Proton magnetic resonance studies of ribonucleic acid complexes. I. Complexes of biological bases and oligonucleotides with RNA. II. Template recognition and the degeneracy of the genetic code

Part I. Complexes of Biological Bases and Oligonucleotides with RNA

The physical nature of complexes of several biological bases and oligonucleotides with single-stranded ribonucleic acids have been studied by high resolution proton magnetic resonance spectroscopy. The importance of various forces in the stabilization of these complexes is also discussed.

Previous work has shown that purine forms an intercalated complex with single-stranded nucleic acids. This complex formation led to severe and stereospecific broadening of the purine resonances. From the field dependence of the linewidths, T₁ measurements of the purine protons and nuclear Overhauser enhancement experiments, the mechanism for the line broadening was ascertained to be dipole-dipole interactions between the purine protons and the ribose protons of the nucleic acid.

The interactions of ethidium bromide (EB) with several RNA residues have been studied. EB forms vertically stacked aggregates with itself as well as with uridine, 3'-uridine monophosphate and 5'-uridine monophosphate and forms an intercalated complex with uridylyl (3' → 5') uridine and polyuridylic acid (poly U). The geometry of EB in the intercalated complex has also been determined.

The effect of chain length of oligo-A-nucleotides on their mode of interaction with poly U in D₂0 at neutral pD have also been studied. Below room temperatures, ApA and ApApA form a rigid triple-stranded complex involving a stoichiometry of one adenine to two uracil bases, presumably via specific adenine-uracil base pairing and cooperative base stacking of the adenine bases. While no evidence was obtained for the interaction of ApA with poly U above room temperature, ApApA exhibited complex formation of a 1:1 nature with poly U by forming Watson-Crick base pairs. The thermodynamics of these systems are discussed.

Part II. Template Recognition and the Degeneracy of the Genetic Code

The interaction of ApApG and poly U was studied as a model system for the codon-anticodon interaction of tRNA and mRNA in vivo. ApApG was shown to interact with poly U below ~20°C. The interaction was of a 1:1 nature which exhibited the Hoogsteen bonding scheme. The three bases of ApApG are in an anti conformation and the guanosine base appears to be in the lactim tautomeric form in the complex.

Due to the inadequacies of previous models for the degeneracy of the genetic code in explaining the observed interactions of ApApG with poly U, the "tautomeric doublet" model is proposed as a possible explanation of the degenerate interactions of tRNA with mRNA during protein synthesis in vivo.

Structural role of fluoride in aluminophosphate sol-gel glasses: High-resolution double-resonance NMR studies

The local structure of Na-Al-P-O-F glasses, prepared by a novel sol-gel route, was extensively investigated by advanced solid-state NMR techniques. Al-21{F-19} rotational echo double resonance (REDOR) results indicate that the F incorporated into aluminophosphate glass is preferentially bonded to octahedral Al units and results in a significant increase in the concentration of six-coordinated aluminum. The extent of Al-F and Al-O-P connectivities are quantified consistently by analyzing Al-27{P-31} and Al-21{F-19} REDOR NMR data. Two distinct types of fluorine species were identified and characterized by various F-19{Al-27}, F-19{Na-23}, and F-19{P-31} double resonance experiments, which were able to support peak assignments to bridging (Al-F-Al, -140 ppm) and terminal (Al-F, -170 ppm) units. On the basis of the detailed quantitative dipole-dipole coupling information obtained, a comprehensive structural model for these glasses is presented, detailing the structural speciation as a function of composition.

Design and modeling of an integrated device for acoustic resonance spectroscopy

This paper investigates the design and modelling of an integrated device for acoustic resonance spectroscopy (ARS). Miniaturisation of such platforms can be achieved using MEMS technology thereby enabling scaling of device dimensions to investigate smaller specimens while simultaneously operating at higher frequencies. We propose an integrated device where the transducers are mounted in close proximity with the specimen to be analysed (e.g. by integrating ultrasound transducers within a microfluidic channel). A finite element (FE) model and a simplified analytical model have been constructed to predict the acoustic response of a sample embedded in such a device configuration. A FE simulation is performed in COMSOL by embedding the piezoelectric transducers in representative fluid media. Resonant frequencies associated with the measurement can be extracted from this data. The response of various media modelled through FEA matches with analytical predictions for a range of biological media. A variety of biological media may be identified by using the measured resonant frequencies as a signature of relevant physical characteristics. The paper establishes the modelling basis of an integrated acoustic resonant spectrometer that is then applied to examine the impact of geometrical scaling on system resolution. © 2013 IEEE.

Novel fluid grid and voidage calculation techniques for a discrete element model of a 3D cylindrical fluidized bed

A discrete element model (DEM) combined with computational fluid dynamics (CFD) was developed to model particle and fluid behaviour in 3D cylindrical fluidized beds. Novel techniques were developed to (1) keep fluid cells, defined in cylindrical coordinates, at a constant volume in order to ensure the conditions for validity of the volume-averaged fluid equations were satisfied and (2) smoothly and accurately measure voidage in arbitrarily shaped fluid cells. The new technique for calculating voidage was more stable than traditional techniques, also examined in the paper, whilst remaining computationally-effective. The model was validated by quantitative comparison with experimental results from the magnetic resonance imaging of a fluidised bed analysed to give time-averaged particle velocities. Comparisons were also made between theoretical determinations of slug rise velocity in a tall bed. It was concluded that the DEM-CFD model is able to investigate aspects of the underlying physics of fluidisation not readily investigated by experiment. © 2014 The Authors.

Resonance based multi-gaited robot locomotion

In order to understand the underlying mechanisms of animals' agility, dexterity and efficiency in motor control, there has been an increasing interest in the study of gait patterns in biological and artificial legged systems. This paper presents a novel approach to the study of gait patterns which makes use of intrinsic mechanical dynamics of robotic systems. Each of these robots consists of a U-shape elastic beam and exploits free vibration to generate different gait patterns. We developed a conceptual model for these robots, and through simulation and real-world experiments, we show three distinct mechanisms for generating four different gait patterns in these robots. © 2012 IEEE.

Finding resonance: Adaptive frequency oscillators for dynamic legged locomotion

There is much to gain from providing walking machines with passive dynamics, e.g. by including compliant elements in the structure. These elements can offer interesting properties such as self-stabilization, energy efficiency and simplified control. However, there is still no general design strategy for such robots and their controllers. In particular, the calibration of control parameters is often complicated because of the highly nonlinear behavior of the interactions between passive components and the environment. In this article, we propose an approach in which the calibration of a key parameter of a walking controller, namely its intrinsic frequency, is done automatically. The approach uses adaptive frequency oscillators to automatically tune the intrinsic frequency of the oscillators to the resonant frequency of a compliant quadruped robot The tuning goes beyond simple synchronization and the learned frequency stays in the controller when the robot is put to halt. The controller is model free, robust and simple. Results are presented illustrating how the controller can robustly tune itself to the robot, as well as readapt when the mass of the robot is changed. We also provide an analysis of the convergence of the frequency adaptation for a linearized plant, and show how that analysis is useful for determining which type of sensory feedback must be used for stable convergence. This approach is expected to explain some aspects of developmental processes in biological and artificial adaptive systems that "develop" through the embodied system-environment interactions. © 2006 IEEE.

Stochastic resonance for modulated gain in a single-mode laser

Stochastic resonance (SR) induced by the signal modulation is investigated, by introducing the signal-modulated gain into a single-mode laser system. Using the linear approximation method, we detailedly calculate the signal-to-noise ratio (SNR) of a gain-noise model of the single-mode laser, taking the cross-correlation between the quantum noise and pump noise into account. We find that, SR appears in the dependence of the SNR on the intensities of the quantum and the pump noises when the correlation coefficient between both the noises is negative; moreover, when the cross-correlation between the two noises is strongly negative, SR exhibits a resonance and a suppression versus the gain coefficient, meanwhile, the single-peaked SR and multi-peaked SR occur in the behaviors of the SNR as functions of the loss coefficient and the deterministic steady-state intensity. (c) 2005 Elsevier B.V. All rights reserved.

Nonlinear Rashba model and spin relaxation in quantum wells

We find that the Rashba spin splitting is intrinsically a nonlinear function of the momentum, and the linear Rashba model may overestimate it significantly, especially in narrow-gap semiconductors. A nonlinear Rashba model is proposed, which is in good agreement with the numerical results from the eight-band k center dot p theory. Using this model, we find pronounced suppression of the D'yakonov-Perel' spin relaxation rate at large electron densities, and a nonmonotonic dependence of the resonance peak position of the electron spin lifetime on the electron density in [111]-oriented quantum wells, both in qualitative disagreement with the predictions of the linear Rashba model.

Interplay between partial incoherence, partial inelasticity, resonance, and heterogeneity in long-range electron transfer and transport

A generalized scattering matrix formalism is constructed to elucidate the interplay of electron resonance, coherence, dephasing, inelastic scattering, and heterogeneity, which play important roles in the physics of long-range electron transfer/transport. The theory consists of an extension of the standard Buttiker phase-breaking model and an analytical expression of the electron transmission coefficient for donor-bridge-acceptor systems with arbitrary length and sequence. The theory incorporates the following features: Dephasing-assisted off-resonance enhancement, inelasticity-induced turnover, resonance enhancement and its dephasing-induced suppression, dephasing-induced smooth superexchange-hopping transition, and heterogeneity effects. (C) 2002 American Institute of Physics.

High-frequency ferromagnetic resonance on ultrafine cobalt particles

We report on high-frequency (300-700 GHz) ferromagnetic resonance (HF-FMR) measurements on cobalt superparamagnetic particles with strong uniaxial effective anisotropy. We derive the dynamical susceptibility of the system on the basis of an independent-grain model by using a rectangular approach. Numerical simulations give typical line shapes depending on the anisotropy, the gyromagnetic ratio, and the damping constant. HF-FMR experiments have been performed on two systems of ultrafine cobalt particles of different sizes with a mean number of atoms per particles of 150 +/- 20 and 310 +/- 20. In both systems, the magnetic anisotropy is found to be enhanced compared to the bulk value, and increases as the particle size decreases, in accordance with previous determinations from magnetization measurements. Although no size effect has been observed on the gyromagnetic ratio, the transverse relaxation time is two orders of magnitude smaller than the bulk value indicating strong damping effects, possibly originating from surface spin disorders.

High-field ferromagnetic resonance in fine particles

We investigate high-field ferromagnetic resonance of superparamagnetic particles with uniaxial anisotropy, In this case, since the field is large enough to saturate the magnetization, the thermal orientational fluctuations of the magnetic moment of the particle are negligible. Thus, we derive the dynamic susceptibility of the system on the basis of an independent particle model. High-field ferromagnetic resonance has been performed on fine cobalt particles, The analysis of the spectra obtained at different frequencies allows us to estimate the effective magnetic anisotropy, the gyromagnetic ratio, and the transverse relaxation time. (C) 1998 Elsevier Science B.V. All rights reserved.

Magnetophonon resonance in the energy relaxation of electrons in a quantum well

The magnetophonon resonance effect in the energy relaxation rate is studied theoretically for a quasi-two-dimensional electron gas in a semiconductor quantum well. An electron-temperature model is adopted to describe the coupled electron-phonon system. The energy relaxation time, derived from the energy relaxation rate, is found to display an oscillatory behavior as the magnetic-field strength changes, and reaches minima when the optical phonon frequency equals integer multiples of the electron cyclotron frequency. The theoretical results are compared with a recent experiment, and a qualitative agreement is found.

Spin split cyclotron resonance in GaAs quantum wells

The cyclotron resonance (CR) of electrons in GaAs/AlGaAs quantum wells is investigated theoretically to explain a recent CR experiment, where two CR peaks were observed at high magnetic fields when both spin-up and spin-down states of the lowest Landau level are occupied. Our theoretical model takes into account the conduction band non-parabolicity, the electron bulk longitude-optic-phonon coupling, and the self-consistent subband structure. A good agreement is found.

High-field ferromagnetic resonance in fine particles

We investigate high-field ferromagnetic resonance of superparamagnetic particles with uniaxial anisotropy, In this case, since the field is large enough to saturate the magnetization, the thermal orientational fluctuations of the magnetic moment of the particle are negligible. Thus, we derive the dynamic susceptibility of the system on the basis of an independent particle model. High-field ferromagnetic resonance has been performed on fine cobalt particles, The analysis of the spectra obtained at different frequencies allows us to estimate the effective magnetic anisotropy, the gyromagnetic ratio, and the transverse relaxation time. (C) 1998 Elsevier Science B.V. All rights reserved.

Isoscalar Giant Monopole Resonance in Relativistic Continuum Random Phase Approximation

The isoscalar giant monopole resonance (ISGMR) in nuclei is studied in the framework of a fully consistent relativistic continuum random phase approximation (RCRPA). In this method the contribution of the continuum spectrum to nuclear excitations is treated exactly by the single particle Green's function technique. The negative energy states in the Dirac sea are also included in the single particle Green's function in the no-sea approximation. The single particle Green's function is calculated numerically by a proper product of the regular and irregular solutions of the Dirac equation. The strength distributions in the RCRPA calculations, the inverse energy-weighted sum rule m(-1) and the centroid energy of the ISGMR in Sn-120 and Pb-208 are analysed. Numerical results of the RCRPA are checked with the constrained relativistic mean field model and relativistic random phase approximation with a discretized spectrum in the continuum. Good agreement between them is achieved.