CpG island density and its correlations with genomic features in mammalian genomes

Background: CpG islands, which are clusters of CpG dinucleotides in GC-rich regions, are considered gene markers and represent an important feature of mammalian genomes. Previous studies of CpG islands have largely been on specific loci or within one geno

Comparison of quantum chemistry calculation methods of nucleic acid base-quartets

Nine base-quartets were calculated by six semi-empirical methods and ab initio Hartree-Fork method using STO-3G basis set. The results showed that PM3 method can be use to calculate base quartets, the results of PM3 calculations are close to the ab initio

Cardioviral RNA structure logo analysis: entropy, correlations, and prediction

In recent years, there has been an increased number of sequenced RNAs leading to the development of new RNA databases. Thus, predicting RNA structure from multiple alignments is an important issue to understand its function. Since RNA secondary structures are often conserved in evolution, developing methods to identify covariate sites in an alignment can be essential for discovering structural elements. Structure Logo is a technique established on the basis of entropy and mutual information measured to analyze RNA sequences from an alignment. We proposed an efficient Structure Logo approach to analyze conservations and correlations in a set of Cardioviral RNA sequences. The entropy and mutual information content were measured to examine the conservations and correlations, respectively. The conserved secondary structure motifs were predicted on the basis of the conservation and correlation analyses. Our predictive motifs were similar to the ones observed in the viral RNA structure database, and the correlations between bases also corresponded to the secondary structure in the database.

Quantum Confinement Effects and Electronic Properties of SnO2 Quantum Wires and Dots

On the basis of the density functional theory (DFT) within local density approximations (LDA) approach, we calculate the band gaps for different size SnO2 quantum wire (QWs) and quantum dots (QDs). A model is proposed to passivate the surface atoms of SnO2 QWs and QDs. We find that the band gap increases between QWs and bulk evolve as Delta E-g(wire) = 1.74/d(1.20) as the effective diameter d decreases, while being Delta E-g(dot) = 2.84/d(1.26) for the QDs. Though the similar to d(1.2) scale is significantly different from similar to d(2) of the effective mass result, the ratio of band gap increases between SnO2 QWs and QDs is 0.609, very close to the effective mass prediction. We also confirm, although the LDS calculations underestimate the band gap, that they give the trend of band gap shift as much as that obtained by the hybrid functional (PBE0) with a rational mixing of 25% Fock exchange and 75% of the conventional Perdew-Burke-Ernzerhof (PBE) exchange functional for the SnO2 QWs and QDs. The relative deviation of the LDA calculated band gap difference Lambda E-g compared with the corresponding PBE0 results is only within 5%. Additionally, it is found the states of valence band maximum (VBM) and conduction band minimum (CBM) of SnO2 QWs or QDs have a mostly p- and s-like envelope function symmetry, respectively, from both LDA and PBE0 calculations.

The refractive nonlinearities of InAs/GaAs quantum dots above-bandgap energy

The third-order optical nonlinear refractive properties of InAs/GaAs quantum dots grown by molecular beam epitaxy have been measured using the reflection Z-scan technique at above-bandgap energy. The nonlinear refractive index and nonlinear absorption index of the InAs/GaAs quantum dots were determined for wavelengths from 740 to 777 nm. The measured results are compared with the nonlinear refractive response of several typical III-V group semiconductor materials. The corresponding mechanisms responsible for the large nonlinear response are discussed.

Rashba electron transport in one-dimensional quantum waveguides

The properties of Rashba wave function in the planar one-dimensional waveguide are studied, and the following results are obtained. Due to the Rashba effect, the plane waves of electron with the energy E divide into two kinds of waves with the wave vectors k(1)=k(0)+k(delta) and k(2)=k(0)-k(delta), where k(delta) is proportional to the Rashba coefficient, and their spin orientations are +pi/2 (spin up) and -pi/2 (spin down) with respect to the circuit, respectively. If there is gate or ferromagnetic contact in the circuit, the Rashba wave function becomes standing wave form exp(+/- ik(delta)l)sin[k(0)(l-L)], where L is the position coordinate of the gate or contact. Unlike the electron without considering the spin, the phase of the Rashba plane or standing wave function depends on the direction angle theta of the circuit. The travel velocity of the Rashba waves with the wave vector k(1) or k(2) are the same hk(0)/m*. The boundary conditions of the Rashba wave functions at the intersection of circuits are given from the continuity of wave functions and the conservation of current density. Using the boundary conditions of Rashba wave functions we study the transmission and reflection probabilities of Rashba electron moving in several structures, and find the interference effects of the two Rashba waves with different wave vectors caused by ferromagnetic contact or the gate. Lastly we derive the general theory of multiple branches structure. The theory can be used to design various spin polarized devices.

Electrically controllable RKKY interaction in semiconductor quantum wires

We demonstrate in theory that it is possible to all-electrically manipulate the RKKY interaction in a quasi-one-dimensional electron gas embedded in a semiconductor heterostructure, in the presence of Rashba and Dresselhaus spin-orbit interaction. In an undoped semiconductor quantum wire where intermediate excitations are gapped, the interaction becomes the short-ranged Bloembergen-Rowland superexchange interaction. Owing to the interplay of different types of spin-orbit interaction, the interaction can be controlled to realize various spin models, e.g., isotropic and anisotropic Heisenberg-like models, Ising-like models with additional Dzyaloshinsky-Moriya terms, by tuning the external electric field and designing the crystallographic directions. Such controllable interaction forms a basis for quantum computing with localized spins and quantum matters in spin lattices.

Quantum tunneling through graphene nanorings

We investigate theoretically quantum transport through graphene nanorings in the presence of a perpendicular magnetic field. Our theoretical results demonstrate that the graphene nanorings behave like a resonant tunneling device, contrary to the Aharonov-Bohm oscillations found in conventional semiconductor rings. The resonant tunneling can be tuned by the Fermi energy, the size of the central part of the graphene nanorings and the external magnetic field.

Spin injection in the multiple quantum-well LED structure with the Fe/AlO (x) injector

A spin-injection/-detection device has been fabricated based on the multiple quantum well light emitting diode (LED) structure. It is found that only a broad electroluminescence (EL) peak of a full width at half maximum of 8.6 nm appears at the wavelength of 801 nm in EL spectra with a circular luminescence polarization degree of 18%, despite PL spectra always show three well resolved peaks. The kinetic energy gained by injected electrons and holes in their drift along opposite directions broadens the EL peak, and makes three EL peaks converge together. The same process also destroys the injected spin polarization of electrons mainly dominated by the Bir-Aronov-Pikus spin relaxing mechanism.

Theoretical gain of strained GeSn0.02/Ge1-x-y ' SixSny ' quantum well laser

Using effective-mass Hamiltonian model of semiconductors quantum well structures, we investigate the electronic structures of the Gamma-conduction and L-conduction subbands of GeSn/GeSiSn strained quantum well structure with an arbitrary composition. Our theoretical model suggests that the band structure could be widely modified to be type I, negative-gap or indirect-gap type II quantum well by changing the mole fraction of alpha-Sn and Si in the well and barrier layers, respectively. The optical gain spectrum in the type I quantum well system is calculated, taking into account the electrons leakage from the Gamma-valley to L-valley of the conduction band. We found that by increasing the mole fraction of alpha-Sn in the barrier layer and not in the well layer, an increase in the tensile strain effect can significantly enhance the transition probability, and a decrease in Si composition in the barrier layer, which lowers the band edge of Gamma-conduction subbands, also comes to a larger optical gain.

An experimental study about the influence of well thickness on the electroluminescence of InGaN/GaN multiple quantum wells

The influence of well thickness on the electroluminescence (EL) of InGaN/GaN multiple quantum wells (MQWs) grown by metalorganic chemical vapor deposition is investigated. It is found that the peak wavelength of EL increases with the increase of well thickness when the latter is located in the range of 3.0-5.1 nm. The redshift is mainly attributed to the quantum confined Stark effect (QCSE). As a contrast, it is found that the EL intensity of InGaN/GaN MQWs increases with the increase of well thickness in spite of QCSE. The result of X-ray diffraction demonstrates that the interface become smoother with the increase of well thickness and suggests that the reduced interface roughness can be an important factor leading to the increase of EL intensity of InGaN/GaN MQWs. (C) 2009 Elsevier B.V. All rights reserved.

Quantum Mechanical Study on Tunnelling and Ballistic Transport of Nanometer Si MOSFETs

Using self-consistent calculations of million-atom Schrodinger-Poisson equations, we investigate the I-V characteristics of tunnelling and ballistic transport of nanometer metal oxide semiconductor field effect transistors (MOSFET) based on a full 3-D quantum mechanical simulation under nonequilibtium condition. Atomistic empirical pseudopotentials are used to describe the device Hamiltonian and the underlying bulk band structure. We find that the ballistic transport dominates the I-V characteristics, whereas the effects of tunnelling cannot be neglected with the maximal value up to 0.8mA/mu m when the channel length of MOSFET scales down to 25 nm. The effects of tunnelling transport lower the threshold voltage V-t. The ballistic current based on fully 3-D quantum mechanical simulation is relatively large and has small on-off ratio compared with results derived from the calculation methods of Luo et al.

Interference in transport through double barriers in interacting quantum wires

We investigate interference effects of the backscattering current through a double-barrier structure in an interacting quantum wire attached to noninteracting leads. Depending on the interaction strength and the location of the barriers, the backscattering current exhibits different oscillation and scaling characteristics with the applied voltage in the strong and weak interaction cases. However, in both cases, the oscillation behaviors of the backscattering current are mainly determined by the quantum mechanical interference due to the existence of the double barriers.