Curriculum Vitae - Po-Jen Hsu / 許伯任
Name: Po-Jen Hsu / 許伯任
Email: clusterga@gmail.com
Tel: +886-952-335534
Google Scholar: https://goo.gl/U6hWDn
Website: https://goo.gl/jz7sU2
EDUCATION
2014: Ph.D., Molecular Science and Technology, TIGP, Academia Sinica/Physics, National Central University. Supervised by Dr. Siew Ann Cheong, Dr. Arnaldo Rapallo , and Dr. San-Kiong Lai (primary thesis supervisor) [10-16].
2003: M.Sc. in Physics, National Central University [19-20]
2000: B.Sc. in Physics, National Central University
WORK EXPERIENCE
2017/2 - present: System Administrator of High Performance Computing Clusters, Institute of Atomic and Molecular Sciences, Academia Sinica.
2016/8 - present: Postdoctoral Research Fellow, Institute of Atomic and Molecular Sciences, Academia Sinica (supervised by Dr. Jer-Lai Kuo) [1-8].
2015/8 - 2016/7: Postdoctoral Research Fellow, Department of Applied Chemistry, National Chiao Tung University (supervised by Professor Sheng-Hsien Lin) [9].
2015 - 2015/7: Senior Data Scientist, Vpon Big Data Mobile Advertising -- Improved advertisement traffic quality and built real-time bidding engine.
2014 - 2015: Senior Engineer, Innovation Digital System, System Software Development Division, Hon Hai Precision IND. CO., LTD. -- Built hand gesture control algorithms based on computer vision for IoT environment and supported camera subsystem in Android cell phone.
2005 - 2008: Research assistant in Physics department, National Central University. --Built and maintained PC clusters and Unix/Linux servers. Built algorithms and models from scratch to simulate chemical and biological materials under statistical mechanics circumstances [17,18].
2003 - 2005: Military service.
TEACHING
- General Physics
- Statistical Mechanics
- Thermodynamics
- Molecular Dynamics Theory
- Data Science and Applications in Physics
- Pattern Recognition and Machine Learning
- High Performance Computing
PUBLICATION LIST
(Each title links to the paper)
- Liquid Crucible Model for Aggregation of Phenylacetylene in the Gas Phase, Saurabh Mishra, Dipak Kumar Sahoo, Po-Jen Hsu, Yoshiyuki Matsuda, Jer-Lai Kuo, Himansu S. Biswal, and and G. Naresh Patwari, Phys. Chem. Chem. Phys. (submitted).
- Dissociation mechanism of sodiated N-acetylglucosamine and N-acetylgalactosamine, Cheng-chau Chiu, Shang-Ting Tsai, Po-Jen Hsu, Hai Thi Huynh, Jien-Lian Chen, HuuTrong Phan, Shih-Pei Huang, Hou-Yu Lin, Jer-Lai Kuo and Chi-Kung Ni, Phys. Chem. Chem. Phys. (submitted).
- Infrared spectra of neutral dimethylamine clusters: An infrared-vacuum ultraviolet spectroscopic and anharmonic vibrational calculation study, Bingbing Zhang, Qian-Rui Huang, Shukang Jiang, Li-Wei Chen, Po-Jen Hsu, Chong Wang, Ce Hao, Xiangtao Kong, Dongxu Dai, Xueming Yang, Jer-Lai Kuo, and Ling Jiang, J. Chem. Phys. 150, 064317 (2019).
- Competition between hydrogen bonds and van der Waals force in intermolecular structure formation of protonated branched-chain alcohol clusters, Natsuko Sugawara, Po-Jen Hsu, Asuka Fujii, and Jer-Lai Kuo, Phys. Chem. Chem. Phys. 20, 25482 (2018).
- Collision-induced dissociation of sodiated glucose, galactose, and mannose, and the identification of anomeric configurations, Hai Thi Huynh, Huu Trong Phan, Po-Jen Hsu, Jien-Lian Chen, Hock Seng Nguan, Shang-Ting Tsai, Thantip Roongcharoen, Chia Yen Liew, Chi-Kung Ni, and Jer-Lai Kuo, Phys. Chem. Chem. Phys. 20, 19614 (2018).
- Hydrogen bond network structures of protonated short-chain alcohol clusters, Asuka Fujii, Natsuko Sugawara, Po-Jen Hsu, Takuto Shimamori, Ying-Cheng Li, Toru Hamashima, and Jer-Lai Kuo, Phys. Chem. Chem. Phys. 20, 14971 (2018).
- Collision-induced dissociation of sodiated glucose and identification of anomeric configuration, Jien-Lian Chen, Hock-Seng Nguan, Po-Jen Hsu, Shang-Ting Tsai, Chia Yen Liew, Jer-Lai Kuo, Wei-Ping Hu, and Chi-Kung Ni, Phys. Chem. Chem. Phys. 19, 15454 (2017).
- Temperature and size dependence of characteristic hydrogen-bonded network structures with ion core switching in protonated (Methanol)6-10-(Water)1 mixed clusters: A revisit, Marusu Katada, Po-Jen Hsu, Asuka Fujii, and Jer-Lai Kuo, J. Phys. Chem. A 121, 5399 (2017).
- Exploration of hydrogen bond networks and potential energy surfaces of methanol clusters with a two-stage clustering algorithm, P. J. Hsu, K. L. Ho, S. H. Lin, and J. L. Kuo, Phys. Chem. Chem. Phys. 19, 544 (2017).
- Precursory signatures of protein folding/unfolding: from time series correlation analysis to atomistic mechanisms, P. J. Hsu, S. A. Cheong, and S. K. Lai, J. Chem. Phys. 140, 204905 (2014).
- A new perspective of shape recognition to discover the phase transition of finite-size clusters, P. J. Hsu, J. Comput. Chem. 35, 1082 (2014).
- Peptide dynamics by molecular dynamics and diffusion theory methods with improved basis sets, P. J. Hsu, S. K. Lai, and A. Rapallo, J. Chem. Phys. 140, 104910 (2014).
- Melting behavior of Ag14 cluster: An order parameter by instantaneous normal modes, P. H. Tang, T. M. Wu, P. J. Hsu, and S. K. Lai, J. Chem. Phys. 137, 244304 (2012).
- Comparative study of cluster Ag17Cu2 by instantaneous normal mode analysis and by isothermal Brownian-type molecular dynamics simulation, P. H. Tang, T. M. Wu, T. W. Yen, S. K. Lai, and P. J. Hsu, J. Chem. Phys. 135, 094302 (2011).
- Dynamical study of metallic clusters using the statistical method of time series clustering, S. K. Lai, Y. T. Lin, P. J. Hsu, and S. A. Cheong, Compt. Phys. Commun. 182, 1013 (2011).
- Melting behavior of noble-metal-based bimetallic clusters, T. W. Yen, P. J. Hsu, and S. K. Lai, e-J. Surf. Sci. Nanotech. 7, 149-156 (2009).
- Melting scenario in metallic clusters, P. J. Hsu, J. S. Luo, S. K. Lai, J. F. Wax, and J-L Bretonnet, J. Chem. Phys. 129, 194302 (2008).
- Structure of bimetallic clusters, P. J. Hsu and S. K. Lai, J. Chem. Phys. 124, 044711 (2006).
- Multi-canonical basin-hopping: a new global optimization method for complex systems, L. Zhan, B. Piwowar, W. K. Liu, P. J. Hsu, S. K. Lai, and Jeff Z. Y. Chen, J. Chem. Phys. 120, 5536 (2004).
- Structures of metallic clusters: mono- and polyvalent metals, S. K. Lai, P. J. Hsu, K. L. Wu, W. K. Liu, and M. Iwamatsu, J. Chem. Phys. 117, 10715 (2002).
AWARD
- Best Team Presentation Award, 4th Hope Meeting, 2012, Japan.
INVITED TALKS
"Exploring the Potential Energy Surface of Methanol Clusters: An Efficient Two-stage Clustering Algorithm", StatPhys-Taiwan-2016, Taiwan [9]
"Invalid Advertisement Traffic Analysis in the Mobile Advertising Using Python", PyCon 2015, Taiwan (download pycon slides)
"Open Source in Physics", International Conference on Open Source 2009, Taiwan (download slides)
SPECIALTIES
Applied Mathematics and Numerical Computation
- Time series analysis
- Genetic algorithm
- Monte Carlo method
- Optimization techniques
- Mode-coupling approaches for long-time behaviors
First Principle Calculation and Molecular Dynamics Theory
- Gaussian09/2016
- GAMESS
- CP2K
- AMBER
- Gromacs
- Lammps
Programming Skills
- Python
- C/C++
- Fortran
- Matlab/Octave
- Unix/Linux shell script
Parallel Computing Techniques
SQL Database
- Hive: Hadoop database for cloud computing
- SQLite: familiar with python, C++ API and SQL database programming [9].
Computer Vision
- Open source computer vision (OpenCV)
- Linux/Android camera and input subsystems
System Administrator of Servers Since 1999
- High Performance Computing Cluster: with more than 9 years experience in hardware and software.
- GitLab Server: Built a GitLab server for laboratory (Our GitLab Webpage).
- Unix/Linux Servers: with more than 12 years experience.
High performance computing clusters at Institute of Atomic and Molecular Sciences, Academia Sinica.
OPEN SOURCE PROJECTS
(Each title links to the GitHub source code)
TSCA
Two-stage Clustering Algorithm (Python/SQLite)
Framework of TSCA.
TSCA [1-9] archives molecular structures into SQLite databases and performs a two-stage clustering method based on the cluster shape and the bonded networks of the molecules to trim down the number of isomers. This algorithm has been proven efficient in various hydrogen bonded systems such as methanol, alcohol, and ammonia clusters.
PTMBHGA
Parallel Tempering Multicanonical Basin-hopping Plus Genetic Algorithm (Fortran/MPICH)
Framework of PTMBHGA.
PTMBHGA [18-20] combines several state-of-the-art optimization techniques such as genetic algorithm, parallel tempering Monte Carlo method, simulated annealing, basing-hopping method, and multicanonical Monte Carlo method. It is flexible and reliable for searching global strucutre in cluster system. This program has been adopted by research groups in Japan and Malaysia.
PMD
Parallel Molecular Dynamics Simulation (Fortran/MPICH)
Framework of PTMD.
PMD [11, 13-17] is designed for model simulation and several statistical analysis including moments, Fourier transformation, and nearest neighbor analysis. It integrates a task schedule system so that users can perform multiple simulations and analysis in parallel.
CL-VAF
Vector Autocorrelation Function with GPGPU (C++/OpenCL)
GPU-accelerated autocorrelation function.
CL-VAF [12-15] utilizes the power of GPU (Graphical Processing Unit) to accelerate the autocorrelation calculation of multi-dimensional vectors.
GestureCV
Hand gesture control based on histogram analysis (C++/OpenCL/OpenCV)
GestureCV combines image filtering and histogram analysis to accomplish precise real-time hand gesture control on laptops or embedded systems.
Framework of GestureCV.
Demonstration of the hand gesture control.
g09tools
Tools for submission and recovering of Gaussian software (Shell Script)
g09tools [1-9] will scan all the Gaussian input files in a folder and submit the Gaussian jobs to the high-performance computing cluster. It will automatically detect the status of the Gaussian job (failed or running). If failed jobs are detected, it will retrieve the last SCF state and continue the SCF steps. It was written in shell script language.
EDUCATION PROJECT
Chinese translations of PhET education project in Physics (EzGo, OSSACC, Ministry of Education)
OTHER INFORMATION
Molecular dynamics simulations of a fragment of the protein transthyretin and metallic clusters diagnosed by the ultra-fast shape recognition technique, time series segmentation, time series cross correlation analysis and diffusion theory method (download thesis)
