57 citations · 164 across the 6 of their papers we have counts for
6 papers
Recovering a Molecule's 3D Dynamics from Liquid-phase Electron Microscopy Movies
Enze Ye, Yuhang Wang, Hong Zhang +3
The dynamics of biomolecules are crucial for our understanding of their functioning in living systems. However, current 3D imaging techniques, such as cryogenic electron microscopy…
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…
Learning Clustered Representation for Complex Free Energy Landscapes
Jun Zhang, Yao-Kun Lei, Xing Che +3
In this paper we first analyzed the inductive bias underlying the data scattered across complex free energy landscapes (FEL), and exploited it to train deep neural networks which y…
Combine Umbrella Sampling with Integrated Tempering Method for Efficient and Accurate Calculation of Free Energy Changes of Complex Energy Surface
Mingjun Yang, Lijiang Yang, Yiqin Gao +1
Umbrella sampling is an efficient method for the calculation of free energy changes of a system along well-defined reaction coordinates. However, when multiple parallel channels al…
Facile implementation of integrated tempering sampling method to enhance the sampling over a broad range of temperatures
Peng Zhao, Li Jiang Yang, Yi Qin Gao +1
Integrated tempering sampling (ITS) method is an approach to enhance the sampling over a broad range of energies and temperatures in computer simulations. In this paper, a new vers…