arXiv subjects

Zhijun Pan

Publications and source records attributed to Zhijun Pan.

9 recordsLinked to original sources

arXiv2026

A Massively Scalable Ligand-Protein Dissociation Dynamic Database Derived from Atomistic Molecular Modelling

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, we present DD-03B, a massively scalable database providing dynamic, all-atom dissociation trajectories for a broad set of ligand-protein complexes. Utilising and extending a validated computational pipeline, we generated dissociation trajectories for 19,037 ligand-protein complexes sourced from PDBbind+v2020R1, resulting in a repository of approximately 0.3 billion simulation frames totalling 40 TB in size. For these systems-which possess experimental binding affinities (kd) but typically lack measured koff rates-we computed and assigned dissociation rate constants through trajectory reweighting. Our analysis reveals that protein-ligand complexes can be categorised into three mechanistic types (pathway-dominant, open-pocket, and entropy-pocket systems), each requiring distinct strategies for accurate kinetic characterisation. Together with our previously released DD-13M, DD-03B forms the core of the expandable Dissociation Dynamic Database (DDD) project, which will be continuously augmented with new trajectories. This large-scale, publicly available resource establishes a critical foundation for training and benchmarking next-generation generative AI models to predict and optimise drug-protein dissociation kinetics.

physics.comp-ph↗

arXiv2026

Human-AI Collaborative Game Testing with Vision Language Models

As modern video games become increasingly complex, traditional manual testing methods are proving costly and inefficient, limiting the ability to ensure high-quality game experiences. While advancements in Artificial Intelligence (AI) offer the potential to assist human testers, the effectiveness of AI in truly enhancing real-world human performance remains underexplored. This study investigates how AI can improve game testing by developing and experimenting with an AI-assisted workflow that leverages state-of-the-art machine learning models for defect detection. Through an experiment involving 800 test cases and 276 participants of varying backgrounds, we evaluate the effectiveness of AI assistance under four conditions: with or without AI support, and with or without detailed knowledge of defects and design documentation. The results indicate that AI assistance significantly improves defect identification performance, particularly when paired with detailed knowledge. However, challenges arise when AI errors occur, negatively impacting human decision-making. Our findings show the importance of optimizing human-AI collaboration and implementing strategies to mitigate the effects of AI inaccuracies. By this research, we demonstrate AI's potential and problems in enhancing efficiency and accuracy in game testing workflows and offers practical insights for integrating AI into the testing process.

cs.HC↗

arXiv2026

A Novel 4-D Dataset Paradigm for Studying Complete Ligand-Protein Dissociation Dynamics

The kinetics and dynamics of drug-protein binding and dissociation are crucial to understanding drug absorption and metabolism. Despite advances in artificial intelligence (AI) tools for drug-protein interaction studies, existing training datasets remain limited to static structures or quasi-static conformations. This paper proposes a novel computational approach for rapidly generating drug-protein dissociation trajectories and presents the inaugural dynamically time-resolved 4-D (t, x, y, z) trajectory database DD-13M. This dataset captures over 26,000 complete dissociation processes for 565 ligand-protein complexes, providing nearly 13 million frames of all-atom simulation trajectories. A deep equivariant generative model, UnbindingFlow, was trained using the DD-13M dataset. This model has the capacity to produce dissociation trajectories for novel targets whilst accurately predicting their rate constants (koff). DD-13M introduces a new type of training dataset for AI models, establishing a de novo paradigm for studying the dynamics of drug-protein interactions.

physics.comp-ph↗

arXiv2026

Great Restraining Wall in Multidimensional Collective Variable Space

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 sampling becomes computationally prohibitive. While techniques like metadynamics (MetaD) and path-CV enable targeted free energy surface (FES) reconstruction, they often struggle with confinement stability, hyperparameter sensitivity, and geometric flexibility. This work introduces the Great Restraining Wall (GW) method, a robust framework for efficient FES sampling within predefined CV subspaces, addressing these limitations through a novel kernel density estimation (KDE)-derived restraining potential. GW operates by constructing a bias potential that confines sampling to user defined regions ranging from multidimensional masks to 1D pathways via asymptotically half-harmonic barriers. Unlike MetaD variants requiring iterative bias deposition, GW potential is derived from a cumulative distribution function, ensuring confinement without manual hyperparameter tuning. GW provides a versatile, stable, and efficient framework for targeted FES sampling, particularly beneficial for complex biomolecular systems with intricate CV landscapes. Its integration with existing enhanced sampling protocols opens avenues for studying ligand binding, conformational transitions, and other rare events with unprecedented precision. Future work will explore GW extension to adaptive regions and machine learning-guided CV discovery.

physics.comp-ph↗

arXiv2026

Guiding Generative Storytelling with Knowledge Graphs

Large language models (LLMs) have shown great potential in story generation, but challenges remain in maintaining long-form coherence and effective, user-friendly control. Retrieval-augmented generation (RAG) has proven effective in reducing hallucinations in text generation; while knowledge-graph (KG)-driven storytelling has been explored in prior work, this work focuses on KG-assisted long-form generation and an editable KG coupled with LLM generation in a two-stage user study. This work investigates how KGs can enhance LLM-based storytelling by improving narrative quality and enabling user-driven modifications. We propose a KG-assisted storytelling pipeline and evaluate it in a user study with 15 participants. Participants created prompts, generated stories, and edited KGs to shape their narratives. Quantitative and qualitative analysis finds improvements concentrated in action-oriented, structurally explicit narratives under our settings, but not for introspective stories. Participants reported a strong sense of control when editing the KG, describing the experience as engaging, interactive, and playful.

cs.CL↗

arXiv2025

A Sinking Approach to Explore Arbitrary Areas in Free Energy Landscapes

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 energy landscapes. A commonly employed approach accelerates the sampling of degrees of freedom associated with pre-defined collective variables (CVs), which typically tends to traverse the entire CV range. However, in many scenarios, the focus of interest is on specific regions within the CV space. This paper introduces a novel "sinking" approach that enables enhanced sampling of arbitrary areas within the CV space. We begin by proposing a gridded convolutional approximation that productively replicates the effects of metadynamics, a powerful CV-based enhanced sampling technique. Building on this, we present the SinkMeta method, which "sinks" the interior bias potential to create restraining potential "cliffs" at the grid edges. This technique can confine the exploration of CVs in MD simulations to a preset area. Our experimental results demonstrate that SinkMeta requires minimal sampling steps to estimate the free energy landscape for CV subspaces of various shapes and dimensions, including irregular two-dimensional regions and one-dimensional pathways between metastable states. We believe that SinkMeta will pioneer a new paradigm for sampling partial phase spaces, especially offering an efficient and flexible solution for sampling minimum free energy paths in high-dimensional spaces.

physics.comp-ph↗

arXiv2024

RaTrack: Moving Object Detection and Tracking with 4D Radar Point Cloud

Mobile autonomy relies on the precise perception of dynamic environments. Robustly tracking moving objects in 3D world thus plays a pivotal role for applications like trajectory prediction, obstacle avoidance, and path planning. While most current methods utilize LiDARs or cameras for Multiple Object Tracking (MOT), the capabilities of 4D imaging radars remain largely unexplored. Recognizing the challenges posed by radar noise and point sparsity in 4D radar data, we introduce RaTrack, an innovative solution tailored for radar-based tracking. Bypassing the typical reliance on specific object types and 3D bounding boxes, our method focuses on motion segmentation and clustering, enriched by a motion estimation module. Evaluated on the View-of-Delft dataset, RaTrack showcases superior tracking precision of moving objects, largely surpassing the performance of the state of the art. We release our code and model at https://github.com/LJacksonPan/RaTrack.

cs.CV↗

arXiv2023

AI Nushu: An Exploration of Language Emergence in Sisterhood -Through the Lens of Computational Linguistics

This paper presents "AI Nushu," an emerging language system inspired by Nushu (women's scripts), the unique language created and used exclusively by ancient Chinese women who were thought to be illiterate under a patriarchal society. In this interactive installation, two artificial intelligence (AI) agents are trained in the Chinese dictionary and the Nushu corpus. By continually observing their environment and communicating, these agents collaborate towards creating a standard writing system to encode Chinese. It offers an artistic interpretation of the creation of a non-western script from a computational linguistics perspective, integrating AI technology with Chinese cultural heritage and a feminist viewpoint.

cs.CL↗

arXiv2022

Self-Supervised Scene Flow Estimation with 4-D Automotive Radar

Scene flow allows autonomous vehicles to reason about the arbitrary motion of multiple independent objects which is the key to long-term mobile autonomy. While estimating the scene flow from LiDAR has progressed recently, it remains largely unknown how to estimate the scene flow from a 4-D radar - an increasingly popular automotive sensor for its robustness against adverse weather and lighting conditions. Compared with the LiDAR point clouds, radar data are drastically sparser, noisier and in much lower resolution. Annotated datasets for radar scene flow are also in absence and costly to acquire in the real world. These factors jointly pose the radar scene flow estimation as a challenging problem. This work aims to address the above challenges and estimate scene flow from 4-D radar point clouds by leveraging self-supervised learning. A robust scene flow estimation architecture and three novel losses are bespoken designed to cope with intractable radar data. Real-world experimental results validate that our method is able to robustly estimate the radar scene flow in the wild and effectively supports the downstream task of motion segmentation.

cs.CV↗