Slow isocharged sequence ions with helium collisions: Projectile core dependence

The collisions of the isocharged sequence ions of q=6 (C6+, N6+, O6+, F6+, Ne6+, Ar6+, and Ca6+), q=7 (F7+, Ne7+, S7+, Ar7+, and Ca7+), q=8 (F8+, Ne8+, Ar8+, and Ca8+), q=9 (F9+, Ne9+, Si9+, S9+, Ar9+, and Ca9+) and q=11 (Si11+, Ar11+, and Ca11+) with helium at the same velocities were investigated. The cross-section ratios of the double-electron transfer (DET) to the single-electron capture (SEC) sigma(DET)/sigma(SEC) and the true double-electron capture (TDC) to the double-electron transfer sigma(TDC)/sigma(DET) were measured. It shows that for different ions in an isocharged sequence, the experimental cross-section ratio sigma(DET)/sigma(SEC) varies by a factor of 3. The results confirm that the projectile core is another dominant factor besides the charge state and the collision velocity in slow (0.35-0.49v(0); v(0) denotes the Bohr velocity) highly charged ions (HCIs) with helium collisions. The experimental cross-section ratio sigma(DET)/sigma(SEC) is compared with the extended classical over-barrier model (ECBM) [A. Barany , Nucl. Instrum. Methods Phys. Res. B 9, 397 (1985)], the molecular Coulombic barrier model (MCBM) [A. Niehaus, J. Phys. B 19, 2925 (1986)], and the semiempirical scaling laws (SSL) [N. Selberg , Phys. Rev. A 54, 4127 (1996)]. It also shows that the projectile core properties affect the initial capture probabilities as well as the subsequent relaxation of the projectiles. The experimental cross-section ratio sigma(TDC)/sigma(DET) for those lower isocharged sequences is dramatically affected by the projectile core structure, while for those sufficiently highly isocharged sequences, the autoionization always dominates, hence the cross-section ratio sigma(TDC)/sigma(DET) is always small.

Study of n=2, Delta n=0 transition of Be-, B-, C-, N- and O-like sequence in the beam-foil spectrum of titanium

The foil-excited the spectrum of highly stripped titanium ions between 12-40 nm has been studied. Titanium ions of 80 and 120 MeV were provided by the HI-13 tandem accelerator at the China Institute of Atomic Energy. GIM-957 XUV-VUV monochromator was refocused to get highly-resolved spectra. Our experimental results and the published spectral data of laser-produced plasma show agreement in nearly all cases within +/- 0.03 nm. The spectra contained some weak or strong lines previously unclassified. These spectral lines mainly belong to 2s2p(2) for TiXVIII, 2p(3) for TiXVIII, 2s2p(3) for TiXVII, 2p(6)4p for Ti XII and 2p(6)3d for Ti XII transitions.

Influence of core property on multi-electron process in slow collisions of isocharged sequence ions with neon

Influence of core property on multi-electron process in the collisions of q = 6-9 and 11 isocharged sequence ions with Ne is investigated in the keV/u region The cross-section ratios of double-, triple-, quadruple- and total multi-electron processes to the single electron capture process as well as the partial ratios of different reaction channels to the relevant multi-electron process are measured by using position-sensitive and time-of-flight techniques The experimental data are compared with the theoretical predictions including the extended classical over-barrier model, the molecular Columbic barrier model and the semi-empirical scaling law Results show a core effect on multi-electron process of isocharge ions colliding with Neon, which is consistent with the results of Helium we obtained previously

Real-Time Study of Genomic DNA Structural Changes upon Interaction with Small Molecules Using Dual-Polarization Interferometry

The structural changes of genomic DNA upon interaction with small molecules have been studied in real time using dual-polarization interferometry (DPI). Native or thermally denatured DNA was immobilized on the silicon oxynitride surface via a preadsorbed poly(ethylenimine) (PEI) layer. The mass loading was similar for both types of DNA, however, native DNA formed a looser and thicker layer due to its rigidity, unlike the more flexible denatured DNA, which mixed with PEI to form a denser and thinner layer. Ethidium bromide (EtBr), a classical intercalator, induced the large thickness decrease and density increase of native DNA (double-stranded), but a slight increase in both the thickness and density of denatured DNA (partial single-stranded).

Effect of block sequence and block length on the stimuli-responsive behavior of polyampholyte brushes: hydrogen bonding and electrostatic interaction as the driving force for surface rearrangement

Diblock polyampholyte brushes with different block sequences (Si/SiO2/poly(acrylic acid)-b-poly (2-vinylpyridine) (PAA-b-P2VP) brushes and Si/SiO2/P2VP-b-PAA brushes) and different block lengths were synthesized by sequent surface-initiated atom transfer radical polymerization (ATRP). The PAA block was obtained through hydrolysis from the corresponding poly(tert-butyl acrylate). The polyampholyte brushes demonstrated unique pH-responsive behavior. In the intermediate pH region, the brushes exhibited a less hydrophilic wetting behavior and a rougher surface morphology due to the formation of polyelectrolyte complex through electrostatic interaction between oppositely charged blocks. In the low pH and high pH regions, the rearrangement of polyampholyte brushes showed great dependence on the block sequence and block length. The polyampholyte brushes with P2VP-b-PAA sequence underwent rearrangement during alternative treatment by acidic aqueous solution (low pH value) and basic aqueous solution (high pH value).

Uncovering the rules for protein-protein interactions from yeast genomic data

Identifying protein-protein interactions is crucial for understanding cellular functions. Genomic data provides opportunities and challenges in identifying these interactions. We uncover the rules for predicting protein-protein interactions using a frequent pattern tree (FPT) approach modified to generate a minimum set of rules (mFPT), with rule attributes constructed from the interaction features of the yeast genomic data. The mFPT prediction accuracy is benchmarked against other commonly used methods such as Bayesian networks and logistic regressions under various statistical measures. Our study indicates that mFPT outranks other methods in predicting the protein-protein interactions for the database used. We predict a new protein-protein interaction complex whose biological function is related to premRNA splicing and new protein-protein interactions within existing complexes based on the rules generated.

7-Amino actinomycin D bound to single-stranded hairpin DNA enhanced by loop sequence-dependent luminescent Eu3+ and Tb3+ binding

Lanthanide Eu3+ and Tb3+ ions have been widely used in luminescent resonance energy transfer (LRET) for bioassays to study metal binding microenvironments. We report here that Eu3+ or Tb3+ can increase the binding affinity of antitumor antibiotic drug agent, 7-amino actinomycin D (7AACTD), binding to 5'-GT/TG-5' or 5'-GA/AG-5' mismatched stem region of the single-stranded hairpin DNA. Further studies indicate that the effect of Eu3+ or Tb3+ on 7AACTD binding is related to DNA loop sequence. Our results will provide new insights into how metal ions can enhance antitumor agents binding to their targets.

Comparison for DNA primary sequence

In this article, two schemes are suggested based on three exons of beta-globin gene belonging to 10 species for comparison of DNA primary sequences. At first, the positions of four nucleic acid bases were extracted, and then based on the information, as the numerical characterization of DNA sequences, the sequence invariants were derived. Sequences comparisons of 10 species selected in this work by using these invariants were performed. The results, especially with scheme 2, are quite satisfactory.

A novel invariant and sequence comparison for DNA

We consider numerical characterization of DNA primary sequence based on the positions of bases (a, t, c, g) and the pairs of bases X, Y in DNA (X, Y=a, t, c, g). This leads to a representation of DNA by a numerical sequence. Then, we extract a novel invariant (molecular connectivity index) from the derived numerical sequences. The suitable invariant can offer a characterization of DNA primary sequence. Finally, we provide an illustration of its utility by making a comparison between ten DNA sequences belonging to beta-globin gene in different species. The evolutionary relationships of ten species we have revealed in this contribution accord with phylogenetic tree properly.

Enthalpy/entropy compensation: Influence of DNA flanking sequence on the binding of 7-amino actinomycin D to its primary binding site in short DNA duplexes

The effect of the context of the flanking sequence on ligand binding to DNA oligonucleotides that contain consensus binding sites was investigated for the binding of the intercalator 7-amino actinomycin D. Seven self-complementary DNA oligomers each containing a centrally located primary binding site, 5'-A-G-C-T-3', flanked on either side by the sequences (AT)(n) or (AA)(n) (with n = 2, 3, 4) and AA(AT)(2), were studied. For different flanking sequences, (AA)(n)-series or (AT)(n)-series, differential fluorescence enhancements of the ligand due to binding were observed. Thermodynamic studies indicated that the flanking sequences not only affected DNA stability and secondary structure but also modulated ligand binding to the primary binding site. The magnitude of the ligand binding affinity to the primary site was inversely related to the sequence dependent stability. The enthalpy of ligand binding was directly measured by isothermal titration calorimetry, and this made it possible to parse the binding free energy into its energetic and entropic terms.