Yong Duan

Publications (22)

Publications listed in the lab bibliography, across all years.

2026

Zhen Huang, Ray Luo, Yong Duan (2026). A Density-Consistent, Finite van der Waals Potential from Gaussian Atomic Densities. The Journal of Physical Chemistry Letters.

Yongxian Wu, Piotr Cieplak, Yong Duan, Ray Luo (2026). pGM5P-26: A Polarizable Gaussian Multipole Water Model with Transferable Temperature-Dependent Thermodynamics. Journal of Chemical Theory and Computation.

Piotr Cieplak, Ray Luo, Yong Duan (2026). Charge Transfer Interactions in Quantum Mechanics and in Classical Force Fields. The Journal of Physical Chemistry B.

2025

Zhen Huang, Yong Duan, Xiongwu Wu, Ray Luo (2025). DEGAUSS: A Novel Softcore Force Field Using Double Exponential van der Waals and Gaussian Charge for Molecular Dynamics Simulations I: Theory and Validation. Journal of Chemical Theory and Computation.

Taoyu Niu, Junmei Wang, Zhen Huang, Ray Luo, Piotr Cieplak, Yong Duan (2025). Optimization of Lennard–Jones Parameters for Induced Dipole Polarizable Gaussian Multipole Force Field. The Journal of Physical Chemistry B.

Yongxian Wu, Qiang Zhu, Zhen Huang, Piotr Cieplak, Yong Duan, Ray Luo (2025). Automated Refinement of Property-Specific Polarizable Gaussian Multipole Water Models Using Bayesian Black-Box Optimization. Journal of Chemical Theory and Computation.

Yong Duan, Junmei Wang, Piotr Cieplak, Ray Luo (2025). Refinement of Atomic Polarizabilities for a Polarizable Gaussian Multipole Force Field with Simultaneous Considerations of Both Molecular Polarizability Tensors and In-Solution Electrostatic Potentials. Journal of Chemical Information and Modeling.

Zhen Huang, Yongxian Wu, Yong Duan, Ray Luo (2025). Performance Tuning of Polarizable Gaussian Multipole Model in Molecular Dynamics Simulations. Journal of Chemical Theory and Computation.

2024

Yong Duan, Taoyu Niu, Junmei Wang, Piotr Cieplak, Ray Luo (2024). PCMRESP: A Method for Polarizable Force Field Parameter Development and Transferability of the Polarizable Gaussian Multipole Models Across Multiple Solvents. Journal of Chemical Theory and Computation.

Shiji Zhao, Piotr Cieplak, Yong Duan, Ray Luo (2024). Assessment of Amino Acid Electrostatic Parametrizations of the Polarizable Gaussian Multipole Model. Journal of Chemical Theory and Computation.

2023

Qiang Zhu, Yongxian Wu, Shiji Zhao, Piotr Cieplak, Yong Duan, Ray Luo (2023). Streamlining and Optimizing Strategies of Electrostatic Parameterization. Journal of Chemical Theory and Computation.

Zhen Huang, Shiji Zhao, Piotr Cieplak, Yong Duan, Ray Luo, Haixin Wei (2023). Optimal Scheme to Achieve Energy Conservation in Induced Dipole Models. Journal of Chemical Theory and Computation.

Shiji Zhao, Piotr Cieplak, Yong Duan, Ray Luo (2023). Transferability of the Electrostatic Parameters of the Polarizable Gaussian Multipole Model. Journal of Chemical Theory and Computation.

2022

Shiji Zhao, Haixin Wei, Piotr Cieplak, Yong Duan, Ray Luo (2022). PyRESP : A Program for Electrostatic Parameterizations of Additive and Induced Dipole Polarizable Force Fields. Journal of Chemical Theory and Computation.

Haixin Wei, Piotr Cieplak, Yong Duan, Ray Luo (2022). Stress tensor and constant pressure simulation for polarizable Gaussian multipole model. The Journal of Chemical Physics.

Shiji Zhao, Haixin Wei, Piotr Cieplak, Yong Duan, Ray Luo (2022). PyRESP: A flexible program for polarizable force field parameterizations. Biophysical Journal.

Shiji Zhao, Haixin Wei, Piotr Cieplak, Yong Duan, Ray Luo (2022). Accurate Reproduction of Quantum Mechanical Many-Body Interactions in Peptide Main-Chain Hydrogen-Bonding Oligomers by the Polarizable Gaussian Multipole Model. Journal of Chemical Theory and Computation.

2020

Haixin Wei, Ruxi Qi, Junmei Wang, Piotr Cieplak, Yong Duan, Ray Luo (2020). Efficient formulation of polarizable Gaussian multipole electrostatics for biomolecular simulations. The Journal of Chemical Physics.

2019

Junmei Wang, Piotr Cieplak, Ray Luo, Yong Duan (2019). Development of Polarizable Gaussian Model for Molecular Mechanical Calculations I: Atomic Polarizability Parameterization To Reproduce ab Initio Anisotropy. Journal of Chemical Theory and Computation.

2012

Junmei Wang, Piotr Cieplak, Jie Li, Qin Cai, Meng-Juei Hsieh, Ray Luo, Yong Duan (2012). Development of Polarizable Models for Molecular Mechanical Calculations. 4. van der Waals Parametrization. The Journal of Physical Chemistry B.

2006

Lijiang Yang, Chun-Hu Tan, Meng-Juei Hsieh, Junmei Wang, Yong Duan, Piotr Cieplak, James Caldwell, Peter A. Kollman, Ray Luo (2006). New-Generation Amber United-Atom Force Field. The Journal of Physical Chemistry B.

2003

Yong Duan, Chun Wu, Shibasish Chowdhury, Mathew C. Lee, Guoming Xiong, Wei Zhang, Rong Yang, Piotr Cieplak, Ray Luo, Taisung Lee, James Caldwell, Junmei Wang, Peter Kollman (2003). A point‐charge force field for molecular mechanics simulations of proteins based on condensed‐phase quantum mechanical calculations. Journal of Computational Chemistry.