Calibration-quality adiabatic potential energy surfaces for H3(+) and its isotopologues

Calibration-quality ab initio adiabatic potential energy surfaces (PES) have been determined for all isotopologues of the molecular ion H(3)(+). The underlying Born-Oppenheimer electronic structure computations used optimized explicitly correlated shifted Gaussian functions. The surfaces include diagonal Born-Oppenheimer corrections computed from the accurate electronic wave functions. A fit to the 41,655 ab initio points is presented which gives a standard deviation better than 0.1 cm(-1) when restricted to the points up to 6000 cm(-1) above the first dissociation asymptote. Nuclear motion calculations utilizing this PES, called GLH3P, and an exact kinetic energy operator given in orthogonal internal coordinates are presented. The ro-vibrational transition frequencies for H(3)(+), H(2)D(+), and HD(2)(+) are compared with high resolution measurements. The most sophisticated and complete procedure employed to compute ro-vibrational energy levels, which makes explicit allowance for the inclusion of non-adiabatic effects, reproduces all the known ro-vibrational levels of the H(3)(+) isotopologues considered to better than 0.2 cm(-1). This represents a significant (order-of-magnitude) improvement compared to previous studies of transitions in the visible. Careful treatment of linear geometries is important for high frequency transitions and leads to new assignments for some of the previously observed lines. Prospects for further investigations of non-adiabatic effects in the H(3)(+) isotopologues are discussed. In short, the paper presents (a) an extremely accurate global potential energy surface of H(3)(+) resulting from high accuracy ab initio computations and global fit, (b) very accurate nuclear motion calculations of all available experimental line data up to 16,000 cm(-1), and (c) results suggest that we can predict accurately the lines of H(3)(+) towards dissociation and thus facilitate their experimental observation.     

4',5'-Dichloro-2',7'-dimethoxy-5(6)-carboxyfluorescein (JOE): synthesis and spectral properties of oligonucleotide conjugates

A convenient procedure for the preparation of the fluorescent dye 4',5'-dichloro-2',7'-dimethoxy-5(6)-carboxyfluorescein (JOE) is reported; the overall yield achieved starting from isovanillin is 10 times higher (40% vs 4%) compared to the known procedure. Isomers (5- and 6-) are easily chromatographically separable as pentafluorophenyl esters of 3',6'-O-bis(cyclohexylcarbonyl) derivatives. Four non-nucleoside JOE phosphoramidites based on 5- and 6-isomers and flexible 6-aminohexanol (AH) or rigid 4-trans-aminocyclohexanol (ACH) linkers have been prepared and used for oligonucleotide labeling. Spectral and photophysical properties of 5'-JOE-modified oligonucleotides have been studied. Fluorescence quantum yield of the dye correlates with the nature of the linker (rigid vs flexible) and with the presence of dG nucleosides in close proximity to a JOE residue.     

Column solid phase extraction and determination of ultra-trace Au,Pd and Pt in environmental and geological samples

A new sorbent based on cysteine modified silica gel (SiG-cys) was prepared and studied for preconcentration and separation of noble metals Au(III), Pd(II), Pt(II), Pt(IV). Its extraction efficiency was examined by batch and column solid phase extraction procedures. Laboratory experiments performed showed that sorbent is characterized with high selectivity, permiting quantitative sorption (93–97%) of noble metals Au, Pd and Pt from acidic media 0.1–2 mol L^? 1 HCl and unsignificant sorption (less than 2%) for common base metals like Cu, Fe, Mn and Zn. The analytes retained on the sorbent are effectively eluted with 0.1 mol L^? 1 thiourea in 0.1 mol L^? 1 HCl and measured by ETAAS or ICP OES under optimal instrumental parameters. The sorbent showed high mechanical and chemical stability and extraction efficiency was not changed after 500 cycles of sorption/desorption. The sorbent was successfully applied in analyticals procedures for preconcentration and determination of Au, Pd and Pt in geological and soil samples. Detection limits (3σ criteria) achieved, depending on the instrumental methods used are: ETAAS (0.005 μg L^? 1 for Au in river and sea water, 0.002 μg g^? 1 for Au in copper ore and copper concentrate); ICP OES (0.03 μg L^? 1 for Pd and 0.06 μg L^? 1 for Pt in river and sea water, 0.006 μg g^? 1 for Pd in copper ore and copper concentrate and 0.002 μg g^? 1 for soluble Pt in soil). The accuracy of the procedures developed was confirmed by added/found method for sea and river water; by the analysis of national certified materials (copper ore and copper concentrate for Au and Pd) and by determination of the sum of soluble Pt(II) + Pt(IV) in spiked soil samples.     

Symmetry energy impact in simulations of core-collapse supernovae

In this work we study the effect of the symmetry energy on several properties of neutron stars. First, we discuss its effect on the density, proton fraction and pressure of the neutron star crust-core transition. We show that whereas the first two quantities present a clear correlation with the slope parameter L of the symmetry energy, no satisfactory correlation is seen between the transition pressure and L . However, a linear combination of the slope and curvature parameters at ρ = 0.1 fm^?3 is well correlated with the transition pressure. In the second part we analyze the effect of the symmetry energy on the pasta phase. It is shown that the size of the pasta clusters, number of nucleons and the cluster proton fraction depend on the density dependence of the symmetry energy: a small L gives rise to larger clusters. The influence of the equation of state at subsaturation densities on the extension of the inner crust of the neutron star is also discussed. Finally, the effect of the density dependence of the symmetry energy on the strangeness content of neutron stars is studied in the last part of the work. It is found that charged (neutral) hyperons appear at smaller (larger) densities for smaller values of the slope parameter L. A linear correlation between the radius and the strangeness content of a star with a fixed mass is also found.     

Stabilization of stochastic cycles and control of noise-induced chaos

We study the robustness of symmetrically coupled and clustering-based weighted heterogeneous inter-connected networks with respect to load-failure-induced cascades. This is done under the assumption that the flow dynamics are governed by global redistribution of loads based on weighted betweenness centrality. Our results indicate that no weighting bias should be assigned to inter-links when calculating shortest path between node pairs under the clustering-based weighting scheme; i.e., inter-links shall be treated no differently than intra-links. In contrast with local load redistribution cases, we show that increasing connectivity is preferred for the robustness against global load redistribution-based cascading failures in clustering-based weighted inter-connected networks. Furthermore, comparisons among weighting schemes reveal that, both the clustering-based and degree-based schemes outperform the random one in the sense of requiring lower initial and total investments required to ensure robustness. We also find that clustering-based scheme outperforms degree-based one in terms of requiring lower initial investments. Except in a limited range where weighting is heavily suppressed, clustering-based scheme is shown to outperform degree-based one in terms of total investments. Finally, when there exists a hard investment budget constraint, clustering-based weighting scheme would be a better choice against a two-nodes-induced failure than the degree-based weighting, and the clustering-based scheme is more stable than degree-based scheme against one-or-two-nodes-induced failure. We expect our findings to be significantly useful in designing real-world weighted inter-connected networks that are robust against load-failure-induced cascades.     

Interpolation of harmonic functions based on Radon projections

We consider an algebraic method for reconstruction of a harmonic function in the unit disk via a finite number of values of its Radon projections. The approach is to seek a harmonic polynomial which matches given values of Radon projections along some chords of the unit circle. We prove an analogue of the famous Marr’s formula for computing the Radon projection of the basis orthogonal polynomials in our setting of harmonic polynomials. Using this result, we show unique solvability for a family of schemes where all chords are chosen at equal distance to the origin. For the special case of chords forming a regular convex polygon, we prove error estimates on the unit circle and in the unit disk. We present an efficient reconstruction algorithm which is robust with respect to noise in the input data and provide numerical examples.     

Controllability on Infinite-Dimensional Manifolds: A Chow–Rashevsky Theorem

One of the fundamental problems in control theory is that of controllability, the question of whether one can drive the system from one point to another with a given class of controls. A classical result in geometric control theory of finite-dimensional (nonlinear) systems is Chow–Rashevsky theorem that gives a sufficient condition for controllability on any connected manifold of finite dimension. In other words, the classical Chow–Rashevsky theorem, which is in fact a primary theorem in subriemannian geometry, gives a global connectivity property of a subriemannian manifold. In this paper, following the unified approach of Kriegl and Michor (The Convenient Setting of Global Analysis, Mathematical Surveys and Monographs, vol. 53, Am. Math. Soc., Providence, 1997) for a treatment of global analysis on a class of locally convex spaces known as convenient, we give a generalization of Chow–Rashevsky theorem for control systems in regular connected manifolds modelled on convenient (infinite-dimensional) locally convex spaces which are not necessarily normable. To indicate an application of our approach to the infinite-dimensional geometric control problems, we conclude the paper with a novel controllability result on the group of orientation-preserving diffeomorphisms of the unit circle.     

Knowing when to give up: early-rejection stratagems in ligand docking

Virtual screening is an important resource in the drug discovery community, of which protein–ligand docking is a significant part. Much software has been developed for this purpose, largely by biochemists and those in related disciplines, who pursue ever more accurate representations of molecular interactions. The resulting tools, however, are very processor-intensive. This paper describes some initial results from a project to review computational chemistry techniques for docking from a non-chemistry standpoint. An abstract blueprint for protein–ligand docking using empirical scoring functions is suggested, and this is used to discuss potential improvements. By introducing computer science tactics such as lazy function evaluation, dramatic increases to throughput can and have been realized using a real-world docking program. Naturally, they can be extended to any system that approximately corresponds to the architecture outlined.     

Spectroscopic Investigation of Polypeptide Plane Brushes

Fourier transform infrared spectroscopy (FTIR) was used for determination of orientational and conformational characteristics of plane polypeptide brushes with different density of polypeptide chains grafted to modified silicon surface. The determination of grafting density of polypeptide chains in brushes, which depends on chemical structure of spacer groups, was carried out using ultraviolet (UV) spectroscopy. The influence of chemical structure of modifying spacer groups and outer conditions on the characteristics of plane polypeptide brushes was established. The peculiarities of α-helical structure (random coil transfer of polymer chains in brushes under the action of denaturants) were investigated.