Energy Hyperspace for Stacking Interaction in AU/AU Dinucleotide Step: Dispersion-Corrected Density Functional Theory Study

Double helical structures of DNA and RNA are mostly determined by base pair stacking interactions, which give them the base sequence-directed features, such as small roll values for the purine-pyrimidine steps. Earlier attempts to characterize stacking interactions were mostly restricted to calculations on fiber diffraction geometries or optimized structure using ab initio calculations lacking variation in geometry to comment on rather unusual large roll values observed in AU/AU base pair step in crystal structures of RNA double helices. We have generated stacking energy hyperspace by modeling geometries with variations along the important degrees of freedom, roll, and slide, which were chosen via statistical analysis as maximally sequence dependent. Corresponding energy contours were constructed by several quantum chemical methods including dispersion corrections. This analysis established the most suitable methods for stacked base pair systems despite the limitation imparted by number of atom in a base pair step to employ very high level of theory. All the methods predict negative roll value and near-zero slide to be most favorable for the purine-pyrimidine steps, in agreement with Calladine's steric clash based rule. Successive base pairs in RNA are always linked by sugar-phosphate backbone with C3-endo sugars and this demands C1-C1 distance of about 5.4 angstrom along the chains. Consideration of an energy penalty term for deviation of C1-C1 distance from the mean value, to the recent DFT-D functionals, specifically B97X-D appears to predict reliable energy contour for AU/AU step. Such distance-based penalty improves energy contours for the other purine-pyrimidine sequences also. (c) 2013 Wiley Periodicals, Inc. Biopolymers 101: 107-120, 2014.

Potential energy model for turbulent entrainment across density interface in a linearly stratified fluid

A potential energy model is developed for turbulent entrainment in the absence of mean shear in a linearly stratified fluid. The relation between the entrainment distance D and the time t and the relation between dimensionless entrainment rate E and the local Richardson number are obtained. An experiment is made for examination. The experimental results are in good agreement with the model, in which the dimensionless entrainment distance D is given by DBAR = A(i)(SBAR)-1/4(fBAR)1/2(tBAR)1/8, where A(i) is the proportional coefficient, S is the dimensionless stroke, fBAR is the dimensionless frequency of the grid oscillation, tBAR the dimensionless time.

Density, sp3 content and internal layering of DLC films by X-ray reflectivity and electron energy loss spectroscopy

A variety of hydrogenated and non-hydrogenated amorphous carbon thin films have been characterized by means of grazing-incidence X-ray reflectivity (XRR) to give information about their density, thickness, surface roughness and layering. We used XRR to validate the density of ta-C, ta-C:H and a-C:H films derived from the valence plasmon in electron energy loss spectroscopy measurements, up to 3.26 and 2.39 g/cm3 for ta-C and ta-C:H, respectively. By comparing XRR and electron energy loss spectroscopy (EELS) data, we have been able for the first time to fit a common electron effective mass of m*/me = 0.87 for all amorphous carbons and diamond, validating the `quasi-free' electron approach to density from valence plasmon energy. While hydrogenated films are found to be substantially uniform in density across the film, ta-C films grown by the filtered cathodic vacuum arc (FCVA) show a multilayer structure. However, ta-C films grown with an S-bend filter show a high uniformity and only a slight dependence on the substrate bias of both sp3 and layering.

Temperature and power-density-dependent inter-shell energy states in InAs/GaAs quantum dots

We have investigated the evolution of exciton state filling in InAs/GaAs quantum dot (QD) structures as a function of the excitation power density by using rnicro-photoluminescence spectroscopy at different temperatures. In addition to the emission bands of exciton recombination corresponding to the atom-like S, P and D, etc. shells of QDs, it was observed that some extra states V between the S and P shells, and D' between the P and D shells appear in the spectra with increasing number of excitons occupying the QDs at a certain temperature. The emergence of these inter-shell excitonic levels is power density and temperature dependent, which is an experimental demonstration of strong exciton-exciton exchange interaction, state hybridization, and coupling of a multi-exciton system in QDs. (c) 2006 Elsevier B.V. All rights reserved.

Temperature and power-density-dependent inter-shell energy states in InAs/GaAs quantum dots

We have investigated the evolution of exciton state filling in InAs/GaAs quantum dot (QD) structures as a function of the excitation power density by using rnicro-photoluminescence spectroscopy at different temperatures. In addition to the emission bands of exciton recombination corresponding to the atom-like S, P and D, etc. shells of QDs, it was observed that some extra states V between the S and P shells, and D' between the P and D shells appear in the spectra with increasing number of excitons occupying the QDs at a certain temperature. The emergence of these inter-shell excitonic levels is power density and temperature dependent, which is an experimental demonstration of strong exciton-exciton exchange interaction, state hybridization, and coupling of a multi-exciton system in QDs. (c) 2006 Elsevier B.V. All rights reserved.

DETERMINING THE DENSITY DEPENDENCE OF THE NUCLEAR SYMMETRY ENERGY USING HEAVY-ION REACTIONS

We review recent progress in the determination of the subsaturation density behavior of the nuclear symmetry energy from heavy-ion collisions as well as the theoretical progress in probing the high density behavior of the symmetry energy in heavy-ion reactions induced by high energy radioactive beams. We further discuss the implications of these results for the nuclear effective interactions and the neutron skin thickness of heavy nuclei.

Probing the high density behavior of the symmetry energy by using the free neutron-proton ratio

Based on the isospin- and momentum-dependent transport model IBUU04, the transverse momentum distributions of the free neutron-proton ratio in the Sn-132+(124) Sn reaction system at mid-central collisions with beam energies of 400/A MeV, 600/A MeV and 800/A MeV are studied by using two different symmetry energies. It is found that the free neutron-proton ratio as a function of the transverse momentum at the mid-rapidity is very sensitive to the density dependency of the symmetry energy especially at incident energies around 400/AMeV.

Probing the high density behavior of the symmetry energy by using proton elliptic flow

Based on the isospin- and momentum-dependent transport model IBUU04, we calculated the reaction of the Sn-132+Sn-124 systems in semi-central collisions at beam energies of 400/A MeV, 600/A MeV and 800/A MeV by adopting two different density dependent symmetry energies. It was found that the proton differential elliptic flow as a function of transverse momentum is quite sensitive to the density dependence of symmetry energy, especially for the considered beam energy range. Therefore the proton differential elliptic flow may be considered as a robust probe for investigating the high density behavior of symmetry energy in intermediate energy heavy ion collisions.