Zhiye Tang

• Assistant Professor

Saito Group

Theoretical and Computational Molecular Science, Theoretical Molecular Science I

Institute for Molecular Science, Japan

April 2022-Present

• Project Assistant Professor

Okazaki Group Itoh Lab, Department of Advanced Material Science

Tokyo University, Japan

April 2020-March 2022

• Postdoctoral Researcher

Okazaki Lab, Graduate School of Engineering

Nagoya University, Japan

Jan 2018-March 2020

• Postdoctoral Researcher

Chang Lab, Chemistry Department

University of California, Riverside, US

Sept 2016-Dec 2017

• Substitute Lecturer (General Chemistry A)

University of California Riverside, Riverside, CA, US, 2017

• Teaching Assistant (General Chemistry A, B, C)

University of California Riverside, Riverside, CA, US, 2015-2016

• Teaching Assistant (General Chemistry Laboratory A, B, C)

University of California Riverside, Riverside, CA, US, 2012-2014

• Invited Lecturer

Computational Chemistry and Biology Workshop, Riverside, CA, US, 2013, 2016, 2017

Computational and Modeling Software:

• • Molecular/Brownian Dynamics: Gromacs, Lammps, AMBER, NAMD, Metadynamics, GaMD, GeomBD, NAM

  • Conformational Search/Docking: Autodock, Autodock Vina, VDock, Mining Minima 2

  • Protonation State Determination: MCCE, ProPKa, DelPhiPKa

  • Free Energy Calculation: Umbrella Sampling (WHAM), Milestoning

  • Visualization and Modeling: Vega ZZ, Avogadro, VMD, PyMol

  • Database: Cambridge Crystallographic Data Centre, PDB Data Bank, Pfam

  • Others: In House Packages, Personal Analysis Library and Tools

Programming Languages:

• • Proficient: C/C++, VC, VC#, Fortran, Basic, Mathematica, Direct X, Intel MKL Library, openMP, openMPI, SIMD, LaPACK, ScaLAPACK

  • Sufficient: PERL, PYTHON, R, Cuda

Features of Personal Library:

• Molecular Dynamics File IO: Topology (Gromacs, amber, namd, lammps format), Trajectories (DCD, MDCRD, TRR, PDB, GRO, etc.)

• Trajectory Format Conversion

• Easy Script Templating

• Basic Analysis Scripts: RMSD, RMSF, Hydrogen bond, Geometry, etc.

• Flexible Atom Selection: resemble that in VMD

• Energy Calculation: PME + SIMD + reproduced Verlet algorithm used in Gromacs

• Minimization: steepest decent, l-bfgs

• Internal Coordinate Conversion

• Polymer Preparation: adjustments of entanglements and radius of gyration

• Figure Generation: exporting data to BMP file

• Principal Component Analysis: Cartesian and Dihedral versions

• Data Fitting

General Software:

• • Microsoft Office, 3DS MAX, PHOTOSHOP

Fluent in

• English

• Mandarin Chinese

• Japanese

• Cantonese

Learning in progress

• French

Last Update: Jan 16, 2023