13 citations · 37 across the 13 of their papers we have counts for
13 papers
Spin-Consistency Constraints in Noncollinear Tensor TDA
Wenxian Qin, Tai Wang, Yue Yu +3
TDDFT for open-shell systems, whether spin-conserving or spin-flip, has long suffered from spin contamination. This problem arises because the single-excitation space built upon a…
TDDFT Gradients and Nonadiabatic Couplings with Minimal Auxiliary Basis Set Approximation for Fewest-Switches Surface Hopping Dynamics
Cheng Fan, Zhichen Pu, Zehao Zhou +3
The electronic structure calculations remain a major bottleneck in ab initio nonadiabatic molecular dynamics. We develop an efficient TDDFT-based FSSH implementation in the GPU4PyS…
Analytical Excited-State Gradients and Derivative Couplings in TDDFT with Minimal Auxiliary Basis Set Approximation and GPU Acceleration
Zhichen Pu, Xiaojie Wu, Yuanheng Wang +5
Calculating excited-state gradients and derivative couplings using time-dependent density functional theory (TDDFT) remains a computationally demanding task. An efficient variant,…
CryoDyna: Multiscale end-to-end modeling of cryo-EM macromolecule dynamics with physics-aware neural network
Chengwei Zhang, Shimian Li, Yihao Niu +4
Single-particle cryo-EM has transformed structural biology but still faces challenges in resolving conformational heterogeneity at atomic resolution. Existing cryo-EM heterogeneity…
TRIDS: AI-native molecular docking framework for accelerating high-throughput virtual screening with physically valid binding poses
Xuhan Liu, Baohua Zhang, Yue Xue +7
Molecular docking is a cornerstone of drug discovery for unveiling the mechanism of ligand-receptor interactions. With the recent advances of deep learning (DL), AI-powered molecul…
Large Language Models as AI Agents for Digital Atoms and Molecules: Catalyzing a New Era in Computational Biophysics
Yijie Xia, Xiaohan Lin, Zicheng Ma +9
In computational biophysics, where molecular data is expanding rapidly and system complexity is increasing exponentially, large language models (LLMs) and agent-based systems are f…
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…
Different intermediate water cluster with distinct nucleation dynamics among mono layer ice nucleation
Yuheng Zhao, Yi Qin Gao
Recent first-principle calculations unveiled a distinctive dynamic behavior in water molecule rotation during the melting process of highly confined water, indicating a notable tim…
Generating High-Precision Force Fields for Molecular Dynamics Simulations to Study Chemical Reaction Mechanisms using Molecular Configuration Transformer
Sihao Yuan, Xu Han, Jun Zhang +5
Theoretical studies on chemical reaction mechanisms have been crucial in organic chemistry. Traditionally, calculating the manually constructed molecular conformations of transitio…
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…
DSDP: A Blind Docking Strategy Accelerated by GPUs
YuPeng Huang, Hong Zhang, Siyuan Jiang +4
Virtual screening, including molecular docking, plays an essential role in drug discovery. Many traditional and machine-learning based methods are available to fulfil the docking t…
Unsupervisedly Prompting AlphaFold2 for Few-Shot Learning of Accurate Folding Landscape and Protein Structure Prediction
Jun Zhang, Sirui Liu, Mengyun Chen +12
Data-driven predictive methods which can efficiently and accurately transform protein sequences into biologically active structures are highly valuable for scientific research and…
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…