I am a postdoctoral researcher in Structural Bioinformatics and Computational Biochemistry Unit in the Department of Biochemistry at the University of Oxford. My research focuses on the use of molecular dynamics simulations to investigate signal transduction mechanisms in bacterial chemotaxis, especially through the  study of the molecular structure and function of bacterial chemosensory arrays. My work is jointly advised by Professor Mark Sansom and Dr. Phill Stansfeld and funded by the BBSRC. Before coming to Oxford, I held a postdoctoral position with Professor Zan Luthey-Schulten in the Department of Chemistry and the NSF Center for the Physics of Living Cells at the University of Illinois at Urbana-Champaign (UIUC). In December 2016, I received my Ph. D. in Physics from UIUC under the guidance of Professor Klaus Schulten at the NIH Center for Biomolecular Modeling and Bioinformatics.

Below are listed selected publications and presentations associated with my research. Contact me.

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Publications

• Concerted dynamics of an LPS translocon in the presence of substrate and an antimicrobial peptide. Fiorentino F., Sauer J., Qiu X., Corey R.A., Cassidy C.K., Mynors-Wallis B., Mehmood S., Bolla J., Stansfeld P.J., Robinson C.V., (2020), Nature Chemical Biology, In Press.

• The unconventional cytoplasmic sensing mechanism for ethanol chemotaxis in Bacillus subtilis. Tohidifar P., Bodhankar G.A., Pei S., Cassidy C.K., Walukiewicz H.E., Orodal G.W., Stansfeld P.J., Rao C., (2020), MBio, In Press.

• Complete structure of the chemosensory array core signalling unit in an E. coli minicell strain. *Burt A., *Cassidy C.K., Ames P., Bacia-Verloop M., Baulard M., Huard K., Luthey-Schulten Z., Desfosses A., Stansfeld P.J., Margolin W., Parkinson J.S., Gutsche I., (2020), Nature Communications, 11, 743.

• Structure and dynamics of the E. coli chemotaxis core signaling complex by cryo-electron tomography and molecular simulations. Cassidy C.K., Himes B.A., Sun D., Ma J., Zhao G., Parkinson J.S., Stansfeld P.J., Luthey-Schulten Z., Zhang P., (2020), Communications Biology, 3, 24.

  • PDB: 6S1K; EMDB: 10050

• In situ conformational changes of the Escherichia coli serine chemoreceptor in different signaling states. Yang W., Cassidy C.K., Ames P., Diebolder C.A., Schulten K., Luthey-Schulten Z., Parkinson J.S., Briegel A., (2019), MBio, 10(4):e00973-19.

• CryoEM-based hybrid modeling approaches for structure determination. Cassidy C.K., Himes B.A., Luthey-Schulten Z., Zhang P., (2018), Current Opinion in Microbiology, 31:64-74.

• GPU-accelerated molecular dynamics clustering analysis with openACC. Stone J.E., Perilla J.R., Cassidy C.K., Schulten K., (2016). In Parallel Programming with openACC, Elsevier.

• CryoEM and computer simulations reveal a novel kinase conformational switch in bacterial chemotaxis signaling. *Cassidy C.K., *Himes B.A., *Alvarez J.A., Ma J., Zhao G., Perilla J.R., Schulten K., Zhang P., (2015), Elife, 4:e08419.

  • In the news: Researchers resolve structure of a key component of bacterial decision-making

  • PDB: 3JA6; EMDB: 6319, 6320

• Computational methodologies for real-space structural refinement of large macromolecular complexes. Goh B.C., Hadden J.A., Bernardi R.C., Singharoy A., McGreevy R., Rudack T., Cassidy C.K., Schulten K., (2016), Annual Review of Biophysics, 45:253-278.

• Molecular dynamics simulations of large macromolecular complexes. Perilla J.R., Goh B.C., Cassidy C.K., Liu B., Bernardi R.C., Rudack T., Yu H., Wu Z., and Schulten K., (2015), Current Opinion in Structural Biology, 31:64-74.

• CheY’s acetylation sites responsible for generating clockwise flagellar rotation in Escherichia coli. Fraiberg M., Afanzar O., Cassidy C.K., Gabashvili A., Schulten K., Levin Y., Eisenbach M., (2015), Molecular Microbiology, 95(2):231-244.

  • Selected for Faculty of 1000 Prime

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Presentations

• Gordon Research Conference: Sensory Transduction in Microorganisms. 2020. Ventura Beach, California (Poster)
• OxBacNet Seminar. 2020. Oxford U., Oxford, England (Talk)
• Center for the Physics of Living Cells (CPLC) Seminar. 2019. UIUC, Urbana, IL (Invited Talk)
• Department of Physics Careers Seminar. 2019. UIUC, Urbana, IL (Invited Talk)
• Receptor Fest 22nd Annual Meeting. 2019. U. Oregon, Eugene, Oregon (Talk)
• Receptor Fest 21st Annual Meeting. 2018. Cornell U., Ithaca, New York (Talk)
• Gordon Research Conference: Sensory Transduction in Microorganisms. 2018. Ventura Beach, California (Poster)
• Biochemistry Seminar. 2017. Oxford U., Oxford, England (Invited Talk)
• Biology Seminar. 2017. Leiden U., Leiden, Netherlands (Invited Talk)
• Receptor Fest 20th Annual Meeting. 2017. U. Utah, Salt Lake City, Utah (Talk)
• Blue Waters Annual Symposium. 2017. Sunriver, Oregon (Video of Talk)
• Receptor Fest 19th Annual Meeting. 2016. UCSB, Santa Barbara, California (Talk)
• Gordon Research Conference: Sensory Transduction in Microorganisms. 2016. Ventura Beach, California (Invited Talk)
• Gordon Research Seminar: Sensory Transduction in Microorganisms. 2016. Ventura Beach, California (Poster)
• Medical Microbiology and Immunology Seminar. 2015. U. Wisconsin, Madison, Wisconsin (Invited Talk)
• Receptor Fest 18th Annual Meeting. 2015. U. Colorado, Boulder, Colorado (Talk)
• Biophysical Society 59th Annual Meeting. 2015. Baltimore, Maryland (Poster)
• Bacterial Signaling and Locomotion XIII. 2015. Tucson, Arizona (Invited Talk)
• Receptor Fest 17th Annual Meeting. 2014. U. Utah, Salt Lake City, Utah (Talk)
• Blue Waters Annual Symposium. 2014. Urbana, Illinois (Talk)
• Biophysical Society 58th Annual Meeting. 2014. San Francisco, California (Poster)
• SOPS 4th Annual Postdoctoral Research Symposium. 2014. UIUC, Urbana, Illinois (Poster)
• Beckman Institute Graduate Student Seminar. 2013. UIUC, Urbana, Illinois (Talk)