Sookkyung Lim , Ph.D.

Personal website http://homepages.uc.edu/~limsg/

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

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

2006 -2012 Assistant Professor, Department of Mathematical Sciences, University of Cincinnati

2003 -2006 Postdoctoral Researcher, Mathematical Biosciences Institute, Ohio State University

2012 -2017 Associate Professor, Department of Mathematical Sciences, University of Cincinnati

2017 -To Present Professor, Department of Mathematical Sciences, University of Cincinnati

Grant: #DMS-1410886 Investigators:Lim, Sookkyung 08-15-2014 -07-31-2018 National Science Foundation Collaborative Research: Understanding bacterial flagellar propulsion (with Boyce Griffith) Role:PI $200K Active

Grant: #DMS 0815751 Investigators:Lim, Sookkyung 08-15-2008 -07-31-2011 National Science Foundation Understanding the Hydrodynamic Interaction Among Flagella of E.Coli using the Immersed Boundary Method Combined with the Kirchhoff Rod Theory Role:PI $144,874.00 Completed

Grant: #D12AP00005 Investigators:Sookkyung Lim, Seongho Song, Chris Hong, Sean Moore 01-01-2012 -12-31-2015 DARPA BAA Biochronicity Uncovering general principles of network dynamics of circadian rhythms, cell cycle, DNA damage response, and metabolism as interconnected modules Role:co-PI $3.85million (Lim - $897K) Active Type:Grant

Investigators:S. Lim 09-01-2012 -08-30-2013 Taft Research Center Uncovering general principles of network dynamics $5000 Completed Type:Fellowship

Investigators:Sookkyung Lim 06-01-2008 -07-30-2008 The Charles Phelps Taft Research Center Mathematical modeling of blood flow in abnormal arteries Role:PI $9500 Completed Type:Fellowship

09-01-2003 -08-31-2006 Mathematical Biosciences Institute Postdoctoral Researcher Fellowship Role:Postdoc Completed Type:Fellowship

Investigators:Sookkyung Lim 06-01-2010 -09-20-2010 The Charles Phelps Taft Research Center Mathematical modeling of valveless pumping Role:PI $9400 Completed Type:Fellowship

Investigators:Sookkyung Lim, Benjamin Vaughan, Donald French, Daniel Hassett, Margaret Kupferle 07-01-2011 -06-30-2012 University Research Council Pathogen Persistence Mediated by Biofilms in Urban Water Distribution Systems and River Networks Role:co-PI $25000 Completed Type:Grant

Grant: #585683 Investigators:Lim, Sookkyung 09-01-2018 -08-31-2023 Simons Foundation Mathematical modeling of fluid-structure interaction problems in biology Role:PI $8,400.00 Awarded Level:Private Non-Profit

Grant: #DMS-1853591 Investigators:Lim, Sookkyung 08-01-2019 -07-31-2022 National Science Foundation Fluid-mechanical Interaction of a Bacterial Swimmer with Flagella and Bacterial Chemotaxis Role:PI $150,000.00 Awarded Level:Federal

Investigators:Hong, Christian; Kim, Hang Joon; Lim, Sookkyung 09-01-2024 -08-31-2029 National Institute of General Medical Sciences Fundamental properties of circadian rhythms Role:Collaborator 0.00 Hold Level:Federal

Grant: #CBET-2415406 Investigators:Lim, Sookkyung 07-01-2024 -06-30-2027 National Science Foundation Collaborative Research: A study of the collective dynamics of multiple flagella in a bacterial bundle Role:PI 195656.00 Active Level:Federal

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' 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's suggestion

T. Matsu-ura, A. Dovzhenok, S.T. Coradetti, K.R. Subramanian, D.R. Meyer, J.J. Kwon, C. Kim, N. Salomonis, N. Louise Glass, S. Lim, and C.I. Hong, Synthetic gene network with positive feedback loop amplifies cellulase gene expression in Neurospora crassa, ACS Synth. Biol. (2018)

J. Bellman, J.K. Kim, C.I. Hong, S. Lim, Modeling reveals a key mechanism for light-dependent phase shitfs of Neurospora circadian clock, Biophys. J. 115(6):1093-1102 (2018)

W. Lee, Y. Kim, B.E. Griffith and S. Lim, Bacterial flagellar bundling and unbundling via polymorphic transformations, PRE, 98:052405 (2018).

Invited Presentations

S. Lim (11-2014. ) KSIAM, A special session on Biofluids .Jeju, Korea, Conference. . Level:International

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, Conference. . Level:International

S. Lim (07-2014. ) WCCM, Mini-Symposium on Fluid-structure interaction algorithms and application .Barcelona, Spain, Conference. . Level:International

S. Lim (05-2014. ) Seminar. .NIMS, Daejeon, Korea. Level:Local

Sookkyung Lim (12-2013. ) Mathematical modeling of circadian clock .Konkuk University, Seoul, Korea. Level:Department

S. Lim (12-2013. ) Electro-hydrodynamic effect on DNA dynamics .Chung-Ang University, Seoul, Korea. Level:Department

S. Lim (11-2013. ) Flagellar bundling and unbundling . 66th Annual Meeting of the APS DFD, Pittsburgh, PA. Conference. . Level:International

S. Lim (11-2013. ) Mathematical modeling in life sciences .KSEA, Ohio Chapter, Cincinnati. Workshop. . Level:Local

S. Lim (08-2013. ) DNA dynamics under thermal fluctuation .US-Korea, Teaneck, NJ. Conference. . Level:National

S. Lim (06-2013. ) 7th MIT conference on Computational Fluid and Solid Mechanics, Cambridge, MA. Conference. . Level:International

S. Lim (06-2013. ) Special Highlight on Mathematical Biology .NIMS, Daejeon, Korea. Workshop. . Level:Regional

S. Lim (03-2013. ) 3rd Ohio River Analysis Meeting , Cincinnati. Workshop. . Level:Regional

S. Lim (10-2012. ) (In Press. ) Workshop on mathematical and computational challenges in cilia- and flagella- induced fluid dynamics .Ohio State Univ., Columbus, OH. Workshop. . Level:National

S. Lim (10-2012. ) (In Press. ) Hydrodynamics of bundling/unbundling helical flagella driven by rotary motors .WPI, Worcester, MA. Other Institution. . Level:Department

S. Lim (08-2012. ) (In Press. ) Modeling biological thin filaments in fluid flow .San Diego, CA. Conference. . Level:International

S. Lim (07-2012. ) (In Press. ) Generalized immersed boundary method applied to mathematical modeling in biology .Inha University, Inchon, South Korea. Other Institution. . Level:Department

S. Lim (07-2012. ) (In Press. ) Mathematical modeling of circadian rhythms .Konkuk University, Seoul, Korea. Other Institution. . Level:Department

S. Lim (12-2011. ) (In Press. ) Fluid-mechanical interaction of bacterial flagella by the generalized immersed boundary method .NIMS, Daejeon, South Korea. Level:International

S. Lim (09-2011. ) (In Press. ) Generalized immersed boundary method applied to mathematical modeling in biology .Computational Science and Engineering, Yonsei University, Seoul, South Korea. Other Institution. . Level:Department

S. Lim (09-2011. ) (In Press. ) A general version of the immersed boundary method and its biological applications .Chung-Ang University, Seoul, South Korea. Level:Department

S. Lim (08-2011. ) (In Press. ) A general version of the immersed boundary method and its biological applications .Ulsan National Institute of Science and Technology, Ulsan, South Korea. Conference. . Level:National

S. Lim (03-2011. ) (In Press. ) Generalized immersed boundary method applied to mathematical modeling in biology .Center for Computational Science, Tulane University, New Orleans, LA. Other Institution. . Level:Department

S. Lim (09-2010. ) (In Press. ) The immersed boundary method for fluid-structure interaction problems in biology .Sungkyunkwan University, Suwon, South Korea. Level:Department

S. Lim (09-2010. ) (In Press. ) A general version of the immersed boundary method applied to biological problems .Seoul National University, Seoul, South Korea. Level:Department

S. Lim (08-2010. ) (In Press. ) The generalized immersed boundary method and its applications .Field Institute, Toronto, Cadana. Workshop. . Level:International

S. Lim (07-2010. ) (In Press. ) Flagellar behavior of E. Coli by the immersed boundary method .World Congress on Computational Mechanics, Sydney, Austrailia. Conference. . Level:International

S. Lim (07-2010. ) (In Press. ) Fluid-mechanical interaction of bacterial flagella by the generalized immersed boundary method .SIAM LS and SIAM annual meeting, Pittsburgh, PA . Conference. . Level:International

S. Lim (04-2010. ) (In Press. ) Electrostatic effects on a charged rod in fluid .SIAM Great Lakes conference on Modeling and Numerical PDEs in Mathematical Biology, University of Michigan, Dearborn. Conference. . Level:Regional

S. Lim (04-2010. ) (In Press. ) Dynamics of an electrostatically charged DNA in fluid by the generalized immersed boundary method .Georgia Institute of Technology, Atlanta, GA. Level:Department

S. Lim (12-2009. ) (In Press. ) The immersed boundary method applied to biology .Konkuk University, Seoul, South Korea. Level:Department

S. Lim (12-2009. ) (In Press. ) Dynamics of an electrically charged rod in a viscous fluid by the immersed boundary method .Konkuk University, Seoul, South Korea. Workshop. . Level:Department

S. Lim (12-2009. ) (In Press. ) The hydrodynamic interaction of bacterial flagella .Korean Institute of Advanced Studies, Seoul, South Korea. Other Institution. . Level:Local

S. Lim (12-2009. ) (In Press. ) Fluid-mechanical interaction of flexible bacterial flagella by the immersed boundary method .Ewha Women's University, Seoul, South Korea. Conference. . Level:International

S. Lim (11-2009. ) (In Press. ) Flexible bacterial flagella motion by the immersed boundary method .University of Pittsburgh, Pittsburgh, PA. Other Institution. . Level:Department

S. Lim (07-2009. ) (In Press. ) Supercoiling dynamics of a circular DNA in fluid by the immersed boundary method .US national congress on computational mechanics, Columbus, OH. Conference. . Level:International

S. Lim (07-2009. ) (In Press. ) Fluid-mechanical interaction of flexible bacterial flagella by the immersed boundary method .Chung-Ang University, Seoul, South Korea. Level:Department

S. Lim (06-2009. ) (In Press. ) Fluid-mechanical interaction of flexible bacterial flagella by the immersed boundary method .Konkuk University, Seoul, South Korea. Level:Department

S. Lim (06-2009. ) (In Press. ) Supercoiling dynamics of DNA in fluid .Coupled problems in science and engineering, Ischia Island, Italy. Level:International

S. Lim (08-2008. ) (In Press. ) Generalized immersed boundary method combined with the Kirchhoff rod theory .Hanyang University, Seoul, South Korea. Level:Department

S. Lim (08-2008. ) (In Press. ) Dynamics of a ring with twist and bend in a fluid .KAIST, Seoul, South Korea. Other Institution. . Level:International

S. Lim (08-2008. ) (In Press. ) Mini-Symposium on Modeling, Analysis and Simulation in blood flow .SIAM Conferences on Life Sciences, Montreal, Canada. Conference. . Level:International

S. Lim (04-2008. ) (In Press. ) Simulation of blood flow in a compliant vessel by the immersed boundary method .Cleveland State University, Cleveland, OH. Other Institution. . Level:University

S. Lim (09-2007. ) (In Press. ) Macroscopic modeling of a circular rod with twist and bend in fluid .IMA, University of Minnesota, Twin Cities, Minnesota. Workshop. . Level:International

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. Level:International

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.. Level:National

S. Lim (07-2017. ) Contributed Talk .Society for Mathematical Biology, Salt Lake City, Utah. Level:International

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.

Colloquium

Sookkyung Lim (03-15-2011). Generalized immersed boundary method applied to mathematical modeling in biology . Department of Mathematics, Tulane University. Other Institution. Level:Department

Sookkyung Lim (05-08-2009). The generalized immersed boundary method applied to mathematical modeling in biology . Department of Mathematics, Cincinnati, OH. UC. Level:Department

Lecture

Sookkyung Lim (07-21-2011. ) Stokes formulation combined with the Kirchhoff rod theory .Konkuk University, South Korea. Other Institution. Level:Department

Sookkyung Lim (08-17-2011. ) The generalized immersed boundary method .Konkuk University, South Korea. Other Institution. Level:Department

S. Lim (12-2013. ) Regularized Stokes formulation combined with Kirchhoff rod theory .Seoul, Korea. Level:Department

S. Lim (06-2017. ) Lecture series on Perturbation theory .Seoul, Korea.

Event Organized

ESMTB: Minisymposium on Fluid-structure interaction problems in biomechanics Conference 06-28-2011 07-02-2011 Krakow, Poland Level:International

Nonlinear Dynamics Seminar Other 10-2011 To Present UC Level:Department

Mathematical Biology Seminar Other 2006 2011 UC Level:Department

Barnett Lecture 04-2008 04-2008 Cincinnati, OH Level:Department

SIAM Conference on Life Sciences: Minisymposium on Biological locomotion Conference 08-07-2012 08-10-2012 San Diego, CA, USA Level:International

Hot Topic Workshop Workshop 06-03-2013 06-05-2013 NIMS, Daejeon, Korea Level:Regional

US-Korea Conference Conference 08-11-2013 08-14-2013 Teaneck, Nj Level:National

ICIAM: Minisymposium Conference 08-10-2015 08-14-2015 Beijing, China Level:International

KSIAM: Special Session Conference 11-20-2014 11-23-2014 Jeju Island, Korea Level:National

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 08-12-2017 Washington D.C. Level:National

(Hiring committee ) Committee Member Type:Departmental Service Level:Department 10-2009 -03-2010

Department of Mathematical Sciences (Excutive Committee ) Committee Member Type:Departmental Service Level:Department 09-2007 -06-2009

Graduate Student Seminar Coordinator Type:Departmental Service Level:Department 09-2011 -To Present

(Undergraduate advising ) Member Type:Departmental Service Level:Department 09-2011 -05-2012

MBI (Institute Partners meeting ) Type:Departmental Service Level:University 11-2009 -11-2009

UC Show Case (Poster Presenter ) Other Type:University/College Service Level:University 2008 -2008

NSF (Review Panel ) Reviewer Type:Grant Panel Level:National

Journal of Computational Physics Reviewer Type:Service to Professional Associations Level:International

International Journal of Multiscale Computational Engineering Reviewer Type:Service to Professional Associations Level:International

Journal of Theoretical Biology Reviewer Type:Service to Professional Associations

Journal of Computational Methods in Applied Mechanics and Engineering Reviewer Type:Service to Professional Associations Level:International

Journal of Experimental Biology Reviewer Type:Service to Professional Associations

Barnett Lecture Coordinator Type:Departmental Service Level:Department 05-2007 -05-2007

Math Bowl Member Type:Departmental Service Level:Department

(Academic Committee ) Committee Member Type:Departmental Service Level:Department 09-01-2012 -05-30-2013

(Graduate Affair Committee ) Committee Member Type:Departmental Service Level:Department 09-01-2012 -05-30-2013

MBI Mentor Type:Departmental Service Level:University 01-2011 -To Present

Systems Biology Program Committee Member Type:Service to Professional Development Programs Level:College 08-2013 -To Present

(Search Committee ) Committee Member Type:Departmental Service Level:Department 11-2013 -05-2014

(KAMSA ) Executive Board Type:Service to Professional Associations Level:National 08-2013 -07-2015

KSEA Council Member Type:Community Service Level:International 07-2014 -06-2017

PLOS ONE Reviewer Type:Service to Professional Associations Level:International

Applied Calculus II Coordinator Type:Departmental Service

European Society for Mathematical and Theoretical Biology

The Society for Mathematical Biology

Society for Industrial and Applied Mathematics

15-MATH-911 SEMINAR-APPLD MATH Level:Graduate

15 MATH 3006 MATH MODELING Level:Undergraduate

15 MATH 1045 APPLIED CAL II Level:Undergraduate

15 MATH 6051 APPLIED ODEs Level:Graduate

15-MATH-913 SEMINAR-APPLD MATH Level:Graduate

15 MATH-518 Special Topics in Mathematical Biology Level:Graduate

15-MATH-951 SEM MATH BIOL Level:Graduate

15-MATH-252 CALCULUS II Level:Undergraduate

15-MATH-264 CALC & AN GEOM IV Level:Undergraduate

15-MATH-710 ADV NUMERICAL ANAL Level:Graduate

15-MATH-264 CALC & AN GEOM IV Level:Undergraduate

15-MATH-253 CALCULUS III Level:Undergraduate

15-MATH-227 APPLIED CALC II Level:Undergraduate

Advanced Math Modeling Level:Graduate

Scientific Computing Level:Graduate

ODEs Level:Graduate

09-19-2012 -09-21-2012 Mathematical Biology: Looking at the Future MBI, OSU Columbus, OH Type:Workshop

05-13-2013 -05-15-2013 Stochastic modeling of biological processes IMA Minnesota Type:Workshop

08-14-2013 -08-16-2013 International Conference on Computational Cell Biology Virginia Tech Blacksburg, VA Type:Conference Attendance