Dynamics of pulled desorption with effects of excluded-volume interaction: The p-Laplacian diffusion equation and its exact solution

We analyze the dynamics of desorption of a polymer molecule which is pulled at one of its ends with force f, trying to desorb it. We assume a monomer to desorb when the pulling force on it exceeds a critical value f(c). We formulate an equation for the average position of the n-th monomer, which takes into account excluded-volume interaction through the blob-picture of a polymer under external constraints. The approach leads to a diffusion equation with a p-Laplacian for the propagation of the stretching along the chain. This has to be solved subject to a moving boundary condition. Interestingly, within this approach, the problem can be solved exactly in the trumpet, stem-flower and stem regimes. In the trumpet regime, we get tau = tau(0)n(d)(2), where n(d) is the number of monomers that have desorbed at the time tau. tau(0) is known only numerically, but for f close to f(c), it is found to be tau(0) similar to f(c)/(f(2/3) - f(c)(2/3)) If one used simple Rouse dynamics, this result would change to tau similar to f(c)n(d)(2)/(f - f(c)). In the other regimes too, one can find exact solution, and interestingly, in all regimes tau similar to n(d)(2). Copyright (C) EPLA, 2011

Effect of ester chemical structure and peptide bond conformation in fragmentation pathways of differently metal cationized cyclodepsipeptides

Fragmentation behavior of two classes of cyclodepsipeptides, isariins and isaridins, obtained from the fungus Isaria, was investigated in the presence of different metal ions using multistage tandem mass spectrometry (MS(n)) with collision induced dissociation (CID) and validated by NMR spectroscopy. During MS(n) process, both protonated and metal-cationized isariins generated product ions belonging to the identical `b-ion' series, exhibiting initial backbone cleavage explicitly at the beta-ester bond. Fragmentation behavior for the protonated and metal-cationized acyclic methyl ester derivative of isariins was very similar. On the contrary, isaridins during fragmentation produced ions belonging to the `b' or/and the `y' ion series depending on the nature of interacting metal ions, due to initial backbone cleavages at the beta-ester linkage or/and at a specific amide linkage. Interestingly, independent of the nature of the interacting metal ions, the product ions formed from the acyclic methyl ester derivative of isaridins belonged only to the `y-type'. Complementary NMR data showed that, while all metal ions were located around the beta-ester group of isariins, the metal ion interacting sites varied across the backbone for isaridins. Combined MS and NMR data suggest that the different behavior in sequence specific charge-driven fragmentation of isariins and isaridins is predetermined because of the constituent beta-hydroxy acid residue in isariins and the cis peptide bond in isaridins.

Tryptophan-water interaction in Monellin:Hydration patterns from molecular dynamics simulations

Femtosecond spectroscopy carried out earlier on Monellin and some other systems has given insights into the hydration dynamics of the proteins. In the present work, molecular dynamics simulations have been performed on Monellin to study the hydration dynamics. A method has been described to follow up the molecular events of the protein–water interactions in detail. The time constants of the survival correlation function match well with the reported experimental values. This validates the procedure, adapted here for Monellin, to investigate the hydration dynamics in general.

Interaction anisotropy and shear instability of aspirin polymorphs established by nanoindentation

Nanoindentation is applied to the two polymorphs of aspirin to examine and differentiate their interaction anisotropy and shear instability. Aspirin provides an excellent test system for the technique because: (i) polymorphs I and II exhibit structural similarity in two dimensions, thereby facilitating clear examination of the differences in mechanical response in relation to well-defined differences between the two crystal structures; (ii) single crystals of the metastable polymorph II have only recently become accessible; (iii) shear instability has been proposed for II. Different elastic moduli and hardness values determined for the two polymorphs are correlated with their crystal structures, and the interpretation is supported by measured thermal expansion coefficients. The stress-induced transformation of the metastable polymorph II to the stable polymorph I can be brought about rapidly by mechanical milling, and proceeds via a slip mechanism. This work establishes that nanoindentation provides ``signature'' responses for the two aspirin polymorphs, despite their very similar crystal structures. It also demonstrates the value of the technique to quantify stability relationships and phase transformations in molecular crystals, enabling a deeper understanding of polymorphism in the context of crystal engineering.

Direct evidence of redox interaction between metal ion and support oxide in Ce(0.98)Pd(0.02)O(2-delta) by a combined electrochemical and XPS study

A combined electrochemical method and X-ray photo electron spectroscopy (XPS) has been utilized to understand the Pd(2+)/CeO(2) interaction in Ce(1-x)Pd(x)O(2-delta) (x = 0.02). A constant positive potential (chronoamperometry) is applied to Ce(0.98)Pd(0.02)O(2-delta) working electrode which causes Ce(4+) to reduce to Ce(3+) to the extent of similar to 35%, while Pd remains in the +2 oxidation state. Electrochemically cycling this electrode between 0.0-1.2 V reverts back to the original state of the catalyst. This reversibility is attributed to the reversible reduction of Ce(4+) to Ce(3+) state. CeO(2) electrode with no metal component reduces to CeO(2-y) (y similar to 0.4) after applying 1.2 V which is not reversible and the original composition of CeO(2) cannot be brought back in any electrochemical condition. During the electro-catalytic oxygen evolution reaction at a constant 1.2 V for 1000 s, Ce(0.98)Pd(0.02)O(2-delta) reaches a steady state composition with Pd in the +2 states and Ce(4+) : Ce(3+) in the ratio of 0.65 : 0.35. This composition can be denoted as Ce(0.63)(4+)Ce(0.35)(4+)Pd(0.02)O(2-delta-y) (y similar to 0.17). When pure CeO(2) is put under similar electrochemical condition, it never reaches the steady state composition and reduces almost to 85%. Thus, Ce(0.98)Pd(0.02)O(2-delta) forms a stable electrode for the electro-oxidation of H(2)O to O(2) unlike CeO(2) due to the metal support interaction.

Interaction between oxygen and silver dissolved in liquid copper

The effect of silver on the activity of oxygen in solution in liquid copper has been measured at 1373 K. The results are compared with those of other authors who have studied the system; it is found that the results are in good agreement with Alcock and Richardson's quasichemical model when a coordination number of 2 is assigned to all atoms in the ternary solution.

Ferroelectric interaction and polarization studies in BaTiO3/SrTiO3 superlattice

Ferroelectric superlattice structures consisting of alternating layers of BaTiO3 and SrTiO3 with variable interlayer thickness were grown on Pt (111)/TiO2/SiO2/Si (100) substrates by pulsed laser deposition. The presence of superlattice reflections in the x-ray diffraction pattern clearly showed the superlattice behavior of the fabricated structures over a range of 6.4–20 nm individual layer thicknesses. Depth profile conducted by secondary ion mass spectrometry analysis showed a periodic concentration of Ba and Sr throughout the film. Polarization hysteresis and the capacitance-voltage characteristics of these films show clear size dependent ferroelectric characteristics. The spontaneous (Ps) and remnant (Pr) polarizations increase gradually with decreasing periodicity, reach a maximum at a finite thickness and then decrease. The competition between the size effect and long-range ferroelectric interaction is suggested as a possible reason for this phenomenon. The temperature dependence of Ps and Pr shows a single ferroelectric phase transition, and the Curie temperature is estimated to be about 316 K. The curve shows that the ferroelectric superlattice tends to form an artificial material, responding as a single structure with an averaged behavior of both the parent systems.

Interaction of G-Quadruplexes with Nonintercalating Duplex-DNA Minor Groove Binding Ligands

The enzyme telomerase synthesizes the G-rich DNA strands of the telomere and its activity is often associated with cancer. The telomerase may be therefore responsible for the ability of a cancer cell-to escape apoptosis. The G-rich DNA sequences often adopt tetra-stranded structure, known as the G-quadruplex DNA (G4-DNA). The stabilization of the telomeric DNA into the G4-DNA structures by small molecules has been the focus of many researchers for the design and development of new anticancer agents. The compounds which stabilize the G-quadruplex in the telomere inhibit the telomerase activity. Besides telomeres, the G4-DNA forming sequences are present in the genomic regions of biological significance including the transcriptional regulatory and promoter regions of several oncogenes. Inducing a G-quadruplex structure within the G-rich promoter sequences is a potential way of achieving selective gene regulation. Several G-quadruplex stabilizing ligands are known. Minor groove binding ligands (MGBLs) interact with the double-helical DNA through the minor grooves sequence-specifically and interfere with several DNA associated processes. These MGBLs when suitably modified switch their preference sometimes from the duplex DNA to G4-DNA and stabilize the G4-DNA as well. Herein, we focus on the recent advances in understanding the G-quadruplex structures, particularly made by the human telomeric ends, and review the results of various investigations of the interaction of designed organic ligands with the G-quadruplex DNA while highlighting the importance of MGBL-G-quadruplex interactions.

A resistometric study of solute–solute interaction in dilute aluminium–silver alloys

The experimentally determined apparent vacancy formation energy values in dilute aluminium—silver alloys showed a divergence from calculated values at higher solute fractions. This is explained in terms of a solute—solute interaction energy of the order of 0.10 ev which exists when the binding energy between a vacancy and a solute atom pair is reduced to zero.

Role of Nonplanar Peptide Unit in Regular Polypeptide Helices - New Model for Pply-Beta-Benzyl-L-Aspartate

The effect of non-planarity of the peptide unit on helical structures stabilized by intrachain hydrogen bonds is discussed. While the present calculations generally agree with those already reported in the literature for right-handed helical structures, it is found that the most stable left-handed structure is a novel helix, called the delta-helix. Its helical parameters are close to these reported for poly-beta-benzyl-L -aspartate. Conformational energy calculations show that poly-beta-benzyl-L -aspartate with the delta-helical structure is considerably more stable than the structure it is generally believed to take up (the omega-helix) by about 15 kcal/mol-residue.