Comparison of different lattice definitions of the topological charge

We present a comparison of different definitions of the topological charge on the lattice, using a small-volume ensemble with 2 flavours of dynamical twisted mass fermions. The investigated definitions are: index of the overlap Dirac operator, spectral projectors, spectral flow of the HermitianWilson- Dirac operator and field theoretic with different kinds of smoothing of gauge fields (HYP and APE smearings, gradient flow, cooling). We also show some results on the topological susceptibility.

Depth dependent lattice disorder and strain in Mn-implanted and post-annealed InAs thin films

The lattice order degree and the strain in as-grown, Mn-implanted and post-implantedannealedInAsthinfilms were investigated with depth resolution by means of Rutherford backscattering spectrometry in channeling conditions (RBS/C). Three main crystallographic axes were analyzed for both In and As sublattices. The behaviour of the induced defects was evaluated in two regions with different native defects: the interface and the surface. The results show that Mn implantation and post-implantation annealing are anisotropic processes, affecting in a different way the In and As sublattices. The mechanisms influencing the enhancement and deterioration of the crystal quality during the implantation are discussed in relation to the as-grown defects and the segregation of the elements

High quality InAlN single layers lattice-matched to GaN grown by molecular beam epitaxy

We report on properties of high quality ~60 nm thick InAlN layers nearly in-plane lattice-matched to GaN, grown on c-plane GaN-on-sapphire templates by plasma-assisted molecular beam epitaxy. Excellent crystalline quality and low surface roughness are confirmed by X-ray diffraction, transmission electron microscopy, and atomic force microscopy. High annular dark field observations reveal a periodic in-plane indium content variation (8 nm period), whereas optical measurements evidence certain residual absorption below the band-gap. The indium fluctuation is estimated to be +/- 1.2% around the nominal 17% indium content via plasmon energy oscillations assessed by electron energy loss spectroscopy with sub-nanometric spatial resolution.

Optimization of a label-free biosensor vertically characterized based on a periodic lattice of high aspect ratio SU-8 nano-pillars with a simplified 2D theoretical model

We have recently demonstrated a biosensor based on a lattice of SU8 pillars on a 1 μm SiO2/Si wafer by measuring vertically reflectivity as a function of wavelength. The biodetection has been proven with the combination of Bovine Serum Albumin (BSA) protein and its antibody (antiBSA). A BSA layer is attached to the pillars; the biorecognition of antiBSA involves a shift in the reflectivity curve, related with the concentration of antiBSA. A detection limit in the order of 2 ng/ml is achieved for a rhombic lattice of pillars with a lattice parameter (a) of 800 nm, a height (h) of 420 nm and a diameter(d) of 200 nm. These results correlate with calculations using 3D-finite difference time domain method. A 2D simplified model is proposed, consisting of a multilayer model where the pillars are turned into a 420 nm layer with an effective refractive index obtained by using Beam Propagation Method (BPM) algorithm. Results provided by this model are in good correlation with experimental data, reaching a reduction in time from one day to 15 minutes, giving a fast but accurate tool to optimize the design and maximizing sensitivity, and allows analyzing the influence of different variables (diameter, height and lattice parameter). Sensitivity is obtained for a variety of configurations, reaching a limit of detection under 1 ng/ml. Optimum design is not only chosen because of its sensitivity but also its feasibility, both from fabrication (limited by aspect ratio and proximity of the pillars) and fluidic point of view. (© 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

Classification of discrete systems on a square lattice

We consider the classification up to a Möbius transformation of real linearizable and integrable partial difference equations with dispersion defined on a square lattice by the multiscale reduction around their harmonic solution. We show that the A1, A2, and A3 linearizability and integrability conditions constrain the number of parameters in the equation, but these conditions are insufficient for a complete characterization of the subclass of multilinear equations on a square lattice.

Preliminary temperature accelerated life test (ALT) on lattice mismatched triple-junction concentrator solar cells-on-carriers

A temperature accelerated life test on concentrator lattice mismatched Ga0.37In0.63P/Ga0.83In0.17As/Ge triple-junction solar cells-on-carrier is being carried out. The solar cells have been tested at three different temperatures: 125, 145 and 165°C and the nominal photo-current condition (500X) is emulated by injecting current in darkness. The final objective of these tests is to evaluate the reliability, warranty period, and failure mechanism of these solar cells in a moderate period of time. Up to now only the test at 165°C has finished. Therefore, we cannot provide complete reliability information, but we have carried out preliminary data and failure analysis with the current results.

Spin-lattice relaxation of laser-polarized xenon in human blood

The nuclear spin polarization of 129Xe can be enhanced by several orders of magnitude by using optical pumping techniques. The increased sensitivity of xenon NMR has allowed imaging of lungs as well as other in vivo applications. The most critical parameter for efficient delivery of laser-polarized xenon to blood and tissues is the spin-lattice relaxation time (T1) of xenon in blood. In this work, the relaxation of laser-polarized xenon in human blood is measured in vitro as a function of blood oxygenation. Interactions with dissolved oxygen and with deoxyhemoglobin are found to contribute to the spin-lattice relaxation time of 129Xe in blood, the latter interaction having greater effect. Consequently, relaxation times of 129Xe in deoxygenated blood are shorter than in oxygenated blood. In samples with oxygenation equivalent to arterial and venous blood, the 129Xe T1s at 37°C and a magnetic field of 1.5 T were 6.4 s ± 0.5 s and 4.0 s ± 0.4 s, respectively. The 129Xe spin-lattice relaxation time in blood decreases at lower temperatures, but the ratio of T1 in oxygenated blood to that in deoxygenated blood is the same at 37°C and 25°C. A competing ligand has been used to show that xenon binding to albumin contributes to the 129Xe spin-lattice relaxation in blood plasma. This technique is promising for the study of xenon interactions with macromolecules.

Adsorption from a one-dimensional lattice gas and the Brunauer–Emmett–Teller equation

An exact treatment of adsorption from a one-dimensional lattice gas is used to eliminate and correct a well-known inconsistency in the Brunauer–Emmett–Teller (B.E.T.) equation—namely, Gibbs excess adsorption is not taken into account and the Gibbs integral diverges at the transition point. However, neither model should be considered realistic for experimental adsorption systems.

Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: Application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K

The conformational space annealing (CSA) method for global optimization has been applied to the 10-55 fragment of the B-domain of staphylococcal protein A (protein A) and to a 75-residue protein, apo calbindin D9K (PDB ID code 1CLB), by using the UNRES off-lattice united-residue force field. Although the potential was not calibrated with these two proteins, the native-like structures were found among the low-energy conformations, without the use of threading or secondary-structure predictions. This is because the CSA method can find many distinct families of low-energy conformations. Starting from random conformations, the CSA method found that there are two families of low-energy conformations for each of the two proteins, the native-like fold and its mirror image. The CSA method converged to the same low-energy folds in all cases studied, as opposed to other optimization methods. It appears that the CSA method with the UNRES force field, which is based on the thermodynamic hypothesis, can be used in prediction of protein structures in real time.

Stretching lattice models of protein folding

A new class of experiments that probe folding of individual protein domains uses mechanical stretching to cause the transition. We show how stretching forces can be incorporated in lattice models of folding. For fast folding proteins, the analysis suggests a complex relation between the force dependence and the reaction coordinate for folding.

Cooperative enhancement of specificity in a lattice of T cell receptors

Two of the most important models to account for the specificity and sensitivity of the T cell receptor (TCR) are the kinetic proofreading and serial ligation models. However, although kinetic proofreading provides a means for individual TCRs to measure accurately the length of time they are engaged and signal appropriately, the stochastic nature of ligand dissociation means the kinetic proofreading model implies that at high concentrations the response of the cell will be relatively nonspecific. Recent ligand experiments have revealed the phenomenon of both negative and positive crosstalk among neighboring TCRs. By using a Monte Carlo simulation of a lattice of TCRs, we integrate receptor crosstalk with the kinetic proofreading and serial ligation models and discover that receptor cooperativity can enhance T cell specificity significantly at a very modest cost to the sensitivity of the response.

Folding funnels and frustration in off-lattice minimalist protein landscapes

A full quantitative understanding of the protein folding problem is now becoming possible with the help of the energy landscape theory and the protein folding funnel concept. Good folding sequences have a landscape that resembles a rough funnel where the energy bias towards the native state is larger than its ruggedness. Such a landscape leads not only to fast folding and stable native conformations but, more importantly, to sequences that are robust to variations in the protein environment and to sequence mutations. In this paper, an off-lattice model of sequences that fold into a β-barrel native structure is used to describe a framework that can quantitatively distinguish good and bad folders. The two sequences analyzed have the same native structure, but one of them is minimally frustrated whereas the other one exhibits a high degree of frustration.

Lattice model for rapidly folding protein-like heteropolymers.

Protein folding is a relatively fast process considering the astronomical number of conformations in which a protein could find itself. Within the framework of a lattice model, we show that one can design rapidly folding sequences by assigning the strongest attractive couplings to the contacts present in a target native state. Our protein design can be extended to situations with both attractive and repulsive contacts. Frustration is minimized by ensuring that all the native contacts are again strongly attractive. Strikingly, this ensures the inevitability of folding and accelerates the folding process by an order of magnitude. The evolutionary implications of our findings are discussed.