Ion current calculations based on three dimensional Poisson-Nernst-Planck theory for a cyclic peptide nanotube

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 implemented using a finite difference method. The influence of dipolar lipid molecules on the ion currents is also examined by turning on or off the charges of the lipid dipoles in dipalmitoylphosphatidylcholine (DPPC). Comparisons between the calculated and experimentally measured ion currents show that the PNP approach agrees well with the measurements at low ion concentrations but overestimates the currents at higher concentrations. Concentration profiles reveal the selectivity of the peptide nanotube to cations, which is attributed to the negatively charged carbonyl oxygens inside the nanotube. The dominant cation and the minimum anion concentrations inside the cyclic peptide nanotube suggest that these cyclic peptide nanotubes can be employed as ion sensors. In the case of the polar DPPC bilayer, smaller currents are obtained in the calculation. The variation of current with polarity of the lipids implies that both polar and nonpolar lipid bilayer membranes can be utilized to regulate ion currents in the peptide nanotube and other ion channels. Strengths and limitations of the PNP theory are also discussed.     

Manipulating the optical properties of pyramidal nanoparticle arrays

This paper reports the orientation-dependent optical properties of two-dimensional arrays of anisotropic metallic nanoparticles. These studies were made possible by our simple procedure to encapsulate and manipulate aligned particles having complex three-dimensional (3D) shapes inside a uniform dielectric environment. Using dark field or scattering spectroscopy, we investigated the plasmon resonances of 250-nm Au pyramidal shells embedded in a poly(dimethylsiloxane) (PDMS) matrix. Interestingly, we discovered that the scattering spectra of these particle arrays depended sensitively on the direction and polarization of the incident white light relative to the orientation of the pyramidal shells. Theoretical calculations using the discrete dipole approximation support the experimentally observed dependence on particle orientation with respect to incident field. This work presents an approach to manipulate--by hand--ordered arrays of particles over cm(2) areas and provides new insight into the relationship between the shape of well-defined, 3D particles and their supported plasmon resonance modes.     

Atomic-scale roughness effect on capillary force in atomic force microscopy

We study the capillary force in atomic force microscopy by using Monte Carlo simulations. Adopting a lattice gas model for water, we simulated water menisci that form between a rough silicon-nitride tip and a mica surface. Unlike its macroscopic counterpart, the water meniscus at the nanoscale gives rise to a capillary force that responds sensitively to the tip roughness. With only a slight change in tip shape, the pull-off force significantly changes its qualitative variation with humidity.     

Structures of DNA-linked nanoparticle aggregates

The room-temperature structure of DNA-linked gold nanoparticle aggregates is investigated using a combination of experiment and theory. The experiments involve extinction spectroscopy measurements and dynamic light scattering measurements of aggregates made using 60 and 80 nm gold particles and 30 base-pair DNA. The theoretical studies use calculated spectra for models of the aggregate structures to determine which structure matches the observations. These models include diffusion-limited cluster-cluster aggregation (DLCA), reaction-limited cluster-cluster aggregation (RLCA), and compact (nonfractal) cluster aggregation. The diameter of the nanoparticles used in the experiments is larger than has been considered previously, and this provides greater sensitivity of spectra to aggregate structure. We show that the best match between experiment and theory occurs for the RLCA fractal structures. This indicates that DNA hybridization takes place under irreversible conditions in the room-temperature aggregation. Some possible structural variations which might influence the result are considered, including the edge-to-edge distance between nanoparticles, variation in the diameter of the nanoparticles, underlying lattice structures of on-lattice compact clusters, and positional disorders in the lattice structures. We find that these variations do not change the conclusion that the room-temperature structure of the aggregates is fractal. We also examine the variation in extinction at 260 nm as temperature is increased, showing that the decrease in extinction at temperatures below the melting temperature is related to a morphological change from fractal toward compact structures.     

Tunable infrared generation in KTA and applications

Noncollinear difference frequency mixing of dye laser and Nd:YAG second harmonic (fundamental) radiation from a commercial laser system is employed for the generation of 2.7–5.3 μm (1.6–1.7 μm) radiations in a flux-grown KTiOAsO₁ crystal. The generated radiation is used to scan the methane absorption in the fundamental (v ₃) and its first overtone (2v ₃) band at pressure 90 torr in a laboratory made single pass gas cell of length 33 cm.     

Quadrupole interaction at111Cd nuclein in single-crystalline thallium

The quadrupole interaction of¹¹¹Cd nuclei in a single crystal of hexagonal thallium has been investigated for different geometries and sample temperatures employing the perturbed - angular correlation technique. The observed variation of the electric field gradient with temperature is attributed to local modes of thermal vibrations of the Cd impurities. An analytical relationship has been derived from lattice-dynamical models, expressing the temperature dependence in terms of impurity-host mass ratios and local force-constants.     

Mitochondrial Oxidative Phosphorylation

Mitochondria can form ATP from ADP and inorganic phosphate, the required energy being supplied by respiration. This coupled process, which in sufficiently aerated normal animal cells furnishes the bulk of the cellular ATP, is termed oxidative phosphorylation. The overall reaction is intimately associated with the mitochondrial inner membrane and proceeds via a primary high-energy intermediate. This intermediate, in a manner as yet unknown, energizes the anhydride formation between ADP and inorganic phosphate. The coupling between respiration and ATP synthesis is mediated by proteins of the mitochondrial inner membrane which are known as “coupling factors”. The mechanism of oxidative phosphorylation is at present being discussed in terms of three hypotheses which are generally referred to as “chemical”, “chemiosmotic”, and “conformational” hypotheses. None of these hypotheses has as yet been experimentally verified.     

Finite lifetime effects on the polarizability within time-dependent density-functional theory

We present an implementation for considering finite lifetime of the electronic excited states into linear-response theory within time-dependent density-functional theory. The lifetime of the excited states is introduced by a common phenomenological damping factor. The real and imaginary frequency-dependent polarizabilities can thus be calculated over a broad range of frequencies. This allows for the study of linear-response properties both in the resonance and nonresonance cases. The method is complementary to the standard approach of calculating the excitation energies from the poles of the polarizability. The real and imaginary polarizabilities can then be calculated in any specific energy range of interest, in contrast to the excitation energies which are usually solved only for the lowest electronic states. We have verified the method by investigating the photoabsorption properties of small alkali clusters. For these systems, we have calculated the real and imaginary polarizabilities in the energy range of 1-4 eV and compared these with excitation energy calculations. The results showed good agreement with both previous theoretical and experimental results.     

DNA as helical ruler: exciton-coupled circular dichroism in DNA conjugates

The structure and properties of oligonucleotide conjugates possessing stilbenedicarboxamide chromophores at both ends of a poly(dA):poly(dT) base-pair domain of variable length have been investigated using a combination of spectroscopic and computational methods. These conjugates form capped hairpin structures in which one stilbene serves as a hairpin linker and the other as a hydrophobic end-cap. The capping stilbene stabilizes the hairpin structures by ca. 2 kcal/mol, making possible the formation of a stable folded structure containing a single A:T base pair. Exciton coupling between the stilbene chromophores has little effect on the absorption bands of capped hairpins. However, exciton-coupled circular dichroism (EC-CD) can be observed for capped hairpins possessing as many as 11 base pairs. Both the sign and intensity of the EC-CD spectrum are sensitive to the number of base pairs separating the stilbene chromophores, as a consequence of the distance and angular dependence of exciton coupling. Calculated spectra obtained using a static vector model based on canonical B-DNA are in good agreement with the experimental spectra. Molecular dynamics simulations show that conformational fluctuations of the capped hairpins result in large deviations of the averaged spectra in both the positive and negative directions. These results demonstrate for the first time the ability of B-DNA to serve as a helical ruler for the study of electronic interactions between aligned chromophores. Furthermore, they provide important tests for atomistic theoretical models of DNA.