Optimization of the Lennard-Jones parameters for a combined ab initio quantum mechanical and molecular mechanical potential using the 3-21G basis set. - Marek Freindorf; Jiali Gao (J. Comput. Chem., 1996)

Energy components of aqueous solution: Insight from hybrid QM/MM simulations using a polarizable solvent model. - Jiali Gao (J. Comput. Chem., 1997)

A molecular mechanics force field for NAD+ NADH, and the pyrophosphate groups of nucleotides. - Joseph J. Pavelites; Jiali Gao; Paul A. Bash; Alexander D. MacKerell Jr. (J. Comput. Chem., 1997)

Hydrogen-bonding interactions in the active site of a low molecular weight protein-tyrosine phosphatase. - Cristóbal Alhambra; Jiali Gao (J. Comput. Chem., 2000)

Ab initio QM/MM simulations with a molecular orbital-valence bond (MOVB) method: application to an SN2 reaction in water. - Yirong Mo; Jiali Gao (J. Comput. Chem., 2000)

Combined QM/MM study of the opsin shift in bacteriorhodopsin. - Ramkumar Rajamani; Jiali Gao (J. Comput. Chem., 2002)

Hydride transfer catalyzed by xylose isomerase: Mechanism and quantum effects. - Mireia Garcia-Viloca; Cristóbal Alhambra; Donald G. Truhlar; Jiali Gao (J. Comput. Chem., 2003)

Implementation of an adaptive umbrella sampling method for the calculation of multidimensional potential of mean force of chemical reactions in solution. - Ramkumar Rajamani; Kevin J. Naidoo; Jiali Gao (J. Comput. Chem., 2003)

Combined QM/MM and path integral simulations of kinetic isotope effects in the proton transfer reaction between nitroethane and acetate ion in water. - Jiali Gao; Kin-Yiu Wong; Dan Thomas Major (J. Comput. Chem., 2007)

CHARMM: The biomolecular simulation program. - Bernard R. Brooks; Charles L. Brooks III; Alexander D. MacKerell Jr.; Lennart Nilsson; Robert J. Petrella; Benoît Roux; Y. Won; G. Archontis; Christian Bartels; Stefan Boresch; Amedeo Caflisch; Leo S. D. Caves; et al. (J. Comput. Chem., 2009)

The opsin shift and mechanism of spectral tuning in rhodopsin. - Ramkumar Rajamani; Yen-Lin Lin; Jiali Gao (J. Comput. Chem., 2011)

Dipole preserving and polarization consistent charges. - Peng Zhang; Peng Bao; Jiali Gao (J. Comput. Chem., 2011)

A self-consistent coulomb bath model using density fitting. - Xin Chen 050; Zexing Qu; Bingbing Suo; Jiali Gao (J. Comput. Chem., 2020)

Community Reaction Network Reduction for Constructing a Coarse-Grained Representation of Combustion Reaction Mechanisms. - Lin Ji; Yue Li; Jie Wang; An Ning; Naixin Zhang; Shengyao Liang; Jiyun He; Tianyu Zhang; Zexing Qu; Jiali Gao (J. Chem. Inf. Model., 2022)

Research on Diabetes Prediction Model Based on Machine Learning Algorithms. - Na Hu; Jiali Gao (CIPAE, 2023)

A Fractional-Order Recurrent Neural Network Model for Time-Variant Quadratic Programming in Robot Motion Planning. - Yi Yang 049; Puchen Zhu; Xuchen Wang; Weibing Li; Jiali Gao; Richard M. Voyles; Xin Ma (AIM, 2024)

Layer-wise surface quality improvement in laser powder bed fusion through surface anomaly detection and control. - Chenguang Ma; Di Wang; Kai Zhao; Jiali Gao; Heng Wang; Aoming Zhang; Lang Cheng; Yingjie Zhang (Comput. Ind. Eng., 2024)

CPPCGM: A Highly Efficient Sequence-Based Tool for Simultaneously Identifying and Generating Cell-Penetrating Peptides. - Qiufen Chen; Yuewei Zhang; Jiali Gao; Jun Zhang (J. Chem. Inf. Model., 2025)