Use of very long-distance NOEs in a fully deuterated protein: an approach for rapid protein fold determination

The high sensitivity of modern NMR instrumentation, in combination with full deuteration, enabled the measurement of long-range NOEs between amide protons in a fully deuterated protein corresponding to distances up to 8A. These are beyond the limit normally observed in protonated samples. Such long-distance NOEs could be observed using long mixing times, which became possible due to reduced spin diffusion and T1 relaxation of the amide protons in the fully deuterated sample. This information was used in combination with secondary structure restraints derived from secondary chemical shifts for structure calculations. With these backbone amide proton NOEs only, a unique fold could be obtained with positional root mean square deviations from the average of 1.30 and 2.25 A for backbone and heavy atoms, respectively. Despite the low density of restraints, no mirror image problems were observed. Addition of sidechain NOE information increased the precision of the ensemble and in particular of the core packing. The structures obtained in this way were close to the published crystal structure. NOE completeness analysis revealed that the cumulative completeness is still more than 80% for an 8.0 A cut-off distance.     

A theoretical analysis of a piezoelectric ultrasound device with an active matching layer

This paper investigates the use of magnetically active materials in the matching layer of a piezoelectric transducer. This then allows the performance of the device to be dynamically altered by applying an external field. The effect that this new matching layer has on the performance of a typical device is theoretically investigated here. It transpires that the additional flexibility of an active matching layer can be used to maintain the efficiency of the device as the external load is varied.     

The electrochemical reduction of CO2 on a copper electrode in 1‐n‐butyl‐3‐methyl imidazolium tetrafluoroborate (BMI.BF4) monitored by surface‐enhanced Raman scattering (SERS)

The electrochemical conversion of CO₂ into value‐added products using room temperature ionic liquids as solvent/electrolyte has been proposed as an alternative to minimize the environmental effects of CO₂ emissions. A key issue in the design of electrochemical systems for the reduction of CO₂ is the in situ identification of intermediate surface species as well as reaction products. Copper electrodes, besides being used as cathodes in the electrochemical reduction of CO₂, present surface‐enhanced Raman scattering (SERS) when properly activated. In this sense, the electrochemical reduction of CO₂ over a copper electrode in the room temperature ionic liquids 1‐n‐butyl‐3‐methyl imidazolium tetrafluoroborate (BMI.BF₄) was investigated by cyclic voltammetry and by in situ SERS. The cyclic voltammetries have shown that the presence of CO₂ on the BMI.BF₄ anticipates the reduction of BMI⁺ to the corresponding carbene. Fourier‐transform‐SERS spectra excited at 1064 nm and SERS spectra excited at 632.8 nm have shown vibrational signals from adsorbed CO. These SERS results indicated that CO adsorbs on the copper surface at two different surface sites. The observation of a 2275 cm⁻¹ vibration in the SERS spectra also confirmed the presence of chemically adsorbed CO₂. Other products of CO₂ reduction in BMI.BF₄, besides CO, were identified, including BMI carbene and the BMI‐CO₂ adduct. The SERS results also suggest that the presence of a thin film of Cu₂O on the copper surface anticipates the reduction of CO₂ to CO, an important component of syngas. Copyright © 2016 John Wiley & Sons, Ltd.     

Second Order Integrability Conditions for Difference Equations: An Integrable Equation

Integrability conditions for difference equations admitting a second order formal recursion operator are presented and the derivation of symmetries and canonical conservation laws are discussed. In a generic case, some of these conditions yield nonlocal conservation laws. A new integrable equation satisfying the second order integrability conditions is presented and its integrability is established by the construction of symmetries, conservation laws and a 3 × 3 Lax representation. Finally, via the relation of the symmetries of this equation to the Bogoyavlensky lattice, an integrable asymmetric quad equation and a consistent pair of difference equations are derived.     

Inferring topological features of proteins from amino acid residue networks

Topological properties of native folds are obtained from statistical analysis of 160 low homology proteins covering the four structural classes. This is done analyzing one, two and three-vertex joint distribution of quantities related to the corresponding network of amino acid residues. Emphasis on the amino acid residue hydrophobicity leads to the definition of their center of mass as vertices in this contact network model with interactions represented by edges. The network analysis helps us to interpret experimental results such as hydrophobic scales and fraction of buried accessible surface area in terms of the network connectivity. Moreover, those networks show assortative mixing by degree. To explore the vertex-type dependent correlations, we build a network of hydrophobic and polar vertices. This procedure presents the wiring diagram of the topological structure of globular proteins leading to the following attachment probabilities between hydrophobic–hydrophobic 0.424(5), hydrophobic-polar 0.419(2) and polar–polar 0.157(3) residues.     

Quasi-superradiant soliton state of matter in quantum metamaterials

Strong interaction of a system of quantum emitters (e.g., two-level atoms) with electromagnetic field induces specific correlations in the system accompanied by a drastic increase of emitted radiation (superradiation or superfluorescence). Despite the fact that since its prediction this phenomenon was subject to a vigorous experimental and theoretical research, there remain open question, in particular, concerning the possibility of a first order phase transition to the superradiant state from the vacuum state. In systems of natural and charge-based artificial atom this transition is prohibited by “no-go” theorems. Here we demonstrate numerically and confirm analytically a similar transition in a one-dimensional quantum metamaterial – a chain of artificial atoms (qubits) strongly interacting with classical electromagnetic fields in a transmission line. The system switches from vacuum state to the quasi-superradiant (QS) phase with one or several magnetic solitons and finite average occupation of qubit excited states along the transmission line. A quantum metamaterial in the QS phase circumvents the “no-go” restrictions by considerably decreasing its total energy relative to the vacuum state by exciting nonlinear electromagnetic solitons.     

Structural characterization of SiGe nanoclusters formed by rapid thermal annealing

This work presents the structural characterization of nanoclusters formed from a-Si:H/Ge heterostructures processed by rapid thermal annealing (RTA) at 1000 °C for annealing times varying between 30 s and 70 s. The a-Si:H layers were grown on electron cyclotron resonance (ECR) using SiH₄ and Ar precursor gases. The Ge layer was grown in an e-beam evaporation system. The structural characterizations were performed by high-resolution X-ray diffractometer (HRXRD) on grazing incidence X-ray reflection mode (GIXRR) and micro-Raman measurements. The average grain size, Ge concentration (x_Ge) and strain were estimated from Lorentzian GIXRR peak fit. The average grain size varied from 3 nm to 7.5 nm and decreased with annealing time. The x_Ge increase with annealing time and varied from 8% to 19%, approximately. The strain calculated for (1 1 1), (2 2 0) and (3 1 1) peaks at 40 s, 50 s, 60 s and 70 s annealing time suggest the geometrical changes in nanoclusters according to process time.     

Multiple scattering of ultrasound in weakly inhomogeneous media: application to human soft tissues

Waves scattered by a weakly inhomogeneous random medium contain a predominant single-scattering contribution as well as a multiple-scattering contribution which is usually neglected, especially for imaging purposes. A method based on random matrix theory is proposed to separate the single- and multiple-scattering contributions. The experimental setup uses an array of sources/receivers placed in front of the medium. The impulse responses between every couple of transducers are measured and form a matrix. Single-scattering contributions are shown to exhibit a deterministic coherence along the antidiagonals of the array response matrix, whatever the distribution of inhomogeneities. This property is taken advantage of to discriminate single- from multiple-scattered waves. This allows one to evaluate the absorption losses and the scattering losses separately, by comparing the multiple-scattering intensity with a radiative transfer model. Moreover, the relative contribution of multiple scattering in the backscattered wave can be estimated, which serves as a validity test for the Born approximation. Experimental results are presented with ultrasonic waves in the megahertz range, on a synthetic sample (agar-gelatine gel) as well as on breast tissues. Interestingly, the multiple-scattering contribution is found to be far from negligible in the breast around 4.3 MHz.