(3eq) Dynamics of Living Matter: Modeling Biology with the Physics of Fluids and Reactions

The puzzle of the intelligence arising from the structure of matter remains standing. The living matter senses the external environment/stimuli and regulates the inner system through feedback loop to maintain homeostasis and avoid danger. With the advancement of experimental discovery, modeling has become the efficient and informative approach to build up the complexity and understand the dynamics of the living system. My research interests span three topics around the living matter:

• “Biology of stability”: In cell biology, homeostasis manages the stability of the living system. The failure of maintaining the stability could profoundly impact cell functionality and even the health of being. In collaboration with experimentalist, I am interested in the epigenetics where I model the effect of herbicide on the dynamic change of methylation.
• “The dynamics of bacterial physiology”: The intrinsic antibiotic resistance in bacterial physiology could compromise the well-being in a healthcare facility. For bacteria/pathogens, antimicrobial resistance can be acquired through the conjugation. I am interested in investigating the conjugation behavior under both the internal gene regulatory pathway and extracellular substances.
• “Functional Morphology”: I am interested in cellular morphologies as they evolve specific traits to survive in their aquatic environment. With the aid of the microfluidic design, this fundamental question lies at the heart of biomedical device for cell separation and diagnostic applications. I am developing the fundamental theory of ellipsoidal microhydrodynamics to investigate the first principle of anisotropicity.

Research Accomplishments

During my Ph.D., I worked with Prof Arezoo Ardekani at the University of Notre Dame and my research topic is about active matter with a focus of flow physics in swimming at microscale. I worked on the motion of small planktonic organisms: their locomotion (unsteady or impulsive) could affect the speed, swimming efficiency, and detection volume that alerts a predator in the aquatic system (JFM 2012, Phys Fluids 2012). By collaborating with experimentalists, I have developed a model to understand the interaction between bacteria and soft interface (PRE 2013, PRE 2019). I performed direct numerical simulation to explore the mixing generated by swimmers and It has created the numerical framework of high fidelity simulation for organism swimming in stratified fluids (Sci Rep 2015).

At Purdue, I worked with Prof Sangtae Kim to study the dynamics of ellipsoid in a general quadratic flow (Phys Fluids 2019(1,2), JFM 2020(2)) and formed an industrial collaboration with the director of unconventional energy, Nate Schultheiss. Currently, I am a research associate and also working with Prof Doraiswami Ramkrishna, Prof Chongli Yuan and Prof Vivek Narsimhan to study epigenetics and antimicrobial transfer using bio-reaction model and to develop sampling method for modeling polymer chain. In the meantime, I also collaborated with Dr. Mattheiu Mercier at IMFT, France.

Teaching Interests

Many areas of Chemical Engineering, including transport phenomena and quantitative biology, are interdisciplinary and require a strong background in analytical skills such as programming and physics. These analytical skills benefit students as they pursue their goals—whether working as an engineer, being an entrepreneur, or pursuing other professions such as business or law. To attract students to a math program, a well-structured training process is needed to provide students with a solid foundation, keep them engaged, and encourage them to make breakthroughs. My goal as an educator is to strengthen the process of training creative young minds in Applied Mathematics. After gaining experience as a teaching assistant and mentoring undergraduates at both the University of Notre Dame and Purdue University, I have developed an understanding of how I would like to approach this goal. For undergraduate education, my approaches are (1) cultivating students’ interests in the classes and (2) providing students with adequate academic help. For graduate students, my method is (3) helping students acquire in-depth physics and mathematical knowledge.

Selected publications (out of 13 total, google scholar: https://scholar.google.com/citations?user=uEmQO5cAAAAJ&hl=en)

First-author contributions are underlined

Wang, S., Ramkrishna, D., Narsimhan, V. “Exact sampling of polymer conformations in an external field using Brownian bridges” Journal of Chemical Physics (accepted).

Wang, S., Martin, C.P. and Kim, S., 2019. Improper integrals as a puzzle for creeping flow around an ellipsoid. Physics of Fluids, 31(2), p.021101. (Invited papers on transport phenomena in celebration of Prof. Robert Byron Bird’s 95^th birthday)

Wang, S. and Ardekani, A.M., 2015. Biogenic mixing induced by intermediate Reynolds number swimming in stratified fluids. Scientific reports, 5, p.17448. (Highlighted on Physics.org, Futurity, Geology Page, Purdue College of Engineering News Page, Purdue Research Computing Cluster)

Wang, S. and Ardekani, A.M., 2012. Unsteady swimming of small organisms. Journal of Fluid Mechanics, 702, pp.286-297.

Author

Shiyan Wang

Purdue University