湯 之也

TANG, Zhiye

Zhiye Tang

Assistant Professor

Institute for Molecular Science, Japan

Work Email: zhiyetang[at]ims.ac.jp

Personal Email: ztang006[at]ucr.edu

Research Experiences

  • 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

Education

Ph.D. in Chemistry

University of California, Riverside, USA

September 2011-August 2016

Bachelor of Science in Chemistry

Wuhan University, China

September 2007-June 2011

Teaching Experiences

  • 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

Computer and Computational Skills

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

Language Skills

Fluent in

  • English

  • Mandarin Chinese

  • Japanese

  • Cantonese

Learning in progress

  • French

Last Update: Jan 16, 2023