. Minary, Z. Zhu and M. E. Tuckerman, J. Chem. Phys. 116, 4389 (2002).
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A new reciprocal space based treatment of long range interactions on surfaces
P. Minary, M. E. Tuckerman, K. Pihakari and G. J. Martyna, J. Chem. Phys. 116, 5351(2002).
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Using novel variable transformations to enhance conformational sampling in molecular dynamics
Z. Zhu, M. E. Tuckerman, S. O. Samuelson and G. J. Martyna, Phys. Rev. Lett. 88, 100201 (2002).
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Structural properties of molten silicates from ab initio molecular dynamics simulations: Comparison between CaO-Al2O 3-SiO2 and SiO2
M. Benoit, S. Ispas and M. E. Tuckerman, Phys. Rev. B 64, 224205 (2001).
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Non-Hamiltonian molecular dynamics: Generalizing Hamiltonian phase space principles to non-Hamiltonian systems.
M. E. Tuckerman, Y. Liu, G. Ciccotti and G. J. Martyna, J. Chem. Phys., 115, 1678 (2001).
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A dual length scale method for plane wave based simulation studies of chemical systems modeled using mixed ab initio/empirical force field descriptions.
D. A. Yarne, M. E. Tuckerman, and G. J. Martyna, J. Chem. Phys.115, 3531 (2001).
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Heavy-atom skeleton quantization and proton tunneling in ``intermediate barrier'' hydrogen bonds
M. E. Tuckerman and D. Marx, Phys. Rev. Lett. 86, 4946 (2001).
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Protonic defects in hydrogen bonded liquids: Structure and dynamics in ammonia and comparison with water.
Y. Liu and M. E. Tuckerman, J. Phys. Chem. B 105, 6598 (2001).

An adiabatic molecular dynamics method for the calculation of free energy profiles
L. Rosso and M. E. Tuckerman, Molec. Sim. 28, 91 (2002).

Structural and dynamical behavior of an azide anion in water from ab initio molecular dynamics calculations
D. A. Yarne, M. E. Tuckerman and M. L. Klein, Chemical Physics 258, 163 (2000).

Exploiting multiple levels of parallelism in molecular dynamics based calculations via modern techniques and software paradigms on distributed memory computers.
M.E. Tuckerman, D. A. Yarne, S. O. Samuelson, A. L. Hughes and G.J. Martyna, Comp. Phys. Comm. 128, 333 (2000).

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Understanding modern molecular dynamics methods: Techniques and Applications .
M.E. Tuckerman and G.J. Martyna, J. Phys. Chem. B 104, 159 (2000).

Generalized Gaussian moment thermostatting: A new continuous dynamical approach to the canonical ensemble.
Y. Liu and M.E. Tuckerman, J. Chem. Phys. 112, 1685 (2000).
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Simulation studies of liquid ammonia by classical ab initio, classical and path integral molecular dynamics .
M. Diraison, G.J. Martyna and M.E. Tuckerman, J. Chem. Phys. 111, 1096 (1999).

Quantum dynamics via adiabatic ab initio centroid molecular dynamics .
D. Marx, M.E. Tuckerman and G.J. Martyna, Comput. Phys. Comm. 118, 166 (1999).

Molecular dynamics algorithms for path integrals at constant pressure .
G.J. Martyna, A. Hughes and M.E. Tuckerman, J. Chem. Phys. 110, 3275 (1999).
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On the Classical Statistical Mechanics of non-Hamiltonian Systems .
M.E. Tuckerman, C.J. Mundy and G.J. Martyna, Europhys. Lett. 45, 149 (1999).

A reciprocal-space based method for treating long range forces in force-field based and ab initio calculations of clusters .
G.J. Martyna and M.E. Tuckerman, J. Chem. Phys. 110, 2810 (1999).
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The nature of the hydrated excess proton in water .
D. Marx, M.E. Tuckerman J. Hutter and M. Parrinello, Nature 397, 601 (1999).

A molecular dynamics study of HIV-1 protease complexes with C60 and fullerene-based anti-viral agents .
H. Mi, M.E. Tuckerman, D.I. Schuster and S.R. Wilson, Proc. Electrochem. Soc. 99, 256 (1999).

Quantum nuclear ab initio molecular dynamics study of water wires .
H.S. Mei, M.E. Tuckerman, D.E. Sagnella and M.L. Klein J. Phys. Chem. B 102, 10446 (1998).

An ab initio path integral molecular dynamics study of double proton transfer in the formic acid dimer .
S. Miura, M.E. Tuckerman and M.L. Klein J. Chem. Phys. 109, 5290 (1998).

An empirical valence bond model for proton transfer in water.
M.E. Tuckerman and D.E. Sagnella J. Chem. Phys. 108, 2073 (1998).

Ab initio molecular dynamics study of solid nitromethane.
M.E. Tuckerman and M.L. Klein Chem. Phys. Lett. 283, 147 (1998).

Path integral molecular dynamics: A computational approach to quantum statistical mechanics.
M.E. Tuckerman and A. Hughes Proc. 1997 CECAM conference on ``Computer simulation of rare events and quantum dynamics in condensed phase systems.

Ab initio molecular dynamics study of crystal hydrates of HCl including path integral results.
T. von Rosenvinge, M.E. Tuckerman, and M.L. Klein, J. Chem. Soc. Faraday Discuss. 106, 273 (1997).

Modified nonequilibrium molecular dynamics for fluid flows with energy conservation.
M.E. Tuckerman, C.J. Mundy, S. Balasubramanian and M.L. Klein, J. Chem. Phys. 106, 5615 (1997).

Toward a statistical thermodynamics of steady states.
M.E. Tuckerman, C.J. Mundy and M.L. Klein, Phys. Rev. Lett. 78, 2042 (1997).

On the quantum nature of the shared proton in hydrogen bonds.
M.E. Tuckerman, D. Marx, M.L. Klein and M. Parrinello, Science 275, 817 (1997).

Ab initio molecular dynamics simulations.
M.E. Tuckerman, P.J. Ungar, T. von Rosenvinge and M.L. Klein, J. Phys. Chem. 100, 12878 (1996).

Efficient Car-Parrinello molecular dynamics algorithms for path integrals.
M.E. Tuckerman, D. Marx, M.L. Klein, and M. Parrinello J. Chem. Phys. 104, 5579 (1996).

Explicit reversible integration algorithms for extended systems.
G.J. Martyna, M.E. Tuckerman, D.J. Tobias, and M.L. Klein, Mol. Phys. 87, 1117 (1996).

Ab initio molecular dynamics simulation of the solvation and transport of hydronium and hydroxyl ions in water.
M.E. Tuckerman, K. Laasonen, M. Sprik, and M. Parrinello J. Chem. Phys. 103, 150 (1995).

Ab initio molecular dynamics simulation of the solvation and transport of H3O+ and OH- ions in water.
M.E. Tuckerman, K. Laasonen, M. Sprik, and M. Parrinello J. Phys. Chem. 99, 5749 (1995).

Integrating the Car-Parrinello equations I, II, and III .
M.E. Tuckerman,J. Hutter, M. Parrinello J. Chem. Phys. 101, 1301,1316 (1994), 102, 859 (1995).

Efficient molecular dynamics and hybrid Monte Carlo algorithms for path integrals.
M.E. Tuckerman, G.J. Martyna, M.L. Klein and B.J. BerneJ. Chem. Phys. 99, 2796 (1993).
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Vibrational relaxation in simple fluids: Comparison of theory and simulation.
M.E. Tuckerman, and B.J. Berne J. Chem. Phys. 98, 7301 (1993).
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Nose-Hoover chains: The canonical ensemble via continuous dynamics.
G.J. Martyna, M.E. Tuckerman, and M.L. Klein J. Chem. Phys. 97, 2635 (1992).
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Reversible multiple time scale molecular dynamics .
M.E. Tuckerman, G.J. Martyna and B.J. Berne J. Chem. Phys. 97, 1990 (1992).
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