Parallelization of the deMon2k code

The parallelization of the LCGTO-KS-DFT code deMon2k is presented. The parallelization of the three-center electron repulsion integrals, the numerical integration using a direct grid algorithm and the matrix multiplication and diagonalization are described. The efficiency of the parallelization is analyzed by selected benchmark calculations. It is shown that geometry optimizations of systems with more than 8,000 basis functions are feasible on cluster architectures.     

2-[(R-phenyl)amine]-1,4-naphthalendiones as photosystem I electron acceptors: structure-activity relationship of m- and p-PAN compounds with QSAR analysis

Nineteen 2-[(R-phenyl)amine]-1,4-naphthalendione derivatives (PAN) were tested on spinach thylakoids for their activity as electron acceptors. These molecules act as photosystem I electron acceptors in the micromolar range. AC(50) values varied from 5 nM to 24 microM. QSAR analysis revealed a linear correlation of the m-PAN derivative log [1/AC(50)] with the energy difference of the LUMO and HOMO orbitals. The biological activity of p-PAN derivatives correlates linearly with structural parameters. Electron affinity is being the most important. The half wave I potential values (E(1/2)) of PAN compounds (from -213 to -569 mV vs. NHE) match with the mid-point potentials of the A(0) to F(X) niche of PSI electron transport carriers. The logP values of PAN derivatives were 3.35 and 3.88, indicating that they are hydrophobic compounds. Therefore PAN compounds accept electrons at the hydrophobic A(0) to F(X) niche of PSI.     

DNA nanomachines and nanostructures involving quadruplexes

DNA is an attractive component for molecular recognition, because of its self-assembly properties. Its three-dimensional structure can differ markedly from the classical double helix. For example, DNA or RNA strands carrying guanine or cytosine stretches associate into four-stranded structures called G-quadruplexes or i-DNA, respectively. Since 2002, several groups have described nanomachines that take advantage of this structural polymorphism. We first introduce the unusual structures that are involved in these devices (i.e., i-DNA and G-quadruplexes) and then describe the opening and closing steps that allow cycling. A quadruplex-duplex molecular machine is then presented in detail, together with the rules that govern its formation, its opening/closing kinetics and the various technical and physico-chemical parameters that play a role in the efficiency of this device. Finally, we review the few examples of nanostructures that involve quadruplexes.     

Comprehensive two-dimensional gas chromatography in the analysis of volatile samples of natural origin: a multidisciplinary approach to evaluate the influence of second dimension column coated with mixed stationary phases on system orthogonality

The study evaluates the influence of selectivity tuning of the stationary phase of the second dimension on the orthogonality of a comprehensive two-dimensional gas chromatography (GC x GC) system. Two different sets of columns, providing independent and semi-independent separation mechanisms were used. The first consisted of a first dimension separating analytes on a volatility basis (i.e. a non-polar polydimethylsiloxane (OV1) column) combined with a second dimension separating by polarity, using columns coated with 100% polyethylene glycol (CW20M), CW20M/OV1 mixtures in ratios of 25-75%, and polydimethylsiloxane, 7% phenyl, 7% cyanopropyl (OV1701). The second set consisted of a first dimension separating analytes on a polarity basis (100% CW20M column) combined with a second dimension separating by volatility, consisting of columns coated with 100% OV1, OV1/CW20M mixtures in ratios of 25-75%, and 100% OV1701. Medium-complexity mixtures of natural origin (i.e. peppermint essential oil and a standard mixture of suspected allergens) consisting of components in a relatively limited range of molecular weights (MW) and volatilities, but belonging to different classes of compounds in a wide range of polarity (mono- and sesquiterpenoids, hydrocarbons and oxygenated compounds) were analysed with the above sets of columns. Different approaches were used to evaluate peak spreading on the GC x GC separation plane and degree of orthogonality of the column sets, namely: (1) a Factor Analysis (FA) approach, estimating the correlation coefficients and spreading angles of the sample components in the two-dimensional chromatographic plane; (2) an Informational Theory (IT) approach, based on determining a group of parameters including: informational entropy, % synentropy and similarity (H); and (3) an approach based on estimating the amount of separation space used, i.e. a practical parameter that directly refers to the experimental separation plane of the GC x GC chromatogram. Results showed that peak spreading in the chromatographic plane, when CW20M and OV1 are combined in different ratios, can be predicted from retention mechanisms, and that the degree of orthogonality measured with different approaches, is consistent with the divergent nature, in terms of polarity of the stationary phases combined in the GC x GC system.     

On the continuity of minimizers for quasilinear functionals

In this paper we establish a continuity result for local minimizers of some quasilinear functionals that satisfy degenerate elliptic bounds. The non-negative function which measures the degree of degeneracy is assumed to be exponentially integrable. The minimizers are shown to have a modulus of continuity controlled by log log(1/|x|)⁻¹. Our proof adapts ideas developed for solutions of degenerate elliptic equations by J. Onninen, X. Zhong: Continuity of solutions of linear, degenerate elliptic equations, Ann. Sc. Norm. Super. Pisa Cl. Sci. (5) 6 (2007), 103–116.     

Capital rationing problems under uncertainty and risk

Capital rationing is a major problem in managerial decision making. The classical mathematical formulation of the problem relies on a multi-dimensional knapsack model with known input parameters. Since capital rationing is carried out in conditions where uncertainty is the rule rather than the exception, the hypothesis of deterministic data limits the applicability of deterministic formulations in real settings. This paper proposes a stochastic version of the capital rationing problem which explicitly accounts for uncertainty. In particular, a mathematical formulation is provided in the framework of stochastic programming with joint probabilistic constraints and a novel solution approach is proposed. The basic model is also extended to include specific risk measures. Preliminary computational results are presented and discussed.     

Bingham Flows in Periodic Domains of Infinite Length

The Bingham fluid model has been successfully used in modeling a large class of non-Newtonian fluids. In this paper, the authors extend to the case of Bingham fluids the results previously obtained by Chipot and Mardare, who studied the asymptotics of the Stokes flow in a cylindrical domain that becomes unbounded in one direction, and prove the convergence of the solution to the Bingham problem in a finite periodic domain, to the solution of the Bingham problem in the infinite periodic domain, as the length of the finite domain goes to infinity. As a consequence of this convergence, the existence of a solution to a Bingham problem in the infinite periodic domain is obtained, and the uniqueness of the velocity field for this problem is also shown. Finally, they show that the error in approximating the velocity field in the infinite domain with the velocity in a periodic domain of length 2? has a polynomial decay in ?, unlike in the Stokes case(see [Chipot,M. and Mardare, S., Asymptotic behaviour of the Stokes problem in cylinders becoming unbounded in one direction, Journal de Math′ematiques Pures et Appliqu′ees, 90(2), 2008,133–159]) where it has an exponential decay. This is in itself an important result for the numerical simulations of non-Newtonian flows in long tubes.     

Aldol Reactions of the trans-o-Hydroxybenzylidenepyruvate Hydratase-Aldolase (tHBP-HA) from Pseudomonas fluorescens N3

In this paper, a recombinant trans-o-hydroxybenzylidenepyruvate hydratase-aldolase (tHBP-HA) of Pseudomonas fluorescens N3 was used as a new catalyst for aldol condensation reactions. The reaction of some aldehydes with a different electronic activation catalyzed by tHBP-HA is presented and discussed together with some hints on the product structure. The enzyme is strictly pyruvate-dependent but uses different aldehydes as acceptors. The structure of the products is highly dependent on the electronic characteristics of the aldehyde. The results are interesting for both their synthetic importance and the mechanism of the formation of the products. Not only the products obtained and the recognition power are reported, but also some characteristics of its mechanism are analyzed. The results clearly show that the enzyme is efficiently prepared, purified, and stored, that it recognizes many different substrates, and that the products depend on the substrate electronic nature.