Analysis of the energies of the triple base triplets

Sixty-four sets of three-dimensional models of DNA triplex base triplets (TBT) were built up based on codons by homologous modeling method and their energies were minimized. According to sequence of TBT and orientation of the third ODN strand third, the energies of monomers and water-K+-TBT ternary complexes of TBT were analyzed. The results showed: (i) The energies of the symmetric parallel monomers are generally lower than those of the symmetric anti-parallel monomers of TBT, but the energies of the symmetric parallel ternary complexes are higher than those of the symmetric anti-parallel ternary complexes of TBT. (ii) No matter TBTs are monomers or ternary complexes, the energies of asymmetric parallel TBTs are generally lower than those of the asymmetric anti-parallel ones. (iii) Although the energies of the parallel TBTs are correlated with those of the anti-parallel ones, the energy differences are significant between them. The results here suggest the sequences of TBTs and the orientations of the third ODN strands are two of the key factors that can influence the formation and stability of TBT. (C) 2002 Elsevier Science B.V. All rights reserved.

The comparative analysis of the energies of conjugated triple base triplets and their applications

We built 64 sets of 3D models of DNA triplex base triplets (TBT) and minimized their energies. The TBTs were divided into 32 pairs of conjugated ones on the basis of their sequence characteristic, and the energies of each pair of them were compared and analyzed, the results showed: (i) The duplex DNA of which any strand contains at least a couple of A or T, has a preference for selecting the oligodeoxyribonucleic acid (ODN) strand containing abundant T to form TBT. (ii) The duplex DNA of which any strand contains at least a couple of G or C has a preference for selecting ODN containing abundant G to form symmetric antiparallel TBT, but selecting ODN containing abundant C to form asymmetric parallel TBT. (iii) The duplex DNA of which any strand contains only one of A, T, G or C has a preference for selecting ODN containing abundant pyrimidines (T or C) to form antiparallel TBT. Additionally, two examples of TBTs applications, in designing ODN to form triplex with duplex were presented. The energy calculation result revealed that 15-TCG is the best ligand of the HIV PPT duplex. The comparative analysis of energies of the conjugated TBTs provides directive significance for designing ODN strand that is easy to form triplex in theory. (C) 2002 Elsevier Science B.V. All rights reserved.

Sixfold symmetry of excitonic transition energies in c-plane for wurtzite GaN

The optical properties of the strained wurtzite GaN are investigated theoretically within the nearest neighbor tight-binding method. The piezoelectric effect is also taken into account. The empirical rule has been used in the strained band-structure calculation. The results show that the excitonic transition energies are anisotropic in the c-plane in a high electronic concentration system and have a 60 degrees periodicity, which is in agreement with experiment. (C) 2008 American Institute of Physics. [DOI: 10.1063/1.3001937]

Electronic structure of paramagnetic In1-xMnx as nanowires

The electronic structure, spin splitting energies, and g factors of paramagnetic In1-xMnxAs nanowires under magnetic and electric fields are investigated theoretically including the sp-d exchange interaction between the carriers and the magnetic ion. We find that the effective g factor changes dramatically with the magnetic field. The spin splitting due to the sp-d exchange interaction counteracts the Zeeman spin splitting. The effective g factor can be tuned to zero by the external magnetic field. There is also spin splitting under an electric field due to the Rashba spin-orbit coupling which is a relativistic effect. The spin-degenerated bands split at nonzero k(z) (k(z) is the wave vector in the wire direction), and the spin-splitting bands cross at k(z) = 0, whose k(z)-positive part and negative part are symmetrical. A proper magnetic field makes the k(z)-positive part and negative part of the bands asymmetrical, and the bands cross at nonzero k(z). In the absence of magnetic field, the electron Rashba coefficient increases almost linearly with the electric field, while the hole Rashba coefficient increases at first and then decreases as the electric field increases. The hole Rashba coefficient can be tuned to zero by the electric field.

Energy bands and acceptor binding energies of GaN

The energy bands of zinc-blende and wurtzite GaN are calculated with the empirical pseudopotential method, and the pseudopotential parameters for Ga and N atoms are-given. The calculated energy bands are in agreement with those obtained by the ab initio method. The effective-mass theory for the semiconductors of wurtzite structure is established, and the effective-mass parameters of GaN for both structures are given The binding energies of acceptor states are calculated by solving strictly the effective-mass equations. The binding energies of donor and acceptor are 24 and 142 meV for the zinc-blende structure, 20 and 131, and 97 meV for the wurtzite structure, respectively, which are consistent with recent experimental results. It is proposed that there are two kinds of acceptor in wurtzite GaN. One kind is the general acceptor such as C, which substitutes N, which satisfies the effective-mass theory. The other kind of acceptor includes Mg, Zn, Cd, etc., the binding energy of these accepters is deviated from that given by the effective mass theory. In this report, wurtzite GaN is grown by the molecular-beam epitaxy method, and the photoluminescence spectra were measured. Three main peaks are assigned to the donor-acceptor transitions from two kinds of accepters. Some of the transitions were identified as coming from the cubic phase of GaN, which appears randomly within the predominantly hexagonal material. [S0163-1829(99)15915-0].

Tuning the Exciton Binding Energies in Single Self-Assembled InGaAs/GaAs Quantum Dots by Piezoelectric-Induced Biaxial Stress

We study the effect of an external biaxial stress on the light emission of single InGaAs/GaAs(001) quantum dots placed onto piezoelectric actuators. With increasing compression, the emission blueshifts and the binding energies of the positive trion (X+) and biexciton (XX) relative to the neutral exciton (X) show a monotonic increase. This phenomenon is mainly ascribed to changes in electron and hole localization and it provides a robust method to achieve color coincidence in the emission of X and XX, which is a prerequisite for the possible generation of entangled photon pairs via the recently proposed "time reordering'' scheme.

Free radial oscillation of a sphere in relativistic elasticity theory

The spherically symmetric free radial oscillation in the first post-Newtonian approximation for a homogeneous and isotropic elastic sphere with a constant density is studied. Based on the Xu, Wu, and Soffel formalism, the relation of the oscillation frequency of the sphere with the radius, mass density, and elastic constants of the sphere is derived by using the successive approximation method.

1ST PRINCIPLE CALCULATIONS OF QUASI-PARTICLE ENERGIES FOR BAND STRUCTURES OF SI AND GAAS

We have applied the Green function theory in GW approximation to calculate the quasiparticle energies for semiconductors Si and GaAs. Good agreements of the calculated excitation energies and fundamental energy gaps with the experimental band structures were achieved. We obtained the calculated fundamental gaps of Si and GaAs to be 1.22 and 1.42 eV in comparison to the experimental values of 1.17 and 1.52 eV, respectively. Ab initio pseudopotential method has been used to generate basis wavefunctions and charge densities for calculating dielectric matrix elements and electron self-energies.

1ST-PRINCIPLES CALCULATIONS FOR QUASI-PARTICLE ENERGIES OF GAP AND GAAS

We have applied the Green-function method in the GW approximation to calculate quasiparticle energies for the semiconductors GaP and GaAs. Good agreement between the calculated excitation energies and the experimental results was achieved. We obtained calculated direct band gaps of GaP and GaAs of 2.93 and 1.42 eV, respectively, in comparison with the experimental values of 2.90 and 1.52 eV, respectively. An ab initio pseudopotential method has been used to generate basis wave functions and charge densities for calculating the dielectric matrix elements and self-enegies. To evaluate the dynamical effects of the screened interaction, the generalized-plasma-pole model has been utilized to extend the dielectric matrix elements from static results to finite frequencies. We presen the calculated quasiparticle energies at various high-symmetry points of the Brillouin zone and compare them with the experimental results and other calculations.

1ST PRINCIPLE CALCULATIONS OF QUASI-PARTICLE ENERGIES FOR BAND STRUCTURES OF SEMICONDUCTORS

We successfully applied the Green function theory in GW approximation to calculate the quasiparticle energies for semiconductors Si and GaAs. Ab initio pseudopotential method was adopted to generate basis wavefunctions and charge densities for calculating dielectric matrix elements and electron self-energies. To evaluate dynamical effects of screened interaction, GPP model was utilized to extend dieletric matrix elements from static results to finite frequencies. We give a full account of the theoretical background and the technical details for the first principle pseudopotential calculations of quasiparticle energies in semiconductors and insulators. Careful analyses are given for the effective and accurate evaluations of dielectric matrix elements and quasiparticle self-energies by using the symmetry properties of basis wavefunctions and eigenenergies. Good agreements between the calculated excitation energies and fundamental energy gaps and the experimental band structures were achieved.

2-DELTA-FUNCTION GENERALIZED PLASMA POLE MODEL FOR 1ST PRINCIPLE CALCULATIONS OF QUASI-PARTICLE ENERGIES IN MANY-ELECTRON SYSTEMS

To evaluate the dynamical effects of the screened interaction in the calculations of quasiparticle energies in many-electron systems a two-delta-function generalized plasma pole model (GPP) is introduced to simulate the dynamical dielectric function. The usual single delta-function GPP model has the drawback of over simplifications and for the crystals without the center of symmetry is inappropriate to describe the finite frequency behavior for dielectric function matrices. The discrete frequency summation method requires too much computation to achieve converged results since ab initio calculations of dielectric function matrices are to be carried out for many different frequencies. The two-delta GPP model is an optimization of the two approaches. We analyze the two-delta GPP model and propose a method to determine from the first principle calculations the amplitudes and effective frequencies of these delta-functions. Analytical solutions are found for the second order equations for the parameter matrices entering the model. This enables realistic applications of the method to the first principle quasiparticle calculations and makes the calculations truly adjustable parameter free.

DETERMINATION OF THE X-CONDUCTION-SUBBAND ENERGIES IN TYPE-II GAAS/ALAS/GAAS QUANTUM-WELL BY DEEP-LEVEL TRANSIENT SPECTROSCOPY

Using deep level transient spectroscopy (DLTS) the X conduction-subband energy levels in an AlAs well sandwiched by double GaAs layers were determined. Calculation gives eight subbands in the well with well width of 50 Angstrom. Among them, five levels and the other three remainders are determined by using the large longitudinal electron effective mass m(1)(1.1m(0)) and transverse electron effective mass m(t)(0.19m(0)) at X valley, respectively. Two subbands with the height energies were hardly detectable and the other six ones with lower energies are active in the present DLTS study. Because these six subbands are close to each other, we divided them into three groups. Experimentally, we observed three signals induced from the three groups. A good agreement between the calculation and experiment was obtained. (C) 1995 American Institute of Physics.