Publications, preprints, and book chapters

Publications

J. Lee, S. Goker, S. Lim, and C.I. Hong, Development of circadian rhythms in mammalian systems, Biochemical J. in press (2024). Biochem2024 -->
J. Park, Y. Kim, W. Lee, V. Pfeifer, V. Muraveva, C. Beta, and S. Lim, Bundling instability of lophotrichous bacteria, Physics of Fluids, 36, 101917 (2024). PoF2024
A. Barrett, A.L. Fogelson, M.G. Forest, C. Gruninger, S. Lim and B.E. Griffith, Flagellum Pumping Efficiency in Shear-Thinning Viscoelastic Fluids, J. Fluid Mech., 999, A2 (2024). JFM2024
A. Goity, A. Dovzhenok, S. Lim, C.I. Hong, J. Loros, J.C. Dunlap and L.F. Larrondo, Transcriptional rewiring of an evolutionary conserved circadian clock, The EMBO Journal, 43(10):2015-2034 (2024). EMBO2024
S. Kamdar, D. Ghosh, W. Lee, M. Ttulea-Codrean, Y. Kim, S. Ghosh, Y. Kim, T. Cheepuru, E. Lauga, S. Lim, and X. Cheng, Multiflagellarity leads to the size-independent swimming speed of peritrichous bacteria, PNAS, 120 (48) e2310952120 (2023). PNAS2023
W. Lee, Y. Kim, and S. Lim, Bio-inspired in silico microswimmer: Run and tumble kinematics, Physics of Fluids, 35, 031908 (2023) - Editor's Pick. PoF2023
J. Park, Y. Kim, W. Lee, and S. Lim, Modeling of lophotrichous bacteria reveals key factors for swimming reorientation, Scientific Reports (Nature Publishing Group), 12, 6482 (2022). SciRep2022
D. Kim, Y. Kim, and S. Lim, Effects of swimming environment on bacterial motility, Physics of Fluids, 34, 031907 (2022) - Featured Article. PoF2022
W. Lee, Y. Kim, C.S. Peskin, and S. Lim, A novel computational approach to simulate microswimmers propelled by bacterial flagella, Physics of Fluids, 33, 111903 (2021) - Featured Article. PoF2021
Y. Pourfarjam, S. Kasson, L. Tran; C. Ho, S. Lim, and I. Kim, PARG has a robust endo-glycohydrolase activity that releases protein-free poly(ADP-ribose) chains, Biochemical and Biophysical Research Communications 527(3):818-823 (2020). BBRC2020
Y. Park, Y. Kim and S. Lim, Flagellated bacteria swim in circles near a rigid wall, Phys. Rev. E 100: 063112 (2019). PRE2019
X. Liu, A. Chen, A. Caicedo-Casso, G. Cui, M. Du, Q. He, S. Lim, H.J. Kim, C.I. Hong and Y. Liu, FRQ-CK1 interaction determines the period of circadian rhythms in Neurospora, Nature Communications, 10(1):4352 (2019). NatureCommun2019
M. Baek, S. Virgilio, T. Lamb, O. Ibarra, J.M. Andrade, R. Gonçalves, A. Dovzhenok, S. Lim, D. Bell-Pedersen, M.C. Bertolini, C.I. Hong, Circadian clock regulation of the glycogen synthase (gsn) gene by WCC is critical for rhythmic glycogen metabolism in Neurospora crassa, PNAS 1815360116 (2019). PNAS2019
Y. Park, Y. Kim and S. Lim, Locomotion of a single-flagellated bacterium, J. Fluid Mech., 859:586-612 (2019) JFM2019
W. Lee, Y. Kim, B.E. Griffith and S. Lim, Bacterial flagellar bundling and unbundling via polymorphic transformations, PRE, 98:052405 (2018). PRE2018
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). BiophysJ2018
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., 7(5):1395-1405 (2018). ACS2018
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) - Editors' Suggestion. PRE2017b
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. PRE2017a
W. Lee, S. Lim, and Y. Kim, The role of myosin II in glioma invasion: A mathematical model, PLOS ONE (2017) PLOSone2017
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) MoleCell2016
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. Kim, Y. Park, and S. Lim, 3D simulations of blood flow dynamics in compliant vessels, Comm. Comput. Phys. 19(05):1167-1190 (2016) CiCP2016
A. Caicedo, H. Kang, C.I. Hong, and S. Lim, Robustness and period sensitivity analysis of minimal models for biochemical oscillators, Scientific Reports (Nature Publishing Group), 5:13161 (2015) SciRep2015
A. Dovzhenok, M Baek, S. Lim, and C.I. Hong, Mathematical modeling and validation of glucose compensation of the Neurospora circadian clock, Biophys. J. 108(7):1830-1839 (2015) BiophyJ2015
W. Lee, Y. Kim, S. Olson, and S. Lim, Nonlinear dynamics of a rotating elastic rod in a viscous fluid, Phys. Rev. E 90:033012(2014) PRE2014
Y. Kim, J. Lee, and S. Lim, Nodal flow simulations by the immersed boundary method, SIAM J. Appl. Math. 74(2):263-283 (2014) SIAM2014
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) JCP2013
D. Swigon, S. Lim, and Y. Kim, Dynamical simulations of DNA supercoiling and compression, Biochem. Soc. Trans. Apr 1;41(2):554-8 (2013). doi: 10.1042/BST20120316 BST2013
S. Lim and C. S. Peskin, Fluid-mechanical interaction of flexible bacterial flagella by the immersed boundary method, Phys. Rev. E, 85, 036307 (2012) PRE2012
W. Lee, S. Lim, and E. Jung, Dynamical motion driven by periodic forcing to an open elastic tube in fluid, Commun. Comput. Phys. 12(2) 494-514 (2012) CiCP2012
B. Griffith and S. Lim, Simulating an elastic ring with bend and twist by an adaptive generalized immersed boundary method, Commun. Comput. Phys. 12(2):433-461 (2012) CiCP2012.pdf
S. Lim, Y. Kim, and D. Swigon, Dynamics of an electrostatically charged elastic rod in fluid, Proc. R. Soc. A 467:569-590 (2011) doi:10.1098/rspa.2010.0174 prsa2011.pdf
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) siap2010
S. Lim, Dynamics of an open elastic rod with intrinsic curvature and twist in a viscous fluid, Phys. Fluids 22, 024104 (2010) pof2010.pdf
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) abme2009.pdf
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) mi09.pdf
S. Lim, Supercoiling dynamics of a circular DNA in fluid, Proceedings of International Conference on Computational Methods for Coupled Problems in Science and Engineering, 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) SIAM08
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) CMAME2008.pdf
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) siam04.pdf
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) mit03.pdf

Book chapters

Y. Kim, W. Lee, H. Jeon, S. Lim, S. Roh, D. Lee, J. Lee and S. Lawler, The role of microenvironment in regulation of cell infiltration in glioblastoma. In: Stolarska M., Tarfulea N. (eds) Cell Movement. Modeling and Simulation in Science, Engineering and Technology. Birkhäuser, p27-60 (2018) CellMovement2018

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