arXiv subjects

Sihao Yuan

Publications and source records attributed to Sihao Yuan.

3 recordsLinked to original sources

arXiv2025

CryoDyna: Multiscale end-to-end modeling of cryo-EM macromolecule dynamics with physics-aware neural network

Single-particle cryo-EM has transformed structural biology but still faces challenges in resolving conformational heterogeneity at atomic resolution. Existing cryo-EM heterogeneity analysis methods either lack atomic details or tend to subject to overfitting due to image noise and limited information in single views. To obtain atomic detailed multiple conformations and make full use of particle images of different orientations, we present here CryoDyna, a deep learning framework to infer macromolecular dynamics directly from 2D projections by integrating cross-view attention and multi-scale deformation modeling. Combining coarse-grained MARTINI representation with atomic backmapping, CryoDyna achieves near-atomic interpretation of protein conformational landscapes. Validated on multiple simulated and experimental datasets, CryoDyna demonstrates improved modeling accuracy and robustly recovers multi-scale complex structure changes hidden in the cryo-EM particle stacks. As examples, we generated protein-RNA coordinated motions, resolved dynamics in the unseen region of RAG signal end complex, mapped translocating ribosome states in a one-shot manner, and revealed step-wise closure of a membrane-anchored protein multimer. This work bridges the gap between cryo-EM heterogeneity analysis and atomic-scale structural dynamics, offering a promising tool for exploration of complex biological mechanisms.

q-bio.BM↗

arXiv2025

Performing Path Integral Molecular Dynamics Using Artificial Intelligence Enhanced Molecular Simulation Framework

This study employed an artificial intelligence-enhanced molecular simulation framework to enable efficient Path Integral Molecular Dynamics (PIMD) simulations. Owing to its modular architecture and high-throughput capabilities, the framework effectively mitigates the computational complexity and resource-intensive limitations associated with conventional PIMD approaches. By integrating machine learning force fields (MLFFs) into the framework, we rigorously tested its performance through two representative cases: a small-molecule reaction system (double proton transfer in formic acid dimer) and a bulk-phase transition system (water-ice phase transformation). Computational results demonstrate that the proposed framework achieves accelerated PIMD simulations while preserving quantum mechanical accuracy. These findings show that nuclear quantum effects can be captured for complex molecular systems, using relatively low computational cost.

physics.chem-ph↗

arXiv2024

Generating High-Precision Force Fields for Molecular Dynamics Simulations to Study Chemical Reaction Mechanisms using Molecular Configuration Transformer

Theoretical studies on chemical reaction mechanisms have been crucial in organic chemistry. Traditionally, calculating the manually constructed molecular conformations of transition states for chemical reactions using quantum chemical calculations is the most commonly used method. However, this way is heavily dependent on individual experience and chemical intuition. In our previous study, we proposed a research paradigm that uses enhanced sampling in molecular dynamics simulations to study chemical reactions. This approach can directly simulate the entire process of a chemical reaction. However, the computational speed limits the use of high-precision potential energy functions for simulations. To address this issue, we present a scheme for training high-precision force fields for molecular modeling using a previously developed graph-neural-network-based molecular model, molecular configuration transformer. This potential energy function allows for highly accurate simulations at a low computational cost, leading to more precise calculations of the mechanism of chemical reactions. We applied this approach to study a Claisen rearrangement reaction and a Carbonyl insertion reaction catalyzed by Manganese.

physics.chem-ph↗