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Zhang, Jonathan

Associate Professor

Dr. Zhiwen Jonathan Zhang is an associate professor of the Bioengineering Department in the School of Engineering at SCU, starting September of 2011. Dr. Zhang received his Ph.D. degree in Chemistry and Biochemistry from University of Texas at Austin in 2001 by developing the first generation E. coli two-hybrid system, engineering peptide-binding peptides, pioneering the concept of "substrate-targeted enzyme inhibitors". He then carried out his postdoctoral research in The Scripps research Institute from 2001 to 2004, researching on engineering unnatural proteins via expanding genetic codes and hijacking cellular protein synthesis machinery. From 2004 to 2011, Dr. Zhang has been an assistant professor of Medicinal Chemistry in College of Pharmacy, Department of Biomedical Engineering and Institute of Cellular and Molecular Biology at University of Texas at Austin.

Dr. Zhang’s classroom teaching ranges from the fundamental “Biomolecular Engineering” to highly interdisciplinary capstone “Molecular Biodevice Engineering”.

Zhang lab has graduated 6 postdocs and visiting professors and 5 PhD students, numerous Master students and undergraduate research students from his lab.

Dr. Zhang has established his highly interdisciplinary research programs at the crossroad of biomolecular and biodevice engineering, genetic engineering, biochemistry, chemical biology and drug discovery. Recently Dr. Zhang’ a research has spearheaded into BIOAI in medicinal and medical applications.  The theme of research in Dr. Zhang's lab has been "bioengineering towards medicine". The idea is to engineer novel materials (particularly proteins and peptides) and devices and apply them to study basic biological and medical questions that can ultimately lead to drug discovery and patient care. Research from Dr. Zhang's lab has led to the development of technologies such as unnatural genetic codes in mammalian cells, trM2H system, site-specific protein cross-linking technology, synthetic antibody and cell LASIK. Recently, 15 years after its discovery, Zhang lab has established the molecular mechanism of communication between the mammalian cells and Gram-positive bacterial cells, which not only paves the way to develop new therapies to combat the super-bacterial infection but also provides the implication of the new therapy towards viral infection such as COV-19 and HIV.

Dr. Zhang’s research has been supported by major grants from NIH, NSF, American Heart Association, Welch Research Foundation, etc.

Dr. Zhang has been awarded with eight US and international patents (more pending) and he has co-founded companies in the area of pharmaceutics, regenerative medicines and bio-devices and been invited to serve as consultant for biotech and pharmaceutical companies.

Current Research Area

  1. BIOAI and machine vision for anti-infectious drug discovery
  2. Origin of Life and Reverse-Directed-Evolution

Funding and Acknowledgement

We appreciate the grants from NIH NCI R01, NSF SBIR, American Heart Association, Welch Foundation, JOINN Foundation, Santa Clara University School of Engineering Internal Research grants, as well as the awards from the scientific community. We are deeply grateful to the close collaborations with biotech and high-tech industry at Bay Area as well as the esteemed academic scholars across the nation and internationally.


  • Biomolecular Engineering I (BIOE 175) labs (BIOE175L)
  • Biomolecular Engineering II (BIOE 176)
  • Biodevice Engineering (BIOE 163) labs (BIOE 163L)
  • Biomaterial Engineering (BIOE 153)
  • Senior Design Projects (BIOE 194, 195, 196)
  • Biotechnology (BIOE 186/286 graduate)
  • Clinical Biomaterial Engineering (BIOE 386 graduate)

For a list of Bioengineering course descriptions, visit the Undergraduate Course Descriptions page or the Graduate Course Descriptions page.


Published more than 20 scientific journal articles.

Jonathan Zhang 2016

Associate Professor, Department of Bioengineering