Wei-Tse Hsu

Wei-Tse Hsu

Postdoctoral Research Associate in Drug Design

Department of Biochemistry, ‎ ‎ University of Oxford

About Me

Hi! I’m Wei-Tse Hsu, a Postdoctoral Research Associate in Drug Design in the Biggin Group at the University of Oxford. I am passionate about developing neural networks for binding affinity predictions and unraveling biophysical phenomena. I am proficient in molecular dynamics, enhanced sampling methods, and deep learning applications in computational molecular sciences. My Ph.D. work in the Shirts Group primarily focused on understanding the structural determinants of glycosylated insulin’s properties, as well as developing improved free energy methods such as alchemical metadynamics and replica exchange of expanded ensembles (REXEE). With the ultimate goal of becoming a professor, I have been enjoying making convoluted scientific topics more accessible, engaging, and inspiring. I also love sharing my insights on this website. (Check my recent posts and mini-courses for more!) In my spare time, I enjoy long-distance running, cooking, photography, and playing the guitar. Feel free to reach out to me at wei-tse.hsu@bioch.ox.ac.uk – I’d love to connect!

Download my curriculum vitae.

Interests
  • Molecular dynamics
  • Enhanced sampling methods
  • Computational biophysics
  • Deep learning
Education
  • Ph.D. in Chemical Engineering, 2018-2024

    University of Colorado, Boulder

  • B.Sc. in Chemical Engineering, 2013-2017

    National Taiwan University

Research Experience

See Research Projects and Publications for more details.

 
 
 
 
 
Department of Chemical Engineering, University of Colorado Boulder
Ph.D. researcher in the Shirts Research Group
Department of Chemical Engineering, University of Colorado Boulder
Sep 2018 – Nov 2023 Colorado, U.S.A.
  • Advisor: Prof. Michael R. Shirts
  • Developed synchronous ensemble of expanded ensembles (EEXE) by combining the working principles of expanded ensemble (EXE) and Hamiltonian replica exchange (HREX).
  • Developed alchemical metadynamics, which enables alchemical biases in the metadynamics framework and overcomes limitations of traditional alchemical free energy methods.
  • Developed methods based on molecular dynamics to predict the proteolytic stability and monomeric propensity of glycosylated insulin.
  • Helped design SCALE-MS, an extensible framework aiming to support adapative and asynchronous executions of simulation ensembles.
  • Maintained physical_validation, a Python package aimed at testing the physical validity of results from molecular dynamics.
 
 
 
 
 
Department of Chemical Engineering, National Taiwan University
Undergraduate researcher/research assistant in Biomolecular Engineering Laboratory
Department of Chemical Engineering, National Taiwan University
Jul 2016 – Apr 2018 Taipei, Taiwan
  • Advisor: Prof. Steven Sheng-Shih Wang
  • Explored the effects of various small molecules on amyloid fibrillogensis of hen egg-white lysozyme (HEWL) with a wide array of spectroscopic experiments.
  • Investigated the aggregation process of human $\gamma$D-crystallin (HGDC) using molecular dynamics and molecular docking.
 
 
 
 
 
Department of Chemiecal Engineering, National Taiwan University
Undergraduate researcher in Biomimetic Membrane Interfacial Phenomena and Engineering Laboratory
Department of Chemiecal Engineering, National Taiwan University
Jul 2015 – Feb 2016 Taipei, Taiwan
  • Advisor: Prof. Ling Chao
  • Developed MATLAB codes to accurately estimate fluorophore diffusivity on lipid membranes by fitting fluorescence intensity curves from FRAP (fluorescence recovery after photobleaching) experiments ($R^2>0.97$).
  • Experimented methods for depositing giant plasma membrane vesicles (GPMVs) on polymer cushions.
  • Constructed supported lipid bilayer (SLB) platforms to study membrane protein properties.

Research Projects

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Publications

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physical_validation: A Python package to assess the physical validity of molecular simulation results
Exploring the influence of brilliant blue G on amyloid fibril formation of lysozyme
Lysozyme amyloid fibrillization in presence of tacrine/acridone-coumarin heterodimers
Brilliant blue R dye is capable of suppressing amyloid fibril formation of lysozyme
Investigating the effects of erythrosine B on amyloid fibril formation derived from lysozyme