Structural Characterization of Act c 10.0101 and Pun g 1.0101—Allergens from the Non-Specific Lipid Transfer Protein Family

(1) Background: Non-specific lipid transfer proteins (nsLTPs), which belong to the prolamin superfamily, are potent allergens. While the biological role of LTPs is still not well understood, it is known that these proteins bind lipids. Allergen nsLTPs are characterized by significant stability and resistance to digestion. (2) Methods: nsLTPs from gold kiwifruit (Act c 10.0101) and pomegranate (Pun g 1.0101) were isolated from their natural sources and structurally characterized using X-ray crystallography (3) Results: Both proteins crystallized and their crystal structures were determined. The proteins have a very similar overall fold with characteristic compact, mainly α-helical structures. The C-terminal sequence of Act c 10.0101 was updated based on our structural and mass spectrometry analysis. Information on proteins’ sequences and structures was used to estimate the risk of cross-reactive reactions between Act c 10.0101 or Pun g 1.0101 and other allergens from this family of proteins. (4) Conclusions: Structural studies indicate a conformational flexibility of allergens from the nsLTP family and suggest that immunoglobulin E binding to some surface regions of these allergens may depend on ligand binding. Both Act c 10.0101 and Pun g 1.0101 are likely to be involved in cross-reactive reactions involving other proteins from the nsLTP family.     

A Neumann-Neumann algorithm for a mortar discretization of elliptic problems with discontinuous coefficients

Summary. Neumann-Neumann algorithm have been well developed for standard finite element discretization of elliptic problems with discontinuous coefficients. In this paper, an algorithm of this kind is designed and analyzed for a mortar finite element discretization of problems in three dimensions. It is established that its rate of convergence is independent of the discretization parameters and jumps of coefficients between subregions. The algorithm is well suited for parallel computations.Mathematics Subject Classification (1991): 65N55, 65N10, 65N30, 65N22.The work was supported in part by the U.S. Department of Energy under contract DE-FG02-92ER25127 and in part by Polish Science Foundation under grant 2P03A00524.AcknowledgmentThe author would like to thank Olof Widlund for many fruitful discussions and valuable remarks and suggestions on how to improve the presentation of our results.     

BDDC methods for discontinuous Galerkin discretization of elliptic problems

A discontinuous Galerkin (DG) discretization of Dirichlet problem for second-order elliptic equations with discontinuous coefficients in 2-D is considered. For this discretization, balancing domain decomposition with constraints (BDDC) algorithms are designed and analyzed as an additive Schwarz method (ASM). The coarse and local problems are defined using special partitions of unity and edge constraints. Under certain assumptions on the coefficients and the mesh sizes across ∂Ω_i, where the Ω_i are disjoint subregions of the original region Ω, a condition number estimate C(1+max_ilog(H_i/h_i))² is established with C independent of h_i, H_i and the jumps of the coefficients. The algorithms are well suited for parallel computations and can be straightforwardly extended to the 3-D problems. Results of numerical tests are included which confirm the theoretical results and the necessity of the imposed assumptions.     

Neumann‐Neumann methods for a DG discretization on geometrically nonconforming substructures

A discontinuous Galerkin discretization for second order elliptic equations with discontinuous coefficients in 2D is considered. The domain of interest Ω is assumed to be a union of polygonal substructures Ω_i of size O(H_i). We allow this substructure decomposition to be geometrically nonconforming. Inside each substructure Ω_i, a conforming finite element space associated to a triangulation \begin{align*} {\mathcal{T}}_{h_i}(\Omega_i)\end{align*} is introduced. To handle the nonmatching meshes across ?Ω_i, a discontinuous Galerkin discretization is considered. In this article, additive and hybrid Neumann‐Neumann Schwarz methods are designed and analyzed. Under natural assumptions on the coefficients and on the mesh sizes across ?Ω_i, a condition number estimate \begin{align*} C(1 + \max_i\log \frac{H_i}{h_i})^2\end{align*} is established with C independent of h_i, H_i, h_i/h_j, and the jumps of the coefficients. The method is well suited for parallel computations and can be straightforwardly extended to three dimensional problems. Numerical results are included. © 2011 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq 2012     

Additive Schwarz Methods for Elliptic Mortar Finite Element Problems

Summary. Two variants of the additive Schwarz method for solving linear systems arising from the mortar finite element discretization on nonmatching meshes of second order elliptic problems with discontinuous coefficients are designed and analyzed. The methods are defined on subdomains without overlap, and they use special coarse spaces, resulting in algorithms that are well suited for parallel computation. The condition number estimate for the preconditioned system in each method is proportional to the ratio H/h, where H and h are the mesh sizes, and it is independent of discontinuous jumps of the coefficients. For one of the methods presented the choice of the mortar (nonmortar) side is independent of the coefficients.This work has been supported in part by the Norwegian Research Council, grant 113492/420This work has been supported in part by the National Science Foundation, grant NSF-CCR-9732208 and in part by the Polish Science Foundation, grant 2P03A02116 Mathematics Subject Classification (2000):65N55     

A finite element — Capacitance method for elliptic problems on regions partitioned into subregions

Summary A method is given for the solution of linear equations arising in the finite element method applied to a general elliptic problem. This method reduces the original problem to several subproblems (of the same form) considered on subregions, and an auxiliary problem. Very efficient iterative methods with the preconditioning operator and using FFT are developed for the auxiliary problem.     

Effect of perchlorates on the infrared bands of water: III. The structural model

The splitting of OD bands of HDO in the presence of perchlorates is studied and a structural model of solution is proposed. The assignment of D₂O and H₂O stretching bands in perchlorate solutions is discussed and the effect of temperature and of perchlorate on the vibrational bands of water are compared. Two other band-splitting anions are presented and the problem of anion-water hydrogen bonding is analysed.     

Parylene insulated probes for scanning electrochemical-atomic force microscopy

Scanning electrochemical-atomic force microscopy (SECM-AFM) is a powerful technique that can be used to obtain in situ information related to electrochemical phenomena at interfaces. Fabrication of probes to perform SECM-AFM experiments remains a challenge. Herein, we describe a method for formation of microelectrodes at the tip of commercial conductive AFM probes and demonstrate application of these probes to SECM-AFM. Probes were first insulated with a thin parylene layer, followed by subsequent exposure of active electrodes at the probe tips by mechanical abrasion of the insulating layer. Characterization of probes was performed by electron microscopy and cyclic voltammetry. In situ measurement of localized electrochemical activity with parylene-coated probes was demonstrated through measurement of the diffusion of Ru(NH)(6)(3+) across a porous membrane.     

UV plasmonic-based sensing properties of aluminum nanoconcave arrays

For several decades the plasmonic behavior of materials has been almost exclusively studied in visible region. Emerging applications require, however, the development of efficient materials operating in UV range. In UV nanoplasmonics aluminum (Al) can play a leading role due to its advantageous electronic properties. Yet, there is still lack of reproducible method to obtain Al nanostructures with desired parameters. Al nanoconcaves can provide a way to overcome these limitations. Here, two different periodicities of the Al nanoconcaves arrays were analyzed. It was observed that the Al concaves can dramatically reduce the optical reflectivity as compared to flat, unstructured Al. At the same time pronounced reflectivity dips were discernible, which were ascribed to (0,1) plasmonic mode. The positions of the dips were at around 250 nm and 350 nm for Al concaves with interpores distance (D_c) of 246.3 nm and 456.7 nm, respectively. The refractive index sensitivity (RIS) was: ∼191 nm/RIU for the Al concaves with D_c = 246.3 nm, and ∼291 nm/RIU for the Al nanoconcaves arrays with D_c = 456.7 nm.