Search results for: Mark E. Tuckerman

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article

An interoperable implementation of collective‐variable based enhanced sampling methods in extended phase space within the OpenMM package

Shitanshu Bajpai, Brian K. Petkov, Muchen Tong, Charlles R. A. Abreu, more

Journal of Computational Chemistry > 44 > 28 > 2166 - 2183

Collective variable (CV)‐based enhanced sampling techniques are widely used today for accelerating barrier‐crossing events in molecular simulations. A class of these methods, which includes temperature accelerated molecular dynamics (TAMD)/driven‐adiabatic free energy dynamics (d‐AFED), unified free energy dynamics (UFED), and temperature accelerated sliced sampling (TASS), uses an extended variable...

chapter

New Developments in Plane-Wave Based ab initio Calculations

Glenn J. Martyna, Mark E. Tuckerman

Lecture Notes in Physics > Bridging Time Scales: Molecular Simulations for the Next Decade > Perpectives in ab initio MD > 381-411

New developments in plane-wave based ab initio calculations are reviewed. First, a general framework for electrostatic calculations is presented that allows 3-dimensional periodic systems (solids, liquids), 2-dimensional periodic systems (surfaces), and non-periodic systems (clusters) to be treated properly and easily (J. Chem. Phys. 110, 2810–2821 (1999) and J. Chem. Phys. 115...

chapter

Basic Concepts and Trends in ab Initio Molecular Dynamics

Mark E. Tuckerman

NATO Science Series II: Mathematics, Physics and Chemistry > Novel Approaches to the Structure and Dynamics of Liquids: Experiments, Theories and Simulations > 53-91

The field of ab initio molecular dynamics, in which finite temperature molecular dynamics trajectories are generated using forces obtained from electronic structure calculations performed “on the fly”, is a rapidly evolving and growing technology that allows chemical processes in condensed phases to be studied in an accurate and unbiased way. This article is intended to present the basics of the ab initio...

chapter

Generating Equilibrium Ensembles Via Molecular Dynamics

Mark E. Tuckerman

Handbook of Materials Modeling > Atomistic Scale > 589-611

Over the last several decades, molecular dynamics (MD) has become one of the most important and commonly used approaches for studying condensed phase systems. MD calculations generally serve two often complementary purposes. First, an MD simulation can be used to study the dynamics of a system starting from particular initial conditions. Second, MD can be employed as a means of generating a collection...

article

First principles molecular dynamics study of proton dynamics and transport in phosphoric acid/imidazole (2:1) system

Linas Vilčiauskas, Mark E. Tuckerman, Jan P. Melchior, Gabriel Bester, more

Solid State Ionics > 2013 > 252 > Complete > 34-39

Phosphoric acid based polymer electrolyte membranes (e.g. poly(benzimidazole)/phosphoric acid) are the only quasi-anhydrous separator electrolytes for medium temperature fuel cells currently in use. Pure phosphoric acid has the highest known intrinsic proton conductivity of any substance, which is very sensitive towards doping with Brønsted–Lowry bases or even acids. Proton conductivity shows the...

article

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

Chemical Physics Letters > 2011 > 511 > 4-6 > 177-182

The properties of the hydrated hydroxide ion OH−(aq) stand in sharp contrast to those of most other aqueous ions. Chief among these is its anomalously high mobility, which is shared only by the aqueous hydronium ion H3O+(aq). However, while the transport mechanism of H3O+(aq) is now well understood, the details of OH−(aq) diffusion at ambient conditions are just beginning to emerge, and the effects...

article

On the Use of the SiC(100)-c(2×2) Surface as a Substrate for the Creation of Ordered Organic–Semiconductor Interfaces

Yanli Zhang, Mark E. Tuckerman

The Journal of Physical Chemistry Letters > 2011 > 2 > 14 > 1814 - 1819

article

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

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

The Journal of Physical Chemistry A > 2011 > 115 > 23 > 6112 - 6124

article

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 ^†

Alexander Witt, Francesco Sebastianelli, Mark E. Tuckerman, Zlatko Bačić

The Journal of Physical Chemistry C > 2010 > 114 > 48 > 20775 - 20782

article

Enhanced Conformational Sampling of Peptides via Reduced Side-Chain and Solvent Masses

I-Chun Lin, Mark E. Tuckerman

The Journal of Physical Chemistry B > 2010 > 114 > 48 > 15935 - 15940

article

Failure of Perturbative DFT-Derived STM Images of Organic Molecules on Semiconductor Surfaces

Robin L. Hayes, Mark E. Tuckerman

The Journal of Physical Chemistry C > 2010 > 114 > 35 > 15102 - 15108

article

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

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

Journal of the American Chemical Society > 2010 > 132 > 33 > 11510 - 11515

article

Concerted Proton−Electron Transfer to Dioxygen in Water

Ophir Snir, Yifeng Wang, Mark E. Tuckerman, Yurii V. Geletii, more

Journal of the American Chemical Society > 2010 > 132 > 33 > 11678 - 11691

article

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, more

Chemical Physics > 2010 > 370 > 1-3 > 294-305

The Liouville operator approach is employed to derive a new measure-preserving geometric integrator for molecular dynamics simulations in the isothermal–isobaric (NPT) ensemble. Recently, we introduced such a scheme for NPT simulations with isotropic cell fluctuations in the absence of holonomic constraints [M.E. Tuckerman et al., J. Phys. A 39 (2006) 5629]. Here, we extend this approach to include...

article

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

Dominik Marx, Amalendu Chandra, Mark E. Tuckerman

Chemical Reviews > 2010 > 110 > 4 > 2174 - 2216

article

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

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

The Journal of Physical Chemistry B > 2009 > 113 > 52 > 16574 - 16589

article

Hydroxide anion at the air–water interface

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

Chemical Physics Letters > 2009 > 481 > 1-3 > 2-8

Whether aqueous interfaces are acidic or basic has implications for interfacial chemistry, but the question remains open. We employ first-principles molecular dynamics simulations to determine the intrinsic propensity of OH ⁻ for the air–water interface and find that OH ⁻ is stabilized by roughly k _B T at the interface vs. the bulk. We predict, therefore, that the surface population...

article

Ab Initio Molecular Dynamics Studies of the Liquid−Vapor Interface of an HCl Solution ^†

Hee-Seung Lee, Mark E. Tuckerman

The Journal of Physical Chemistry A > 2009 > 113 > 10 > 2144 - 2151

article

Efficient and Direct Generation of Multidimensional Free Energy Surfaces via Adiabatic Dynamics without Coordinate Transformations

Jerry B. Abrams, Mark E. Tuckerman

The Journal of Physical Chemistry B > 2008 > 112 > 49 > 15742 - 15757

article

The Structure and Proton Transport Mechanisms in the Superprotonic Phase of CsH ₂ PO ₄ : An Ab Initio Molecular Dynamics Study

Hee-Seung Lee, Mark E. Tuckerman

The Journal of Physical Chemistry C > 2008 > 112 > 26 > 9917 - 9930

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INFONA - science communication portal

Search results for: Mark E. Tuckerman

An interoperable implementation of collective‐variable based enhanced sampling methods in extended phase space within the OpenMM package

New Developments in Plane-Wave Based ab initio Calculations

Basic Concepts and Trends in ab Initio Molecular Dynamics

Generating Equilibrium Ensembles Via Molecular Dynamics

First principles molecular dynamics study of proton dynamics and transport in phosphoric acid/imidazole (2:1) system

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

On the Use of the SiC(100)-c(2×2) Surface as a Substrate for the Creation of Ordered Organic–Semiconductor Interfaces

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

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 ^†

Enhanced Conformational Sampling of Peptides via Reduced Side-Chain and Solvent Masses

Failure of Perturbative DFT-Derived STM Images of Organic Molecules on Semiconductor Surfaces

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

Concerted Proton−Electron Transfer to Dioxygen in Water

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

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

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

Hydroxide anion at the air–water interface

Ab Initio Molecular Dynamics Studies of the Liquid−Vapor Interface of an HCl Solution ^†

Efficient and Direct Generation of Multidimensional Free Energy Surfaces via Adiabatic Dynamics without Coordinate Transformations

The Structure and Proton Transport Mechanisms in the Superprotonic Phase of CsH ₂ PO ₄ : An Ab Initio Molecular Dynamics Study

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