PUBLICATIONS

 
In Process  2016+
2011-2015
2006-2010
2001-2005
1996-2000
1990-1995

  1. “Locating landmarks on the free energy surfaces of organic crystals”
    E. Schneider, L. Vogt, M. Chen, T. -Q. Yu, and M. E. Tuckerman  (in preparation)
  2. “A perturbative analysis of the adiabatic/temperature-accelerated free energy dynamics approach based on the Fokker-Planck equation”
    M. Chen and M. E. Tuckerman  (in preparation)
  3. Ab initio molecular dynamics simulation of a mixture of phosphoric acid and imidazole”
    M. Kumar and M. E. Tuckerman  (in preparation)
  4. “The dielectric constant of neat phosphoric acid”
    M. Kumar, L. Vilciauskas and M. E. Tuckerman  (in preparation)

  5. “Stochastic neural network approach for learning high-dimensional free energy surfaces”
    Elia Schneider, Luke Dai, Robert Q. Topper, Christof Drechsel-Grau, and Mark E. Tuckerman Phys. Rev. Lett. (in press)
  6. “By-passing the Kohn-Sham equations with machine learning”
    F. Brockherde, L. Vogt, L. Li, M. E. Tuckerman, K. Burke, K.-R. Mueller (in press).
  7. “Importance of a Fully Anharmonic Treatment of Equilibrium Isotope Fractionation Properties of Dissolved Ionic Species As Evidenced by Li+(aq)”
    Romain Dupuis, Magali Benoit, M. E. Tuckerman, Merlin Méheut Acc. Chem. Res. 50(7), 1597 (2017).
  8. “Mesoscale Simulations of Anion Exchange Membranes Based on Quaternary Ammonium Tethered Triblock Copolymers”
    F. Sepehr, H. Liu, X. Luo, C. Bae, M. E. Tuckerman, M. A. Hickner, S. J. Paddison Macromolecules 50(11), 4397 (2017).
  9. “Powder diffraction and crystal structure prediction identify four new coumarin polymorphs”
    A. G. Shtukenberg, Q. Zhu, D. J. Carter, L. Vogt, J. Hoja, E. Schneider, H. Song, B. Pokroy, I. Polishchuk, A. Tkatchenko, A. R. Oganov, A. L. Rohl, M. E. Tuckerman, B. Kahr Chem. Sci. 8, 4926-4940 (2017).
  10. “Competing quantum effects in the free energy profiles and diffusion rates of hydrogen and deuterium molecules through clathrate hydrates”
    J. R. Cendagorta, A. Powers, T. J. H. Hele, O. Marsalek, Z. Bacic, and M. E.Tuckerman Phys. Chem. Chem. Phys. 18, 32169 (2016).
  11. “Advanced potential energy surfaces for molecular simulation”
    A. Albaugh, H. A. Boateng, R. T. Bradshaw, O. N. Demerdash, J. Dziedzic, Y. Mao, D. T. Margul, J. Swails, Q. Zeng, D. A. Case, P. Eastman, J. W. Essex, M. Head-Gorgon, V.S. Pande, J. W. Ponder, Y. Shao, C.-K. Skylaris, I. T.Todorov, M. E. Tuckerman, and T. Head-Gordon J. Phys. Chem. B 120, 9811 (2016).
  12. “Isostructural Cocrystals of 1,3,5-Trinitrobenzene Assembled by Halogen Bonding”
    J. C. Bennion, L. Vogt, M. E. Tuckerman, A. J. Matzger Cryst. Growth & Design 16, 4688 (2016).
  13. “Report on the sixth blind test of organic crystal-structure prediction methods”
    A. M. Reilly, R. I. Copper, C. S. Adjiman, S. Bhattacharya, A. D. Boese, J. G. Brandenburg, P. J. Bygrave, R. Bylsma, J. Campbell, R. Car, D. H. Case, R. Chadha, J. C. Cole, K. Cosburn, H. M. Cuppen, F. Curtis, G. M. Day, R. A. DiStasio, Jr., A. Dzyabchenko, B. P. van Eijck, D. Elking, J. A. van den Ende, J. C. Facelli, M. B. Ferraro, L. Fusti-Molnar, L. M. Ghiringhelli, H. Goto, S. Grimme, R. Guo, D. W. M. Hofmann, J. Hoja, R. K. Hylton, J. Iuzzolino, W. Jankiewicz, D. T. de Jong, J. Kendrick, N. J. J. de Klerk, H. -Y. Ko, L. N. Kuleshova, X. Li, S. Lohani, F. J. J. Leusen, A. M. Lund, J. Lv, Y. Ma, N. Marom, A. Masunov, P. McCabe, D. P. McMahon, H. Meekes, M. P. Metz, A. J. Misquitta, S. Mohamed, B. Monserrat, R. J. Needs, M. A. Neumann, J. Nyman, S. Obata, H. Oberhofer, A. Oganov, A. M. Orendt, G. I. Pagola, C. C. Pantelides, C. J. Pickard, R. Podeszwa, L. S. Price, S. L. Price, A. Pulido, M. Read, K. Reuter, E. Schneider, C. Schober, G. P. Shields, P. Singh, I. J. Sugden, K. Szalewicz, C. R. Taylor, A. Tkatchenko, M. E. Tuckerman, F. Vacarro, M. Vasileiadis, A. Vazquez-Mayagoitia, L. Vogt, Y. Wang, R. E. Watson, G. A. de Wlis, J. Yang, Q. Zhu, C. R. Groom. Acta Cryst. B72, 439 (2016).
  14. “Exploring polymorphism of benzene and naphthalene with free energy based enhanced molecular dynamics”
    E. Schneider, L. Vogt, and M. E. Tuckerman, Acta Cryst. B72, 542 (2016).
  15. “A stochastic, resonance-free multiple time-step algorithm for polarizable models that permits very large time steps”
    D. Margul and M. E. Tuckerman, J. Chem. Theor. Comput. 12, 2170 (2016).
  16. “Resorcinol crystallization from the melt: A new ambient phase and new “riddles”.”
    Q. Zhu, A. Shtukenberg, D. Carter, T. -Q. Yu, J. Yang, M. Chen. P. Raiteri, A. R. Oganov, B. Pokroy, I. Polishchuk, P. J. Bygrave, G. M. Day, A. L. Rohl, M. E. Tuckerman, B. Kahr, J. Am. Chem. Soc. 138, 4881 (2016).
  17. “Impact of the condensed-phase environment on the translation-rotation eigenstates and spectra of a hydrogen molecule in clathrate hydrates”
    A. Powers, O. Marsalek, M. Xu, L. Ulivi, D. Colognesi, M. E. Tuckerman, and Z. Bacic, J. Phys. Chem. Lett. 7, 308 (2016).

  18. “From classical to quantum and back: Hamiltonian adaptive coupling of classical and path integral models of atoms”
    K. Kreis, M. E. Tuckerman, D. Donadio, K. Kremer, and R. Potestio J. Chem. Theor. Comput. 12, 3030 (2015).
  19. “Locating landmarks on high-dimensional free energy surfaces”
    M. Chen, T. -Q. Yu, and M. E. Tuckerman Proc. Natl. Acad. Sci. U.S.A 112, 3235 (2015).
  20. “Microscopic mechanism of the equilibrium melting of a solid”
    A. Samanta, W. E., T. -Q. Yu, and M. E. Tuckerman Science 346, 729 (2014).
  21. “Free energy reconstruction from metadynamics or adiabatic free energy dynamics simulations”
    M. Cuendet and M. E. Tuckerman J. Chem. Theor. Comput. 10, 2975 (2014).
  22. “How accurately do current force fields predict experimental peptide conformations? An adiabatic free energy dynamics study”
    A. T. Tzanov, M. Cuendet, and M. E. Tuckerman J. Phys. Chem. B 118, 6539 (2014).
  23. “Order-parameter-aided temperature-accelerated sampling for the exploration of crystal polymorphism and solid-liquid phase transitions”
    T. -Q. Yu, E. Vanden-Eijnden, P. Chen, M. Chen, A. Samanta, and M. E. Tuckerman J. Chem. Phys. 140, 214109 (2014).
  24. “Sampling saddle points on a free energy surface”
    A. Samanta, M. Chen, T. -Q. Yu,M. E. Tuckerman, and W. E J. Chem. Phys. 140, 164109 (2014).
  25. Ab Initio Molecular Dynamics Study of the Aqueous HOO Ion”
    Z. Ma, D. Anick, and M. E. Tuckerman J. Phys. Chem. B 118, 7937 (2014).
  26. “Efficient calculation of free energy differences associated with isotopic substitution using path-integral molecular dynamics”
    O. Marsalek, P. Chen, R. Dupuis, M. Benoit, M. M´eheut, Z. Baˇci´c, and M. E. Tuckerman J. Chem. Theor. Comput. 10, 1440 (2014).
  27. “Computational techniques for density functional based molecular dynamics calculations in plane-wave and localized basis sets”
    A. T. Tzanov and M. E. Tuckerman in Many-Electron Approaches in Physics, Chemistry, and Math-ematics: A Multidisciplinary View, Springer, Berlin (2014).
  28. “Stochastic, resonance-free multiple time-step algorithm for molecular dynamics with very large time steps”
    B. Leimkuhler, D. T. Margul, and M. E. Tuckerman Mol. Phys. 111, 3579 (2013).
  29. “First principles molecular dynamics study of proton dynamics and transport in phosphoric acid/imidazole (2:1) system”
    L. Vilciauskas, M. E. Tuckerman, G. Bester, and K. -D. Kreuer Solid State Ionics 252, 35 (2013).
  30. Ab initio molecular dynamics study of water at constant pressure using converged basis sets and empirical dispersion corrections”
    Z. Ma and M. E. Tuckerman J. Chem. Phys. 137, 044506 (2012).
  31. “Alchemical free energy Differences in Flexible Molecules from Thermodynamic Integration or Free Energy Perturbation Combined with Driven Adiabatic Dynamics”
    M. Cuendet and M. E. Tuckerman, J. Chem. Theor. Comput. 8, 3504 (2012).
  32. “The mechanism of proton conduction in liquid phosphoric acid”
    L. Vilciauskas, K. D. Kreuer, S. J. Paddison, and M. E. Tuckerman Nature Chemistry 4, 461 (2012).
  33. “Heating and Flooding: A unified approach for the rapid generation of free energy surfaces”
    M. Chen, M. Cuendet, and M. E. Tuckerman J. Chem. Phys. 137, 024102 (2012).
    Top 20 most downloaded articles in July, 2012.
  34. “Macromolecular systems understood through multiscale and enhanced sampling techniques”
    P. J. Ortoleva, T. Keyes, M. E. Tuckerman J. Phys. Chem. B 116, 8335 (2012).
  35. Ab initio molecular dynamics studies of conjugated dienes on semiconductor surfaces”
    M. E. Tuckerman and Y. Zhang in Functionalization of Semiconductor Surfaces, F. Tao and S. Bernasek, eds. Wiley, Hoboken, NJ (2012).
  36. “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. (Frontiers Article) 511, 177 (2011).
  37. “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).
  38. “Constrained molecular dynamics in the isothermal-isobaric ensemble and its adaptation for adiabatic free energy dynamics”
    T. -Q. Yu and M. E. Tuckerman European Phys. J. Special Topics 200, 183 (2011).
  39. “On the use of the SiC(100)-c(2×2) surface as a substrate for the creation of ordered organic-semiconductor interfaces”
    Y. Zhang and M. E. Tuckerman J. Phys. Chem. Lett. 2, 1814 (2011).
  40. “Temperature-accelerated approach for exploring polymorphism in molecular crystals based on free energy”
    T. -Q. Yu and M. E. Tuckerman Phys. Rev. Lett. 107, 015701 (2011).
  41. “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).

  42. “Path Integral Molecular Dynamics Study of Small H2 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).
  43. “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).
  44. “Constant pressure ab initio molecular dynamics with discrete variable representation basis sets”
    Z. Ma and M. E. Tuckerman J. Chem. Phys. 133, 184110 (2010).
  45. “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).
  46. “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).
  47. “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).
  48. 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).
  49. “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).
  50. “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).
  51. “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).
  52. “Measure-preserving integrators for molecular dynamics in the isothermal-isobaric ensemble derived from the Liouville operator”
    T.-Q. Yu, J. Alejandre, R. L´opez-Rend´on, G. J. Martyna, and M. E. Tuckerman Chem. Phys. 370, 294 (2010).
  53. “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).
  54. “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).
  55. “Hydroxide anions 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).
  56. 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).
  57. “A comparative study of the centroid and ring-polymer methods for approximating quantum time correlation functions from path integrals”
    A. Perez, M. M¨user. and M. E. Tuckerman J. Chem. Phys. 130, 184105 (2009).
  58. “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).
  59. “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).
  60. “The structure and proton transport mechanism 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).
  61. “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).
  62. “Fine grained parallelization of the Car-Parrinello ab initio molecular dynamics method on the IBM Blue Gene/L supercomputer”
    E. Bohm, A. Bhatele, L. Kale, M. E. Tuckerman, S. Kumar, J. A. Gunnels, and G. J. Martyna IBM J. Res. Devel. 52, 177 (2008).
  63. “Dynamical spatial warping: A novel method for the conformational sampling of biophysical structure”
    P. Minary, Mark E. Tuckerman and G. J. Martyna. SIAM J. Sci. Comput. 30, 2055 (2007).
  64. “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).
  65. “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).
  66. “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).
  67. “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).
    Top 20 most downloaded articles in May, 2007
  68. “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).
  69. “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).
  70. “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).
    Top 20 most downloaded articles in October, 2006
  71. “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).
    Top 20 most downloaded articles in October, 2006.
  72. Ab initio molecular dynamics with discrete variable representation basis sets: Techniques and application to liquid water”
    H. E. Lee and M. E. Tuckerman J. Phys. Chem. A 110, 5549 (2006).
  73. “A Liouville-operator derived measure-preserving integrator for molecular dynamics simulations in the isothermal-isobaric ensemble”
    J. Alejandre, R. L´opez-Rend´on, A. L. Jochim and M. E. Tuckerman J. Phys. A: Mathematical and General 39, 5629 (2006).
  74. “Revisiting the structures of (LiCH3)n aggregates using Car-Parrinello molecular dynamics”
    H. G´erard, A. de la Lande, J. Maddaluno, O. Parisel and M. E. Tuckerman, J. Phys. A 110, 4787 (2006).
  75. “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. Zhang, J. Am. Chem. Soc. 128, 4530 (2006).
  76. 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).
  77. “Structure and dynamics of OH(aq)”
    M. E. Tuckerman, A. Chandra and D. Marx Accounts Chem. Res. 39, 151 (2006).
    Top 20 most cited articles in 2006
  78. “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. Engl. 45, 1144 (2006).

  79. “Efficient evaluation of nonlocal pseudopotentials via Euler exponential spline interpolation”
    H. S. Lee, G. J. Martyna and M. E. Tuckerman, ChemPhysChem 6, 1827 (2005).
  80. Ab initio molecular dynamics: Concepts, recent developments and future trends”
    P. Minary, R. Iftimie and M. E. Tuckerman, Proc. Natl. Acad. Sci.  102, 6654 (2005).
  81. “First-principles calculation of the 17O 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).
  82. “Reaction mechanism of cis-1,3-butadiene addition the Si(100)-2×1 surface”
    P. Minary and M. E. Tuckerman J. Am. Chem. Soc. 127, 1110 (2005).
  83. “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).
  84. “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).
  85. “Mapping the backbone dihedral free-energy surfaces in small peptides in solution using adiabatic free-energy dynamics”
    L. Rosso, J. B. Abrams, and M. E. Tuckerman J. Phys. Chem. B 109, 4162 (2005).
  86. “Reaction pathway [4+2] Diels-Alder adduct formation on Si(100)-2×1”
    P. Minary and M. E. Tuckerman J. Am. Chem. Soc. 126, 13920 (2004).
  87. “Long range interactions on wires: A reciprocal space based formalism”
    P. Minary, J. A. Morrone, G. J. Martyna, and M. E. Tuckerman J. Chem. Phys. 121, 11949 (2004).
  88. “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).
  89. “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, G. J. Martyna and M. E. Tuckerman J. Comp. Chem. 25, 2006 (2004).
  90. “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).
  91. “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).
  92. “Solid-state proton conduction: An ab initio molecular dynamics investigation of ammonium perchlorate doped with neutral ammonia”
    L. Rosso and M. E. Tuckerman Pure Appl. Chem. 76, 49 (2004).
  93. Ab initio molecular dynamics calculations with simple, localized, orthonormal real-space basis sets”
    Y. Liu, D. Yarne, and M. E. Tuckerman Phys. Rev. B 68, 125110 (2003).
  94. “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).
  95. “A simple quantum mechanical/molecular mechanical (QM/MM) model for methanol”
    J. A. Morrone and M. E. Tuckerman, Chem. Phys. Lett. 370, 406 (2003).
  96. “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).
  97. “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).
  98. “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).
  99. Ab initio molecular dynamics: Basic concepts, current trends, and novel applications”
    M. E. Tuckerman, J. Phys. Condens. Matter 14, R1297 (2002)
  100. Ab initio molecular dynamics study of proton mobility in liquid methanol”
    J. A. Morrone and M. E. Tuckerman, J. Chem. Phys. 117, 4403 (2002).
  101. 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).
  102. “The nature and transport mechanism of hydrated hydroxide ions in aqueous solution”
    M.E. Tuckerman, D. Marx and M. Parrinello, Nature 417, 925 (2002).
  103. “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).
  104. “On the use of the adiabatic molecular dynamics technique in the calculation of free energy profiles”
    L. Rosso, P. Minary, Z. Zhu and M.E. Tuckerman, J. Chem. Phys. 116, 4389 (2002).
  105. “An adiabatic molecular dynamics method for the calculation of free energy profiles”
    L. Rosso and M.E. Tuckerman, Mol. Simulat. 28, 91 (2002).
  106. “Using novel variable transformations to enhance conformational sampling in molecular dynamics”
    Z. Zhu, M. E. Tuckerman, and G. J. Martyna, Phys. Rev. Lett. 88, 100201 (2002).
  107. “Structural properties of molten silicates from ab initio molecular-dynamics: Comparison between CaO-Al2O3-SiO2 and SiO2
    S. Ispas, M. Benoit and M.E. Tuckerman, Phys. Rev. B 64, 224205 (2001).
  108. “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).
  109. “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).
  110. “Constrained isothermal-isobaric molecular dynamics with full atomic virial”
    M.E. Tuckerman, S. Melchionna, G. J. Martyna and G. Ciccotti, J. Phys. Chem. B 105, 6710 (2001).
  111. “Heavy-atom skeleton quantization and proton tunneling in ”intermediate-barrier” hydrogen bonds”
    M.E. Tuckerman and D. Marx, Phys. Rev. Lett., 86, 4946 (2001).
  112. “Non-Hamiltonianmolecular 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).

  113. “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, Chem. Phys. 258, 163 (2000).
  114. “Solvated excess protons in water: quantum effects on the hydration structure”
    D. Marx, M.E. Tuckerman and M. Parrinello, J. Phys. Condens. Matter 12, A153 (2000).
  115. “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).
  116. “Understanding modern molecular dynamics: Techniques and applications”
    M.E. Tuckerman and G.J. Martyna J. Phys. Chem. B 104, 159 (2000).
  117. “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).
  118. “Nonequilibrium molecular dynamics”
    C.J. Mundy, K. Bagchi, S. Balasubramanian, M.E. Tuckerman and M. L. Klein, Rev. Comp. Chem. 14, 291 (1999).
  119. Ab initio molecular dynamics study of crystalline nitric acid trihydrate”
    D. M. Sullivan, K. Bagchi, M.E. Tuckerman and M. L. Klein, J. Phys. Chem. A 103, 8678 (1999).
  120. “A Molecular dynamics study of the HIV-1 protease complexes with C60, and fullerene-based antiviral agents”
    H. Mi, D.I. Schuster, S. R. Wilson and M.E. Tuckerman, Proc. Electrochem. Soc. 99, 256 (1999).
  121. “Quantum dynamics via adiabatic ab initio centroid molecular dynamics”
    D. Marx, M.E. Tuckerman and G.J. Martyna, Comp. Phys. Comm. 118, 166 (1999).
  122. “Effect of N-H· · ·S amide-thiolate hydrogen bonding on bond lengths in rubredoxin models [(CH3)3NCH2CONH2]2[M(S2o-xyl)2]”
    W.P. Chung, J.C. Dewan, M.E. Tuckerman and M.A. Walters, Inorg. Chim. Acta 291, 388 (1999).
  123. “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).
  124. “The nature of the hydrated excess proton in water”
    D. Marx, M.E. Tuckerman and M. Parrinello, Nature 397, 601 (1999).
  125. “Molecular dynamics algorithm for path integrals at constant pressure”
    M.E. Tuckerman, A. Hughes, and G.J. Martyna, J. Chem. Phys. 110, 3275 (1999).
  126. “A reciprocal space based method for treating long range interactions in ab initio and force-field-based calculations in clusters”
    G.J. Martyna and M.E. Tuckerman, J. Chem. Phys. 110, 2810 (1999).
  127. “On the classical statistical mechanics of non-Hamiltonian systems”
    M.E. Tuckerman, C.J. Mundy and G.J. Martyna, Europhys. Lett. 45, 149 (1999).
  128. “Quantum nuclear ab initio molecular dynamics study of water wires”
    H.S. Mei, M.E. Tuckerman and M. L. Klein, J. Phys. Chem. B 102, 10446 (1998).
  129. 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).
  130. Ab initio molecular dynamics study of solid nitromethane”
    M.E. Tuckerman and M. L. Klein, Chem. Phys. Lett. 283, 147 (1998).
  131. “An empirical valence bond model for proton transfer in water”
    D. Sagnella and M.E. Tuckerman, J. Chem. Phys. 108, 2073 (1998).
  132. “Path integral molecular dynamics: A computational approach to quantum statistical mechanics”
    M.E. Tuckerman and A.L. Hughes, Proc. 1997 CECAM workshop on computer simulation of rare events, Villa Marigola, Lerici, Italy.
  133. “Toward a statistical thermodynamics of steady states”
    M.E. Tuckerman, C.J. Mundy, and M. L. Klein, Phys. Rev. Lett. 78, 2042 (1997).
  134. “On the quantum nature of the shared proton in a hydrogen bonds”
    M.E. Tuckerman, D. Marx, M. L. Klein, and M. Parrinello, Science, 275 817 (1997).
  135. “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).
  136. Ab initio molecular dynamics study of crystal hydrates of HCl including path integral results”
    M.E. Tuckerman, T. von Rosenvinge, and M. L. Klein, J. Chem. Soc. Faraday Trans. 106, 273 (1997).
  137. Ab initio molecular dynamics simulations of molecular crystals”
    M.E. Tuckerman, T. von Rosenvinge, and M. L. Klein, Mater. Res. Soc. Symp. Proc. 408, 477 (1996).
  138. Ab initio molecular dynamics simulations”
    M.E. Tuckerman, P.J. Ungar, T. von Rosenvinge, and M. L. Klein, J. Phys. Chem. 100, 12878 (1996).
  139. “Efficient and general algorithms for path integrals Car-Parrinello molecular dynamics”
    M.E. Tuckerman, D. Marx, M. L. Klein, and M. Parrinello, J. Chem. Phys. 104, 5579 (1996).
  140. “Explicit reversible integrators for extended systems dynamics”
    G. Martyna, M.E. Tuckerman, D.J. Tobias and M.L. Klein, Mol. Phys. 87, 1117 (1996).

  141. 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, 150-161 (1995).
  142. “Symplectic reversible integrators – predictor corrector methods”
    G.J. Martyna and M.E. Tuckerman, J. Chem. Phys. 102, 8071-8077 (1995).
  143. 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, 5749-5752 (1995).
  144. “Integrating the Car-Parrinello equations III: techniques for ultrasoft pseudopotentials”
    J. Hutter, M.E. Tuckerman and M. Parrinello, J. Chem. Phys. 102, 859-871 (1995).
  145. “Ab initio simulations of water and water ions”
    M.E. Tuckerman, K. Laasonen, M. Sprik and M. Parrinello, J. Phys.: Condensed Matter 6, A93-A100 (1994).
  146. “Integrating the Car-Parrinello equations I: Basic integration techniques”
    M.E. Tuckerman and M. Parrinello, J. Chem. Phys. 101, 1302-1315 (1994).
    “Integrating the Car-Parrinello equations II: Multiple scale techniques”
    M.E. Tuckerman and M. Parrinello, J. Chem. Phys. 101, 1316-1326 (1994).
  147. “Multiple time scale simulation of a flexible model of CO2
    M.E. Tuckerman and W. Langel, J. Chem. Phys. 100, 6368-6371 (1994).
  148. “Efficient molecular dynamics and hybrid Monte Carlo algorithms for path integrals”
    M. Tuckerman, B.J. Berne, G.J. Martyna and M.L. Klein, J. Chem. Phys. 99, 2796 (1993).
  149. “Vibrational relaxation in simple fluids: Comparison of theory and simulation”
    M.E. Tuckerman and B.J. Berne, J. Chem. Phys. 98, 7301-7318 (1993).
  150. “Nosé-Hoover chains: The canonical ensemble via continuous dynamics”
    G.J. Martyna, M.E. Tuckerman and M.L. Klein, J. Chem. Phys. 97, 2635-2643 (1992).
  151. “Reversible multiple time scale molecular dynamics”
    M.E. Tuckerman, G.J. Martyna and B. J. Berne, J. Chem. Phys. 97, 1990-2001 (1992).
  152. “Molecular dynamics in systems with multiple time scale: Systems with stiff and soft degrees of freedom and with short and long range forces”
    M.E. Tuckerman and B. J. Berne, J. Chem. Phys. 95, 8362-8364 (1991).
  153. “Comparison of rate theories for generalized Langevin dynamics and memory friction”
    S.C. Tucker, M.E. Tuckerman, B.J. Berne and E. Pollak, J. Chem. Phys. 95, 5809-5826 (1991).
  154. “Stochastic molecular dynamics in systems with multiple time scales and memory friction”
    M.E. Tuckerman and B.J. Berne, J. Chem. Phys. 95, 4389-4396 (1991).
  155. “Molecular dynamics algorithm for multiple time scales: Systems with long range forces”
    M.E. Tuckerman, G.J. Martyna and B. J. Berne, J. Chem. Phys. 94, 6811-6815 (1991).
  156. “Molecular dynamics algorithm for multiple time scales: Systems with disparate masses”
    M.E. Tuckerman, B.J. Berne and A. Rossi, J. Chem. Phys. 94, 1465-1469 (1991).
  157. “Dynamic friction on rigid and flexible bonds”
    B.J. Berne, M.E. Tuckerman, J.E.Straub and A.R.L. Bug, J. Chem. Phys. 93, 5084-5095 (1990).
  158. “Molecular dynamics algorithm for condensed systems with multiple time scales”
    M.E. Tuckerman, G.J. Martyna and B. J. Berne, J. Chem. Phys. 93, 1287-1291 (1990).