Coulomb distortion and medium corrections in nucleon-removal reactions

One-nucleon removal reactions at or above the Fermi energy are important tools to explore the single-particle structure of exotic nuclei. Experimental data must be compared with calculations to extract structure information, evaluate correlation effects in nuclei or determine reaction rates for nuclear astrophysics. However, there is insufficient knowledge to calculate accurately the cross sections for these reactions. We evaluate the contributions of the final state interaction (FSI) and of the medium modifications of the nucleon-nucleon interactions and obtain the shapes and magnitudes of momentum distributions. Such effects have been often neglected in the literature. Calculations for reactions at energies 35 - 1000 MeV/nucleon are reported and compared to published data. For consistency, the state-of-the-art eikonal method for stripping and diffraction dissociation is used. We find that the two effects are important and their relative contributions vary with the energy and with the atomic and mass number of the projectile involved. These two often neglected effects modify considerably the one-nucleon removal cross sections. As expected, the effect are largest at lower energies, around 50 MeV/nucleon and on heavy targets.Comment: 12 pages, 10 figures. Accpeted for publication in the Physical Review C. arXiv admin note: text overlap with arXiv:nucl-th/0407026 by other author

Approximate solution of the Duffin-Kemmer-Petiau equation for a vector Yukawa potential with arbitrary total angular momenta

The usual approximation scheme is used to study the solution of the Duffin-Kemmer-Petiau (DKP) equation for a vector Yukawa potential in the framework of the parametric Nikiforov-Uvarov (NU) method. The approximate energy eigenvalue equation and the corresponding wave function spinor components are calculated for arbitrary total angular momentum in closed form. Further, the approximate energy equation and wave function spinor components are also given for case. A set of parameter values is used to obtain the numerical values for the energy states with various values of quantum levelsComment: 17 pages; Communications in Theoretical Physics (2012). arXiv admin note: substantial text overlap with arXiv:1205.0938, and with arXiv:quant-ph/0410159 by other author

Approximate k-state solutions to the Dirac-Yukawa problem based on the spin and pseudospin symmetry

Using an approximation scheme to deal with the centrifugal (pseudo-centrifugal) term, we solve the Dirac equation with the screened Coulomb (Yukawa) potential for any arbitrary spin-orbit quantum number {\kappa}. Based on the spin and pseudospin symmetry, analytic bound state energy spectrum formulas and their corresponding upper- and lower-spinor components of two Dirac particles are obtained using a shortcut of the Nikiforov-Uvarov method. We find a wide range of permissible values for the spin symmetry constant C_{s} from the valence energy spectrum of particle and also for pseudospin symmetry constant C_{ps} from the hole energy spectrum of antiparticle. Further, we show that the present potential interaction becomes less (more) attractive for a long (short) range screening parameter {\alpha}. To remove the degeneracies in energy levels we consider the spin and pseudospin solution of Dirac equation for Yukawa potential plus a centrifugal-like term. A few special cases such as the exact spin (pseudospin) symmetry Dirac-Yukawa, the Yukawa plus centrifugal-like potentials, the limit when {\alpha} becomes zero (Coulomb potential field) and the non-relativistic limit of our solution are studied. The nonrelativistic solutions are compared with those obtained by other methods.Comment: 21 pages, 6 figure

Physiochemical property space distribution among human metabolites, drugs and toxins

<p>Abstract</p> <p>Background</p> <p>The current approach to screen for drug-like molecules is to sieve for molecules with biochemical properties suitable for desirable pharmacokinetics and reduced toxicity, using predominantly biophysical properties of chemical compounds, based on empirical rules such as Lipinski's "rule of five" (Ro5). For over a decade, Ro5 has been applied to combinatorial compounds, drugs and ligands, in the search for suitable lead compounds. Unfortunately, till date, a clear distinction between drugs and non-drugs has not been achieved. The current trend is to seek out drugs which show metabolite-likeness. In identifying similar physicochemical characteristics, compounds have usually been clustered based on some characteristic, to reduce the search space presented by large molecular datasets. This paper examines the similarity of current drug molecules with human metabolites and toxins, using a range of computed molecular descriptors as well as the effect of comparison to clustered data compared to searches against complete datasets.</p> <p>Results</p> <p>We have carried out statistical and substructure functional group analyses of three datasets, namely human metabolites, drugs and toxin molecules. The distributions of various molecular descriptors were investigated. Our analyses show that, although the three groups are distinct, present-day drugs are closer to toxin molecules than to metabolites. Furthermore, these distributions are quite similar for both clustered data as well as complete or unclustered datasets.</p> <p>Conclusion</p> <p>The property space occupied by metabolites is dissimilar to that of drugs or toxin molecules, with current drugs showing greater similarity to toxins than to metabolites. Additionally, empirical rules like Ro5 can be refined to identify drugs or drug-like molecules that are clearly distinct from toxic compounds and more metabolite-like. The inclusion of human metabolites in this study provides a deeper insight into metabolite/drug/toxin-like properties and will also prove to be valuable in the prediction or optimization of small molecules as ligands for therapeutic applications.</p

smyRNA: A Novel Ab Initio ncRNA Gene Finder

Background: Non-coding RNAs (ncRNAs) have important functional roles in the cell: for example, they regulate gene expression by means of establishing stable joint structures with target mRNAs via complementary sequence motifs. Sequence motifs are also important determinants of the structure of ncRNAs. Although ncRNAs are abundant, discovering novel ncRNAs on genome sequences has proven to be a hard task; in particular past attempts for ab initio ncRNA search mostly failed with the exception of tools that can identify micro RNAs. Methodology/Principal Findings: We present a very general ab initio ncRNA gene finder that exploits differential distributions of sequence motifs between ncRNAs and background genome sequences. Conclusions/Significance: Our method, once trained on a set of ncRNAs from a given species, can be applied to a genome sequences of other organisms to find not only ncRNAs homologous to those in the training set but also others that potentially belong to novel (and perhaps unknown) ncRNA families. Availability

Targeted Gene Panel Sequencing for Early-onset Inflammatory Bowel Disease and Chronic Diarrhea

Background: In contrast to adult-onset inflammatory bowel disease (IBD), where many genetic loci have been shown to be involved in complex disease etiology, early-onset IBD (eoIBD) and associated syndromes can sometimes present as monogenic conditions. As a result, the clinical phenotype and ideal disease management in these patients often differ from those in adult-onset IBD. However, due to high costs and the complexity of data analysis, high-throughput screening for genetic causes has not yet become a standard part of the diagnostic work-up of eoIBD patients. Methods: We selected 28 genes of interest associated with monogenic IBD and performed targeted panel sequencing in 71 patients diagnosed with eoIBD or early-onset chronic diarrhea to detect causative variants. We compared these results to whole-exome sequencing (WES) data available for 25 of these patients. Results: Target coverage was significantly higher in the targeted gene panel approach compared with WES, whereas the cost of the panel was considerably lower (approximately 25% of WES). Disease-causing variants affecting protein function were identified in 5 patients (7%), located in genes of the IL10 signaling pathway (3), WAS (1), and DKC1 (1). The functional effects of 8 candidate variants in 5 additional patients (7%) are under further investigation. WES did not identify additional causative mutations in 25 patients. Conclusions: Targeted gene panel sequencing is a fast and effective screening method for monogenic causes of eoIBD that should be routinely established in national referral centers.info:eu-repo/semantics/publishedVersio