Baryon Binding Energy in Sakai-Sugimoto Model

The binding energy of baryon has been studied in the dual $AdS_5\times S^5$ string theory with a black hole interior. In this picture baryon is constructed of a $D_5$ brane vertex wrapping on $S^5$ and $N_c$ fundamental strings connected to it. Here, we calculate the baryon binding energy in Sakai-Sugimoto model with a $D_4/D_8/\bar{D_8}$ in which the supersymmetry is completely broken. Also we check the $T$ dependence of the baryon binding energy. We believe that this model represents an accurate description of baryons due to the existence of Chern-Simones coupling with the gauge field on the brane. We obtain an analytical expression for the baryon binding energy . In that case we plot the baryon binding energy in terms of radial coordinate. Then by using the binding energy diagram, we determine the stability range for baryon configuration. And also the position and energy of the stable equilibrium point is obtained by the corresponding diagram. Also we plot the baryon binding energy in terms of temperature and estimate a critical temperature in which the baryon would be dissociated.Comment: 14 pages, 1 fi

Study of fragmentation using clusterization algorithm with realistic binding energies

We here study fragmentation using \emph{simulated annealing clusterization algorithm} (SACA) with binding energy at a microscopic level. In an earlier version, a constant binding energy (4 MeV/nucleon) was used. We improve this binding energy criterion by calculating the binding energy of different clusters using modified Bethe-Weizs\"{a}cker mass (BWM) formula. We also compare our calculations with experimental data of ALADiN group. Nearly no effect is visible of this modification

Energy scaling law for nanostructured materials

The equilibrium binding energy is an important factor in the design of materials and devices. However, it presents great computational challenges for materials built up from nanostructures. Here we investigate the binding-energy scaling law from first-principles calculations. We show that the equilibrium binding energy per atom between identical nanostructures can scale up or down with nanostructure size. From the energy scaling law, we predict finite large-size limits of binding energy per atom. We find that there are two competing factors in the determination of the binding energy: Nonadditivities of van der Waals coefficients and center-to-center distance between nanostructures. To uncode the detail, the nonadditivity of the static multipole polarizability is investigated. We find that the higher-order multipole polarizability displays ultra-strong intrinsic nonadditivity, no matter if the dipole polarizability is additive or not.Comment: 13 pages, 4 figures, 7 table

The Okamoto-Nolen-Schiffer anomaly without rho-omega mixing

We examine the effect of isospin-violating meson-nucleon coupling constants and of $\pi$-$\eta$ mixing on the binding-energy differences of mirror nuclei in a model that possesses no contribution from $\rho$-$\omega$ mixing. The ${}^{3}$He-${}^{3}$H binding-energy difference is computed in a nonrelativistic approach using a realistic wave function. We find the ${}^{3}$He-${}^{3}$H binding-energy difference very sensitive to the short-distance behavior of the nucleon-nucleon potential. We conclude that for the typically hard Bonn form factors such models can not account for the observed binding-energy difference in the three-nucleon system. For the medium-mass region (A=15--41) the binding-energy differences of mirror nuclei are computed using a relativistic mean-field approximation to the Walecka model. We obtain large binding-energy differences---of the order of several hundred keV---arising from the pseudoscalar sector. Two effects are primarily responsible for this new finding: a) the inclusion of isospin breaking in the pion-nucleon coupling constant, and b) the in-medium enhancement of the small components of the bound-state wave functions. We look for off-shell ambiguities in these results and find them to be large.Comment: 19 LaTeX pages and 2 postscript figures. Revisions/additions: Manuscript now includes a treatment of the binding-energy difference in the three-nucleon system as well as a study of possible off-shell ambiguities in the binding-energy differences of (A=15-41) mirror nucle

Effect of shell thickness on exciton and biexciton binding energy of a ZnSe/ZnS core/shell quantum dot

The exciton and biexciton binding energy have been studied for a ZnSe/ZnS core/shell quantum dot using WKB (Wentzel-Kramers-Brillouin) approximation. The exciton binding energy increases for small shell thickness and for large thickness, the binding energy again starts decreasing. A similar result is obtained for biexcitons where for thicker shells, the biexciton attains antibonding.Comment: 5 Figure

Genome-wide organization of eukaryotic pre-initiation complex is influenced by nonconsensus protein-DNA binding

Genome-wide binding preferences of the key components of eukaryotic pre-initiation complex (PIC) have been recently measured with high resolution in Saccharomyces cerevisiae by Rhee and Pugh (Nature (2012) 483:295-301). Yet the rules determining the PIC binding specificity remain poorly understood. In this study we show that nonconsensus protein-DNA binding significantly influences PIC binding preferences. We estimate that such nonconsensus binding contribute statistically at least 2-3 kcal/mol (on average) of additional attractive free energy per protein, per core promoter region. The predicted attractive effect is particularly strong at repeated poly(dA:dT) and poly(dC:dG) tracts. Overall, the computed free energy landscape of nonconsensus protein-DNA binding shows strong correlation with the measured genome-wide PIC occupancy. Remarkably, statistical PIC binding preferences to both TFIID-dominated and SAGA-dominated genes correlate with the nonconsensus free energy landscape, yet these two groups of genes are distinguishable based on the average free energy profiles. We suggest that the predicted nonconsensus binding mechanism provides a genome-wide background for specific promoter elements, such as transcription factor binding sites, TATA-like elements, and specific binding of the PIC components to nucleosomes. We also show that nonconsensus binding influences transcriptional frequency genome-wide

Binding of Nucleobases with Single-Walled Carbon Nanotubes

We have calculated the binding energy of various nucleobases (guanine (G), adenine (A), thymine (T) and cytosine (C)) with (5,5) single-walled carbon nanotubes (SWNTs) using ab-initio Hartre-Fock method (HF) together with force field calculations. The gas phase binding energies follow the sequence G $>$ A $>$ T $>$ C. We show that main contribution to binding energy comes from van-der Wall (vdW) interaction between nanotube and nucleobases. We compare these results with the interaction of nucleobases with graphene. We show that the binding energy of bases with SWNTs is much lower than the graphene but the sequence remains same. When we include the effect of solvation energy (Poisson-Boltzman (PB) solver at HF level), the binding energy follow the sequence G $>$ T $>$ A $>$ C $>$, which explains the experiment\cite{zheng} that oligonucleotides made of thymine bases are more effective in dispersing the SWNT in aqueous solution as compared to poly (A) and poly (C). We also demonstrate experimentally that there is differential binding affinity of nucleobases with the single-walled carbon nanotubes (SWNTs) by directly measuring the binding strength using isothermal titration (micro) calorimetry. The binding sequence of the nucleobases varies as thymine (T) $>$ adenine (A) $>$ cytosine (C), in agreement with our calculation.Comment: 7 pages, 6 figure