Publications by authors named "Bae-Yeun Ha"

28Publications

Nematic ordering of worm-like polymers near an interface.

J Chem Phys 2020 May;152(20):204907

Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.

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May 2020

Toward building a physical model for membrane selectivity of antimicrobial peptides: making a quantitative sense of the selectivity.

Soft Matter 2019 Sep;15(37):7509-7526

Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.

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September 2019

Confinement induces helical organization of chromosome-like polymers.

Sci Rep 2019 01 29;9(1):869. Epub 2019 Jan 29.

Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada.

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January 2019

Opposing effects of cationic antimicrobial peptides and divalent cations on bacterial lipopolysaccharides.

Phys Rev E 2017 Oct 9;96(4-1):042405. Epub 2017 Oct 9.

Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.

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October 2017

A ring-polymer model shows how macromolecular crowding controls chromosome-arm organization in Escherichia coli.

Sci Rep 2017 09 19;7(1):11896. Epub 2017 Sep 19.

Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada.

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September 2017

How are molecular crowding and the spatial organization of a biopolymer interrelated.

Soft Matter 2016 Dec;12(48):9786-9796

Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada. and School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, Korea.

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December 2016

Effects of molecular crowding and confinement on the spatial organization of a biopolymer.

Soft Matter 2016 Nov;12(47):9436-9450

Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada. and School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, Korea.

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November 2016

Chromosome-like organization of an asymmetrical ring polymer confined in a cylindrical space.

Soft Matter 2015 Nov;11(41):8179-93

Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1.

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November 2015

How Cell Concentrations Are Implicated in Cell Selectivity of Antimicrobial Peptides.

Langmuir 2015 Jul 17;31(29):8052-62. Epub 2015 Jul 17.

†Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.

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July 2015

Polymers under confinement: single polymers, how they interact, and as model chromosomes.

Soft Matter 2015 Mar;11(12):2333-52

Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1.

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March 2015

A polymer in a crowded and confined space: effects of crowder size and poly-dispersity.

Soft Matter 2015 Mar;11(10):1877-88

Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea.

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March 2015

Activation kinetics of zipper molecular beacons.

J Phys Chem B 2015 Jan 18;119(1):44-53. Epub 2014 Dec 18.

Department of Medical Biophysics, Ontario Cancer Institute, University of Toronto , Toronto, Ontario, Canada M5G 1L7.

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January 2015

Surface-lattice model describes electrostatic interactions of ions and polycations with bacterial lipopolysaccharides: ion valence and polycation's excluded area.

Langmuir 2014 Nov 7;30(45):13631-40. Epub 2014 Nov 7.

Department of Physics and Astronomy, University of Waterloo , Waterloo, Ontario N2L 3G1, Canada.

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November 2014

Electrostatic modification of the lipopolysaccharide layer: competing effects of divalent cations and polycationic or polyanionic molecules.

Soft Matter 2014 Oct;10(38):7528-44

Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.

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October 2014

Physical manipulation of the Escherichia coli chromosome reveals its soft nature.

Proc Natl Acad Sci U S A 2012 Oct 14;109(40):E2649-56. Epub 2012 Sep 14.

Department of Physics and Section of Molecular Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.

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October 2012

Overlapping two self-avoiding polymers in a closed cylindrical pore: Implications for chromosome segregation in a bacterial cell.

Phys Rev E Stat Nonlin Soft Matter Phys 2010 Nov 22;82(5 Pt 1):051926. Epub 2010 Nov 22.

Supercomputing Center, Korea Institute of Science and Technology Information, Yuseong-gu, Daejeon 305-806, Korea.

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November 2010

Electrostatic bending of lipid membranes: how are lipid and electrostatic properties interrelated?

Langmuir 2010 Sep;26(18):14737-46

Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada.

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September 2010

Self-avoiding polymer trapped inside a cylindrical pore: Flory free energy and unexpected dynamics.

Phys Rev E Stat Nonlin Soft Matter Phys 2009 Jun 9;79(6 Pt 1):061912. Epub 2009 Jun 9.

Supercomputing Center, Korea Institute of Science and Technology Information, P.O. Box 122, Yuseong-gu, Daejeon 305-806, Korea.

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June 2009

Compression and stretching of a self-avoiding chain in cylindrical nanopores.

Phys Rev Lett 2008 Sep 22;101(13):138101. Epub 2008 Sep 22.

FAS Center for Systems Biology, Harvard University, 7 Divinity Avenue, Cambridge, Massachusetts 02138, USA.

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September 2008

Unexpected relaxation dynamics of a self-avoiding polymer in cylindrical confinement.

J Chem Phys 2007 Oct;127(16):164903

FOM-Institute AMOLF, Kruislaan 407, 1098 SJ Amsterdam, The Netherlands.

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October 2007

Physical basis for membrane-charge selectivity of cationic antimicrobial peptides.

Phys Rev Lett 2007 Apr 16;98(16):168101. Epub 2007 Apr 16.

Department of Physics and Astronomy, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.

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April 2007

Confined space and effective interactions of multiple self-avoiding chains.

Phys Rev Lett 2007 Mar 23;98(12):128303. Epub 2007 Mar 23.

FOM-Institute AMOLF, Kruislaan 407, 1098 SJ Amsterdam, The Netherlands.

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March 2007

Thermal denaturation of double-stranded DNA: effect of base stacking.

Phys Rev E Stat Nonlin Soft Matter Phys 2006 Jan 11;73(1 Pt 1):011905. Epub 2006 Jan 11.

Department of Applied Mathematics, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.

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January 2006

Charge renormalization and inversion of a highly charged lipid bilayer: effects of dielectric discontinuities and charge correlations.

Phys Rev E Stat Nonlin Soft Matter Phys 2005 Aug 19;72(2 Pt 1):021508. Epub 2005 Aug 19.

Department of Physics, University of Waterloo, Ontario N2L 3G1, Canada.

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August 2005

Nonzero ionic size and charge-correlation forces between fluid membranes.

Authors:
Yang Li Bae-Yeun Ha

Phys Rev E Stat Nonlin Soft Matter Phys 2004 Dec 3;70(6 Pt 1):061503. Epub 2004 Dec 3.

Department of Physics, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1.

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December 2004

Chain persistency in single-stranded DNA.

Phys Rev E Stat Nonlin Soft Matter Phys 2004 Jun 15;69(6 Pt 1):061913. Epub 2004 Jun 15.

Department of Physics, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1.

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June 2004

Effect of divalent counterions on asymmetrically charged lipid bilayers.

Authors:
Bae-Yeun Ha

Phys Rev E Stat Nonlin Soft Matter Phys 2003 Mar 18;67(3 Pt 1):030901. Epub 2003 Mar 18.

Department of Physics, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1.

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March 2003