Biomedical subjects

Bae-Yeun Ha

Publications and source records attributed to Bae-Yeun Ha.

5 recordsLinked to original sources

PubMed2006

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

We study the thermal denaturation of double-stranded DNA, i.e., separation of its two strands upon heating. A simple homo-polymer model is used to account for the effect of base stacking on the thermal stability of DNA. We find that stacking influences the stability in a nontrivial way: It not only enhances the stability but also makes the denaturation transition sharp. While stacking between bound monomers stabilizes DNA as does base pairing, stacking in unbound parts (or loops) rather destabilizes DNA--the overall stability is, however, enhanced by stacking.

Journal Article↗

PubMed2005

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

We reexamine the problem of charge renormalization and inversion of a highly charged surface of a low dielectric constant immersed in ionic solutions. To be specific, we consider an asymmetrically charged lipid bilayer, in which only one layer is negatively charged. In particular, we study how dielectric discontinuities and charge correlations (among lipid charges and condensed counterions) influence the effective charge of the surface. When counterions are monovalent (e.g., Na+), our mean-field approach implies that dielectric discontinuities can enhance counterion condensation. A simple scaling picture shows how the effects of dielectric discontinuities and surface-charge distributions are intertwined: Dielectric discontinuities diminish condensation if the backbone charge is uniformly smeared out while counterions are localized in space; they can, however, enhance condensation when the backbone charge is discrete. In the presence of asymmetric salts such as CaCl2 , we find that the correlation effect, treated at the Gaussian level, is more pronounced when the surface has a lower dielectric constant, inverting the sign of the charge at a smaller value of Ca2+ concentration.

Calcium↗

PubMed2004

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

We present a theoretical approach to charge-correlation attractions between like-charged membranes with neutralizing counterions assumed to be localized to the membrane surface. In particular, we study the effect of nonzero ionic sizes on the attraction by treating the membrane charges (both backbone charges and localized counterions) as forming a two-dimensional ionic fluid of hard spheres of the same diameter D . Using a two-dimensional Debye-Huckel approach to this system, we examine how ion sizes influence the attraction. We find that the attraction gets stronger as surface charge densities or counterion valency increase, consistent with long-standing observations. Our results also indicate a nontrivial dependence of the attraction on separations h: The attraction is enhanced by ion sizes for intermediate h ranges, while it crosses over to the known D -independent universal behavior as h-->infinity; it remains finite as h-->0, as expected for a system of finite-sized ions.

Journal Article↗

PubMed2004

Chain persistency in single-stranded DNA.

We develop a theoretical approach to hairpin-loop formation of single-stranded (ss) DNA by treating the strand as a two-state system in which bases are either "stacked" or "unstacked." The looping kinetics of ssDNA is shown to be intrinsically different from that of a wormlike chain; it is mainly controlled by stacking-breakage probability, not by the mean curvature of loops, and highly sensitive to the composition of the loop as seen in recent experiments. Our estimate of a stacking energy for poly ( dA ), -3.9 kcal/mol, is consistent with known results.

Base Sequence↗

PubMed2003

Effect of divalent counterions on asymmetrically charged lipid bilayers.

We study an asymmetrically charged lipid bilayer in which the inner layer is negatively charged, while the outer one is neutral. In particular, we focus on the interplay between the asymmetrical charge distribution and counterion valency in determining the preferred curvature state of the bilayer. We show that, at low ionic strength, an entropic effect associated with counterion release tends to expand the inner layer-surprisingly, the excess charge of the bilayer opposes this. In the absence of multivalent ions, the entropic effect is dominant and gives rise to a tendency towards negative mean curvature. The presence of divalent counterions, however, counterbalances the entropic effect-they tend to shrink the inner layer, leading to positive mean curvature.

Biophysical Phenomena↗