57 citations · 117 across the 10 of their papers we have counts for
10 papers
A Massively Scalable Ligand-Protein Dissociation Dynamic Database Derived from Atomistic Molecular Modelling
Maodong Li, Dechin Chen, Zhijun Pan +2
Understanding the kinetics of drug-protein interactions is paramount for drug design, yet the field lacks large-scale, dynamic data to move beyond static structural analysis. Here,…
Collective Variables Based on Multipole Expansion of Ewald Summation for Crystallization
YaoKun Lei, MaoDong Li, Yi Isaac Yang
Crystallization, a fundamental phase transition process governing material formation in natural and industrial contexts, involves the spontaneous emergence of long-range structural…
Great Restraining Wall in Multidimensional Collective Variable Space
Zhijun Pan, Maodong Li, Dechin Chen +1
Enhanced sampling methods are pivotal for exploring rare events in molecular dynamics (MD), yet face challenges in high-dimensional collective variable (CV) spaces where exhaustive…
A Novel 4-D Dataset Paradigm for Studying Complete Ligand-Protein Dissociation Dynamics
Maodong Li, Jiying Zhang, Zhe Wang +7
The kinetics and dynamics of drug-protein binding and dissociation are crucial to understanding drug absorption and metabolism. Despite advances in artificial intelligence (AI) too…
Performing Path Integral Molecular Dynamics Using Artificial Intelligence Enhanced Molecular Simulation Framework
Cheng Fan, Maodong Li, Sihao Yuan +4
This study employed an artificial intelligence-enhanced molecular simulation framework to enable efficient Path Integral Molecular Dynamics (PIMD) simulations. Owing to its modular…
A Sinking Approach to Explore Arbitrary Areas in Free Energy Landscapes
Zhijun Pan, Maodong Li, Dechin Chen +1
To address the time-scale limitations in molecular dynamics (MD) simulations, numerous enhanced sampling methods have been developed to expedite the exploration of complex free ene…
A Generalized Nucleation Theory for Ice Crystallization
Maodong Li, Yupeng Huang, Yijie Xia +5
Despite the simplicity of the water molecule, the kinetics of ice nucleation under natural conditions can be complex. We investigated spontaneously grown ice nuclei using all-atom…
Atomistic View of Homogeneous Nucleation of Water into Polymorphic Ices
Maodong Li, Jun Zhang, Niu Haiyang +6
Water is one of the most abundant substances on Earth, and ice, i.e., solid water, has more than 18 known phases. Normally ice in nature exists only as Ice Ih, Ice Ic, or a stackin…
Deep Reinforcement Learning of Transition States
Jun Zhang, Yao-Kun Lei, Zhen Zhang +5
Combining reinforcement learning (RL) and molecular dynamics (MD) simulations, we propose a machine-learning approach (RL) to automatically unravel chemical reaction mechanisms…
A Perspective on Deep Learning for Molecular Modeling and Simulations
Jun Zhang, Yao-Kun Lei, Zhen Zhang +6
Deep learning is transforming many areas in science, and it has great potential in modeling molecular systems. However, unlike the mature deployment of deep learning in computer vi…