Sensitivity-enhanced IPAP experiments for measuring one-bond C–C and C–H residual dipolar couplings in proteins

Sensitivity-enhanced 2D IPAP experiments using the accordion principle for measuring one-bond 13C'-13Calpha and 1Halpha-13Calpha dipolar couplings in proteins are presented. The resolution of the resulting spectra is identical to that of the decoupled HSQC spectra and the sensitivity of the corresponding 1D acquisitions are only slightly lower than those obtained with 3D HNCO and 3D HN(COCA)HA pulse sequences due to an additional delay 2Delta. For cases of limited resolution in the 2D 15N-1HN HSQC spectrum the current pulse sequences can easily be modified into 3D versions by introducing a poorly digitized third dimension, if so desired. The experiments described here are a valuable addition to the suites available for determination of residual dipolar couplings in biological systems.     

Minimum energy pulse synthesis via the inverse scattering transform

This paper considers a variety of problems in the design of selective RF-pulses. We apply a formula of Zakharov and Manakov to directly relate the energy of an RF-envelope to the magnetization profile and certain auxiliary parameters used in the inverse scattering transform (IST) approach to RF-pulse synthesis. This allows a determination of the minimum possible energy for a given magnetization profile. We give an algorithm to construct both the minimum energy RF-envelope as well as any other envelope that produces a given magnetization profile. This includes an algorithm for solving the Gel'fand-Levitan-Marchenko equations with bound states. The SLR method is analyzed in terms of traditional scattering data, and shown to be a special (singular) case of the IST approach. RF-envelopes are computed for a variety of examples.     

Correction of spin diffusion during iterative automated NOE assignment

Indirect magnetization transfer increases the observed nuclear Overhauser enhancement (NOE) between two protons in many cases, leading to an underestimation of target distances. Wider distance bounds are necessary to account for this error. However, this leads to a loss of information and may reduce the quality of the structures generated from the inter-proton distances. Although several methods for spin diffusion correction have been published, they are often not employed to derive distance restraints. This prompted us to write a user-friendly and CPU-efficient method to correct for spin diffusion that is fully integrated in our program ambiguous restraints for iterative assignment (ARIA). ARIA thus allows automated iterative NOE assignment and structure calculation with spin diffusion corrected distances. The method relies on numerical integration of the coupled differential equations which govern relaxation by matrix squaring and sparse matrix techniques. We derive a correction factor for the distance restraints from calculated NOE volumes and inter-proton distances. To evaluate the impact of our spin diffusion correction, we tested the new calibration process extensively with data from the Pleckstrin homology (PH) domain of Mus musculus beta-spectrin. By comparing structures refined with and without spin diffusion correction, we show that spin diffusion corrected distance restraints give rise to structures of higher quality (notably fewer NOE violations and a more regular Ramachandran map). Furthermore, spin diffusion correction permits the use of tighter error bounds which improves the distinction between signal and noise in an automated NOE assignment scheme.     

Standing waves, clustering, and phase waves in 1D simulations of kinetic relaxation oscillations in NO+NH3 on Pt(1 0 0) coupled by diffusion

The Lombardo–Imbihl–Fink (LFI) ODE model of the NO+NH₃ reaction on a Pt(1 0 0) surface shows stable relaxation oscillations with very sharp transitions for temperatures T between 404 and 433 K. Here we study numerically the effect of linear diffusive coupling of these oscillators in one spatial dimension. Depending on the parameters and initial conditions we find a rich variety of spatio-temporal patterns which we group into four main regimes: bulk oscillations (BOs), standing waves (SW), phase clusters (PC), and phase waves (PW). Two key ingredients for SW and PC are identified, namely the relaxation type of the ODE oscillations and a nonlocal (and nonglobal) coupling due to relatively fast diffusion of the kinetically slaved variables NH₃ and H. In particular, the latter replaces the global coupling through the gas phase used to obtain SW and PC in models of related surface reactions. The PW exist only under the assumption of (relatively) slow diffusion of NH₃ and H.     

Dynamic supercoiling bifurcations of growing elastic filaments

Certain bacteria form filamentous colonies when the cells fail to separate after dividing. In Bacillus subtilis, Bacillus thermus, and Cyanobacteria, the filaments can wrap into complex supercoiled structures as the cells grow. The structures may be solenoids or plectonemes, with or without branches in the latter case. Any microscopic theory of these morphological instabilities must address the nature of pattern selection in the presence of growth, for growth renders the problem nonautonomous and the bifurcations dynamic. To gain insight into these phenomena, we formulate a general theory for growing elastic filaments with bending and twisting resistance in a viscous medium, and study an illustrative model problem: a growing filament with preferred twist, closed into a loop. Growth depletes the twist, inducing a twist strain. The closure of the loop prevents the filament from unwinding back to the preferred twist; instead, twist relaxation is accomplished by the formation of supercoils. Growth also produces viscous stresses on the filament which even in the absence of twist produce buckling instabilities. Our linear stability analysis and numerical studies reveal two dynamic regimes. For small intrinsic twist the instability is akin to Euler buckling, leading to solenoidal structures, while for large twist it is like the classic writhing of a twisted filament, producing plectonemic windings. This model may apply to situations in which supercoils form only, or more readily, when axial rotation of filaments is blocked. Applications to specific biological systems are proposed.     

Two types of the effective mass divergence and the Grüneisen ratio in heavy-fermion metals

The behavior of the specific heat c_p, effective mass M^*, and the thermal expansion coefficient of a Fermi system located near the fermion condensation quantum phase transition (FCQPT) is considered. We observe the first type behavior if the system is close to FCQPT: the specific heat , , while the thermal expansion coefficient . Thus, the Grüneisen ratio Γ(T)=/c_p does not diverges. At the transition region, where the system passes over from the non-Fermi liquid to the Landau Fermi liquid, the ratio diverges as . When the system becomes the Landau Fermi liquid, Γ(T,r)∝1/r, with r being a distance from the quantum critical point. Provided the system has undergone FCQPT, the second type takes place: the specific heat behaves as , M^*∝1/T, and =a+bT with a,b being constants. Again, the Grüneisen ratio diverges as .     

Pseudo-Kähler metrics on six-dimensional nilpotent Lie algebras

It is well known that any symplectic manifold (M,Ω) has an almost complex structure J which is compatible with Ω. In this paper, we deal with the existence of compatible pairs (J,Ω) on nilpotent Lie algebras of dimension ≤6, J being an integrable almost complex structure. We prove that if such a pair exists, J must satisfy some extra conditions, namely J must be nilpotent in the sense of [Trans. Am. Math. Soc. 352 (2000) 5405]. Associated to any such a compatible pair, there is a pseudo-Kähler metric g which cannot be positive definite unless be abelian. All these metrics are Ricci flat, although many of them are nonflat, and we study the behaviour of its curvature tensor under deformation.     

Temperature measurements using fiber optic polarization interferometer

A novel measurement method of temperature based on the phenomena that the phase difference between principle polarization states in the optical retarder is function of temperature is described. The polarization state of optical beam is changed as it passes through the optical retarder, which depends on the temperature. The temperature of optical retarder is determined by comparison of the power difference between principal polarization states. We demonstrate successfully the temperature measurement by using a polarization maintaining fiber as the optical retarder. With a 100 mm length of the fiber optic retarder, the change rate of phase difference on temperature was 0.236 rad/°C and the measurement error was ±0.038°C over the temperature range of −2.6 – +3.4°C. With a 11.5 mm length of the fiber optic retarder, the change rate of phase difference on temperature was 0.021 rad/°C and the measurement error was ±0.79°C over the temperature range of −8.5 – +86.5°C.     

Low noise double pass L-band erbium-doped fiber amplifier

A new double pass long wavelength band erbium-doped fiber amplifier with enhanced noise figure characteristics is demonstrated. The noise figure is improved by about 2.6 dB with the incorporation of broadband conventional-band fiber Bragg grating (FBG) in between the two segments of erbium-doped fiber. By incorporating both the pre-amplifier and the FBG, the noise figure is further improved, which varies from 4.0 to 5.0 dB in the flat gain region from 1570 to 1600 nm. The gain varies from 32.0 to 33.4 dB within this region. The new amplifier with high gain and low noise figure can be useful as an inline amplifier in a wavelength division multiplexing transmission system.     

Time-resolved imaging of latent fingerprints with nanosecond resolution

Imaging of latent fingerprints using time-resolved (TR) method offers a broader platform to eliminate the unwanted background emission. In this paper, a novel TR imaging technique is demonstrated and implemented, which facilitates the detection of latent fingerprints with nanosecond resolution. Simulated experiments were carried out with two overlapping fingerprints treated with two fluorescent powders having different lifetimes in nanosecond range. The dependence of the fluorescence emission intensity in nanosecond resolution of TR imaging is also revealed.