Nature and properties of ultrathin nanocrystalline gold films formed at the organic-aqueous interface

Ultrathin nanocrystalline films of gold formed at different temperatures at the organic-aqueous interface have been investigated by X-ray diffraction, electron microscopy, atomic force microscopy, and electronic spectroscopy. The films are smooth and continuous over relatively large length scales and are generally approximately 100 nm thick. The size of the nanocrystals is sensitive to the reaction temperature, which also determines whether the film is metallic or an activated conductor. The surface plasmon band of gold is highly red-shifted in the films. Alkanethiols perturb the structure of the films, with the magnitude of the effect depending on the chain length. Accordingly, the position of the plasmon band and the electrical resistance of the films are affected by interaction with alkanethiols; the plasmon band approaches that of isolated nanocrystals in the presence of long-chain thiols.     

Potts ferromagnets on coexpressed gene networks: identifying maximally stable partitions

Clustering gene expression data by exploiting phase transitions in granular ferromagnets requires transforming the data to a granular substrate. We present a method using the recently introduced homogeneity order parameter Lambda [H. Agrawal, Phys. Rev. Lett. 89, 268702 (2002)]] for optimizing the parameter controlling the "granularity" and thus the stability of partitions. The model substrates obtained for gene expression data have a highly granular structure. We explore properties of phase transition in high q ferromagnetic Potts models on these substrates and show that the maximum of the width of superparamagnetic domain, corresponding to maximally stable partitions, coincides with the minimum of Lambda.     

Combustion Behaviour of Nitrocellulose and its Complexes with Copper Oxide. Hot stage microscopic studies

Complexes of nitrocellulose (NC – low and high nitrogen content) with copper oxide (CuO) have been synthesized and studied for morphological behaviour on heating from room temperature to 500°C with the help of hot stage microscopy (HSM). During decomposition, NC:CuO complexes show contraction of fibrous boundaries followed by mass movement of matrix, with the evolution of brown yellow colour gas at higher temperatures as compared to NC alone. This revised version was published online in July 2006 with corrections to the Cover Date.     

Viscous potential flow analysis of Kelvin-Helmholtz instability with mass transfer and vaporization

Viscous potential flow analysis of Kelvin-Helmholtz instability with heat and mass transfer has been studied. A dispersion relation has been obtained. Stability criterion is given by a critical value of relative velocity. It has been found that heat and mass transfer has destabilizing effect on relative velocity when lower fluid viscosity is low while it has stabilizing effect when lower fluid viscosity is high. Various graphs have been plotted for relative velocity and growth rate. In statically unstable situation viscosity has stabilizing effect while in statically stable situation it has destabilizing effect.     

Surface pattern recording in amorphous chalcogenide layers

Investigations of light-induced volume expansion and surface pattern recording in amorphous chalcogenide layers and nano-layered structures (NLS) were extended to direct electron-beam recording on Se/As₂S₃ and Sb/As₂S₃ NLS. Light as well as e-beam induced bleaching occurs in all NLS, while volume expansion occurs only in chalcogenide–chalcogenide NLS and in homogeneous Se or As₂S₃ layers. Comparison of these two phenomena revealed the possible role of purely electronic and thermal processes in the interdiffusion and relief formation. The latter is supposed to be connected with radiation-induced defect creation, free volume increase under the increased fluidity conditions as well as with the possible additional influence of electrostatic forces and stress.     

Topological estimation of proton-ligand formation constants of potential antitumour agents: Salicylhydroxamic acids

Proton-ligand formation constants of salicylhydroxamic acids (SHA) and their nuclear substituted derivatives have been estimated topologically using the normalized Wiener index, referred to as mean square Wiener index (Wms). Regression analysis of the data indicates that Wms can be used successfully for estimating and monitoring proton-ligand formation constants.     

Power spectra and spatial pattern dynamics of a ring laser

Experimental measurements of power spectra of a single longitudinal and transverse mode ring dye laser are presented that reveal the critical slowing down of the laser near threshold. External pump noise serves as a probe of the frequency response of the dye laser. Detailed comparisons of the spectral characteristics with computer simulations and an approximate analytic theory are given. The dynamics of spatial pattern formation in a multimode dye laser is examined through measurements of first-passage-time distributions. A comparison of the experiments with computer simulations based on a simple theoretical model of the two-mode laser shows qualitative agreement. These measurements indicate that there are a variety of complex phenomena associated with the transverse mode pattern formation dynamics that need to be addressed theoretically and studied further experimentally.     

Finite-Time Optimal Control of Polynomial Systems Using Successive Suboptimal Approximations

It is shown in this paper that the finite-time optimal control of polynomial systems can be obtained by solving a sequence of optimal control problems for the linearized problem. The paper provides proof of convergence as well as illustration of the procedure by two examples.     

Rapid and accurate estimation of protein–ligand relative binding affinities using site-identification by ligand competitive saturation

Predicting relative protein–ligand binding affinities is a central pillar of lead optimization efforts in structure-based drug design. The site identification by ligand competitive saturation (SILCS) methodology is based on functional group affinity patterns in the form of free energy maps that may be used to compute protein–ligand binding poses and affinities. Presented are results obtained from the SILCS methodology for a set of eight target proteins as reported originally in Wang et al. (J. Am. Chem. Soc., 2015, 137, 2695–2703) using free energy perturbation (FEP) methods in conjunction with enhanced sampling and cycle closure corrections. These eight targets have been subsequently studied by many other authors to compare the efficacy of their method while comparing with the outcomes of Wang et al. In this work, we present results for a total of 407 ligands on the eight targets and include specific analysis on the subset of 199 ligands considered previously. Using the SILCS methodology we can achieve an average accuracy of up to 77% and 74% when considering the eight targets with their 199 and 407 ligands, respectively, for rank-ordering ligand affinities as calculated by the percent correct metric. This accuracy increases to 82% and 80%, respectively, when the SILCS atomic free energy contributions are optimized using a Bayesian Markov-chain Monte Carlo approach. We also report other metrics including Pearson''s correlation coefficient, Pearlman''s predictive index, mean unsigned error, and root mean square error for both sets of ligands. The results obtained for the 199 ligands are compared with the outcomes of Wang et al. and other published works. Overall, the SILCS methodology yields similar or better-quality predictions without a priori need for known ligand orientations in terms of the different metrics when compared to current FEP approaches with significant computational savings while additionally offering quantitative estimates of individual atomic contributions to binding free energies. These results further validate the SILCS methodology as an accurate, computationally efficient tool to support lead optimization and drug discovery.

Predicting relative protein–ligand binding affinities is a central pillar of lead optimization efforts in structure-based drug design.     

Studies on drug–DNA complexes,adriamycin–d‐(TGATCA)2 and 4′‐epiadriamycin–d‐(CGATCG)2, by phosphorus‐31 nuclear magnetic resonance spectroscopy

The complexes of adriamycin–d‐(TGATCA)₂ and 4′‐epiadriamycin–d‐(CGATCG)₂ are studied by one‐ and two‐dimensional ³¹P nuclear magnetic resonance spectroscopy (NMR) at 500 MHz in the temperature range 275–328 K and as a function of drug to DNA ratio (0.0–2.0). The binding of drug to DNA is clearly evident in ³¹P? ³¹P exchange NOESY spectra that shows two sets of resonances in slow chemical exchange. The phosphate resonances at the intercalating steps, T1pG2/C1pG2 and C5pA6/C5pG6, shift downfield up to 1.7 ppm and that at the adjacent step shift downfield up to 0.7 ppm, whereas the central phosphate A3pT4 is relatively unaffected. The variations of chemical shift with drug to DNA ratio and temperature as well as linewidths are different in each of the two complexes. These observations reflect change in population of B_I/B_II conformation, stretching of backbone torsional angle ζ, and distortions in O? P? O bond angles that occur on binding of drug to DNA. To the best of our knowledge, there are no solution studies on 4′‐epiadriamycin, a better tolerated drug, and binding of daunomycin or its analogue to d‐(TGATCA)₂ hexamer sequence. The studies report the use of ³¹P NMR as a tool to differentiate various complexes. The specific differences may well be the reasons that are responsible for different antitumor action of these drugs due to different binding ability and distortions in DNA. Copyright © 2009 John Wiley & Sons, Ltd.