Direct synthesis of polymer nanocapsules with a noncovalently tailorable surface.
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Capsules↗
Biomedical subjects
Wokyung Sung
Publications and source records attributed to Wokyung Sung.
The effect of sequence correlation on bubble statistics in double-stranded DNA.
DNA exists stably in the double-stranded structure at physiological temperatures, but base pairs are observed to unbind locally, giving way to bubbles (i.e., locally denatured states) due to thermal fluctuation. In this study, we consider the effect of sequence on the bubble statistics. On the basis of the Edwards equation description [W. Sung and J.-H. Jeons, Phys. Rev. E 69, 031902 (2004) ], we develop a stochastic model incorporating the sequence randomness as a dichotomic noise, where the bubble and its size are identified as a returning random walk and its first passage time, respectively. By simulating the model Langevin equation, we obtain the bubble size distribution and show how it is affected by the sequence correlation. We find that the bubble size distribution of DNA with finite sequence correlation deviates from the Poland-Scheraga-type distribution. In particular, the formation of large bubbles is dramatically enhanced as sequence correlation length gets longer.
Base Sequence↗
Static and dynamic correlations in a charged membrane.
We study static and dynamic correlations of two fluctuations, the charge density fluctuation and height fluctuation (undulation), on a fluid membrane with a finite excess charge in a viscous fluid. For a planar and symmetrical membrane, we consider a model Hamiltonian inclusive of the fluctuations at the Gaussian level, and construct their equations of motion. Within the model, there exists no coupling, either static or dynamic, between the two fluctuations. The correlation function of the charge density has a short-range damped oscillation over the size of lipid heads due to Coulomb attraction between unlike-charged lipids. Its dynamic correlation function is shown to decay much faster in time than that in simple diffusion. The correlation function of height undulation, on the other hand, has a long-range damped oscillation (bud) over the membrane size, due to Coulomb repulsion among the excess charges. As the excess charge density increases to a critical value, a bending instability sets in, where a minute perturbation on the membrane can cause a large bud to form. Due to the excess charge, the dynamic correlation of the undulation decays slowly in time; at the critical density of the instability, the decay becomes infinitely slow.
Lipid Bilayers↗
A semiflexible chain model of local denaturation in double-stranded DNA.
Double-stranded DNA (dsDNA) is known to form a locally denatured structure ("bubble") below its denaturation temperature (T(c)). We have investigated the physical behavior of the bubbles using a model of dsDNA as two wormlike chains containing interacting complementary base pairs. The model incorporates two biologically relevant features, i.e., semiflexibility of the strand and overdamping nature of aqueous background. Computer simulations using the Langevin equation are performed to examine the size distribution and dynamics of bubbles. The results show that the entropy associated with semiflexibility of DNA sensitively affects the size distribution and lifetime of bubble. In particular, the lifetime grows with bubble size m as m(2.7) at temperature close to T(c), which is consistent with our analysis based on a stochastic model of bubble size dynamics.
Algorithms↗
Effect of surface undulation on polymer adsorption.
We study the adsorption of a long, flexible polymer (ideal or self-avoiding chain) interacting with a rough surface via a finite-range attraction. Within the Edwards equation approach, we develop a variational method to find the segmental distribution and the free energy of an adsorbed chain. As adsorption becomes strong, the segments tend to be localized within the valleys rather than above the hills of the undulating surface, resulting in a decrease of adsorption thickness. Consequently, the surface undulation enhances adsorption in the case of a strongly adsorbed chain whereas the undulation suppresses it for a weakly adsorbed one, since the enhanced entropic repulsion is dominant over the attraction from the surface. Considering the surface with undulation characterized by a Gaussian correlation as an example, we find an optimal correlation length at which the adsorption becomes the strongest and a critical correlation length below which desorption is induced.
Journal Article↗
Conformation of local denaturation in double-stranded DNA.
Double-stranded DNA (dsDNA) undergoes a denaturing transition above which the strands unbind completely. At temperatures (including the physiological temperature) below the transition the base pairs tend to unbind locally, giving way to loops, i.e., locally denatured states. In the flexible-chain model, the imaginary time Schrödinger equation describes the interstrand distance distribution of dsDNA with the time variable replaced by the sequence number. We transform the equation to the Fokker-Planck equation (FPE), which provides a convenient and powerful analytical method and, via the equivalent Langevin equation, a simulation scheme. The temperature-dependent potential that emerges in the FPE manifests how the DNA conformation changes dramatically near the transition temperature. We present several simulation plots along with analytical results illustrating the order parameter (concentration of bound base pairs), base pair distance correlation function, and loop size distribution at different temperatures.
Base Pairing↗
Effects of charge fluctuation on two-membrane instability and fusion.
Membrane fusion is fundamental to diverse biological processes ranging from intercellular and intracellular transport to egg fertilization. We study the effects of coupling between membrane undulation and charge fluctuation on its fusion. We find that, at concentrations of millimolar range, multivalent cations such as calcium in solution induce a strong correlated-charge fluctuation on each membrane, leading to inversion and overcondensation of surface charges. When the charge fluctuation is cooperatively coupled to undulation, two apposing membranes undergo a dynamic instability to spontaneous growth of in-phase undulation with submicron wavelengths, thereby greatly reducing fusion barrier.
Calcium↗