Honghui Zhang

Honghui Zhang

PHD from CUHKSZ, specialised in biological science

Sitemap

A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.

Pages

Posts

WASP: An R package for complex system modelling and prediction

15 minute read

Published:

The wavelet-based variance transformation method is used for system modelling and prediction. It refines predictor spectral representation using Wavelet Theory, which leads to improved model specifications and prediction accuracy. A supporting open-source software, Wavelet System Prediction (WASP), can be found under page of Software.

GitHub Pages: A site to host your personal homepage

3 minute read

Published:

GitHub Pages is a static site hosting service that takes HTML, CSS, and JavaScript files straight from a repository on GitHub, optionally runs the files through a build process, and publishes a website.

Word to Latex: Writing papers the right way

1 minute read

Published:

LaTeX is a document preparation system for high-quality typesetting. It is most often used for medium-to-large technical or scientific documents, but it can be used for almost any form of publishing.

people

projects

publications

Revealing the Interaction Mechanism Stabilizing Crystalline Cellulose Iβ by Molecular Dynamics Simulations

Published in Journal of Fiber Bioengineering and Informatics,, 2017

This paper unevils the interaction mechanism that stabilizes crystalline cellulose Iβ through in-depth molecular dynamics simulations.

Recommended citation: Jiang X., Zhang H., Zhong A. Revealing the Interaction Mechanism Stabilizing Crystalline Cellulose Iβ by Molecular Dynamics Simulations. Journal of Fiber Bioengineering and Informatics. 10(3): 141-154 (2017). https://doi.org/10.3993/jfbim00267

Revealing the Weak Interaction Mechanism of Crystalline Cellulose Iα by Molecular Dynamics Simulations

Published in Journal of Fiber Bioengineering and Informatics , 2019

This paper reveals the weak interaction mechanism stabilizing crystalline cellulose Iα, using molecular dynamics simulations.

Recommended citation: Zhang H., Jiang X. Revealing the Weak Interaction Mechanism of Crystalline Cellulose Iα by Molecular Dynamics Simulations. Journal of Fiber Bioengineering and Informatics. 12(4): 167-178 (2019). https://doi.org/10.3993/jfbim00324

The analysis of the effects of high hydrostatic pressure (HHP) on amylose molecular conformation at atomic level based on molecular dynamics simulation

Published in Food Chemistry, 2020

This paper analyses the effects of high hydrostatic pressure (HHP) on the molecular conformation of amylose using molecular dynamics simulation at the atomic level.

Recommended citation: Chen Z.†, Zhang H.† Wade K. et al. The analysis of the effects of high hydrostatic pressure (HHP) on amylose molecular conformation at atomic level based on molecular dynamics simulation. Food Chemistry.327: 127047 (2020). https://doi.org/10.1016/j.foodchem.2020.127047

Predicting Mutational Effects on Receptor Binding of the Spike Protein of SARS-CoV-2 Variants

Published in Journal of the American Chemical Society, 2021

This paper analysis the impact of mutations on receptor binding of SARS-CoV-2 spike protein, with direct implications in tracking viral variants.

Recommended citation: Bai C., Wang J., Chen G., Zhang H. et al. Predicting Mutational Effects on Receptor Binding of the Spike Protein of SARS-CoV-2 Variants. Journal of the American Chemical Society, 143(42): 17646-17654 (2021). https://doi.org/10.1021/jacs.1c07965

Application of Coarse-Grained (CG) Models to Explore Conformational Pathway of Large-Scale Protein Machines

Published in Entropy, 2022

This paper utilizes coarse-grained (CG) models to explore the conformational pathways of large-scale protein machines, advancing understanding in protein structure and dynamics.

Recommended citation: Shi D. †, An K.†, Zhang H.† et al. "Application of Coarse-Grained (CG) Models to Explore Conformational Pathway of Large-Scale Protein Machines". Entropy, 24(5), 620 (2022). https://doi.org/10.3390/e24050620

Mechanism of Regio- and Enantioselective Hydroxylation of Arachidonic Acid Catalyzed by Human CYP2E1: A Combined Molecular Dynamics and Quantum Mechanics/Molecular Mechanics Study

Published in Journal of Chemical Information and Modeling, 2025

We combine molecular dynamics and QM/MM to clarify how human CYP2E1 hydroxylates arachidonic acid and what determines its regio- and enantioselectivity.

Recommended citation: Zhang, H., , Hirao, H., Mechanism of Regio- and Enantioselective Hydroxylation of Arachidonic Acid Catalyzed by Human CYP2E1: A Combined Molecular Dynamics and Quantum Mechanics/Molecular Mechanics Study" Journal of Chemical Information and Modeling, 65(4), 2080-2092 (2025). https://doi.org/10.1021/acs.jcim.5c00115

software

Installation of AMBER

Amber is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules.

Installation of Chemshell

ChemShell is a script-based chemistry code focusing on hybrid QM/MM calculations with support for standard quantum chemical or force field calculations.

Installation of CP2K

CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems.

Installation of VASP

The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles.

Installation of Orca

ORCA is a general-purpose quantum chemistry program package that features virtually all modern electronic structure methods (density functional theory, many-body perturbation and coupled cluster theories, and multireference and semiempirical methods).

talks

The Van der Waals and Electrostatic Interaction Studying of Crystalline Cellulose Iβ Based on Molecular Dynamics

Published:

Recommended citation: Xuewei Jiang; Honghui Zhang; Anhua Zhong. “The Van der Waals and Electrostatic Interaction Studying of Crystalline Cellulose Iβ Based on Molecular Dynamics.” 10th International Conference on Textile Bioengineering and Informatics, 16-19 May 2017, Wuhan, China. Talk. link Download ppt here

Award:
Outstanding Student Paper in the 10th International Conference on Textile Bioengineering and Informatics

teaching

Textile Material Science

Undergraduate course, Wuhan Textile University, 2017

  • Teaching period: T2, 2017.
  • Position: Teacher
  • Role: Teaching
  • Number of students: ~100

BIM3018: Biophysical Chemistry

Undergraduate course, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong (Shenzhen), 2022

  • Teaching period: T2, 2022
  • Position: Teaching Assistant
  • Role: Demonstrator and Tutor
  • Number of students: 15
  • Student evaluation (overall): [5.72/6]. Teaching Evaluation Report
  • Course Profile: Download

CHM2004: Biophysical Chemistry

Undergraduate course, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong (Shenzhen), 2023

  • Teaching period: T2, 2023.
  • Position: Teaching Assistant
  • Role: Demonstrator and Tutor
  • Number of students: 32
  • Student evaluation (overall): [5.67/6]. Teaching Evaluation Report
  • Course Profile: Download

CHM2004: Biophysical Chemistry

Undergraduate course, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong (Shenzhen), 2024

  • Teaching period: T1, 2023.
  • Position: Teaching Assistant
  • Role: Demonstrator and Tutor
  • Number of students: 28
  • Student evaluation (overall): [5.58/6]. Teaching Evaluation Report
  • Course Profile: Download