Bae-Yeun Ha

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Bae Yeun HaAssociate Professor

Office: PHY 372
Phone: (519) 888-4567 ext. 37004
Email: byha@uwaterloo.ca

Research interests

  • Theoretical molecular biophysics & soft matter
  • Biomolecular electrostatics, confinement, dynamics & association
  • Polyelectrolytes and polyampholytes
  • Confined polymers: statics, dynamics, & chain miscibility
  • Polymer models for chromosome organization & segregation
  • Membrane electrostatics
  • Membrane selectivity of cationic antimicrobial peptides

Recent publications

  • Y. Jung and B.-Y. Ha, “Overlapping two self-avoiding chains in a closed cylindrical pore: implications for chromosome segregation in a bacterial cell,” Phys. Rev. E 82, 051926-1- - 051926-5 (2010).
  • S. Taheri-Araghi and B.-Y. Ha, “Electrostatic bending of lipid membranes: how are lipid and electrostatic properties interrelated?” Langmuir 26, 14737-14746 (2010).
  • S. Taheri-Araghi and B.-Y. Ha, “Cationic antimicrobial peptides: a physical basis for their selective membrane-disrupting activity,” Soft Matter 6, 1933-1940 (2010).
  • Y. Jung, S. Jun, and B.-Y. Ha, “Self-avoiding polymer trapped inside a cylindrical pore: Flory free energy and unexpected dynamics,” Phys. Rev. E 79, 061912-1--061912-8 (2009).
  • S. Jun, D. Thirumalai, and B.-Y. Ha, “Compression and Stretching of a Self-Avoiding Chain in Cylindrical Nanopores,” Phys. Rev. Lett. 101, 138101-1--138101-4 (2008).
  • S. Taheri-Araghi and B.-Y. Ha, "Physical Basis for Membrane-Charge Selectivity of Cationic Antimicrobial Peptides," Phys. Rev. Lett. 98, 168101-1 -- 168101-4 (2007).
  • S. Jun, A. Arnold, and B.-Y. Ha, "Confined Space and Effective Interactions of Multiple Self-Avoiding Chains," Phys. Rev. Lett. 98, 128303-1 -- 128303-4 (2007).
  • A. Arnold, B. Bozorgui, and D. Frenkel, B.-Y. Ha, and S. Jun, "Unexpected relaxation dynamics of a self-avoiding polymer in cylindrical confinement," J. Chem. Phys. 127, 164903-1 -- 164903-9 (2007).
  • G. Morrison, C. Hyeon, N. M. Toan, B.-Y. Ha, and D. Thirumalai, "Stretching Homopolymers," Macromolecules 40, 7343-7353 (2007).
  • M. Kohandel and B.-Y. Ha, "Thermal denaturation of double-stranded DNA: effect of base stacking," Phys. Rev. E 73, 011905-1 -- 011905-8 (2006).
  • A. Sain, J. Z.Y. Chen, and B.-Y. Ha, "Persistency of single-stranded DNA: the interplay between base sequences and base stacking," Physica A 369, 697-687 (2006).
  • S. Taheri-Araghi and B.-Y. Ha, "Charge renormalization and inversion of a highly-charged lipid bilayer: effects of dielectric discontinuities and charge correlations," Phys. Rev. E 72, 021508-1 -- 021508-10 (2005).
  • Y. Li and B.-Y. Ha, "Molecular theory of asymmetrically charged bilayers: preferred curvatures," Europhys. Lett. 70, 411-417 (2005).
  • Y. Li and B.-Y. Ha, "Nonzero ionic size and charge-correlation forces between fluid membranes", Phys. Rev. E, 70, 061503-1 -- 061503-9 (2004).
  • S. Jun, Y. Hong, H. Imamura, B.-Y. Ha, J. Bechhoefer, and P. Chen, "Self-Assembly of the Ionic Peptide EAK16: The Effect of Charge Distributions on Self-Assembly", Biophys. J. 87, 1249-1259 (2004).
  • A. Sain, B.-Y. Ha, H.-K. Tsao, and J.Z.Y Chen, "Chain persistency in single-stranded DNA", Phys. Rev. E 69, 61913-61916 (2004).
  • S. Jun, J. Bechhoefer, and B.-Y. Ha, "Diffusion-limited loop-formation of semiflexible polymers: Kramers theory and the intertwined time scales of chain relaxation and closing", Europhys. Lett. 64, 420-426 (2003).
  • B.-Y. Ha and D. Thirumalai, "Bending rigidity of stiff polyelectrolyte chains: A Single chain and a bundle of multichains", Macromolecules 36, 9658-9666 (2003).
  • B.-Y. Ha, "Effect of divalent counterions on asymmetrically charged lipid bilayers", Phys. Rev. E 67, 030901-030904, Rapid Communication (2003).
  • A. Sain and B.-Y. Ha, "Counterion distribution and charge-fluctuation-interactions between like-charged fluid membranes", Physica A 320, 67-76 (2003).
  • B.-Y. Ha, "Stabilization and destabilization of cell membranes by multivalent ions", Phys. Rev. E 64, 051902-051905 (2001).
  • B.-Y. Ha, "Modes of charge fluctuations and counterion-mediated attractions between like-charged fluid membranes", Phys. Rev. E 64, 031507-1--031507-9 (2001).
  • B.-Y. Ha and A.J. Liu, "Effect of nonzero chain diameter on DNA condensation", Phys. Rev. E 63, 021503-021507 (2001).
  • B.-Y. Ha and A. J. Liu, Reply to Comment on "The nature of attraction between two charged rods", Phys. Rev. Lett. 83, 2681-2681 (1999).
  • B.-Y. Ha and A. J. Liu, "Counterion-mediated, non-pairwise additive attractions in bundles of like-charged rods", Phys. Rev. E 60, 803-813 (1999).
  • B.-Y. Ha and A. J. Liu, "Kinetics of bundle growth in DNA condensation", Europhys. Lett. 46, 624-630 (1999).
  • R. M. Nyquist, B.-Y. Ha, and A. J. Liu, "Counterion condensation in solutions of rigid polyelectrolytes", Macromolecules 32, 3481-3487 (1999).
  • B.-Y. Ha and D. Thirumalai, "Persistence length of flexible polyelectrolyte chains", J. Chem. Phys. 110, 7533-7540 (1999).
  • B.-Y. Ha and A. J. Liu, "Charge oscillations and many-body effects in bundles of like-charged rods", Phys. Rev. E 58, 6281-6286 (1998).
  • B.-Y. Ha and A. J. Liu, "Interfaces in solutions of randomly charged rods", Physica A 259, 235-244 (1998).
  • B.- Y. Ha and A. J. Liu, "Effect of non-pairwise-additive interactions on bundles of rodlike polyelectrolytes", Phys. Rev. Lett. 81, 1011-1014 (1998).
  • B.-Y. Ha and A.J. Liu, "Counterion-mediated attraction between two like-charged rods", Phys. Rev. Lett. 79, 1289-1292 (1997).
  • B.-Y. Ha and D. Thirumalai, "Persistence length of intrinsically stiff polyampholyte chains", J. de Phys. II 7, 887-902 (1997).
  • B.-Y. Ha and D. Thirumalai, "Semiflexible chains under tension", J. Chem. Phys. 106, 4243-4247 (1997).

Other publications

  • S. Jun, J. Bechhoefer, and B.-Y. Ha, "Looping of semiflexible polymers: from statics to dynamics", published as a chapter in Phenomena of Polymers & Biopolymers ed. by P. Chen (Woodhead Publishing Limited, 2005).
  • B.-Y. Ha and A.J. Liu, "Physical Questions Posed by DNA Condensation'', in physical Chemistry of Polyelectrolytes, edited by T.Radeva (Marcel Dekker, NY, 2001), p163-180.
  • B.-Y. Ha, "How DNA packages itself into finite bundles of a well-defined size'', (Stochastic Dynamics and Pattern Formation in Biological and Complex Systems. APCTP Conference, Seoul, South Korea, 7-10 July 1999). AIP Conference Proceedings, 2000 (no.501), p137-145.
  • D. Thirumalai and B.- Y. Ha, "Statistical Mechanics of Semiflexible Chains: A meanfield variational approach'' in Theoretical and Mathematical Models in Polymer Research, edited by A. Y. Grosberg (Academic Press, 1998), p1-35.