Residual dipolar couplings and some specific models for motional averaging

The measurement of residual dipolar couplings (RDCs) from partially oriented molecules is now widely used to provide restraints for NMR structure determination. Bond vibrations, random angular fluctuations around bond vectors and conformational exchange all influence the magnitude of the experimental RDCs. The effect that angular fluctuations have upon the magnitude of RDCs is quantitatively compared using three new models (elliptic, uni-dimensional, and equally populated two site jump) and three established models (static, isotropic motion in a cone and free diffusion about a fixed symmetry axis: Woessner's model) for motional averaging in the limit that the amplitude of motion beta < or = (max)15-20 degrees. The influence of the different motional models on the value of R(obs) determined from the distribution of RDCs is explored. The consequences of the different types of angular motion for the accurate determination of bond vector orientation, with respect to the alignment tensor, A, is investigated. The extent to which motion influences the magnitude of RDCs is compared to some non-dynamic factors affecting RDC size.     

Variation of molecular alignment as a means of resolving orientational ambiguities in protein structures from dipolar couplings

Residual dipolar couplings for pairs of proximate magnetic nuclei in macromolecules can easily be measured using high-resolution NMR methods when the molecules are dissolved in dilute liquid crystalline media. The resulting couplings can in principle be used to constrain the relative orientation of molecular fragments in macromolecular systems to build a complete structure. However, determination of relative fragment orientations based on a single set of residual dipolar couplings is inherently hindered by the multi-valued nature of the angular dependence of the dipolar interaction. Even with unlimited dipolar data, this gives rise to a fourfold degeneracy in fragment orientations. In this Communication, we demonstrate a procedure based on an order tensor analysis that completely removes this degeneracy by combining residual dipolar coupling measurements from two alignment media. Application is demonstrated on (15)N-(1)H residual dipolar coupling data acquired on the protein zinc rubredoxin from Clostridium pasteurianum dissolved in two different bicelle media.     

Dark resonances as a probe for the motional state of a single ion

Single, rf-trapped ions find various applications ranging from metrology to quantum computation. High-resolution interrogation of an extremely weak transition under best observation conditions requires an ion almost at rest. To avoid line-broadening effects such as the second-order Doppler effect or rf heating in the absence of laser cooling, excess micromotion has to be eliminated as far as possible. In this paper the motional state of a confined three-level ion is probed, taking advantage of the high sensitivity of observed dark resonances to the trapped ion’s velocity. Excess micromotion is controlled by monitoring the dark-resonance contrast with varying laser-beam geometry. The influence of different parameters such as the cooling laser intensity has been investigated experimentally and numerically.     

Metallic helix array as a broadband wave plate

This study demonstrates theoretically and experimentally that a metallic helix array can operate as a highly transparent broadband wave plate in propagation directions perpendicular to the axis of helices. The functionality arises from a special property of the helix array, namely, that two branches of elliptically right-handed and left-handed polarized states are nearly rigidly shifted in frequency and their dispersions are controlled by different mechanisms that can be independently tuned by structural parameters.     

Protein backbone dynamics from N-HN dipolar couplings in partially aligned systems: a comparison of motional models in the presence of structural noise

Residual dipolar couplings (RDCs) provide excellent probes for the exploration of dynamics in biomolecules on biologically relevant time-scales. Applying geometric motional models in combination with high-resolution structures to fit experimental RDCs allows the extraction of local dynamic amplitudes of peptide planes in proteins using only a limited number of data points. Here we compare the behaviour of three simple and intuitive dynamic modes: the Gaussian axial fluctuation model (1D-GAF), the two-site jump model, and a model supposing axially symmetric motion about a mean orientation. The requirement of a structural model makes this kind of methodology potentially very sensitive to structural imprecision. Numerical simulations of RDC dynamic averaging under different regimes show that the anisotropic motional models are more geometrically stringent than the axially symmetric model making it more difficult to alias structural noise as artificial dynamic amplitudes. Indeed, it appears that the model extracts accurate motional amplitudes even in the presence of significant structural error. We also show that a two-site jump model, also assuming the (alpha)C(i-1)-(alpha)C(i) as rotation axis, can only be distinguished from the previously developed GAF model beyond amplitude/jumps of around 40 degrees. The importance of appropriate estimation of the molecular alignment tensor for determination of local motional amplitudes is also illustrated here. We demonstrate a systematic scaling of extracted dynamic amplitudes if a static structure is assumed when determining the alignment tensor from dynamically averaged RDCs. As an example an artificial increase of 0.14 (0.85 compared to the expected 0.71) is observed in the extracted S2 if a pervasive 20 degrees GAF motion is present that is ignored in the tensor determination. Finally we apply a combined approach using the most appropriate motional model, to complete the analysis of dynamic motions from protein G.     

Supernova bangs as a tool to study big bang

Supernovae and gamma-ray bursts are the most powerful explosions in observed Universe. This educational review tells about supernovae and their applications in cosmology. It is explained how to understand the production of light in the most luminous events with minimum required energy of explosion. These most luminous phenomena can serve as primary cosmological distance indicators. Comparing the observed distance dependence on red shift with theoretical models one can extract information on evolution of the Universe from Big Bang until our epoch.     

Intense laser alignment in dissipative media as a route to solvent dynamics

We extend the concept of alignment by short intense pulses to dissipative environments within a density matrix formalism and illustrate the application of this method as a probe of the dissipative properties of dense media. In particular, we propose a means of disentangling rotational population relaxation from decoherence effects via strong laser alignment. We illustrate also the possibility of suppressing rotational relaxation to prolong the alignment lifetime through choice of the field parameters. Implications to several disciplines and a number of potential applications are proposed.     

Nonlinear photonic engineering: from NLO as a goal to NLO as a tool

Engineering of new nonlinear materials, structures and devices with enhanced figures of merit has acted over the last two decades as a major force to help drive nonlinear optics from the laboratory to real applications. In this perspective, electrooptic polymers have triggered a currently maturing integrated optics technology with a variety of industrial applications in view. We report here on a possibly major turning point in this field whereby nonlinear optical phenomena, while remaining a major functional end-goal per se, are being now implemented at the core of the elaboration process itself. Cycles of angularly selective optical pumping based on quantum interferences between multiphoton excitation pathways followed by relaxation via a randomizing diffusion process are able to break the isotropy of adequate photosensitive media into a rich variety of controllable multipolar patterns. Their photoinduced symmetry reflects the multipolar symmetry of controllable polarization states of the coherent writing beams which can be permanently or dynamically imprinted on a variety of currently explored structures including films, waveguides, gratings or microcavities.     

Thermal noise as a spectroscopic tool to determine transport properties

The utilization of thermal fluctuations or Johnson/Nyquist noise as a spectroscopic method to determine transport properties in conductors or semiconductors is developed. The autocorrelation function is obtained from power spectral density measurements thus enabling electronic transport property calculation through the Green–Kubo formalism. This experimental approach is distinct from traditional numerical methods such as molecular dynamics simulations, which have been used to extract the autocorrelation function and directly related physics only. This work reports multi-transport property measurements consisting of the electronic relaxation time, resistivity, mobility, diffusion coefficient, electronic contribution to thermal conductivity and Lorenz number from experimental data. Double validation of the experiment was accomplished through the use of a standard reference material and a standard measurement method, i.e. four-probe collinear resistivity technique. Thermal noise measurements resulted in a 1.1 and 5% agreement with the reference material and four-probe values, respectively. Additional measurements were also taken on nanoscale Au and Cu thin films. Specifically, the validated spectroscopic methodology was applied to 30 nm Au and Cu thin films to obtain transport property data that was again compared to four-probe resistivity measurements. Comparative analysis of the resistivity data showed agreement within 13.6 and 4.8% for the Au and Cu samples, respectively, thus lending further credibility to the experimental method and theory.     

Nanothermodynamics as a tool to describe small objects of nature

An apparatus based on a thermodynamic method is developed to determine the parameters of nanoparticles. The essence of the applied approaches is an optimization procedure. In terms of this procedure, the sizes and structures of the objects are determined using the potential energy and Helmholtz energy as objective functions for solid and liquid particles, respectively. To find the thermodynamic functions of nanoparticles, the generally accepted frame of reference, the concept of supramolecule, and the main points of statistical thermodynamics are used. It is shown that the energy stored in nanoparticles is much higher than in macroscopic objects and also that the number of atomic and molecular species entering into nanoparticles should be considered as a state variable. Using the notion of phase as applied to nanoparticles, phase transformations are considered and an analogue of the capillary pressure is found in the frame of the classical approach.     

Observation of a motional Stark effect to determine the second-order Doppler effect

The high resolution two-photon spectroscopy of hydrogen is often limited by the second-order Doppler effect. To determine this effect, we apply a magnetic field perpendicular to the atomic beam. This field induces a quadratic motional Stark shift proportional, as the second-order Doppler effect, to v(2) (v atomic velocity). For some magnetic field, these two effects are opposite and the total shift due to the atomic velocity is reduced. We present the first observation of this effect for the 1S-3S transition in hydrogen.     

Di-Higgs production as a probe of flavor changing neutral Yukawa couplings

Top partners are well motivated in many new physics models.Usually,vector like quarks,T_(L,R),are introduced to circumvent the quantum anomaly.Therefore,it is crucial to probe their interactions with standard model particles.However,flavor changing neutral couplings are always difficult to detect directly in current and future experiments.In this paper,we demonstrate how to constrain the flavor changing neutral Yukawa coupling Tth indirectly,via the di-Higgs production.We consider the simplified model,including a pair of gauge singlet T_(L,R).Under the perturbative unitarity and experimental constraints,we select m_T=400 GeV,s_L=0.2,and m_T=800 GeV,s_L=0.1 as benchmark points.After the analysis on the amplitude and evaluation of the numerical cross sections,we infer that the present constraints from di-Higgs production have already surpassed the unitarity bound because of the(y_(L,R)~(tT))~4 behavior.For the case of m_T=400 GeV and s_L=0.2,Rey_(L,R)~(tT) and Imy_(L,R)~(tT)can be bounded optimally in the range(-0.4,0.4) at the HL-LHC with 2σ CL.For the case of m_T=800 GeV and s_L=0.1,Rey_(L,R)~(tT)and Imy_(L,R)~(tT) can be bounded optimally in the range(-0.5,0.5) at the HL-LHC with 2σ CL.The anomalous triple Higgs coupling δ_(hhh) can also affect the constraints on y_(L,R)~(tT).Finally,we determine that the top quark electric dipole moment can provide stronger bounds in the off-axis regions for some scenarios.     

Silver nanorods used to promote SERS as a quantitative analytical tool

We have fabricated silver nanorod arrays by electrodepositing the nanorods evenly in the shallow pores of porous anodic aluminum oxide (AAO) templates. The diameter and length were 28 and 44 nm, respectively. The maxima of the transverse and longitudinal modes of the surface plasmon were near 417 and 511 nm, respectively. A good surface‐enhanced Raman scattering (SERS) spectrum was observed by excitation with the 514.5‐nm laser line. The SERS intensity increased almost linearly upon malachite green isothiocyanate adsorption on the tips of the silver nanorods as the concentration of the mother solutions increased. Our results show that silver nanorods fabricated on AAO templates could be used as an SERS substrate for quantitative analyses. Copyright © 2009 John Wiley & Sons, Ltd.     

Curcumin as a tool to assess the surface hydrophobicity of proteins

ABSTRACT

Curcumin is non-fluorescent in aqueous media; however, in the vicinity of hydrophobic surface it fluoresces. This property is used to assess the use of curcumin as a surface hydrophobic probe. The surface hydrophobicity of proteins was measured by calculating the binding affinity and surface hydrophobicity index value. Surface hydrophobicity of bovine serum albumin, β-lactoglobulin, soy lipoxygenase-1, ovalbumin, and lysozyme is in the following order: bovine serum albumin?>?β-lactoglobulin?>?soy lipoxygenase-1?>?ovalbumin?>?lysozyme. The binding affinities of curcumin decreased with the decrease in surface hydrophobicity of proteins. The orders of surface hydrophobicity index value, determined using curcumin, show similar trend with the reported values of standard probes, viz. cis-parinaric acid and 1-anilinonaphthalene-8-sulfonate. The surface hydrophobicity index value of proteins determined using curcumin decreased in the presence of urea, suggesting the possible use of curcumin as a probe to determine the surface hydrophobicity of proteins.     

EIT as a tool to observe dual wavelength operation of a semiconductor laser

We propose a simplified technique for dual wavelength operation of an extended cavity semiconductor laser, and its characterization using electromagnetically induced transparency (EIT). In this laser cavity scheme light beam is made converging before it incidences on the cavity grating. The converging angle of the beam creates two longitudinal oscillating modes of resonating cavity. Frequency separation between the longitudinal modes are measured with the help of beat frequency generation in a photodiode and creating pair of EIT spectra in Rb vapor. The pair of EIT dips that are generated due to dual wavelength of this laser (that is used as control laser) can be used to estimate frequency difference between the generated wavelengths. Width of EIT spectra can be used to estimate linewidth of individual wavelength components.