Probing Proteins in Solution by Xe NMR Spectroscopy

The interaction of xenon with different proteins in aqueous solution is investigated by ¹²⁹Xe NMR spectroscopy. Chemical shifts are measured in horse metmyoglobin, hen egg white lysozyme, and horse cytochrome c solutions as a function of xenon concentration. In these systems, xenon is in fast exchange between all possible environments. The results suggest that nonspecific interactions exist between xenon and the protein exteriors and the data are analyzed in term of parameters which characterize the protein surfaces. The experimental data for horse metmyoglobin are interpreted using a model in which xenon forms a 1:1 complex with the protein and the chemical shift of the complexed xenon is reported (Locci et al., Keystone Symposia “Frontiers of NMR in Molecular Biology VI”, Jan. 9–15, 1999, Breckenridge, CO, Abstract E216, p. 53; Locci et al., XeMAT 2000 “Optical Polarization and Xenon NMR of Materials”, June 28–30, 2000, Sestri Levante, Italy, p. 46).     

Interdependence of in-cell xenon density and temperature during Rb/129Xe spin-exchange optical pumping using VHG-narrowed laser diode arrays

The (129)Xe nuclear spin polarization (P(Xe)) that can be achieved via spin-exchange optical pumping (SEOP) is typically limited at high in-cell xenon densities ([Xe](cell)), due primarily to corresponding reductions in the alkali metal electron spin polarization (e.g. P(Rb)) caused by increased non-spin-conserving Rb-Xe collisions. While demonstrating the utility of volume holographic grating (VHG)-narrowed lasers for Rb/(129)Xe SEOP, we recently reported [P. Nikolaou et al., JMR 197 (2009) 249] an anomalous dependence of the observed P(Xe) on the in-cell xenon partial pressure (p(Xe)), wherein P(Xe) values were abnormally low at decreased p(Xe), peaked at moderate p(Xe) (~300 torr), and remained surprisingly elevated at relatively high p(Xe) values (>1000 torr). Using in situ low-field (129)Xe NMR, it is shown that the above effects result from an unexpected, inverse relationship between the xenon partial pressure and the optimal cell temperature (T(OPT)) for Rb/(129)Xe SEOP. This interdependence appears to result directly from changes in the efficiency of one or more components of the Rb/(129)Xe SEOP process, and can be exploited to achieve improved P(Xe) with relatively high xenon densities measured at high field (including averaged P(Xe) values of ~52%, ~31%, ~22%, and ~11% at 50, 300, 500, and 2000 torr, respectively).     

Resonant scattering of an X-ray photon by a heavy atom

The influence of many-body and relativistic effects on the absolute values and shape of the double differential cross section for the resonant scattering of a linearly polarized X-ray photon by a free xenon atom near the K-shell ionization threshold has been theoretically analyzed. The evolution of the spatially extended structure of the scattering cross section to the K _{α, β} structure of the X-ray spectrum of the xenon atom emission has been demonstrated. The calculations have been performed in the dipole approximation for the anomalous dispersion component of the total inelastic scattering amplitude and in the impulse approximation for the contact component of this amplitude. The contribution of the Rayleigh (elastic) scattering component is taken into account using the methods developed in Hopersky et al., J. Phys. B 30, 5131 (1997). The effects of the radial relaxation of the electron shells, spin-orbit splitting, double excitation/ionization of the atomic ground state, as well as the Auger and radiative decays of the produced main vacancies, are considered. Using the results obtained by Tulkki, Phys. Rev. A 32, 3153 (1985) and Biggs et al., At. Data Nucl. Data Tables 16, 201 (1975), the nonrelativistic Hartree-Fock wavefunctions are changed to the relativistic Dirac-Hartree-Fock wavefunctions of the single-particle scattering states when constructing the process probability amplitude. The calculations are predicting and are in good agreement with the synchrotron experiment on the measurement of the absolute values and shape of the double differential cross section for the resonant scattering of an X-ray photon by a free xenon atom reported by Czerwinski et al., Z. Phys. A 322, 183 (1985).     

The extended Fourier transform for 2D spectral estimation.

We present a linear algebraic method, named the eXtended Fourier Transform (XFT), for spectral estimation from truncated time signals. The method is a hybrid of the discrete Fourier transform (DFT) and the regularized resolvent transform (RRT) (J. Chen et al., J. Magn. Reson. 147, 129-137 (2000)). Namely, it estimates the remainder of a finite DFT by RRT. The RRT estimation corresponds to solution of an ill-conditioned problem, which requires regularization. The regularization depends on a parameter, q, that essentially controls the resolution. By varying q from 0 to infinity one can "tune" the spectrum between a high-resolution spectral estimate and the finite DFT. The optimal value of q is chosen according to how well the data fits the form of a sum of complex sinusoids and, in particular, the signal-to-noise ratio. Both 1D and 2D XFT are presented with applications to experimental NMR signals.     

Infrared spectrum involving forbidden transitions & coriolis interaction and identification of optically pumped far infrared laser lines in asymmetrically mono-deuterated methanol (Methanol-D1)

In this paper new type of ΔK = 2 and 0 transitions have been identified in the Fourier Transform spectrum of Methanol-D₁ (CH₂DOH). These transitions are normally forbidden but a “Coriolis” type interaction with nearby states is believed to be contributing sufficient transition strength through intensity borrowing effect. This is the first time such forbidden transitions are reported to be identified in the excited states, in this molecule. The present conjecture is supported by observation of a many strong allowed transitions to upper terminating levels which are seen to be highly perturbed. This conclusion has been reached by comparing calculated energy levels using known molecular parameters (Pearson et al., 2012; Coudert et al., 2014; El Hilali et al., 2011; Quade et al., 1998; Richard Quade, 1998, 1999; Mukhopadhyay, 1997) and the actually observed FIR lines. The upper levels are seen to be upshifted from expected position. A closer look at the calculated energy values seems to indicate a possible interaction between the above states and other proximate torsional–rotational states could occur. The possible candidates for the interacting level manifolds are narrowed down through the presence of the forbidden transition. We also take the opportunity to propose alternate rotational quantum numbers for some of the assignments recently reported in the literature (El Hilali et al., 2011). Some ambiguities are pointed out on the data and the reported analysis. There remain too many such irregularities and we propose to gather a large body assigned transitions in a future catalog. Assignments and relevant comments on optically pumped FIR laser radiation are also made.     

Direct evidence of a magnetization transfer between laser-polarized xenon and protons of a cage-molecule in water

In a dedicated experimental setup, we directly prepare liquid-state NMR samples containing laser-polarized xenon with nuclear polarization larger than 5% at pressures up to 4 bars. Coating of the NMR tube surface allows us to increase the self-relaxation time of xenon in the gaseous phase to approximately 4.5 hours. Using a modified SPINOE pulse sequence, we present the first direct detection of a regioselective proton signal enhancement of a molecule -cyclodextrin) dissolved in water resulting from cross-polarization between laser-polarized xenon and protons. Received 16 March 2000 and Received in final form 22 May 2000     

Nanoscale Spontaneous Patterning

The SMB equation describing nanoscale spontaneous patterning is studied both analytically and numerically. In contradiction to the claim in the original SMB paper [D. Srolovitz, A. Mazor, B. Bukiet, J. Vac. Sci. Technol. A6(4) (1988), 2371--2380.] that some steady states are stable, we found that all the steady states are unstable. A dynamical system reason for this is given. We also found that typical small initial data solutions undergo an exponential growth followed by an almost linear growth. Such a feature is consistent with the experimental data in the paper [J. Erlebacher et al., J. Vac. Sci. Technol., A18(1) (2000), 115--120, Figure 3]. On the other hand, we never observed the decay portion of the numerical solution reported in this paper. We invent an elegant energy principle which supports our findings.     

Moduli Stabilization in Warped Compactifications at One Loop

We review the moduli stabilization mechanism found in Garriga et al. (Garriga, J., Pujolas, O., and Tanaka, T. (2000). Preprint hep-th/0111277.) for a class of five-dimensional warped brane-world scenarios. Specifically, we consider solutions with a power-law warp factor and a bulk dilaton with logarithmic profile in terms of the proper distance in the extra dimension. This includes the Heterotic M-theory brane-world of Lukas et al. (Lukas, A., Ovrut, B. A., Stelle, K. S., and Waldram, D. (1999). Physical Review D 59, 086001.) and Khoury et al. (Khoury, J., Ovrut, B. A., Steinhardt, P. J., and Turok, N. (2001). Preprint hep-th/0103239.) and the Randall–Sundrum (RS) model as a limiting case. In general, there are two moduli fields y _±, corresponding to the positions of two branes. Classically, the moduli are massless due to a scaling symmetry of the action. However, in the absence of supersymmetry, they develop an effective potential at one loop. Local terms proportional to some powers of the local curvature scale at the location of the corresponding brane are needed in order to remove the divergences in the effective potential. Such terms break the scaling symmetry and therefore act as stabilizers for the moduli. Moreover, for q 10, the observed hierarchy can be naturally generated by this potential, and the lightest modulus mass is of order m _– TeV.     

The Role of Coherence Transfer Efficiency in Design of TROSY-Type Multidimensional NMR Experiments

An improved method for TROSY-type (Pervushin et al., Proc. Natl. Acad. Sci. USA 94, 12366-12371 (1997)) heteronuclear two-dimensional correlation involving protons of negligible CSA is presented. Rather than applying a simple INEPT sequence for back-transfer to protons (Pervushin et al., J. Am. Chem. Soc. 120, 6394-6400 (1998)), we replace the pi/2 proton pulse in INEPT by a spin-state-selective coherence transfer element (Sorensen et al., J. Biomol. NMR 10, 181-186 (1997)) and maintain broadband decoupling during acquisition. Theoretically that results in a sensitivity enhancement of a factor of 2. The new method is demonstrated using a (13)C,(15)N-labeled protein sample, RAP 18-112 (N-terminal domain of alpha(2)-macroglobulin receptor associated protein), at 750 MHz.     

Physics of novel site controlled InGaAs quantum dots on (1 1 1) oriented substrates

Recent work has shown that site-controlled dots (QD) grown on (1 1 1)B GaAs substrates, pre-patterned with tetrahedral pyramidal recesses (Baier et al., 2006) [1], (Pelucchi et al., 2007) [2], (Zhu et al., 2007) [3] are suitable for the generation of single and entangled photons (Young et al., 2009) [4]. We recently introduced InGaAs/GaAs site controlled QD structures which demonstrated record breaking spectral purity, and we showed that increasing the indium concentration of the active region allows easy tunability of the emission wavelength (Mereni et al., 2009) [5], [6]. We present here the first theoretical analysis of the emission energies and optical properties of this system as a function of QD height and In concentration. We model the dots using an 8 band k.p theory chosen to provide the best convergence and performance for structures oriented specifically along the (1 1 1) crystallographic direction.     

Neutral kaon production in p+p and p+Nb collisions

The kaon nucleus (KN) interaction in dense nuclear matter is predicted to be repulsive and increasing with density. However, determined values for this potential are not yet consistent with each other (Benabderrahmane et al., Phys Rev Lett 102:182501, 2009; Agakishiev et?al., Phys Rev C 82:044907, 2010; Büscher et?al., Eur Phys J A 22:301–317, 2004). We analyze $K^0_S$ mesons identified with the HADES detector in p+p and p+?⁹³Nb reactions at 3.5?GeV kinetic beam energy. To determine the KN potential at normal nuclear density we propose to compare the $K^0_S$ differential distributions in p+?⁹³Nb and p+p collisions. High statistics of low p _t -kaons (p _t ?<?100?MeV/c) ensure the sensitivity of our measurements to the nuclear matter effects. We present the data analysis method and first results.     

Cochlear power flux as an indicator of mechanical activity

The question of whether one can conclude just from basilar membrane (BM) vibration data that the cochlea is an active mechanical system is addressed. To this end, a method is developed which computes the power flux through a channel cross section of a short-wave cochlear model from a given BM vibration pattern. The power flux is an important indicator of mechanical activity because a rise in this function corresponds to creation of mechanical energy. The power flux method is applied to BM velocity patterns as measured by Johnstone and Yates [J. Acoust. Soc. Am. 55, 584-587 (1974)] and by Sellick et al. [Hear. Res. 10, 101-108 (1983)] in the guinea pig and by Robles et al. [Peripheral Auditory Mechanisms, edited by J.B. Allen, J.L. Hall, A.E. Hubbard, S.T. Neely, and A. Tubis (Springer, New York, 1986a), pp. 121-128, and J. Acoust. Soc. Am. 80, 1364-1374 (1986b)] in the chinchilla. Before the calculations are performed, the BM data are interpolated and smoothed in order to avoid numerical errors as a result of too few and noisy data points. The choice of the smoothing method influences the computed power flux function considerably. Nevertheless, the calculations appear to make a clear distinction between the "old" data, showing broad BM tuning (Johnstone and Yates, 1974), and the "new" data, in which the response is much more peaked (Sellick et al., 1983; Robles et al., 1986a, b). The former do not give rise to a significant increase of the power flux; the latter do, although less convincingly for the Sellick et al. (1983) data than for the Robles et al. (1986a,b) data. It is thus concluded that the recently obtained, sharply tuned BM responses reflect the presence of mechanical activity in the cochlea.     

Measurement of the principal values of the anisotropic diffusion tensor in an unoriented sample by exploiting the chemical shift anisotropy: (19)F PGSE NMR with homonuclear decoupling

NMR methods (S. V. Dvinskikh et al., J. Magn. Reson. 142, 102-110 (2000) and S. V. Dvinskikh and I. Furó, J. Magn. Reson. 144, 142-149 (2000)) that combine PGSE with dipolar decoupling are extended to polycrystalline solids and unoriented liquid crystals. Decoupling suppresses dipolar dephasing not only during the gradient pulses but also under signal acquisition so that the detected spectral shape is dominated by the chemical shift tensor of the selected nucleus. The decay of the spectral intensity at different positions in the powder spectrum provides the diffusion coefficient in sample regions with their crystal axes oriented differently with respect to the direction of the field gradient. Hence, one can obtain the principal values of the diffusion tensor. The method is demonstrated by (19)F PGSE NMR with homonuclear decoupling in a lyotropic lamellar liquid crystal.     

Coarse-graining the computations of surface reactions: Nonlinear dynamics from atomistic simulators

We review and discuss the use of equation-free computation in extracting coarse-grained, nonlinear dynamics information from atomistic (lattice-gas) models of surface reactions. The approach is based on circumventing the explicit derivation of macroscopic equations for the system statistics (e.g., average coverage). Short bursts of appropriately initialized computational experimentation with the lattice-gas simulator are designed “on demand” and processed in the spirit of the coarse timestepper introduced in Theodoropoulos et al. (2000) (K. Theodoropoulos, Y.-H. Qian, I.G. Kevrekidis, Proc. Natl. Acad. Sci. USA 97 (2000) 9840). The information derived from these computational experiments, processed through traditional, continuum numerical methods is used to solve the macroscopic equations without ever deriving them in closed form. The approach is illustrated through two computational examples: the CO oxidation reaction, and the NO + CO/Pt(1 0 0) reaction.     

Flow visualization in arteriovenous fistula and aneurysm using computational fluid dynamics

The arteriovenous fistula (AVF) is characterized by enhanced blood flow and is the most widely used vascular access for chronic haemodialysis (Sivanesan et al., 1998). A large proportion of the AVF late failures are related to local haemodynamics (Sivanesan et al., 1999a). As in AVF, blood flow dynamics plays an important role in growth, rupture, and surgical treatment of aneurysm. Several techniques have been used to study the flow patterns in simplified models of vascular anastomose and aneurysm. In the present investigation, Computational Fluid Dynamics (CFD) is used to analyze the flow patterns in AVF and aneurysm through the velocity waveform obtained from experimental surgeries in dogs (Galego et al., 2000), as well as intra-operative blood flow recordings of patients with radiocephalic AVF (Sivanesan et al., 1999b) and physiological pulses (Aires, 1991), respectively. The flow patterns in AVF for dog and patient surgeries data are qualitatively similar. Perturbation, recirculation and separation zones appeared during cardiac cycle, and these were intensified in the diastole phase for the AVF and aneurysm models. The values of wall shear stress presented in this investigation of AVF and aneurysm models oscillated in the range that can both cause damage to endothelial cells and develop atherosclerosis.     

NMR study of the dissolution of laser-polarized xenon

NMR of laser-polarized xenon is used to probe the dissolution behaviour of the noble gas in different liquids. The dissolution and self-relaxation rates are extracted via a macroscopic model, and comparison of the decay rate of the xenon magnetization in deuterated and non-deuterated solvent pairs allows the determination of the pure dipole-dipole contribution to relaxation. A transient convective effect, tentatively assigned to the xenon concentration gradient, is observed and characterized by diffusion encoding MRI experiments. The flow of xenon penetrates inside the solvent near the walls of the NMR tube, the longitudinal images showing a “” shape, the transverse ones a “O” shape. This convection effect has implications for delivery conditions of laser-polarized xenon in continuous flow experiments and magnetic resonance imaging. Received 29 April 2002 / Received in final form 26 July 2002 Published online 22 October 2002 RID="a" ID="a"e-mail: hdesvaux@cea.fr RID="b" ID="b"URA CNRS/CEA 331     

The nonsinglet spin-dependent structure function evolution by Laplace and characteristics methods

We evaluate the non-singlet spin-dependent structure function g₁^NS at leading order (LO) and next-to-leading order (NLO) by using the Laplace-transform technique and method of characteristics and also obtain its first moment at NLO. The polarized non-singlet structure function results are compared with the data from HERMES (A. Airapetian et al., Phys. Rev. D 75, 012007 (2007)) and E143 (K. Abe et al. (E143 Collab.), Phys. Rev. D 58, 112003 (1998)) at LO and NLO analyses and the first-moment the result at NLO is compared with the result of the NLO GRSV2000 fit. Considering the solution, this method is valid at low- and large-x regions.     

Relaxivities of human liver and spleen ferritin

Ferritin, the iron-storing protein of mammals, is known to darken T₂-weighted magnetic resonance images. This darkening can be used to noninvasively measure an organ's iron content. Significant discrepancies exist between T₂ data obtained with ferritin-containing tissues and with aqueous solutions of horse spleen ferritin (HSF). The NMR properties of stable human ferritin have never been studied in aqueous solutions. Relaxometry results on human liver and spleen ferritin are reported here, showing that the relaxation induced in aqueous solutions by human ferritins is comparable to that induced by HSF. As a consequence, the differences between ferritin-containing human tissues and ferritin solutions cannot be attributed to different NMR properties of human and horse ferritins, but probably to a clustering of the protein in vivo.     

High harmonic generation in a gas-filled hollow-core photonic crystal fiber

High harmonic generation (HHG) of intense infrared laser radiation (Ferray et al., J. Phys. B: At. Mol. Opt. Phys. 21:L31, 1988; McPherson et al., J. Opt. Soc. Am. B 4:595, 1987) enables coherent vacuum-UV (VUV) to soft-X-ray sources. In the usual setup, energetic femtosecond laser pulses are strongly focused into a gas jet, restricting the interaction length to the Rayleigh range of the focus. The average photon flux is limited by the low conversion efficiency and the low average power of the complex laser amplifier systems (Keller, Nature 424:831, 2003; Südmeyer et al., Nat. Photonics 2:599, 2008; Röser et al., Opt. Lett. 30:2754, 2005; Eidam et al., IEEE J. Sel. Top. Quantum Electron. 15:187, 2009) which typically operate at kilohertz repetition rates. This represents a severe limitation for many experiments using the harmonic radiation in fields such as metrology or high-resolution imaging. Driving HHG with novel high-power diode-pumped multi-megahertz laser systems has the potential to significantly increase the average photon flux. However, the higher average power comes at the expense of lower pulse energies because the repetition rate is increased by more than a thousand times, and efficient HHG is not possible in the usual geometry. So far, two promising techniques for HHG at lower pulse energies were developed: external build-up cavities (Gohle et al., Nature 436:234, 2005; Jones et al., Phys. Rev. Lett. 94:193, 2005) and resonant field enhancement in nanostructured targets (Kim et al., Nature 453:757, 2008). Here we present a third technique, which has advantages in terms of ease of HHG light extraction, transverse beam quality, and the possibility to substantially increase conversion efficiency by phase-matching (Paul et al., Nature 421:51, 2003; Ren et al., Opt. Express 16:17052, 2008; Serebryannikov et al., Phys. Rev. E (Stat. Nonlinear Soft Matter Phys.) 70:66611, 2004; Serebryannikov et al., Opt. Lett. 33:977, 2008; Zhang et al., Nat. Phys. 3:270, 2007). The interaction between the laser pulses and the gas occurs in a Kagome-type Hollow-Core Photonic Crystal Fiber (HC-PCF) (Benabid et al., Science 298:399, 2002), which reduces the detection threshold for HHG to only 200 nJ. This novel type of fiber guides nearly all of the light in the hollow core (Couny et al., Science 318:1118, 2007), preventing damage even at intensities required for HHG. Our fiber guided 30-fs pulses with a pulse energy of more than 10 μJ, which is more than five times higher than for any other photonic crystal fiber (Hensley et al., Conference on Lasers and Electro-Optics (CLEO), IEEE Press, New York, 2008).     

Circular polarization excitation and detection in (14)N NQR

Circular polarization excitation and detection of (14)N NQR signal are reported. A theoretical model is presented in terms of fictitious spin-1/2 operators and is compared to experiments performed on a powder crystalline sample of RDX. It is shown that in spin-1 systems with finite asymmetry--unlike previously reported NMR and symmetric spin-3/2 NQR systems (Chen et al., J. Magn. Reson. 54, 324--327, 1983; Weber and Hahn, Phys. Rev. 120, 365--375, 1960)-the circular polarization nature of the signal is due to powder orientation effects in polycrystalline samples. Sensitivity improvements up to a factor of the square root of 2 are reported using the same hardware and switching modes from linear polarization to circular polarization; this also is shown to result from the polycrystalline nature of the samples.