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
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