Hyonseok Hwang

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Ion current calculations based on Poisson-Nernst-Planck (PNP) theory are performed for a synthetic cyclic peptide nanotube that consists of eight or ten cyclo[(-L-Trp-D-Leu-)4] embedded in a lipid bilayer membrane to investigate the ion transport properties of the nanotube. To explore systems with arbitrary geometries, three-dimensional PNP theory is(More)
Coarse-grained (CG) molecular dynamics (MD) simulations are performed to study the insertion of cyclic peptide nanotubes into cell membranes and to examine whether cyclic peptide nanotubes can function as an ion channel and thereby as an antibacterial agent. To do so, the two coarse-grained (CG) models for lipid molecules and for proteins developed by(More)
Potential of mean force (PMF) profiles of a single Na+ or K+ ion passing through a cyclic peptide nanotube, cyclo[-(D-Ala-Glu-D-Ala-Gln)2-], in water are calculated to provide insight into ion transport and to understand the conductance difference between these two ions. The PMF profiles are obtained by performing steered molecular dynamics (SMD)(More)
In this study, we demonstrate the potentials and pitfalls of using various waterfall plots, such as conventional waterfall plots, two-dimensional (2D) gradient maps, moving window two-dimensional analysis (MW2D), perturbation-correlation moving window two-dimensional analysis (PCMW2D), and moving window principal component analysis two-dimensional(More)
  • Hyonseok Hwang, George C Schatz, Mark A Ratner
  • The journal of physical chemistry. A
  • 2007
To deal with inhomogeneous diffusion coefficients of ions without altering the lattice spacing in the kinetic lattice grand canonical Monte Carlo (KLGCMC) simulation, an algorithm that incorporates diffusion coefficient variation into move probabilities is proposed and implemented into KLGCMC calculations. Using this algorithm, the KLGCMC simulation method(More)
An algorithm in which kinetic lattice grand canonical Monte Carlo simulations are combined with mean field theory (KLGCMC/MF) is presented to calculate ion currents in a model ion channel system. In this simulation, the relevant region of the system is treated by KLGCMC simulations, while the rest of the system is described by modified Poisson-Boltzmann(More)
In order to develop a more complete understanding of the limitations of mixed quantum-classical simulation methods, the origins of electronic dephasing are analyzed in a simple model of the condensed phase, namely, the spin-boson model with an ohmic spectral density. We focus on the decay of the thermally averaged nuclear overlap/phase function (NOPF).(More)
Novel salen-Al/triarylborane dyad complexes were prepared and characterized with their corresponding mononuclear compounds. The UV-vis and photoluminescence experiments for dyads exhibited photoinduced energy transfer from borane to the salen-Al moiety in an intramolecular manner. Theoretical calculation and fluoride titration results further supported(More)
The design and synthesis of the first asymmetrically "two-walled"meso-substituted calix[4]pyrrole tethered by a fluorophore and its subsequent implication as an archetype sequential 'on-off-on-off' fluorescent single-molecular switch are reported. The current system permits us to extend the sensitivity up to sub-nanomolar levels with the detection limit as(More)
Potential of mean force (PMF) profiles and position-dependent diffusion coefficients of Na+ and K+ are calculated to elucidate the translocation of ions through a cyclic peptide nanotube, composed of 8 × cyclo[-(d-Leu-Trp)4-] rings, in water and in hydrated DMPC bilayers. The PMF profiles and PMF decomposition analysis for the monovalent cations show that(More)