Surface electrostatic effects in oligonucleotide microarrays: control and optimization of binding thermodynamics

We present a theoretical thermodynamic framework for the design of more efficient oligonucleotide microarrays. A general thermodynamic relation is derived to describe the electrostatic surface effects on the binding of the assayed biomolecule to a surface-tethered molecular probe. The relation is applied to analyze how the nucleic acid target, the oligonuleotide probe, and their DNA duplex electrostatic interactions with the surface affect the hybridization on DNA arrays. Taking advantage of a closed form exact solution of the linear Poisson-Boltzmann equation for a charged ion-penetrable sphere in electrolyte solution interacting with a plane wall, we study the effects of the surface and solution conditions. Binding free energy is found as a function of the surface material, dielectric or metal, the surface charge density, linker molecule length, temperature, and added salt content. The charge or electric potential of the dielectric or metal surface, respectively, is shown to dominate the hybridization, especially at low added salt or short linker length. We predict that substantial enhancement of sensitivity, selectivity, and reliability of microarrays can be achieved by control of the surface conditions. As examples, we discuss how to overcome two limitations of current technologies: nonequal sensitivity of the probes with different GC and AT bases content, and poor match/mismatch discrimination. In addition, we suggest the design of microarray conditions where the tested nucleic acid is unfolded, thus making possible the screening of a larger sequence with single nucleotide resolution. These promising findings are discussed and further experimental tests suggested.     

The electrostatic contribution to DNA base-stacking interactions.

Base-stacking and phosphate-phosphate interactions in B-DNA are studied using the finite difference Poisson-Boltzmann equation. Interaction energies and dielectric constants are calculated and compared to the predictions of simple dielectric models. No extant simple dielectric model adequately describes phosphate-phosphate interactions. Electrostatic effects contribute negligibly to the sequence and conformational dependence of base-stacking interactions. Electrostatic base-stacking interactions can be adequately modeled using the Hingerty screening function. The repulsive and dispersive Lennard-Jones interactions dominate the dependence of the stacking interactions on roll, tilt, twist, and propellor. The Lennard-Jones stacking energy in ideal B-DNA is found to be essentially independent of sequence.     

On the Spectra of Natural Waves in a Plasma Waveguide in the Presence of Collisions

Plasma Physics Reports - The dispersion characteristics of surface and evanescent waves in ф metal–dielectric–plasma–dielectric–metal structure in the presence of...     

Ultra-Uniform Field Distribution in a Finite-Width Metal–Dielectric–Metal Waveguide

We investigate the propagation characteristics of the fundamental surface plasmon polariton (SPP) mode of a finite-width metal–dielectric–metal waveguide. By changing the refractive index or the thickness of the dielectric layer of the waveguide, the SPP mode can be transformed from a mode confined in the dielectric layer into a mode confined around the metal corners. There always exists a condition at which the mode field distribution in the dielectric layer becomes almost perfectly uniform along the direction parallel to the metal layers, and this condition is insensitive to the width of the waveguide. It is also possible to obtain an ultra-uniform field distribution by controlling the refractive index of a different dielectric placed on both sides of the waveguide. The waveguide can be used as a basic structure for the realization of nanosized photonic devices and sensors.     

Effect of Polymer–Fullerene Interaction on the Dielectric Properties of the Blend

It is commonly believed that large dielectric constants are required for efficient charge separation in polymer photovoltaic devices. However, many polymers used in high‐performance solar cells do not possess high dielectric constants. In this work, the effect of polymer–fullerene interactions on the dielectric environment of the active layer blend and the device performance for several donor–acceptor conjugated polymer systems is investigated. It is found that, while none of the high‐performing polymers studied has a dielectric constant value larger than 3, all polymer–fullerene blends have a significantly larger dielectric constant compared to their pristine constituents. Additionally, it is found that the blend dielectric constant reaches a maximum value in fully optimized devices. Using PTB7:PC₇₁BM blends as an example, it is showed that, in addition to a small increase in the dielectric constant, devices fabricated using the optimum processing additive concentration exhibit almost 3X larger excited state polarizability. This large increase in excited state polarizability results in a substantial difference in short‐circuit current and ultimately device performance. The results show that the excited state polarizability critically depends on polymer–fullerene interactions, and can be a leading indicator of device performance for a given material system.     

Effects of Interaction Between Cadmium and Plumbum on Phytochelatins and Glutathione Production in Wheat (Triticum aestivum L.)

Phytochelatins (PCs) may function as a potential biomarker for metal toxicity. However, less attention has been paid to the effects of metal interactions on the production of PCs and glutathione (GSH),the most prominent cellular thiol. In the present study, the effects of interactions between cadmium (Cd) and plumbum (Pb) on the production of PCs and GSH were monitored over a period of 14 d in wheat (Triticum aestivum L.) tissues. The results showed that combination of Cd and Pb led to synergistic growth inhibition in wheat. Exposure to Cd or Pb increased levels of PCs in a concentration-, tissue-, and time-dependent manner. Cadmium was more effective that Pb in increasing PCs production. Compared with the effects of Cd or Pb alone on the production of PCs, the combination of Cd and Pb acted synergistically, resulting in an enhanced production of PCs. Cadmium also stimulated GSH production in a concentration-, tissue-, and time-dependent manner. However, Pb had no obvious effects on GSH levels. The combination of Pb and Cd antagonized GSH production over the course of the growth period. The results of the present study suggest that metal interactions should be considered in the application of PCs and GSH as potential biomarkers for the evaluation of metal toxicity.     

Optical Properties of Silver-Coated Silicon Nanowires: Morphological and Plasmonic Excitations

The optical extinction spectra of micro- and nanoparticles made up of high-contrast dielectrics exhibit a set of very intense peaks due to the excitations of morphology-dependent resonances (MDRs). These kind of resonances are well known at the microscopic scale as whispering gallery modes. In this work, we study numerically the optical spectra corresponding to a core–shell structure composed by an infinite silicon nanowire coated with a silver shell. This structure shows a combination of both excitations: MDRs and the well-known surface plasmon resonances in dielectric metallic core–shell nanoparticles (Ekeroth Abraham and Lester, Plasmon 2012). We compute in an exact form the complete electromagnetic response for both bare and coated silicon nanowires in the range of 24–200 nm of cross-sectional sizes. We take into account an experimental bulk dielectric function of crystalline silicon and silver by using a correction by size of the metal dielectric function. In this paper, we consider small silver shells in the range of 1–10 nm of thickness as coatings. We analyze the optical response in both the far and near fields, involving wavelengths in the extended range of 300–2,400 nm. We show that the MDRs excited at the core are selectively perturbated by the metallic shell through the bonding and antibonding surface plasmons (SPs). This perturbation depends on both the size of the core and the thickness of the shell, and, as a consequence, we get an efficient tuneable and detectable simple system. Our calculations apply perfectly to long nanotubes compared to the wavelength for the two fundamental polarizations (s, p).     

Extraordinary Optical Transmission Performances of Nanosandwiched Grating for Wideband Multi-Function Integration

In this paper, we present a peculiar metal-dielectric-metal (MDM) nanosandwich grating structure that can achieve extraordinary optical transmission performances at normal incidence in the ultraviolet-visible-near infrared (UV-VIS-NIR) regions. The proposed structure shows three obvious spectrum characteristics: it can obtain high transmittance up to 80 % in NUV region and efficiently blocking visible wavelengths for transverse-magnetic (TM) polarized incidence; a broadband NIR polarizer can be inspired in the wavelength range from 950 to 1400 nm; more surprisingly, these performances do not deteriorated until 30° tilting angle. Compared to other grating structures with single metal overlayer, it shows wider band-stop characteristics and higher broadband transmission transmittance and extinction ratio (ER) in the investigated wavebands. We analyze the underlying physical mechanism by using numerical simulation, which is primarily attributed to metal ultraviolet transparency, surface plasmon polariton (SPP) at metal/dielectric interface, Fabry–Perot (FP)-like cavity mode within this dielectric grating, and optical magnetic resonance especially in the dielectric interlayer of the MDM sandwiched structure. This structure is very important for developing high-performance subwavelength multifunctional integrated optical devices.     

Effects of Interaction Between Cadmium and Plumbum on Phytochelatins and Glutathione Production in Wheat （Triticum aestivum L.）

Phytochelatins (PCs) may function as a potential biomarker for metal toxicity. However, less attention has been paid to the effects of metal interactions on the production of PCs and glutathione (GSH), the most prominent cellular thiol. In the present study, the effects of interactions between cadmium (Cd) and plumbum (Pb) on the production of PCs and GSH were monitored over a period of 14 d in wheat (Triticum aestivum L.) tissues. The results showed that combination of Cd and Pb led to synergistic growth inhibition in wheat. Exposure to Cd or Pb increased levels of PCs in a concentration-, tissue-, and time-dependent manner. Cadmium was more effective that Pb in increasing PCs production. Compared with the effects of Cd or Pb alone on the production of PCs, the combination of Cd and Pb acted synergistically, resulting in an enhanced production of PCs. Cadmium also stimulated GSH production in a concentration-, tissue-, and time-dependent manner. However, Pb had no obvious effects on GSH levels. The combination of Pb and Cd antagonized GSH production over the course of the growth period. The results of the present study suggest that metal interactions should be considered in the application of PCs and GSH as potential biomarkers for the evaluation of metal toxicity.     

On the calculation of electrostatic interactions in proteins

In this paper we present a classical treatment of electrostatic interactions in proteins. The protein is treated as a region of low dielectric constant with spherical charges embedded within it, surrounded by an aqueous solvent of high dielectric constant, which may contain a simple electrolyte. The complete analysis includes the effects of solvent screening, polarization forces, and self energies, which are related to solvation energies. Formulae, and sample calculations of forces and energies, are given for the special case of a spherical protein. Our analysis and model calculations point out that any consistent treatment of electrostatic interactions in proteins should account for the following. Solvent polarization is an important factor in the calculation of pairwise electrostatic interactions. Solvent polarization substantially affects both electrostatic energies and forces acting upon charges. No simple expression for the effective dielectric constant, Deff, can generally be valid, since Deff is a sensitive function of position. Solvent screening of pairwise interactions involving dipolar groups is less effective than the screening of charges. In fact for many interactions involving dipoles, solvent screening can be essentially ignored. The self energy of charges makes a large contribution to the total electrostatic energy of a protein. This must be compensated by specific interactions with other groups in the protein. Strategies for applying our analysis to proteins whose structures are known are discussed.     

Plasmon Features of Coinage Metal Nanoparticles Supported on Zeolites

The plasmonic features in the optical response of coinage metal nanoparticles supported on different type of zeolites were studied. The shifts in the plasmon frequency were analyzed for Cu, Ag, and Au nanoparticles in mordenite, β-zeolite, and Y-zeolite. It was shown experimentally that the resonance energy is sensitive both to type of zeolite structure and counter-cation of zeolite, as well as to annealing temperature and chemical composition of zeolite, their SiO₂/Al₂O₃ molar ratio. A theoretical framework was employed to identify physical mechanism for this sensitivity. Within a simple model, the width of the absorption window identified in the imaginary part of the bulk dielectric function of the different metals was seen to play the important role in establishing the range of the plasmon energies available. In terms of an effective dielectric function, the composite medium was fully described by the complex dielectric function of the metal involved, the dissipation-free dielectric function of the zeolite matrix, and the filling fraction which relates the volume of metal inclusions as a fraction of the total sample volume. The sensitivity of the optical spectra is understood in terms of variations in both the dielectric response of the zeolite matrix as well as nanoparticle size.     

Localized Surface Plasmon Resonance and Refractive Index Sensitivity of Metal–Dielectric–Metal Multilayered Nanostructures

The localized surface plasmon resonances of multilayered nanostructures are studied using finite difference time domain simulations and plasmon hybridization method. Concentric metal–dielectric–metal (MDM) structure with metal core and nanoshell separated by a thin dielectric layer exhibits a strong coupling between the core and nanoshell plasmon resonance modes. The coupled resonance mode wavelengths show dependence on the dielectric layer thickness and composition of core and outer layer metal. The aluminum-based MDM structures show lower plasmon wavelength compared with Ag- and Au-based MDM nanostructures. The calculated refractive index sensitivity (RIS) factor is in the order Ag–Air–Ag>Au–Air–Au>Al–Air–Al for monometallic multilayered nanostructures. Bimetallic multilayered nanostructures support strong and tunable plasmon resonance wavelengths as well as high RIS factor of 510 nm/refractive index unit (RIU) and 470 nm/RIU for Al–Air–Au and Ag-Air-Au, respectively. The MDM structures not only exhibit higher index sensitivity but also cover a wide ultraviolet–near-infrared wavelengths, making these structures very promising for index sensing, biomolecule sensing, and surface-enhanced Raman spectroscopy.     

Formation of a strong electric field resulting in the excitation of microplasma discharges at the edge of a dielectric film on a metal in a plasma flow

Results are presented from experimental and analytical studies of the processes resulting in the excitation of microplasma discharges (MPDs) on a metal surface partially covered with a thin dielectric film under the action of an external plasma flow in vacuum. It is shown experimentally that MPDs are excited at the interface between the open metal surface and the region covered by the dielectric film. The probability of MPD excitation is investigated as a function of the thickness of the dielectric film deposited on the metal. It is found that, for a film thickness of 1 μm, the probability of MPD excitation is close to unity. As the film thickness decreases below ~10 nm or increases above ~10 μm, the probability of MPD excitation is reduced by more than two orders of magnitude. A two-dimensional kinetic numerical code is developed that allows one to model the processes of Debye sheath formation and generation of a strong electric field near the edge of a finite-thickness dielectric film on a metal surface in a plasma flow for different configurations of the film edge. It is shown that the maximum value of the tangential component of the electric field is reached at the film edge and amounts to E _max ≈ |φ₀|/2d (where φ₀ < 0 is the electric potential applied to the metal and d is the film thickness), which for typical conditions of experiments on the excitation of MPDs on metal surfaces (φ₀ ≈–400 V, d ≈ 1 μm) yields E _max ≈ 2 MV/cm. The results of kinetic simulations confirm the qualitative idea about the mechanism of the formation of a strong electric field resulting in the excitation of MPDs at the edge of a dielectric film on a metal surface in a plasma flow and agree with experimental data.     

Distance-dependent dielectric constants and their application to double-helical DNA

Detailed studies of structures of biological macromolecules, even in simplified models, involve many costly and time-consuming calculations. Any thorough methods require sampling of an extremely large conformation and momentum space. Calculations of electrostatic interactions, which depend on many physical factors, such as the details of solvent, solvent accessibility in macromolecules, and molecular polarizability, are always developed in a compromise between more rigorous, detailed models and the need for immediate application to complicated biological systems. In this paper, a middle ground is taken between the more exact theoretical models and the simplest constant values for the dielectric constant. The effects of solvent, counterions, and molecular polarizability are incorporated through a set of adjustable parameters that should be determined from experimental conditions. Several previous forms for the dielectric function are compared with the new ones. The present methods use Langevin functions to span the region of dielectric constant between bulk solvent and cavity values. Application of such dielectric models to double-helical DNA is important because base-stacking preferences were previously demonstrated [A. Sarai, J. Mazur, R. Nussinov, and R. L. Jernigan (1988) Biochemistry, vol. 27, pp. 8498-8502] to be sensitive to the electrostatic formulation. Here we find that poly(dG).poly(dC) can be A form for high screening and B form for low screening. By contrast, poly(dA).poly(dT) can only take the B form. Base stacking is more sensitive to the form of the dielectric function than are the sugar-phosphate backbone conformations. Also in B form, the backbone conformations are not so affected by the base types as in A form.     

Dielectric screening effect of electronic polarization and intramolecular hydrogen bonding

Recent site‐resolved hydrogen exchange measurements have uncovered significant discrepancies between simulations and experimental data during protein folding, including the excessive intramolecular hydrogen bonds in simulations. This finding indicates a possibility that intramolecular charge–charge interactions have not included sufficient dielectric screening effect of the electronic polarization. Scaling down peptide atomic charges according to the optical dielectric constant is tested in this study. As a result, the number of intramolecular hydrogen bonds is lower than using unscaled atomic charges while reaching the same levels of helical contents or β‐hairpin backbone hydrogen bonds, because van der Waals interactions contribute substantially to peptide folding in water. Reducing intramolecular charge–charge interactions and hydrogen bonding increases conformational search efficiency. In particular, it reduces the equilibrium helical content in simulations using AMBER force field and the energy barrier in folding simulations using CHARMM force field.     

Analysis and Optimum Design of Hybrid Plasmonic Slab Waveguides

Propagation properties of hybrid plasmonic slab waveguides are studied in detail using transfer matrix method considering structural and material aspects. Hybrid metal–insulator, hybrid metal–insulator–metal, and hybrid insulator–metal–insulator waveguides are considered. Propagation length (L _p), spatial length (L _s), and mode length (L _m) are utilized as three common figures of merit to compare and optimize the waveguides according to the layer thicknesses and metal/dielectric materials. The effect of constituting materials including metals (such as silver, gold, copper, and aluminum) and dielectrics (common dielectric materials used in photonic integrated circuit technologies such as silicon and silicon compounds, III–V compounds, and polymers) are discussed. It is found that hybrid waveguides are partially to completely superior to conventional plasmonic waveguides, providing a better balance between confinement and loss.     

Design and Realization of a Perfect Metamaterial Absorber in Terahertz Band

Plasmonics - A metamaterial-based absorber with metal–dielectric–metal (MDM) structure design strategy is proposed and verified in terahertz the band. An absorption peak (amplitude is...     

Tuning Plasmon Resonances for Light Coupling into Silicon: a “Rule of Thumb” for Experimental Design

For Si thin-film solar cells to become efficient, schemes to increase the optical absorption in the films are necessary. Scattering of light using plasmonic resonances in metal nanoparticles has been suggested as a feasible route. When placed on a dielectric layer on the front of a solar cell, such metal nanoparticles can scatter a large fraction of the incident light into the solar cell at the resonance wavelength, and hence increase the light collection. However, many related effects may lead to a reduction in photocurrent. Thus, nanoparticle plasmon resonances must be optimized in order to improve the overall light collection. From an experimentalist’s point of view, simple and fast experimental design tools should be explored. In this work, we investigate the plasmon-related photocurrent enhancements for Si test-solar cells with a number of different metal nanoparticle shapes and materials placed on top of a dielectric layer. The spectral position of the photocurrent-enhancement onset is compared to plasmon resonance calculations based on a fairly simple model. Despite the fact that the optical interactions in nanoparticle solar cell configurations can be quite complex, the photocurrent enhancement in the investigated test-solar cells can be predicted qualitatively well for particles with a plasmon resonance in the visible spectrum. This simple and fast model can be used as a rule of thumb in designing nanoparticle arrays for a specific photocurrent enhancement profile.     

Characterizing metal–biomolecule interactions by mass spectrometry

Metal micronutrients are essential for life and exist in a delicate balance to maintain an organism’s health. The labile nature of metal–biomolecule interactions clouds the understanding of metal binders and metal-mediated conformational changes that are influential to health and disease. Mass spectrometry (MS)-based methods and technologies have been developed to better understand metal micronutrient dynamics in the intra- and extracellular environment. In this review, we describe the challenges associated with studying labile metals in human biology and highlight MS-based methods for the discovery and study of metal–biomolecule interactions.