Dynamics of RNA with A6 bulge loop

In order to understand the behavior of RNAs with large bulges In solution, molecular dynamics was performed on the RNA molecule in water with A6 bulge. The result of simulation showed that nonstacked conformation Is the main conformation in large bulges, and the backbone of large bulge is of great conformational flexibility, but bulges-induced bends are relatively rigid. The fluctuation in bulge has little influence on the bend angle of RNAs.

The relation between translation speed and protein secondary structure

Based on the statistical analysis of 119 human and 92 E. coli proteins it was found that for both human and E. coli, the mRNA sequences consisting of tri-codon and tetra-codon with high translation speed preferably code for alpha helices more than for coils. For beta strand, the preference/ avoidance oscillates with the translation speed. Moreover, the non-homogeneous usages of tri-codon and tetra-codon with different translation speeds in a given secondary structure have also been found. These results cannot be simply explained by the effect of stochastic fluctuation.

Statistical correlation between protein secondary structure and messenger RNA stem-loop structure

Anew integrated sequence-structure database, called IADE (Integrated ASTRAL-DSSP-EMBL), incorporating matching mRNA sequence, amino acid sequence, and protein secondary structural data, is constructed. It includes 648 protein domains. Based on the IADE database, we studied the relation between RNA stem-loop frequencies and protein secondary structure. It was found that the alpha-helices and beta-strands on proteins tend to be preferably "coded" by mRNA stem region, while the coils on proteins tend to be preferably "coded" by mRNA loop region. These tendencies are more obvious if we observe the structural words (SWs). An SW is defined by a four-amino-acid-fragment that shows the pronounced secondary structural (alpha-helix or beta-strand) propensity. It is demonstrated that the deduced correlation between protein and mRNA structure can hardly be explained as the stochastic fluctuation effect. (C) 2003 Wiley Periodicals, Inc.

Blue-phase templated fabrication of three-dimensional nanostructures for photonic applications.

A promising approach to the fabrication of materials with nanoscale features is the transfer of liquid-crystalline structure to polymers. However, this has not been achieved in systems with full three-dimensional periodicity. Here we demonstrate the fabrication of self-assembled three-dimensional nanostructures by polymer templating blue phase I, a chiral liquid crystal with cubic symmetry. Blue phase I was photopolymerized and the remaining liquid crystal removed to create a porous free-standing cast, which retains the chiral three-dimensional structure of the blue phase, yet contains no chiral additive molecules. The cast may in turn be used as a hard template for the fabrication of new materials. By refilling the cast with an achiral nematic liquid crystal, we created templated blue phases that have unprecedented thermal stability in the range -125 to 125 °C, and that act as both mirrorless lasers and switchable electro-optic devices. Blue-phase templated materials will facilitate advances in device architectures for photonics applications in particular.

Blue-phase templated fabrication of three-dimensional nanostructures for photonic applications

A promising approach to the fabrication of materials with nanoscale features is the transfer of liquid-crystalline structure to polymers. However, this has not been achieved in systems with full three-dimensional periodicity. Here we demonstrate the fabrication of self-assembled three-dimensional nanostructures by polymer templating blue phase I, a chiral liquid crystal with cubic symmetry. Blue phase I was photopolymerized and the remaining liquid crystal removed to create a porous free-standing cast, which retains the chiral three-dimensional structure of the blue phase, yet contains no chiral additive molecules. The cast may in turn be used as a hard template for the fabrication of new materials. By refilling the cast with an achiral nematic liquid crystal, we created templated blue phases that have unprecedented thermal stability in the range-125 to 125°C, and that act as both mirrorless lasers and switchable electro-optic devices. Blue-phase templated materials will facilitate advances in device architectures for photonics applications in particular. © 2012 Macmillan Publishers Limited. All rights reserved.

Study of the turbulence in the air-side and water-side boundary layers in experimental laboratory wind induced surface waves

This study detailed the structure of turbulence in the air-side and water-side boundary layers in wind-induced surface waves. Inside the air boundary layer, the kurtosis is always greater than 3 (the value for normal distribution) for both horizontal and vertical velocity fluctuations. The skewness for the horizontal velocity is negative, but the skewness for the vertical velocity is always positive. On the water side, the kurtosis is always greater than 3, and the skewness is slightly negative for the horizontal velocity and slightly positive for the vertical velocity. The statistics of the angle between the instantaneous vertical fluctuation and the instantaneous horizontal velocity in the air is similar to those obtained over solid walls. Measurements in water show a large variance, and the peak is biased towards negative angles. In the quadrant analysis, the contribution of quadrants Q2 and Q4 is dominant on both the air side and the water side. The non-dimensional relative contributions and the concentration match fairly well near the interface. Sweeps in the air side (belonging to quadrant Q4) act directly on the interface and exert pressure fluctuations, which, in addition to the tangential stress and form drag, lead to the growth of the waves. The water drops detached from the crest and accelerated by the wind can play a major role in transferring momentum and in enhancing the turbulence level in the water side.On the air side, the Reynolds stress tensor's principal axes are not collinear with the strain rate tensor, and show an angle α σ≈=-20°to-25°. On the water side, the angle is α σ≈=-40°to-45°. The ratio between the maximum and the minimum principal stresses is σ a/σ b=3to4 on the air side, and σ a/σ b=1.5to3 on the water side. In this respect, the air-side flow behaves like a classical boundary layer on a solid wall, while the water-side flow resembles a wake. The frequency of bursting on the water side increases significantly along the flow, which can be attributed to micro-breaking effects - expected to be more frequent at larger fetches. © 2012 Elsevier B.V.

Effect of laser heating temperature on coating characteristics of Stellite 6 deposited by cold spray

Laser-assisted cold spray (LCS) is a new coating and fabrication process which combines some advantages of CS: solid-state deposition, retain their initial composition and high build rate with the ability to deposit materials which are either difficult or impossible to deposit using cold spray alone. Stellite 6 powder is deposited on medium carbon steels by LCS using N 2 as carrier gas pressure. The topography, cross section thickness, structure of the coatings is examined by SEM, optical microscopy, EDX. The results show that thickness and fluctuation of coating are improved with increased deposition site temperature. Porosity of coating is affected by N 2 and deposition site temperature. In this paper, it presents optimal coating using N 2 at a pressure of 3 MPa and temperature of 450°C and deposition site temperature of 1100°C.

Tm-doped fiber laser mode-locked by graphene-polymer composite

We demonstrate mode-locking of a thulium-doped fiber laser operating at 1.94 μm, using a graphene-polymer based saturable absorber. The laser outputs 3.6 ps pulses, with ∼0.4 nJ energy and an amplitude fluctuation ∼0.5%, at 6.46 MHz. This is a simple, low-cost, stable and convenient laser oscillator for applications where eye-safe and low-photon-energy light sources are required, such as sensing and biomedical diagnostics. © 2012 Optical Society of America.

Verification of periodically controlled hybrid systems: Application to an autonomous vehicle

This article introduces Periodically Controlled Hybrid Automata (PCHA) for modular specification of embedded control systems. In a PCHA, control actions that change the control input to the plant occur roughly periodically, while other actions that update the state of the controller may occur in the interim. Such actions could model, for example, sensor updates and information received from higher-level planning modules that change the set point of the controller. Based on periodicity and subtangential conditions, a new sufficient condition for verifying invariant properties of PCHAs is presented. For PCHAs with polynomial continuous vector fields, it is possible to check these conditions automatically using, for example, quantifier elimination or sum of squares decomposition. We examine the feasibility of this automatic approach on a small example. The proposed technique is also used to manually verify safety and progress properties of a fairly complex planner-controller subsystem of an autonomous ground vehicle. Geometric properties of planner-generated paths are derived which guarantee that such paths can be safely followed by the controller. © 2012 ACM.

Periodically controlled hybrid systems verifying a controller for an autonomous vehicle

This paper introduces Periodically Controlled Hybrid Automata (PCHA) for describing a class of hybrid control systems. In a PCHA, control actions occur roughly periodically while internal and input actions may occur in the interim changing the discrete-state or the setpoint. Based on periodicity and subtangential conditions, a new sufficient condition for verifying invariance of PCHAs is presented. This technique is used in verifying safety of the planner-controller subsystem of an autonomous ground vehicle, and in deriving geometric properties of planner generated paths that can be followed safely by the controller under environmental uncertainties.

New application of temperature-dependent modelling of high temperature superconductors: Quench propagation and pulse magnetization

We present temperature-dependent modeling of high-temperature superconductors (HTS) to understand HTS electromagnetic phenomena where temperature fluctuation plays a nontrivial role. Thermal physics is introduced into the well-developed H-formulation model, and the effect of temperature-dependent parameters is considered. Based on the model, we perform extensive studies on two important HTS applications: quench propagation and pulse magnetization. A micrometer-scale quench model of HTS coil is developed, which can be used to estimate minimum quench energy and normal zone propagation velocity inside the coil. In addition, we study the influence of inhomogeneity of HTS bulk during pulse magnetization. We demonstrate how the inhomogeneous distribution of critical current inside the bulk results in varying degrees of heat dissipation and uniformity of final trapped field. The temperature- dependent model is proven to be a powerful tool to study the thermally coupled electromagnetic phenomena of HTS. © 2012 American Institute of Physics.

Design and simulation of SMES system using YBCO tapes for direct drive wave energy converters

The ocean represents a huge energy reservoir since waves can be exploited to generate clean and renewable electricity; however, a hybrid energy storage system is needed to smooth the fluctuation. In this paper a hybrid energy storage system using a superconducting magnetic energy system (SMES) and Li-ion battery is proposed. The SMES is designed using Yttrium Barium Copper Oxide (YBCO) tapes, which store 60 kJ electrical energy. The magnet component of the SMES is designed using global optimization algorithm. Mechanical stress, coupled with electromagnetic field, is calculated using COMSOL and Matlab. A cooling system is presented and a suitable refrigerator is chosen to maintain a cold working temperature taking into account four heat sources. Then a microgrid system of direct drive linear wave energy converters is designed. The interface circuit connecting the generator and storage system is given. The result reveals that the fluctuated power from direct drive linear wave energy converters is smoothed by the hybrid energy storage system. The maximum power of the wave energy converter is 10 kW. © 2012 IEEE.

Spin-cluster effect and lattice-deformation-induced Kondo effect, spin-glass freezing, and strong phonon scattering in La 0.7 Ca 0.3Mn 1-xCr xO 3

Besides the Kondo effect observed in dilute magnetic alloys, the Cr-doped perovskite manganate compounds La0.7 Ca0.3 Mn1-x Crx O3 also exhibit Kondo effect and spin-glass freezing in a certain composition range. An extensive investigation for the La0.7 Ca0.3 Mn1-x Crx O3 (x=0.01, 0.05, 0.10, 0.3, 0.6, and 1.0) system on the magnetization and ac susceptibility, the resistivity and magnetoresistance, as well as the thermal conductivity is done at low temperature. The spin-glass behavior has been confirmed for these compounds with x=0.05, 0.1, and 0.3. For temperatures above Tf (the spin-glass freezing temperature) a Curie-Weiss law is obeyed. The paramagnetic Curie temperature θ is dependent on Cr doping. Below Tf there exists a Kondo minimum in the resistivity. Colossal magnetoresistance has been observed in this system with Cr concentration up to x=0.6. We suppose that the substitution of Mn with Cr dilutes Mn ions and changes the long-range ferromagnetic order of La0.7 Ca0.3 MnO3. These behaviors demonstrate that short-range ferromagnetic correlation and fluctuation exist among Mn spins far above Tf. Furthermore, these interactions are a precursor of the cooperative freezing at Tf. The "double bumps" feature in the resistivity-temperature curve is observed in compounds with x=0.05 and 0.1. The phonon scattering is enhanced at low temperatures, where the second peak of double bumps comes out. The results indicate that the spin-cluster effect and lattice deformation induce Kondo effect, spin-glass freezing, and strong phonon scattering in mixed perovskite La0.7 Ca0.3 Mn1-x Crx O3. © 2005 American Institute of Physics.

An experimental study on engine dynamics model based in-cylinder pressure estimation

The information provided by the in-cylinder pressure signal is of great importance for modern engine management systems. The obtained information is implemented to improve the control and diagnostics of the combustion process in order to meet the stringent emission regulations and to improve vehicle reliability and drivability. The work presented in this paper covers the experimental study and proposes a comprehensive and practical solution for the estimation of the in-cylinder pressure from the crankshaft speed fluctuation. Also, the paper emphasizes the feasibility and practicality aspects of the estimation techniques, for the real-time online application. In this study an engine dynamics model based estimation method is proposed. A discrete-time transformed form of a rigid-body crankshaft dynamics model is constructed based on the kinetic energy theorem, as the basis expression for total torque estimation. The major difficulties, including load torque estimation and separation of pressure profile from adjacent-firing cylinders, are addressed in this work and solutions to each problem are given respectively. The experimental results conducted on a multi-cylinder diesel engine have shown that the proposed method successfully estimate a more accurate cylinder pressure over a wider range of crankshaft angles. Copyright © 2012 SAE International.

Nonlinear analysis of cardiac rhythm fluctuations using DFA method

An approach by which the detrented fluctuation analysis (DFA) method can be used to help diagnose heart failure was demonstrated. DFA was applied to patients suffering from congestive heart failure (CHF) to check correlations between DFA indices and CHF, and determine a correlation between DFA indices and mortality, with a particular attention to the residue parameter, which is a measure of the departure of the DFA from its power law approximation. DFA parameters proved to be useful as a complement to the physiological parameters weber and FE to sort out the patients into three prognostic group.