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1

A Liouville-operator derived measure-preserving integrator for molecular dynamics simulations in the isothermal–isobaric ensemble

Tuckerman, Mark E, Alejandre, José, López-Rendón, Roberto, Jochim, Andrea L, Martyna, Glenn J

Journal:

Journal of Physics A: Mathematical and General Physics

Year:

2006

Language:

english

File:

PDF, 352 KB

english, 2006

2

Explicit reversible integrators for extended systems dynamics

Martyna, Glenn J., Tuckerman, Mark E., Tobias, Douglas J., Klein, Michael L.

Journal:

Molecular Physics

Year:

1996

Language:

english

File:

PDF, 1.81 MB

english, 1996

3

Proton Transport in Triflic Acid Hydrates Studied via Path Integral Car−Parrinello Molecular Dynamics

Hayes, Robin L., Paddison, Stephen J., Tuckerman, Mark E.

Journal:

Journal of Physical Chemistry B

Year:

2009

Language:

english

File:

PDF, 1.20 MB

english, 2009

4

Proton Transport in Triflic Acid Pentahydrate Studied via Ab Initio Path Integral Molecular Dynamics

Hayes, Robin L., Paddison, Stephen J., Tuckerman, Mark E.

Journal:

Journal of Physical Chemistry A

Year:

2011

Language:

english

File:

PDF, 4.87 MB

english, 2011

5

Stochastic, resonance-free multiple time-step algorithm for molecular dynamics with very large time steps

Leimkuhler, Ben, Margul, Daniel T., Tuckerman, Mark E.

Journal:

Molecular Physics

Year:

2013

Language:

english

File:

PDF, 998 KB

english, 2013

6

[WORLD SCIENTIFIC Proceedings of the International School of Physics - LERICI, Villa Marigola (7 – 18 July 1997)] Classical and Quantum Dynamics in Condensed Phase Simulations - Path integral molecular dynamics: a computational approach to quantum statistical mechanics

TUCKERMAN, MARK E., HUGHES, ADAM

Language:

english

File:

PDF, 3.03 MB

english

7

Bypassing the Kohn-Sham equations with machine learning

Brockherde, Felix, Vogt, Leslie, Li, Li, Tuckerman, Mark E., Burke, Kieron, Müller, Klaus-Robert

Journal:

Nature Communications

Year:

2017

Language:

english

File:

PDF, 1.32 MB

english, 2017

8

Measure-preserving integrators for molecular dynamics in the isothermal–isobaric ensemble derived from the Liouville operator

Tang-Qing Yu, José Alejandre, Roberto López-Rendón, Glenn J. Martyna, Mark E. Tuckerman

Journal:

Chemical Physics

Year:

2010

Language:

english

File:

PDF, 1.31 MB

english, 2010

9

Nosé–Hoover chains: The canonical ensemble via continuous dynamics

Martyna, Glenn J., Klein, Michael L., Tuckerman, Mark

Journal:

The Journal of Chemical Physics

Year:

1992

Language:

english

File:

PDF, 821 KB

english, 1992

10

Heating and flooding: A unified approach for rapid generation of free energy surfaces

Chen, Ming, Cuendet, Michel A., Tuckerman, Mark E.

Journal:

The Journal of Chemical Physics

Year:

2012

Language:

english

File:

PDF, 3.08 MB

english, 2012

11

Efficient and general algorithms for path integral Car–Parrinello molecular dynamics

Tuckerman, Mark E., Marx, Dominik, Klein, Michael L., Parrinello, Michele

Journal:

The Journal of Chemical Physics

Year:

1996

Language:

english

File:

PDF, 465 KB

english, 1996

12

Dynamical Spatial Warping: A Novel Method for the Conformational Sampling of Biophysical Structure

Minary, Peter, Tuckerman, Mark E., Martyna, Glenn J.

Journal:

SIAM Journal on Scientific Computing

Year:

2008

Language:

english

File:

PDF, 1012 KB

english, 2008

13

10.1038/17579

Marx, Dominik, Tuckerman, Mark E., Hutter, Jürg, Parrinello, Michele

Journal:

Year:

1999

Language:

english

File:

PDF, 475 KB

english, 1999

14

A reciprocal space based method for treating long range interactions in ab initio and force-field-based calculations in clusters

Martyna, Glenn J., Tuckerman, Mark E.

Journal:

The Journal of Chemical Physics

Year:

1999

Language:

english

File:

PDF, 537 KB

english, 1999

15

Molecular grand-canonical ensemble density functional theory and exploration of chemical space

von Lilienfeld, O. Anatole, Tuckerman, Mark E.

Journal:

The Journal of Chemical Physics

Year:

2006

Language:

english

File:

PDF, 560 KB

english, 2006

16

Non-Hamiltonian molecular dynamics: Generalizing Hamiltonian phase space principles to non-Hamiltonian systems

Tuckerman, Mark E., Liu, Yi, Ciccotti, Giovanni, Martyna, Glenn J.

Journal:

The Journal of Chemical Physics

Year:

2001

Language:

english

File:

PDF, 628 KB

english, 2001

17

Molecular dynamics algorithm for multiple time scales: Systems with long range forces

Tuckerman, Mark E., Berne, Bruce J., Martyna, Glenn J.

Journal:

The Journal of Chemical Physics

Year:

1991

Language:

english

File:

PDF, 686 KB

english, 1991

18

Aqueous Basic Solutions: Hydroxide Solvation, Structural Diffusion, and Comparison to the Hydrated Proton

Marx, Dominik, Chandra, Amalendu, Tuckerman, Mark E.

Journal:

Chemical Reviews

Year:

2010

Language:

english

File:

PDF, 1.63 MB

english, 2010

19

Ab Initio Molecular Dynamics Study of the Aqueous HOO – Ion

Ma, Zhonghua, Anick, David, Tuckerman, Mark E.

Journal:

Journal of Physical Chemistry B

Year:

2014

Language:

english

File:

PDF, 1.85 MB

english, 2014

20

Molecular dynamics algorithm for condensed systems with multiple time scales

Tuckerman, Mark E., Martyna, Glenn J., Berne, Bruce J.

Journal:

The Journal of Chemical Physics

Year:

1990

Language:

english

File:

PDF, 560 KB

english, 1990

21

Molecular dynamics algorithms for path integrals at constant pressure

Martyna, Glenn J., Hughes, Adam, Tuckerman, Mark E.

Journal:

The Journal of Chemical Physics

Year:

1999

Language:

english

File:

PDF, 575 KB

english, 1999

22

Symplectic reversible integrators: Predictor–corrector methods

Martyna, Glenn J., Tuckerman, Mark E.

Journal:

The Journal of Chemical Physics

Year:

1995

Language:

english

File:

PDF, 454 KB

english, 1995

23

A comparative study of the centroid and ring-polymer molecular dynamics methods for approximating quantum time correlation functions from path integrals

Pérez, Alejandro, Tuckerman, Mark E., Müser, Martin H.

Journal:

The Journal of Chemical Physics

Year:

2009

Language:

english

File:

PDF, 481 KB

english, 2009

24

Stochastic Neural Network Approach for Learning High-Dimensional Free Energy Surfaces

Schneider, Elia, Dai, Luke, Topper, Robert Q., Drechsel-Grau, Christof, Tuckerman, Mark E.

Journal:

Physical Review Letters

Year:

2017

Language:

english

File:

PDF, 679 KB

english, 2017

25

Molecular dynamics based enhanced sampling of collective variables with very large time steps

Chen, Pei-Yang, Tuckerman, Mark E.

Journal:

The Journal of Chemical Physics

Year:

2018

Language:

english

File:

PDF, 1.30 MB

english, 2018

26

Hydroxide Ion Diffusion in Anion Exchange Membranes at Low Hydration: Insights from Ab initio Molecular Dynamics

Zelovich, Tamar, Vogt-Maranto, Leslie, Hickner, Michael A., Paddison, Stephen J., Bae, Chulsung, Dekel, Dario R., Tuckerman, Mark E.

Journal:

Chemistry of Materials

Year:

2019

File:

PDF, 937 KB

2019

27

Comparison of the Performance of Machine Learning Models in Representing High-Dimensional Free Energy Surfaces and Generating Observables

Cendagorta, Joseph R., Tolpin, Jocelyn, Schneider, Elia, Topper, Robert Q., Tuckerman, Mark E.

Journal:

Journal of Physical Chemistry B

Year:

2020

File:

PDF, 2.76 MB

2020

28

Liquid Structure and Transport Properties of the Deep Eutectic Solvent Ethaline

Zhang, Yong, Poe, Derrick, Heroux, Luke, Squire, Henry, Doherty, Brian W., Long, Zhuoran, Dadmun, Mark D., Gurkan, Burcu E., Tuckerman, Mark E., Maginn, Edward J.

Journal:

Journal of Physical Chemistry B

Year:

2020

File:

PDF, 2.31 MB

2020

29

The Molecular Origin of the “Continuous” Infrared Absorption in Aqueous Solutions of Acids: A Computational Approach

Radu Iftimie, Mark E. Tuckerman

Journal:

Angewandte Chemie

Year:

2006

Language:

english

File:

PDF, 179 KB

english, 2006

30

The Molecular Origin of the “Continuous” Infrared Absorption in Aqueous Solutions of Acids: A Computational Approach

Radu Iftimie, Mark E. Tuckerman

Journal:

Angewandte Chemie International Edition

Year:

2006

Language:

english

File:

PDF, 179 KB

english, 2006

31

The Nature and Transport Mechanism of Hydrated Hydroxide Ions in Aqueous Solution

Mark E. Tuckerman, Dominik Marx, Michele Parrinello

Journal:

Year:

2002

File:

PDF, 25 KB

2002

32

Efficient Evaluation of Nonlocal Pseudopotentials via Euler Exponential Spline Interpolation

Hee-Seung Lee, Mark E. Tuckerman, Glenn J. Martyna

Journal:

Year:

2005

Language:

english

File:

PDF, 158 KB

english, 2005

33

Scalable fine-grained parallelization of plane-wave–based ab initio molecular dynamics for large supercomputers

Ramkumar V. Vadali, Yan Shi, Sameer Kumar, Laxmikant V. Kale, Mark E. Tuckerman, Glenn J. Martyna

Journal:

Journal of Computational Chemistry

Year:

2004

Language:

english

File:

PDF, 516 KB

english, 2004

34

Hydroxide anion at the air–water interface

Christopher J. Mundy, I-Feng W. Kuo, Mark E. Tuckerman, Hee-Seung Lee, Douglas J. Tobias

Journal:

Chemical Physics Letters

Year:

2009

Language:

english

File:

PDF, 449 KB

english, 2009

35

A simple quantum mechanical/molecular mechanical (QM/MM) model for methanol

Joseph A. Morrone, Mark E. Tuckerman

Journal:

Chemical Physics Letters

Year:

2003

Language:

english

File:

PDF, 133 KB

english, 2003

36

Ab initio molecular dynamics study of solid nitromethane

Mark E. Tuckerman, Michael L. Klein

Journal:

Chemical Physics Letters

Year:

1998

Language:

english

File:

PDF, 99 KB

english, 1998

37

Exploiting multiple levels of parallelism in Molecular Dynamics based calculations via modern techniques and software paradigms on distributed memory computers

Mark E. Tuckerman, D.A. Yarne, Shane O. Samuelson, Adam L. Hughes, Glenn J. Martyna

Journal:

Computer Physics Communications

Year:

2000

Language:

english

File:

PDF, 666 KB

english, 2000

38

Quantum dynamics via adiabatic ab initio centroid molecular dynamics

Dominik Marx, Mark E. Tuckerman, Glenn J. Martyna

Journal:

Computer Physics Communications

Year:

1999

Language:

english

File:

PDF, 1.18 MB

english, 1999

39

Effect of N–H⋯S amide–thiolate hydrogen bonding on bond lengths in rubredoxin models [(CH3)3NCH2CONH2]2[M(S2-o-xyl)2]

Wesley P. Chung, John C. Dewan, Mark Tuckerman, Marc A. Walters

Journal:

Inorganica Chimica Acta

Year:

1999

Language:

english

File:

PDF, 114 KB

english, 1999

40

Direct evidence of an anomalous charge transport mechanism in ammonium perchlorate crystal in an ammonia-rich atmosphere from first-principles molecular dynamics

Lula Rosso, Mark E. Tuckerman

Journal:

Solid State Ionics

Year:

2003

Language:

english

File:

PDF, 763 KB

english, 2003

41

Structural and dynamical behavior of an azide anion in water from ab initio molecular dynamics calculations

Dawne A Yarne, Mark E Tuckerman, Michael L Klein

Journal:

Chemical Physics

Year:

2000

Language:

english

File:

PDF, 180 KB

english, 2000

42

The nature and transport mechanism of hydrated hydroxide ions in aqueous solution

Tuckerman, Mark E., Marx, Dominik, Parrinello, Michele

Journal:

Year:

2002

Language:

english

File:

PDF, 321 KB

english, 2002

43

Structure of liquid water at ambient temperature from ab initio molecular dynamics performed in the complete basis set limit

Lee, Hee-Seung, Tuckerman, Mark E.

Journal:

The Journal of Chemical Physics

Year:

2006

Language:

english

File:

PDF, 711 KB

english, 2006

44

Ab Initio Molecular Dynamics Simulation of the Solvation and Transport of H3O+ and OH- Ions in Water

Tuckerman, Mark, Laasonen, Kari, Sprik, Michiel, Parrinello, Michele

Journal:

Journal of Physical Chemistry

Year:

1995

Language:

english

File:

PDF, 1.25 MB

english, 1995

45

Enol Tautomers of Watson−Crick Base Pair Models Are Metastable Because of Nuclear Quantum Effects

Pérez, Alejandro, Tuckerman, Mark E., Hjalmarson, Harold P., von Lilienfeld, O. Anatole

Journal:

Journal of the American Chemical Society

Year:

2010

Language:

english

File:

PDF, 883 KB

english, 2010

46

On the connection between proton transport, structural diffusion, and reorientation of the hydrated hydroxide ion as a function of temperature

Zhonghua Ma, Mark E. Tuckerman

Journal:

Chemical Physics Letters

Year:

2011

Language:

english

File:

PDF, 738 KB

english, 2011

47

Alchemical Free Energy Differences in Flexible Molecules from Thermodynamic Integration or Free Energy Perturbation Combined with Driven Adiabatic Dynamics

Cuendet, Michel A., Tuckerman, Mark E.

Journal:

Journal of Chemical Theory and Computation

Year:

2012

Language:

english

File:

PDF, 1.85 MB

english, 2012

48

Mapping the Backbone Dihedral Free-Energy Surfaces in Small Peptides in Solution Using Adiabatic Free-Energy Dynamics

Rosso, Lula, Abrams, Jerry B., Tuckerman, Mark E.

Journal:

Journal of Physical Chemistry B

Year:

2005

Language:

english

File:

PDF, 313 KB

english, 2005

49

Molecular Dynamics Study of the Connection between Flap Closing and Binding of Fullerene-Based Inhibitors of the HIV-1 Protease†

Zhu, Zhongwei, Schuster, David I., Tuckerman, Mark E.

Journal:

Year:

2003

Language:

english

File:

PDF, 156 KB

english, 2003

50

Generalized Gaussian moment thermostatting: A new continuous dynamical approach to the canonical ensemble

Liu, Yi, Tuckerman, Mark E.

Journal:

The Journal of Chemical Physics

Year:

2000

Language:

english

File:

PDF, 499 KB

english, 2000

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