[Show abstract][Hide abstract] ABSTRACT: Conformational changes in the envelope proteins of flaviviruses help to expose the highly conserved fusion peptide (FP), a region which is critical to membrane fusion and host cell infection, and which represents a significant target for antiviral drugs and antibodies. In principle, extended timescale atomic-resolution simulations may be used to characterize the dynamics of such peptides. However, the resultant accuracy is critically dependent upon both the underlying force field and sufficient conformational sampling. In the present study, we report a comprehensive comparison of three simulation methods and four force fields comprising a total of more than 40 μs of sampling. Additionally, we describe the conformational landscape of the FP fold across all flavivirus family members. All investigated methods sampled conformations close to available X-ray structures, but exhibited differently populated ensembles. The best force field / sampling combination was sufficiently accurate to predict that the solvated peptide fold is less ordered than in the crystallographic state, which was subsequently confirmed via circular dichroism and spectrofluorometric measurements. Finally, the conformational landscape of a mutant incapable of membrane fusion was significantly shallower than wild-type variants, suggesting that dynamics should be considered when therapeutically targeting FP epitopes.
Full-text · Article · Feb 2016 · Scientific Reports
[Show abstract][Hide abstract] ABSTRACT: Taking advantage of the cluster effect observed in multivalent peptides, this work describes antifungal activity and possible mechanism of action of tetravalent peptide (B4010) which carries 4 copies of the sequence RGRKVVRR through a branched lysine core. B4010 displayed better antifungal properties than natamycin and amphotericin B. The peptide retained significant activity in the presence of monovalent/divalent cations, trypsin and serum and tear fluid. Moreover, B4010 is non-haemolytic and non-toxic to mice by intraperitoneal (200 mg/kg) or intravenous (100 mg/kg) routes. S. cerevisiae mutant strains with altered membrane sterol structures and composition showed hyper senstivity to B4010. The peptide had no affinity for cell wall polysaccharides and caused rapid dissipation of membrane potential and release of vital ions and ATP when treated with C. albicans. We demonstrate that additives which alter the membrane potential or membrane rigidity protect C. albicans from B4010-induced lethality. Calcein release assay and molecular dynamics simulations showed that the peptide preferentially binds to mixed bilayer containing ergosterol over phophotidylcholine-cholesterol bilayers. The studies further suggested that the first arginine is important for mediating peptide-bilayer interactions. Replacing the first arginine led to a 2-4 fold decrease in antifungal activities and reduced membrane disruption properties. The combined in silico and in vitro approach should facilitate rational design of new tetravalent antifungal peptides.
[Show abstract][Hide abstract] ABSTRACT: Effective control of room-temperature electroluminescence of n-ZnMgO/p-GaN light-emitting diodes (LEDs) over both emission intensity and wavelength is demonstrated. With varied Mg concentration, the intensity of LEDs in the near-ultraviolet region is increased due to the effective radiative recombination in the ZnMgO layer. Furthermore, the emission wavelength is shifted to the green/yellow spectral region by employing an indium-tin-oxide thin film as the dopant source, where thermally activated indium diffusion creates extra deep defect levels for carrier recombination. These results clearly demonstrate the effectiveness of controlled metal incorporation in achieving high energy efficiency and spectral tunability of the n-ZnMgO/p-GaN LED devices.
No preview · Article · Dec 2012 · Applied Physics Letters
[Show abstract][Hide abstract] ABSTRACT: Although the dielectric behavior of nanostructured semiconductors has been intensively investigated, the physics behind observations remains disputed with possible mechanisms such as quantum confinement and dangling bond polarization. Here we show that theoretical reproduction of the measured dielectric suppression of Ge nanocrystals asserts that the dielectric suppression originates from the shorter and stronger bonds at the skin-deep surface, the associated local densification and quantum entrapment of energy. Coordination-imperfection induced local quantum entrapment perturbs the Hamiltonian that determines the band gap and hence, the process of electron polarization consequently.
[Show abstract][Hide abstract] ABSTRACT: The bandgap and optical properties (dielectric functions and optical constants) of dome-shaped Ge nanocrystals (nc-Ge) with average sizes of ∼6 nm in height and ∼13 nm in diameter have been investigated using spectroscopic ellipsometry based on the Forouhi-Bloomer optical dispersion model. As compared to bulk crystalline Ge, the nc-Ge exhibited a bandgap expansion of ∼0.2 eV and a significant reduction in the dielectric function. The bandgap expansion and dielectric suppression are discussed in terms of the quantum confinement effect as well as the bond contraction model.
Full-text · Article · Mar 2011 · Journal of Applied Physics
[Show abstract][Hide abstract] ABSTRACT: The split of surface plasmon resonance of self-assembled gold nanoparticles on Si substrate is observed from the dielectric functions of the nanoparticles. The split plasmon resonances are modeled with two Lorentz oscillators: one oscillator at ~1 eV models the polarization parallel to the substrate while the other at ~2 eV represents the polarization perpendicular to the substrate. Both parallel and perpendicular resonances are red-shifted when the nanoparticle size increases. The red shifts in both resonances are explained by the image charge effect of the Si substrate.
[Show abstract][Hide abstract] ABSTRACT: The band gap and optical properties (dielectric functions and optical constants) of Ge thin films with various thicknesses below 50 nm, which were synthesized with electron beam evaporation technique, have been determined using spectroscopic ellipsometry and UV-visible spectrophotometry. The optical properties are well described with the Forouhi–Bloomer model. Both the band gap and optical properties show a strong dependence on the film thickness. For film thickness smaller than ∼10 nm , a band gap expansion is observed as compared to bulk crystalline Ge, which is attributed to the one-dimensional quantum confinement effect. However, a band gap reduction was observed for thickness larger than ∼10 nm , which is explained in terms of the amorphous effect in the Ge layers.
Full-text · Article · Feb 2010 · Journal of Applied Physics
[Show abstract][Hide abstract] ABSTRACT: In this letter, Ni-rich NiO thin film is deposited on p-type Si substrate by dc magnetron sputtering to form a metal-insulator-semiconductor structure. The charge trapping in the Ni nanocrystals (nc-Ni) embedded in NiO matrix induces a flatband voltage shift and capacitance modulation, which could be used for memory applications. The charging of nc-Ni depends on the voltage polarity, as well as the charging time and magnitude of gate voltage. The capacitance modulation can be described by an equivalent circuit model.
[Show abstract][Hide abstract] ABSTRACT: An anti reflective layer for Si photodetectors working at various wavelengths is designed based on a SiO2 film containing Si nanocrystals (nc-Si). It is shown that with a proper amount of nc-Si distributed in the oxide and at the right thickness of the film, a single layer of nc-Si/SiO2 film can serve as a perfect anti reflection coating with very low or insignificant light loss. For example, for a 110 nm layer with an nc-Si volume fraction of 34%, the reflectance and the transmittance at the wavelength of 850 nm can reach 0.008 and 99.99%, respectively.
No preview · Article · Jun 2009 · Japanese Journal of Applied Physics