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Sookkyung Lim

Title: Professor
Office: 4428C French Hall
Tel: 513-556-4127
Email: sookkyung.lim@uc.edu
Web: http://homepages.uc.edu/~limsg/

Personal Website

Education

  • Ph.D., Courant Institute of Mathematical Science, New York University, 2003.

Research Information

Research Interests

Mathematical Biology, Computational Fluid Dynamics, Mathematical modeling, Scientific Computing, Dynamical Systems, Systems Biology

Research Support

  • (PI), Lim, Sookkyung, Collaborative Research: Understanding bacterial flagellar propulsion (with Boyce Griffith), National Science Foundation. (DMS-1410886), $200K. 08/15/2014 to 07/31/2018. Status: Active.
  • (PI), Lim, Sookkyung, Understanding the Hydrodynamic Interaction Among Flagella of E.Coli using the Immersed Boundary Method Combined with the Kirchhoff Rod Theory, National Science Foundation. (DMS 0815751), $144,874.00. 08/15/2008 to 07/31/2011. Status: Completed.
  • (co-PI), Sookkyung Lim, Seongho Song, Chris Hong, Sean Moore, Uncovering general principles of network dynamics of circadian rhythms, cell cycle, DNA damage response, and metabolism as interconnected modules, DARPA BAA Biochronicity. (D12AP00005), $3.85million (Lim - $897K). 01/01/2012 to 12/31/2015. Status: Active.
  • S. Lim, Uncovering general principles of network dynamics, Taft Research Center. $5000. 09/01/2012 to 08/30/2013. Status: Completed.
  • (PI), Sookkyung Lim, Mathematical modeling of blood flow in abnormal arteries, The Charles Phelps Taft Research Center. $9500. 06/01/2008 to 07/30/2008. Status: Completed.
  • (Postdoc), Postdoctoral Researcher Fellowship, Mathematical Biosciences Institute. 09/01/2003 to 08/31/2006. Status: Completed.
  • (PI), Sookkyung Lim, Mathematical modeling of valveless pumping, The Charles Phelps Taft Research Center. $9400. 06/01/2010 to 09/20/2010. Status: Completed.
  • (co-PI), Sookkyung Lim, Benjamin Vaughan, Donald French, Daniel Hassett, Margaret Kupferle, Pathogen Persistence Mediated by Biofilms in Urban Water Distribution Systems and River Networks , University Research Council. $25000. 07/01/2011 to 06/30/2012. Status: Completed.

Publications

Peer Reviewed Publications

  • A. Dovzhenok, M. Baek, S. Lim, C. Hong, Mathematical modeling and experimental validation of glucose compensation of the Neurospora circadian clock. Biophys. J. 108(7):1830–1839 (2015)
  • W. Lee, S. Lim and Y. Kim, The role of myosin II in glioma invasion: A mathematical model. PLoS ONE 12(2):e0171312 (2017)
  • W. Lee, Y. Kim, and S. Olson, and S. Lim, Nonlinear dynamics of a rotating elastic rod in a viscous fluid. Phys. Rev. E 90, 033012 (2014)
  • Y. Kim, J. Lee, and S. Lim, Nodal flow simulations by the immersed boundary method, SIAM App. Math. 74(2):263-283 (2014)
  • A. Caicedo, H. Kang, C.I. Hong, and S. Lim, Robustness and period sensitivity analysis of minimal models for biochemical oscillators, Scientific Reports, 5:13161 (2015)
  • D. Swigon, S. Lim, and Y. Kim, Dynamical simulations of DNA supercoiling and compression, Biochemical Society Transactions Apr 1;41(2):554-8 (2013)
  • S. Olson, S. Lim, and R. Cortez, Modeling the dynamics of an elastic rod with intrinsic curvature and twist using a regularized Stokes formulation, J. Comput. Phys. 238:169-187 (2013)
  • W. Lee, S. Lim, and E. Jung, Dynamical motion driven by periodic forcing to an open elastic tube in fluid, Communications in Computational Physics Vol 12, No 2 pp. 494-514 (2012)
  • S. Lim and C.S. Peskin, Fluid-mechanical interaction of flexible bacterial flagella by the immersed boundary method, Physical Review E 85, 036307 (2012)
  • B. Griffith and S. Lim, Simulating an elastic ring with bend and twist by an adaptive generalized immersed boundary method, Communications in Computational Physics, vol 12 No 2, pp.433-461  (2012)
  • S. Lim, Y. Kim, and D. Swigon, Dynamics of an electrostatically charged elastic rod in fluid, Proc. R. Soc. A 467:569-590 (2011)
  • S. Lim and E. Jung, A three-dimensional model of a closed valveless pump system immersed in a viscous fluid, SIAM J. Appl. Math. 70(6):1999-2022 (2010)
  • S. Lim, Dynamics of an open elastic rod with intrinsic curvature and twist in a viscous fluid, Phys. Fluids 22, 024104 (2010)
  • Y. Kim, S. Lim, S.V. Raman, O.P. Simonetti, and A. Friedman, Blood flow in a compliant vessel by the immersed boundary method, Annals of Biomedical Engineering, Vol. 37, Issue 5, pp. 927-942 (2009)
  • Y. Kim and S. Lim, The role of the micronenvironment in tumor invasion, Proceeding of the SIAM Conference on Mathematics for Industry: Challenges and Frontiers. (MI09) (2009)
  • S. Lim, A. Ferent, X.S. Wang, and C.S. Peskin, Dynamics of a closed rod with twist and bend in fluid, SIAM Journal on Scientific Computing, 31(1):273-302 (2008)
  • E. Jung, S. Lim, W. Lee, and S. Lee, Computational models of valveless pumping using the immersed boundary method, Comput. Methods Appl. Mech. Engrg. 197(25-28): 2329-2339(2008)
  • S. Lim and C. S. Peskin, Simulations of the whirling instability by the immersed boundary method, SIAM Journal on Scientific Computing, 25(6):2066-2083 (2004)
  • S. Lim and C. S. Peskin, Subcritical bifurcation of a rot ating elastic filament in a viscous fluid by the immersed boundary method, Proceedings of the Second MIT Conference on Computational Fluid and Solid Mechanics, pp. 1409-1412 (2003)
  • Y. Kim, Y. Park, and S. Lim, 3D simulations of blood flow dynamics in compliant vessels, Comm. Comput. Phys. 19(05):1167-1190(2016) 
  • T. Matsu-ura, A. Dovzhenok, E. Aihara, J. Rood, Y. Ren, T. Zhang, M.H. Montrose, S. Lim, S.R. Moore, and C.I. Hong, Intercellular coupling of cell cycle and circadian clock in adult stem cell cultures, Molecular Cell 64(5):900-912 (2016).
  • Y. Ren, C.I. Hong, S. Lim, and S. Song, Finding clocks in genes: a Bayesian approach to estimate periodicity, BioMed Research International 3017475 (2016)
  • Y. Park, W. Ko, Y. Kim, and S. Lim, Instabilities of a rotating helical rod in a viscous fluid, Phys. Rev. E, 95:022410(2017) - Editors&39; Suggestion. 
  • W. Ko, S. Lim, W. Lee, Y. Kim, H.C. Berg, C.S. Peskin, Modeling polymorphic transformation of rotating bacterial flagella in a viscous fluid, Phys. Rev. E 95:063106 (2017) - Editor&39;s suggestion

Presentations & Lectures

Invited Presentations

  • S. Lim (11-2014). KSIAM, A special session on Biofluids Jeju, Korea.
  • S. Lim (11-2014). Seminar in Applied Mathematics KAIST, Daejeon, Korea.
  • S. Lim (07-2014). SIAM, Mini-Symposium on The mechanics of flagellar locomotion Chicago, IL.
  • S. Lim (07-2014). WCCM, Mini-Symposium on Fluid-structure interaction algorithms and application Barcelona, Spain.
  • S. Lim (05-2014). Seminar. NIMS, Daejeon, Korea.
  • Sookkyung Lim (12-2013). Mathematical modeling of circadian clock Konkuk University, Seoul, Korea.
  • S. Lim (12-2013). Electro-hydrodynamic effect on DNA dynamics Chung-Ang University, Seoul, Korea.
  • S. Lim (11-2013). Flagellar bundling and unbundling 66th Annual Meeting of the APS DFD, Pittsburgh, PA.
  • S. Lim (11-2013). Mathematical modeling in life sciences KSEA, Ohio Chapter, Cincinnati.
  • S. Lim (08-2013). DNA dynamics under thermal fluctuation US-Korea, Teaneck, NJ.
  • S. Lim (06-2013). 7th MIT conference on Computational Fluid and Solid Mechanics, Cambridge, MA.
  • S. Lim (06-2013). Special Highlight on Mathematical Biology NIMS, Daejeon, Korea.
  • S. Lim (03-2013). 3rd Ohio River Analysis Meeting , Cincinnati.
  • S. Lim (10-2012). Workshop on mathematical and computational challenges in cilia- and flagella- induced fluid dynamics Ohio State Univ., Columbus, OH.
  • S. Lim (10-2012). Hydrodynamics of bundling/unbundling helical flagella driven by rotary motors WPI, Worcester, MA.
  • S. Lim (08-2012). Modeling biological thin filaments in fluid flow San Diego, CA.
  • S. Lim (07-2012). Generalized immersed boundary method applied to mathematical modeling in biology Inha University, Inchon, South Korea.
  • S. Lim (07-2012). Mathematical modeling of circadian rhythms Konkuk University, Seoul, Korea.
  • S. Lim (12-2011). Fluid-mechanical interaction of bacterial flagella by the generalized immersed boundary method NIMS, Daejeon, South Korea.
  • S. Lim (09-2011). Generalized immersed boundary method applied to mathematical modeling in biology Computational Science and Engineering, Yonsei University, Seoul, South Korea.
  • S. Lim (09-2011). A general version of the immersed boundary method and its biological applications Chung-Ang University, Seoul, South Korea.
  • S. Lim (08-2011). A general version of the immersed boundary method and its biological applications Ulsan National Institute of Science and Technology, Ulsan, South Korea.
  • S. Lim (03-2011). Generalized immersed boundary method applied to mathematical modeling in biology Center for Computational Science, Tulane University, New Orleans, LA.
  • S. Lim (09-2010). The immersed boundary method for fluid-structure interaction problems in biology Sungkyunkwan University, Suwon, South Korea.
  • S. Lim (09-2010). A general version of the immersed boundary method applied to biological problems Seoul National University, Seoul, South Korea.
  • S. Lim (08-2010). The generalized immersed boundary method and its applications Field Institute, Toronto, Cadana.
  • S. Lim (07-2010). Flagellar behavior of E. Coli by the immersed boundary method World Congress on Computational Mechanics, Sydney, Austrailia.
  • S. Lim (07-2010). Fluid-mechanical interaction of bacterial flagella by the generalized immersed boundary method SIAM LS and SIAM annual meeting, Pittsburgh, PA .
  • S. Lim (04-2010). Electrostatic effects on a charged rod in fluid SIAM Great Lakes conference on Modeling and Numerical PDEs in Mathematical Biology, University of Michigan, Dearborn.
  • S. Lim (04-2010). Dynamics of an electrostatically charged DNA in fluid by the generalized immersed boundary method Georgia Institute of Technology, Atlanta, GA.
  • S. Lim (12-2009). The immersed boundary method applied to biology Konkuk University, Seoul, South Korea.
  • S. Lim (12-2009). Dynamics of an electrically charged rod in a viscous fluid by the immersed boundary method Konkuk University, Seoul, South Korea.
  • S. Lim (12-2009). The hydrodynamic interaction of bacterial flagella Korean Institute of Advanced Studies, Seoul, South Korea.
  • S. Lim (12-2009). Fluid-mechanical interaction of flexible bacterial flagella by the immersed boundary method Ewha Women's University, Seoul, South Korea.
  • S. Lim (11-2009). Flexible bacterial flagella motion by the immersed boundary method University of Pittsburgh, Pittsburgh, PA.
  • S. Lim (07-2009). Supercoiling dynamics of a circular DNA in fluid by the immersed boundary method US national congress on computational mechanics, Columbus, OH.
  • S. Lim (07-2009). Fluid-mechanical interaction of flexible bacterial flagella by the immersed boundary method Chung-Ang University, Seoul, South Korea.
  • S. Lim (06-2009). Fluid-mechanical interaction of flexible bacterial flagella by the immersed boundary method Konkuk University, Seoul, South Korea.
  • S. Lim (06-2009). Supercoiling dynamics of DNA in fluid Coupled problems in science and engineering, Ischia Island, Italy.
  • S. Lim (08-2008). Generalized immersed boundary method combined with the Kirchhoff rod theory Hanyang University, Seoul, South Korea.
  • S. Lim (08-2008). Dynamics of a ring with twist and bend in a fluid KAIST, Seoul, South Korea.
  • S. Lim (08-2008). Mini-Symposium on Modeling, Analysis and Simulation in blood flow SIAM Conferences on Life Sciences, Montreal, Canada.
  • S. Lim (04-2008). Simulation of blood flow in a compliant vessel by the immersed boundary method Cleveland State University, Cleveland, OH.
  • S. Lim (09-2007). Macroscopic modeling of a circular rod with twist and bend in fluid IMA, University of Minnesota, Twin Cities, Minnesota.
  • S. Lim (08-2015). ICIAM Minisymposium Beijing, China.
  • S. Lim (09-2015). Colloquium NJIT, Newark, NJ.
  • S. Lim (02-2016). MathBio Seminar UC Davis, Davis, CA.
  • S. Lim (03-2016). Applied Math Seminar Ohio State U, Columbus, OH.
  • S. Lim (07-2016). Minisymposium on biofluids World Congress on Computational Mechanics, Seoul, Korea.
  • S. Lim (06-2016). Frontiers in Applied and Computational Mathematics (FACM) NJIT, Newark, NJ.
  • S. Lim (08-2017). Mini-symposium on Applied Mathematics with applications US-Korea Conference, Washington D.C..
  • S. Lim (07-2017). Contributed Talk Society for Mathematical Biology, Salt Lake City, Utah.
  • S. Lim (06-2017). Contributed Talk EASIAM-KSIAM Joint Conference, Seoul, Korea.
  • S. Lim (06-2017). Seminar Ulsan Institute of Science and Technology, Ulsan, Korea.
  • S. Lim (05-2017). Numerical methods for PDEs and their applications Institute Mittag-Leffler, Djursholm, Sweden.
  • S. Lim (05-2017). Applied Seminar Yonsei University, Seoul, Korea.

Colloquia

  • Sookkyung Lim (03/15/2011). Generalized immersed boundary method applied to mathematical modeling in biology. Department of Mathematics, Tulane University.
  • Sookkyung Lim (05/08/2009). The generalized immersed boundary method applied to mathematical modeling in biology. Department of Mathematics, Cincinnati, OH.

Lectures

  • (07/21/2011). Stokes formulation combined with the Kirchhoff rod theory. Summer program in mathematical biology, Konkuk University, South Korea.
  • (08/17/2011). The generalized immersed boundary method. Summer program in mathematical biology, Konkuk University, South Korea.
  • (12-2013). Regularized Stokes formulation combined with Kirchhoff rod theory. Chung-Ang University, Seoul, Korea.
  • (06-2017). Lecture series on Perturbation theory. Konkuk University, Seoul, Korea.

Experience & Service

Work Experience

  • 2006 to 2012, Assistant Professor, Department of Mathematical Sciences, University of Cincinnati.
  • 2003 to 2006, Postdoctoral Researcher, Mathematical Biosciences Institute, Ohio State University.
  • 2012 to 2017, Associate Professor, Department of Mathematical Sciences, University of Cincinnati.
  • 2017 to Present, Professor, Department of Mathematical Sciences, University of Cincinnati.

Events Organized

  • Conference. ESMTB: Minisymposium on Fluid-structure interaction problems in biomechanics (06/28/2011 to 07/02/2011) , Krakow, Poland.
  • Other. Nonlinear Dynamics Seminar (10-2011 to Present) , UC.
  • Other. Mathematical Biology Seminar (2006 to 2011) , UC.
  • Barnett Lecture (04-2008 to 04-2008) , Cincinnati, OH.
  • Conference. SIAM Conference on Life Sciences: Minisymposium on Biological locomotion (08/07/2012 to 08/10/2012) , San Diego, CA, USA.
  • Workshop. Hot Topic Workshop (06/03/2013 to 06/05/2013) , NIMS, Daejeon, Korea.
  • Conference. US-Korea Conference (08/11/2013 to 08/14/2013) , Teaneck, Nj.
  • Conference. ICIAM: Minisymposium (08/10/2015 to 08/14/2015) , Beijing, China.
  • Conference. KSIAM: Special Session (11/20/2014 to 11/23/2014) , Jeju Island, Korea.
  • World Congress on Computational Mechanics, Minisymposium on Biofluids (07-2016, Seoul, Korea.
  • SIAM Conference on Life Sciences, Minisymposia (07-2016.
  • International Council for Industrial and Applied Mathematics, Minisymposium (08-2015.
  • US-Korea Conference, Symposium (08/09/2017 to 08/12/2017) , Washington D.C..

Service

  • Committee Member, Hiring committee, 10-2009 to 03-2010
  • Committee Member, Department of Mathematical Sciences Excutive Committee, 09-2007 to 06-2009
  • Coordinator, Graduate Student Seminar 09-2011 to Present
  • Member, Undergraduate advising, 09-2011 to 05-2012
  • MBI Institute Partners meeting, 11-2009 to 11-2009
  • Other, UC Show Case Poster Presenter, 2008 to 2008
  • Reviewer, NSF Review Panel ,
  • Reviewer, Journal of Computational Physics
  • Reviewer, International Journal of Multiscale Computational Engineering
  • Reviewer, Journal of Theoretical Biology
  • Reviewer, Journal of Computational Methods in Applied Mechanics and Engineering
  • Reviewer, Journal of Experimental Biology
  • Coordinator, Barnett Lecture 05-2007 to 05-2007
  • Member, Math Bowl
  • Committee Member, Academic Committee, 09/01/2012 to 05/30/2013
  • Committee Member, Graduate Affair Committee, 09/01/2012 to 05/30/2013
  • Mentor, MBI 01-2011 to Present
  • Committee Member, Systems Biology Program 08-2013 to Present
  • Committee Member, Search Committee, 11-2013 to 05-2014
  • Executive Board, KAMSA, 08-2013 to 07-2015
  • Council Member, KSEA 07-2014 to 06-2017
  • Reviewer, PLOS ONE
  • Coordinator, Applied Calculus II

Other Experience and Professional Memberships

  • European Society for Mathematical and Theoretical Biology,
  • The Society for Mathematical Biology,
  • Society for Industrial and Applied Mathematics,

Courses Taught

  • 15-MATH-911 SEMINAR-APPLD MATH
    Level: Graduate
    Term: 14FS

  • 15 MATH 3006 MATH MODELING
    Level: Undergraduate
    Term: 14SS

  • 15 MATH 1045 APPLIED CAL II
    Level: Undergraduate
    Term: 14SS

  • 15 MATH 6051 APPLIED ODEs
    Level: Graduate
    Term: 14FS

  • 15-MATH-913 SEMINAR-APPLD MATH
    Level: Graduate
    Term: 13SS

  • 15 MATH-518 Special Topics in Mathematical Biology
    Level: Graduate
    Term: 12W

  • 15-MATH-951 SEM MATH BIOL
    Level: Graduate
    Term: 12W

  • 15-MATH-252 CALCULUS II
    Level: Undergraduate
    Term: 12W

  • 15-MATH-264 CALC & AN GEOM IV
    Level: Undergraduate
    Term: 12S

  • 15-MATH-710 ADV NUMERICAL ANAL
    Level: Graduate
    Term: 11S

  • 15-MATH-264 CALC & AN GEOM IV
    Level: Undergraduate
    Term: 11S

  • 15-MATH-253 CALCULUS III
    Level: Undergraduate
    Term: 11A

  • 15-MATH-227 APPLIED CALC II
    Level: Undergraduate
    Term: 11A

  • Advanced Math Modeling
    Advanced Math Modeling
    Level: Graduate
    Term: 17SS

  • Scientific Computing
    Scientific Computing
    Level: Graduate
    Term: 17SS

  • ODEs
    ODEs
    Level: Graduate
    Term: 17FS

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