Ziyan Zhuang 「庄子岩」

I am currently a Ph.D. student at Tianjin University (Wikipedia) and a jointly trained Ph.D. student at Shenzhen Loop Area Institute (SLAI). My supervisors are Guangrong Zhao at Tianjin University and Yu Li (CUHK) at Shenzhen Loop Area Institute.

Previously, I received my B.S. in Biological Science from Xinjiang University in June 2026, graduating with a GPA of 4.30 and ranking in the top 1%.

Research Interests: AI for Synthetic Biology, bio-inspired algorithm optimization, multi-scale coupling simulation of large biomolecules (cross-system / cross-method), and trustworthy scientific AI agents.

Email: ziyan@tju.edu.cn / ziyanzhuang@slai.edu.cn

CV  /  Github  /  ORCID  /  Google Scholar

Ziyan Zhuang
Hand-drawn scroll depicting the evolution of life

I love biology — more is different.

PKU taught me to see the spatiotemporal complexity emerging from the central dogma and molecular networks; SJTU showed me how AI can map dense, entangled biological signals into higher-dimensional latent spaces to reveal sparse structure. At XJU, Dr. Wen Zhong's developmental biology teaching showed me how nonlinear development makes causal reasoning essential to biological research. These experiences led me to synthetic biology—augmented by AI—as a path to understand, design, and improve living systems. As Feynman said, “What I cannot create, I do not understand.”

In memory of Dr. Wen Zhong, who passed away on 6 March 2026. Rest in peace.

News & Honors

Selected Publications

* denotes corresponding author.

No Image

CYPForge: Auditable Preparation of Cytochrome P450 Molecular Dynamics Systems


Zhuang ZY, Zhao QY, Shao YRS, Zhao GR*, Li Y*, Zhang DC*
ChemRxiv (Preprint), 2026 Preprint
TL;DR: An automated, auditable pipeline that transforms raw PDB/SDF inputs into simulation-ready CYP450 MD systems with gated quality control at every stage.
Paper  |  Code
No Image

Spinetoram resistance in Tuta absoluta: selection, inheritance, biochemical mechanism and fitness cost


Xie JG, Rukiya T, Liu N, Zhuang ZY, Liu XN*, Song Y*.
Pesticide Biochemistry and Physiology, 2025 JCR Q1
TL;DR: Dissected the inheritance mode, biochemical mechanism, and fitness trade-offs of spinetoram resistance in the invasive tomato leafminer.
Paper
Elsevier
CYP380C12 Graphical Abstract

Molecular insights on the function of CYP380C12 in Aphis gossypii Glover (Hemiptera: Aphididae): in silico and RNAi analyses


Zhang LJ, Zhuang ZY (Co-first), Xie JG, Kong WT, Li TT, Wang SF, Liu XN*.
Journal of Economic Entomology, 2025 JCR Q1
TL;DR: Combined homology modeling, molecular docking, and RNAi knockdown to reveal CYP380C12's role in cotton aphid detoxification.
Paper
ESA Oxford
Paper Cover of Journal of Agricultural and Food Chemistry

Functional analysis of lactase phlorizin hydrolase in insect-plant coevolution based on deglycosylation


Li Y, Kong WT, Li TT, Zhang LJ, Zhuang ZY, Liu N*, Liu XN*.
Journal of Agricultural and Food Chemistry, Cover Paper, 2025 JCR Q1
TL;DR: Showed that insect lactase phlorizin hydrolase mediates plant-insect coevolution by deglycosylating plant secondary metabolites to release defensive aglycones.
Paper
ACS
No Image

Exploring the role of CYP6AB328 in spinetoram resistance and growth and development of Phthorimaea absoluta


Xie JG, Wang SY, Zhuang ZY, Wang XH, Lin MH, Liu XN*.
Pesticide Biochemistry and Physiology, 2025 JCR Q1
TL;DR: Showed that CYP6AB328 plays a dual role in both spinetoram detoxification and normal growth and development in the tomato leafminer.
Paper
Elsevier
No Image

Functional Investigation of CYP304F1 in Tuta absoluta (Lepidopteran: Gelechiidae) by RNA Interference


Xie JG, Ali A, Li Y, Zhuang ZY, Liu XN*.
Journal of Economic Entomology, 2024 JCR Q1
TL;DR: RNAi-mediated silencing established CYP304F1's functional importance in the tomato leafminer's xenobiotic response and normal physiology.
Paper
ESA Oxford

Projects & Software

Zhuangzhou System Architecture

Zhuangzhou (庄周): Autonomous Scientific Agent for Enzyme Design & Metabolic Engineering


Ziyan Zhuang & Qianyu Zhao
GitHub

An autonomous scientific intelligence platform that integrates a cross-disciplinary knowledge graph, a multi-agent reasoning system, and hierarchical scientific skills (protein design, molecular simulation, metabolic network analysis) into a closed Think→Act→Observe→Review→Re-decide loop. It enables cross-scale intelligent bioengineering — from catalytic mechanism reasoning and enzyme active-site design to whole-cell metabolic network optimization.

CYPForge workflow diagram

CYPForge: Auditable Preparation of Cytochrome P450 Molecular Dynamics Systems


Ziyan Zhuang & collaborators
GitHub  |  Paper

An auditable workflow for preparing CYP450 protein–heme–ligand systems for Amber molecular dynamics, with manifest-based quality gates across parameterization, solvation, and pre-MD preparation.

Full-protein overview rendered by the biomolecular visualization pipeline

Biomolecular Visualization Agentic Pipeline


Ziyan Zhuang
GitHub

A reproducible pipeline for protein-structure visualization that separates structural facts, chemical topology, interaction evidence, and Blender rendering.

Field Practice & Academic Programs

Westlake AIVC Week

Westlake AIVC Week (Westlake University)


August 2026, Hangzhou, China

Participated in Westlake AIVC Week at the Yungu Campus of Westlake University, a flagship international program advancing the AI Virtual Cell (AIVC) vision. Engaged with frontier directions spanning AI virtual cell modeling, multi-omics integration, deep learning foundation models, and AI for Science, gaining insights into how these converging approaches are reshaping biological research toward data-driven simulation of living systems.

Ancient Ginkgo Tree Sampling at Zhejiang University

Ancient Ginkgo Leaf Collection Volunteer Program (Zhejiang University)


September 2025

Volunteered for Zhejiang University's China Temple Ancient Ginkgo Leaf Collection Initiative, performing standardized sampling of ancient ginkgo trees. Specimen data has been archived in the Zhejiang University Herbarium and incorporated into the GinkgoDB comprehensive ginkgo database, providing important specimens and data for ancient ginkgo germplasm conservation and genetic lineage research.

Shanghai Jiao Tong University Summer School

AI for Bioengineering Summer School (Shanghai Jiao Tong University)


August 2025

Participated in the summer school at the Institute of Natural Sciences, Shanghai Jiao Tong University, focusing on the application of artificial intelligence in bioengineering. Learned cutting-edge techniques including AI-driven protein design and computational biology workflows.

Peking University Summer School

Quantitative Biology Summer School (Peking University)


July 2024

Participated in the summer school at the Center for Life Science (CLS), Peking University, exploring quantitative methods in biological research, including mathematical modeling of biological systems and data-driven experimental design.

Wildlife Monitoring Field Practice (Northern Tianshan Mountains)


June 2024
Ziyan Zhuang, Zifan Zhao, et al.

Participated in field research in the Northern Tianshan Mountains, using infrared camera technology to record and analyze the behavior and distribution of local wild animals. The visual above shows representative footage captured during the internship.