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.

Mutations stabilize small subunit ribosomal RNA in desiccation-tolerant cyanobacteria Nostoc

The ribosomal RNA molecule is an ideal model for evaluating the stability of a gene product under desiccation stress. We isolated 8 Nostoc strains that had the capacity to withstand desiccation in habitats and sequenced their 16S rRNA genes. The stabilities of 16S rRNAs secondary structures, indicated by free energy change of folding, were compared among Nostoc and other related species. The results suggested that 163 rRNA secondary structures of the desiccation-tolerant Nostoc strains were more stable than that of planktonic Nostocaceae species. The stabilizing mutations were divided into two categories: (1) those causing GC to replace other types of base pairs in stems and (2) those causing extension of stems. By mapping stabilizing mutations onto the Nostoc phylogenetic tree based on 16S rRNA gene, it was shown that most of stabilizing mutations had evolved during adaptive radiation among Nostoc spp. The evolution of 16S rRNA along the Nostoc lineage is suggested to be selectively advantageous under desiccation stress.

Analytical study of the antiferromagnetic Heisenberg films

With the variational cumulant expansion (VCE) method, the thermodynamic behaviors of S = 1/2 antiferromagnetic Heisenberg films in simple cubic lattices are studied analytically. From the analytic properties of the free energy, in principle we are able to calculate analytically the critical temperatures T-c(L) and the thermodynamic functions, to any order cumulant as the functions of the number of L (the hyperlayers in the hyperfilm). Explicit expressions for T-c(L) up to the fourth order are given. A comparison with the existing results for 3-dimensional system is given. The effective range of the interaction is obtained from numerical results.

Metamorphosis of self-organized quantum dots into quantum wires

Spontaneous formation of InAs quantum wires in InAlAs on InP(001) via sequential chain-like coalescence of quantum dots along [1 (1) over bar 0] is realized. Theoretical calculations based on the energetics of interacting steps provide a qualitative explanation for the experimental results. Sequential coalescence of initially isolated dots reduces the total free energy strikingly. Thus the wire-like structure is energetically favorable. (C) 1998 Elsevier Science B.V.

Species transformation of trace elements and their distribution prediction in dyestuff residue incineration

The release of heavy metals from the combustion of hazardous wastes is an environmental issue of increasing concern. The species transformation characteristics of toxic heavy metals and their distribution are considered to be a complex problem of mechanism. The behavior of hazardous dyestuff residue is investigated in a tubular furnace under the general condition of hazardous waste pyrolysis and gasfication. Data interpretation has been aided by parallel theoretical study based on a thermodynamic equilibrium model based on the principle of Gibbs free energy minimization. The results show that Ni, Zn, Mn, and Cr are more enriched in dyestuff residue incineration than other heavy metals (Hg, As, and Se) subjected to volatilization. The thermodynamic model calculation is used for explaining the experiment data at 800 degrees C and analyzing species transformation of heavy metals. These results of species transformation are used to predict the distribution and emission characteristics of trace elements. Although most trace element predictions are validated by the measurements, cautions are in order due to the complexity of incineration systems.

Phase equilibria and plate-fluid interfacial tensions for associating hard sphere fluids confined in slit pores

The excess Helmholtz free energy functional for associating hard sphere fluid is formulated by using a modified fundamental measure theory [Y. X. Yu and J. Z. Wu, J. Chem. Phys. 117, 10156 (2002)]. Within the framework of density functional theory, the thermodynamic properties including phase equilibria for both molecules and monomers, equilibrium plate-fluid interfacial tensions and isotherms of excess adsorption, average molecule density, average monomer density, and plate-fluid interfacial tension for four-site associating hard sphere fluids confined in slit pores are investigated. The phase equilibria inside the hard slit pores and attractive slit pores are determined according to the requirement that temperature, chemical potential, and grand potential in coexistence phases should be equal and the plate-fluid interfacial tensions at equilibrium states are predicted consequently. The influences of association energy, fluid-solid interaction, and pore width on phase equilibria and equilibrium plate-fluid interfacial tensions are discussed.

Coherent laser control in attosecond sum-frequency polarization beats using twin noisy driving fields

Based on the phase-conjugate polarization interference between two-pathway excitations, we obtained an analytic closed form for the second-order or fourth-order Markovian stochastic correlation of the V three-level sum-frequency polarization beat (SFPB) in attosecond scale. Novel interferometric oscillatory behavior is exposed in terms of radiation-radiation, radiation-matter, and matter-matter polarization beats. The phase-coherent control of the light beams in the SFPB is subtle. When the laser has broadband linewidth, the homodyne detected SFPB signal shows resonant-nonresonant cross correlation, a drastic difference for three Markovian stochastic fields, and the autocorrelation of the SFPB exhibits hybrid radiation-matter detuning terahertz damping oscillation. As an attosecond ultrafast modulation process, it can be extended intrinsically to any sum frequency of energy levels. It has been also found that the asymmetric behaviors of the polarization beat signals due to the unbalanced controllable dispersion effects between the two arms of interferometer do not affect the overall accuracy in case using the SFPB to measure the Doppler-free energy-level sum of two excited states.

Electronic structure and magnetic coupling properties of Gd-doped AlN: first-principles calculations

In this work, the electronic structure and magnetic coupling properties of Gd doped AlN have been investigated using first-principles method. We found that in the AlN:Gd system, due to the s-f coupling allowed by the symmetry, the exchange splitting of the conduction band is much larger than that of the valence band, which makes the electron-mediated ferromagnetism possible in this material. This property is also confirmed by the energy differences between anti-ferromagnetic and ferromagnetic phase for Al14Gd2N16 with different concentrations of electrons (holes), as well as by the calculated exchange constants. The result indicates that Gd-doped AlN is a promising candidate for the applications in future spintronic devices.

CALCULATION OF SPIN-REORIENTATION TEMPERATURE IN ND2FE14B

The spin-reorientation phenomenon in Nd2Fe14B has been investigated using an angular dependent free energy approach. A magnetic Hamiltonian which includes the crystal electric field term and the exchange term has been established using realistic band structure results. The temperature dependence of the molecular field is accounted for by introducing the Brillouin function and the magnetic Hamiltonian is diagonalized within the ground state multiplet of the Nd ion. The eigenstates are then used to form the partition function for the free energy. At each temperature, the direction of the molecular field is obtained by searching for the minimum in the angular parameter space of the free energy. Our calculations show that for Nd2Fe14B, the net magnetic anisotropy direction is canted away from the c axis at a temperature close to the experimentally reported spin-reorientation temperature of 150 K. The temperature dependence of the magnetic structure is found to be very sensitive to the size of the second order crystal field parameter B20.

Isospin symmetry breaking at high spins in the mirror pair Se-67 and As-67

Recent experimental data have revealed large mirror energy differences (MED) between high-spin states in the mirror nuclei Se-67 and As-67, the heaviest pair where MED have been determined so far. The MED are generally attributed to the isospin symmetry breaking caused by the Coulomb force and by the isospin-nonconserving part of the nucleon-nucleon residual interaction. The different contributions of the various terms have been extensively studied in the fp shell. By employing large-scale shell-model calculations, we show that the inclusion of the g(9/2) orbit causes interference between the electromagnetic spin-orbit and the Coulomb monopole radial terms at high spin. The large MED are attributed to the aligned proton pair excitations from the p(3/2) and f(5/2) orbits to the g(9/2) orbit. The relation of the MED to deformation is discussed.

Isospin dependence of the nuclear equation of state near the critical point

We discuss experimental evidence for a nuclear phase transition driven by the different concentrations of neutrons to protons. Different ratios of the neutron to proton concentrations lead to different critical points for the phase transition. This is analogous to the phase transitions occurring in He-4-He-3 liquid mixtures. We present experimental results that reveal the N/A (or Z/A) dependence of the phase transition and discuss possible implications of these observations in terms of the Landau free energy description of critical phenomena.

THE ISOSPIN DEPENDENCE OF THE NUCLEAR PHASE TRANSITION NEAR THE CRITICAL POINT

The experimental results reveal the isospin dependence of the nuclear phase transition in terms of the Landau Free Energy description of critical phenomena. Near the critical point, different ratios of the neutron to proton concentrations lead to different critical points for the phase transition which is analogous to the phase transitions in He-4-He-3 liquid mixtures. The antisymmetrized molecular dynamics (AMD) and GEMINI models calculations were also performed and the results will be discussed as well.

Computational study on the addition of HCN to methanimine catalyzed by formamidine and formamide

In this paper, we have carried out a theoretical study on the addition of HCN to methanimine with formamidine or formamide using second-order Moller-Plesset perturbation (MP2) method with 6-31 + G(d,p) basis sets. At MP2 level. a high-energy, intermediate has been located for each pathway. The addition of HCN to methanimine with formamidine has the lowest free energy barrier according to the calculations at MP2 level. (C) 2004 Elsevier B.V. All rights reserved.

Lattice Boltzmann study of hydrodynamic effects in lamellar ordering process of two-dimensional quenched block copolymers

By incorporating self-consistent field theory with lattice Boltzmann method, a model for polymer melts is proposed. Compared with models based on Ginzburg-Landau free energy, our model does not employ phenomenological free energies to describe systems and can consider the chain topological details of polymers. We use this model to study the effects of hydrodynamic interactions on the dynamics of microphase separation for block copolymers. In the early stage of phase separation, an exponential growth predicted by Cahn-Hilliard treatment is found. Simulation results also show that the effect of hydrodynamic interactions can be neglected in the early stage.

Studies on coarsening of microdomains in binary polymer mixtures by Lattice Boltzmann methods

An improved free energy approach Lattice Boltzmann model(LBM) is proposed by introducing a forcing term instead of the pressure tensor. This model can reach the proper thermodynamic equilibrium after enough simulation time. On the basis of this model, the phase separation in binary polymer mixtures is studied by applying a Flory-Huggins-type free energy. The numerical results show good agreement with the analytic coexistence curve. This model can also be used to study the coarsening of microdomains in binary polymer mixtures at the early and intermediate stages.