Accurate and Transferable Reactive Molecular Dynamics Models from Constrained Density Functional Theory

CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations

(2020) Thomas D. Kühne et al.   JOURNAL OF CHEMICAL PHYSICS

Multiscale Simulation Reveals Passive Proton Transport Through SERCA on the Microsecond Timescale

(2020) C. Li et al.   BIOPHYSICAL JOURNAL

Deep Potential Molecular Dynamics: A Scalable Model with the Accuracy of Quantum Mechanics

(2018) Linfeng Zhang et al.   PHYSICAL REVIEW LETTERS

Modulating the Chemical Transport Properties of a Transmembrane Antiporter via Alternative Anion Flux

(2018) Zhi Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Quantum Dynamics and Spectroscopy of Ab Initio Liquid Water: The Interplay of Nuclear and Electronic Quantum Effects

(2017) Ondrej Marsalek et al.   Journal of Physical Chemistry Letters

Proton movement and coupling in the POT family of peptide transporters

(2017) Joanne L. Parker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Understanding the essential proton-pumping kinetic gates and decoupling mutations in cytochromecoxidase

(2017) Ruibin Liang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiscale Simulations Reveal Key Aspects of the Proton Transport Mechanism in the ClC-ec1 Antiporter

(2016) Sangyun Lee et al.   BIOPHYSICAL JOURNAL

Perspective: How good is DFT for water?

(2016) Michael J. Gillan et al.   JOURNAL OF CHEMICAL PHYSICS

Computationally Efficient Multiscale Reactive Molecular Dynamics to Describe Amino Acid Deprotonation in Proteins

(2016) Sangyun Lee et al.   Journal of Chemical Theory and Computation

Multistate Density Functional Theory for Effective Diabatic Electronic Coupling

(2016) Haisheng Ren et al.   Journal of Physical Chemistry Letters

The Origin of Coupled Chloride and Proton Transport in a Cl–/H+ Antiporter

(2016) Sangyun Lee et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Multiscale simulations reveal key features of the proton-pumping mechanism in cytochromecoxidase

(2016) Ruibin Liang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Role of Presolvation and Anharmonicity in Aqueous Phase Hydrated Proton Solvation and Transport

(2015) Rajib Biswas et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Multiscale Reactive Molecular Dynamics for Absolute pKa Predictions and Amino Acid Deprotonation

(2014) J. Gard Nelson et al.   Journal of Chemical Theory and Computation

Hydrated Excess Protons Can Create Their Own Water Wires

(2014) Yuxing Peng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

Multiscale reactive molecular dynamics

(2012) Chris Knight et al.   JOURNAL OF CHEMICAL PHYSICS

Computationally Efficient Multiconfigurational Reactive Molecular Dynamics

(2012) Takefumi Yamashita et al.   Journal of Chemical Theory and Computation

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

The Coupled Proton Transport in the ClC-ec1 Cl−/H+ Antiporter

(2011) Yong Zhang et al.   BIOPHYSICAL JOURNAL

Constrained Density Functional Theory

(2011) Benjamin Kaduk et al.   CHEMICAL REVIEWS

Conformational Consequences of Ionization of Lys, Asp, and Glu Buried at Position 66 in Staphylococcal Nuclease

(2010) Daniel A. Karp et al.   BIOCHEMISTRY

Implementing the Nelder-Mead simplex algorithm with adaptive parameters

(2010) Fuchang Gao et al.   COMPUTATIONAL OPTIMIZATION AND APPLICATIONS

Block-Localized Density Functional Theory (BLDFT), Diabatic Coupling, and Their Use in Valence Bond Theory for Representing Reactive Potential Energy Surfaces

(2009) Alessandro Cembran et al.   Journal of Chemical Theory and Computation

Comment on “Free energy simulations of single and double ion occupancy in gramicidin A” [J. Chem. Phys. 126, 105103 (2007)]

(2008) Benoît Roux et al.   JOURNAL OF CHEMICAL PHYSICS

Systematic optimization of long-range corrected hybrid density functionals

(2008) Jeng-Da Chai et al.   JOURNAL OF CHEMICAL PHYSICS

Protons and how they are transported by proton pumps

(2008) M. J. Buch-Pedersen et al.   PFLUGERS ARCHIV-EUROPEAN JOURNAL OF PHYSIOLOGY

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS