cv

Basics

Name Chenlin Lu
Label Postdoctoral Researcher
Email chenlin.helix@gmail.com
Phone (646) 236-6523
Url https://lucl13.github.io

Education

  • 2017.09 - 2022.07

    Beijing, China

    Ph.D.
    Tsinghua University
    Chemical Engineering and Technology
  • 2018.08 - 2019.08

    Tokyo, Japan

    M.S. (Visiting)
    Tokyo Institute of Technology
    Life Science and Technology
  • 2013.09 - 2017.07

    Beijing, China

    B.S.
    Tsinghua University
    Chemical and Industrial Biological Engineering

Research

  • 2022.09 - Present
    Postdoctoral researcher
    Columbia University
    Department: Biochemistry and Molecular Biophysics. Advisor: Prof. Anum Glasgow. Field: computational and experimental biophysics
    • To determine site-resolved energetic information from hydrogen exchange-mass spectrometry (HX-MS) data
    • To elucidate allosteric mechanism using the site-resolved free energies of opening (ΔGop)
    • Developed PIGEON-FEATHER, a Bayesian method to determine site-resolved protection factors from peptide-level HX-MS data via isotopic mass envelope reconstruction
    • Designed PFNet, an end-to-end ML method for predicting protection factors directly from raw mass spectra
    • Unveiled the allosteric ligand regulation mechanism of phosphofructokinase by integrating HX-MS (PIGEON-FEATHER and PFNet) with MD simulations
  • 2018.08 - 2019.08
    Graduate and joint program Researcher
    Tokyo Institute of Technology
    Department: Life Science and Technology. Advisor: Prof. Takafumi Ueno. Field: bioinorganic chemistry, and protein crystallography
    • To determine the X-ray structure of the gold-clustering site in designed Fr-Au
    • Solved high-resolution structures of the tunable gold clustering site
    • Deposited PDBs: 7VIO, 7VIP, 7VIQ, 7VIR, 7VIS, 7VIT, and 7VIU
  • 2017.09 - 2022.07
    Graduate researcher
    Tsinghua University
    Department: Chemical Engineering. Advisor: Prof. Zheng Liu, and Prof. Dianan Lu. Field: bioinorganic chemistry, computational and experimental biophysics
    • To design new-to-nature metalloproteins and metalloenzymes
    • Unveiled the Au ions transport mechanism using a MD-MSMs method
    • Designed novel gold metalloproteins with a precisely tunable structure in apo-ferritin
    • Leveraged Fr-Au metalloproteins as the first artificial metallo-cycloisomerase
    • Elucidated the reaction mechanism using DFT calculations

Presentations

Support

  • 2023.06
    Anton2 allocations
    Pittsburgh Supercomputing Center and the National Research Council
    Co-PI, 330,000 simulation units
  • 2022.10
    ACCESS allocations
    University of Illinois at Urbana-Champaign, and the National Science Foundation
    700,000.0 ACCESS Credits, 2022-2023

Skills

Programming language
Python
Bash
Tcl
Machine learning
Scikit-learn
PyTorch
Lightning
Data analytics and visualization
NumPy, Pandas
Matplotlib, Seaborn
Molecular dynamics
Anton2
Gromacs, OpenMM
VMD, MDTraj, MDAnalysis
Protein design and modeling
Autodock
Rosetta
ProteinMPNN, RFdiffusion
DFT calculations
g16
Experimental Biophysics
Protein expression and purification
Hydrogen exchange/mass spectrometry (HX-MS)
X-ray crystallography
Markov state models
PyEmma
Deeptime