Zhen Zhang
Electrical and Computer Engineering
Assistant Professor
Contact Information
Office Location: EL 176Phone: 435-797-9068
Email: zhen.zhang@usu.edu
Additional Information:
Educational Background
Teaching Interests
I am interested in contributing to a high standard of teaching at both the undergraduate and graduate levels. Courses I have sufficient background to teach include principles of cyber-physical systems, formal methods, stochastic verification, concurrency theory, digital logic design, embedded system design, FPGA design, random process, asynchronous circuit design and synthesis, and modeling and analysis of synthetic biological systems.
Research Interests
My primary interest is in the modeling and verification of concurrent and stochastic systems, ranging from distributed protocols and asynchronous circuits to cyber-physical and synthetic biological systems. I am interested in developing theories and algorithms to advance formal and semi-formal verification techniques in both conventional and stochastic settings, and their applications in controller synthesis, probabilistic hardware and software, and adversarial perturbation detection for image classification conducted by deep neural networks.
Awards
College of Engineering and ECE Dept. Undergraduate Researcher of the Year, 2023
ECE Department, USU
Advisor of the Year , 2020
ECE Department, USU
Publications | Abstracts
- Zhang, Z., A computational model of the effect of VEGF production in wet age-related macular degeneration on neovascularization. Annual Meeting of the Association for Research in Vision and Ophthalmology (ARVO), 2020
An asterisk (*) at the end of a publication indicates that it has not been peer-reviewed.
- Neupane, T., Zhang, Z., (2019). Approximation Techniques for Stochastic Analysis of Biological Systems: Automated Reasoning for Systems Biology and Medicine. Automated Reasoning for Systems Biology and Medicine, Springer, 2019
- Zhang, Z., (2015). Efficient Analysis Methods in Synthetic Biology: Computational Methods in Synthetic Biology. Springer New York
Publications | Book Chapters
An asterisk (*) at the end of a publication indicates that it has not been peer-reviewed.
Publications | Journal Articles
Academic Journal
- Buecherl, L., Roberts, R., Fontanarrosa, P., Mante, J., Zhang, Z., Myers, C.J, (2021). Stochastic Hazard Analysis of Genetic Circuits in iBioSim and STAMINA. ACS Synthetic Biology, 10:10, 2532-2540. doi: 10.1021/acssynbio.1c00159
- Cotner, M., Zhan, J., Zhang, Z., (2021). A Computational Metabolic Model for Engineered Production of Resveratrol in Escherichia coli. ACS Synthetic Biology, 10:8, 1992–2001. doi: 10.1021/acssynbio.1c00163
- Watanabe, L., Nguyen, T., Zhang, M., Zundel, Z., Zhang, Z., Madsen, C., Roehner, N., Myers, C., (2019). iBioSim 3: A Tool for Model-Based Genetic Circuit Design. ACS Synthetic Biology, 8:7, 1560-1563. doi: 10.1021/acssynbio.8b00078
- Sidney, C.R, Curtis, M., Alastair, M.J, Tramy, N., Nicholas, R., Bryan, B., Jacob, B., Michael, B., Kiri, C., Kevin, C., Raik, Gr\"unberg, , Chris, M., Goksel, M., Ernst, O., Matthew, P., Meher, S., Michael, Z., Zhang, Z., Zach, Z., H., G.J, Chris, M., Herbert, S., Anil, W., (2018). Synthetic Biology Open Language (SBOL) Version 2.2.0. Journal of Integrative Bioinformatics, De Gruyter, 15:1, doi: 10.1515/jib-2018-0001
- Zundel, Z., Samineni, M., Zhang, Z., Myers, C.J, (2017). A Validator and Converter for the Synthetic Biology Open Language. ACS Synthetic Biology, 6:7, 1161-1168.
- Zhang, Z., Serwe, W., Wu, J., Yoneda, T., Zheng, H., Myers, C., (2016). An improved fault-tolerant routing algorithm for a Network-on-Chip derived with formal analysis. Science of Computer Programming, 118, 24 - 39.
- Roehner, N., Beal, J., Clancy, K., Bartley, B., Misirli, G., Gr\"unberg, Raik, , Oberortner, E., Pocock, M., Bissell, M., Madsen, C., Nguyen, T., Zhang, M., Zhang, Z., Zundel, Z., Densmore, D., Gennari, J.H, Wipat, A., Sauro, H.M, Myers, C.J, (2016). Sharing Structure and Function in Biological Design with SBOL 2.0. ACS Synthetic Biology, 5:6, 498-506.
- Zhang, Z., Nguyen, T., Roehner, N., Misirli, G., Pocock, M., Oberortner, E., Samineni, M., Zundel, Z., Beal, J., Clancy, K., Wipat, A., Myers, C.J, (2015). libSBOLj 2.0: A Java Library to Support SBOL 2.0. IEEE Life Sciences Letters, 1:4, 34-37.
- Bryan, B., Jacob, B., Kevin, C., Goksel, M., Nicholas, R., Ernst, O., Matthew, P., Michael, B., Curtis, M., Tramy, N., Zhang, Z., H., G.J, Chris, M., Anil, W., Herbert, S., (2015). Synthetic Biology Open Language (SBOL) Version 2.0.0. Journal of Integrative Bioinformatics, 12, 902.
- Roehner, N., Zhang, Z., Nguyen, T., Myers, C.J, (2015). Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language. ACS Synthetic Biology, 4:8, 873-879.
- Zheng, H., Zhang, Z., Myers, C.J, Rodriguez, E., Zhang, Y., (2015). Compositional Model Checking of Concurrent Systems. IEEE Transactions on Computers, 64:6, 1607-1621.
- Madsen, C., Zhang, Z., Roehner, N., Winstead, C.J, Myers, C., (2014). Stochastic Model Checking of Genetic Circuits. J. Emerg. Technol. Comput. Syst., 11:3, 23:1--23:21.
An asterisk (*) at the end of a publication indicates that it has not been peer-reviewed.
Publications | MultiMedia
Software
- Zhang, Z., (2023). VERAPAK software tool: Refutation-based Deep Neural Network verification tool. *
- Israelsen, B., Taylor, L., Zhang, Z., (2023). RAGTIMER software tool: a rare-event formal verification tool for Chemical Reaction Networks. 29th International Symposium on Model Checking of Software (SPIN 2023) *
- Taylor, L., Zhang, Z., (2023). Cycle and Commute expansion for the RAGTIMER software tool for drastic improvement of formal analysis of Chemical Reaction Networks. 23rd Conference on Formal Methods in Computer-Aided Design – FMCAD 2023
- Jeppson, J., Zhang, Z., (2023). STAMINA C++ 2.0 software tool. 20th International Conference on Quantitative Evaluation of Systems (QEST 2023)
An asterisk (*) at the end of a publication indicates that it has not been peer-reviewed.
Publications | Other
Other
- Zhang, Z., (2011). A Fault-Tolerant Routing Algorithm for a Network-on-Chip Using a Link Fault Model.
An asterisk (*) at the end of a publication indicates that it has not been peer-reviewed.