Spectroscopic selection of distance measurements in a protein dimer with mixed nitroxide and Gd3+ spin labels

The pulse DEER (Double Electron-Electron Resonance) technique is frequently applied for measuring nanometer distances between specific sites in biological macromolecules. In this work we extend the applicability of this method to high field distance measurements in a protein assembly with mixed spin labels, i.e. a nitroxide spin label and a Gd(3+) tag. We demonstrate the possibility of spectroscopic selection of distance distributions between two nitroxide spin labels, a nitroxide spin label and a Gd(3+) ion, and two Gd(3+) ions. Gd(3+)-nitroxide DEER measurements possess high potential for W-band long range distance measurements (6 nm) by combining high sensitivity with ease of data analysis, subject to some instrumental improvements.     

Observation of slow light in the noise spectrum of a vertical external cavity surface-emitting laser

The role of coherent population oscillations is evidenced in the noise spectrum of an ultralow noise laser. This effect is isolated in the intensity noise spectrum of an optimized single-frequency vertical external cavity surface-emitting laser. The coherent population oscillations induced by the lasing mode manifest themselves through their associated dispersion that leads to slow light effects probed by the spontaneous emission present in the nonlasing side modes.     

Probing conformational variations at the ATPase site of the RNA helicase DbpA by high-field electron-nuclear double resonance spectroscopy

The RNA helicase DbpA promotes RNA remodeling coupled to ATP hydrolysis. It is unique because of its specificity to hairpin 92 of 23S rRNA (HP92). Although DbpA kinetic pathways leading to ATP hydrolysis and RNA unwinding have been recently elucidated, the molecular (atomic) basis for the coupling of ATP hydrolysis to RNA remodeling remains unclear. This is, in part, due to the lack of detailed structural information on the ATPase site in the presence and absence of RNA in solution. We used high-field pulse ENDOR (electron-nuclear double resonance) spectroscopy to detect and analyze fine conformational changes in the protein's ATPase site in solution. Specifically, we substituted the essential Mg(2+) cofactor in the ATPase active site for paramagnetic Mn(2+) and determined its close environment with different nucleotides (ADP, ATP, and the ATP analogues ATPγS and AMPPnP) in complex with single- and double-stranded RNA. We monitored the Mn(2+) interactions with the nucleotide phosphates through the (31)P hyperfine couplings and the coordination by protein residues through (13)C hyperfine coupling from (13)C-enriched DbpA. We observed that the nucleotide binding site of DbpA adopts different conformational states upon binding of different nucleotides. The ENDOR spectra revealed a clear distinction between hydrolyzable and nonhydrolyzable nucleotides prior to RNA binding. Furthermore, both the (13)C and the (31)P ENDOR spectra were found to be highly sensitive to changes in the local environment of the Mn(2+) ion induced by the hydrolysis. More specifically, ATPγS was efficiently hydrolyzed upon binding of RNA, similar to ATP. Importantly, the Mn(2+) cofactor remains bound to a single protein side chain and to one or two nucleotide phosphates in all complexes, whereas the remaining metal coordination positions are occupied by water. The conformational changes in the protein's ATPase active site associated with the different DbpA states occur in remote coordination shells of the Mn(2+) ion. Finally, a competitive Mn(2+) binding site was found for single-stranded RNA construct.     

Temperature-dependent exchange interaction in molecular magnets Cu(hfac)2L(R) studied by EPR: methodology and interpretations

Exchange-coupled spin triads nitroxide-copper(II)-nitroxide are the key building blocks of molecular magnets Cu(hfac)(2)L(R). These compounds exhibit thermally induced structural rearrangements and spin transitions, where the exchange interaction between spins of copper(II) ion and nitroxide radicals changes typically by 1 order of magnitude. We have shown previously that electron paramagnetic resonance (EPR) spectroscopy is sensitive to the observed magnetic anomalies and provides information on both inter- and intracluster exchange interactions. The value of intracluster exchange interaction is temperature-dependent (J(T)), that can be accessed by monitoring the effective g-factor of the spin triad as a function of temperature (g(eff)(T)). This paper describes approaches for studying the g(eff)(T) and J(T) dependences and establishes correlations between them. The experimentally obtained g(eff)(T) dependences are interpreted using three different models for the mechanism of structural rearrangements on the molecular level leading to different meanings of the J(T) function. The contributions from these mechanisms and their manifestations in X-ray, magnetic susceptibility and EPR data are discussed.     

Exchange bias and anisotropy in the Fe/KCoF3 structure

A new type of ferromagnet/antiferromagnet structure (Fe/KCoF₃) was deposited by molecular beam epitaxy. Unidirectional and uniaxial anisotropies of 5.1 and 3.4 kA/m were measured at 23 K using ferromagnetic resonance. Magnetization measurements at 5 K showed a hysteresis loop shift of 6 kA/m due to exchange bias. Significant enhancement of four-fold anisotropy was found at low temperatures in the samples with polycrystalline KCoF₃ structure.     

Free surface waves in wall-bounded granular flows

We report free-surface waves in granular flows near boundaries in an inclined chute. The chevron-shaped traveling waves spontaneously develop at inclinations close to the angle of repose for both steady and accelerating flows. Two distinct regimes are characterized by internal angle and frequency variations. Experimental measurements indicate that subsurface circulation driven by velocity gradients near frictional walls plays a central role in the pattern formation mechanism, suggesting that wave generation is controlled by the granular analog of a fluid boundary layer.     

Evolution of epitaxial titanium silicide nanocrystals as a function of growth method and annealing treatments

Titanium silicide grows on silicon in a form of discontinuous layers, which is the most serious obstacle to the formation of high-quality epilayers for VLSI applications. At the same time, nanometric dimensions of the epitaxial silicide islands attract interest as quantum nanostructures. However, for this purpose, nanocrystals in a self-assembled array have to be defect-free, and exhibit high shape and size uniformity. In this work titanium silicide was grown on Si(1 1 1) substrates by reactive deposition epitaxy and by solid-phase epitaxy. Since the reaction and phase-formation kinetics depend on the growth method, accordingly different lattice matching and facet energies may result in different morphological shapes of the nanocrystals. Nanocrystals from reaction in a solid-state could be characterized as highly non-uniform in both shape and size, and their evolution due to post-deposition anneals increased that non-uniformity even further. Relaxation of epitaxial mismatch strain by misfit dislocations could be inferred from a gradual reduction of the nanocrystal vertical aspect ratio and development of flat top facets out of the initially sharp conical crests, in accord with generalized Wulf-Kaishew theorem. On the other hand, the silicide nanocrystals formed by reactive deposition exhibited high uniformity and thermal stability. Significant strain relaxation, as could be judged by the nanocrystal flattening, took place only at temperatures in excess of 650 °C, followed by progressive nanocrystal coalescence. It thus could be inferred, that better titanium silicide nanocrystal arrays (in the sense of uniformity and stability) are more easily obtained by reactive deposition epitaxy than by solid-phase epitaxy. While terminal, stable C54-TiSi₂ phase, did eventually form in the epilayers in both methods, different evolution pathways were manifested by different respective morphologies and orientations even in this final state.     

Characteristics of ESEEM and HYSCORE spectra of S>1/2 centers in orientationally disordered systems

One- and two-dimensional electron-spin echo envelope modulation (ESEEM) spectra of Kramers’ multiplets in orientationally disordered systems are simulated using a simple mathematical model. A fairly general high-field spin Hamiltonian is considered with a general g-tensor and arbitrary relative orientations between all tensors involving the electron-spin S, the nuclear spin I, and their interaction. The zero field splitting (ZFS) and the nuclear quadrupole interactions are, however, approximated by their respective secular part in a way that retains all orientation dependencies and it is assumed that the nuclear quadrupole interaction is smaller than the hyperfine interaction. These approximations yield an effective sublevel nuclear Hamiltonian for each EPR transition and are sufficient to account for the most important characteristics of the ESEEM spectra of high electronic multiplets in orientationally disordered systems. Moreover, they allow to obtain some analytical expressions that for I=1/2 illuminate important aspects of 2D hyperfine sublevel correlation (HYSCORE) experiments in S=3/2, 5/2 systems. The pulses are considered as ideal and selective with respect to the different EPR transitions. The contributions of the latter to the echo intensity are weighed according to their different nutation angles and equilibrium Boltzmann populations. For simple axial cases with I=1/2, analytical expressions, analogous to the S=1/2 case, were derived for: (i) the modulation depth, (ii) the lineshapes of the HYSCORE cross-correlation ridges, and (iii) ENDOR powder pattern. Experimental results obtained from Mn(D₂O)₆²⁺ and VO(D₂O)₅²⁺ in frozen solutions are presented, compared, and analyzed in light of the theoretical part.     

Auto-ignition of a polydisperse fuel spray

In the present paper, the effect of fuel spray polydispersity on the auto-ignition process in a fuel cloud is considered. In many engineering applications it is common practice to relate to the actual polydisperse spray as being equivalent to a monodisperse spray with all droplets therein having some average diameter. In combustion systems, the Sauter mean diameter (SMD) is frequently used for this purpose; it is based on the ratio between the total droplet volume and the total droplet surface area of all the droplets in the polydisperse spray. The main purpose of the current work is to examine qualitatively the dynamics of ignition of a truly polydisperse spray in a combustible gas medium and compare it with the dynamics of an equivalent monodisperse spray based on the SMD. Since the system of governing equations represents a multi-scale problem the method of integral manifolds is applied in order to extract the dynamical behavior. Preliminary computed results suggest that the use of the usual SMD-based monodisperse spray leads to quite a significant over-estimate of the ignition time. An alternative modified definition of the SMD, in which the overall liquid fuel volume is also conserved in the averaging process, reduces the discrepancy between the ignition time for the polydisperse spray and that of the equivalent monodisperse spray. However, it seems that some other sort of average droplet size needs to be determined to minimize the aforementioned discrepancy. These results highlight the care that must be exercised before dispensing with the behavior of the actual polydisperse spray in favor of that of an equivalent monodisperse spray, even at the expense of complexity.