Quantitative interpretation of diffusion-ordered NMR spectra:can we rationalize small molecule diffusion coefficients?

Appealingly simple: A new method is described that allows the diffusion coefficient of a small molecule to be estimated given only the molecular weight and the viscosity of the solvent used. This method makes possible the quantitative interpretation of the diffusion domain of diffusion-ordered NMR spectra (see picture). © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Phenotypic effect of mutations in evolving populations of RNA molecules

Background. The secondary structure of folded RNA sequences is a good model to map phenotype onto genotype, as represented by the RNA sequence. Computational studies of the evolution of ensembles of RNA molecules towards target secondary structures yield valuable clues to the mechanisms behind adaptation of complex populations. The relationship between the space of sequences and structures, the organization of RNA ensembles at mutation-selection equilibrium, the time of adaptation as a function of the population parameters, the presence of collective effects in quasispecies, or the optimal mutation rates to promote adaptation all are issues that can be explored within this framework. Results. We investigate the effect of microscopic mutations on the phenotype of RNA molecules during their in silico evolution and adaptation. We calculate the distribution of the effects of mutations on fitness, the relative fractions of beneficial and deleterious mutations and the corresponding selection coefficients for populations evolving under different mutation rates. Three different situations are explored: the mutation-selection equilibrium (optimized population) in three different fitness landscapes, the dynamics during adaptation towards a goal structure (adapting population), and the behavior under periodic population bottlenecks (perturbed population). Conclusions. The ratio between the number of beneficial and deleterious mutations experienced by a population of RNA sequences increases with the value of the mutation rate µ at which evolution proceeds. In contrast, the selective value of mutations remains almost constant, independent of µ, indicating that adaptation occurs through an increase in the amount of beneficial mutations, with little variations in the average effect they have on fitness. Statistical analyses of the distribution of fitness effects reveal that small effects, either beneficial or deleterious, are well described by a Pareto distribution. These results are robust under changes in the fitness landscape, remarkably when, in addition to selecting a target secondary structure, specific subsequences or low-energy folds are required. A population perturbed by bottlenecks behaves similarly to an adapting population, struggling to return to the optimized state. Whether it can survive in the long run or whether it goes extinct depends critically on the length of the time interval between bottlenecks. © 2010 Stich et al; licensee BioMed Central Ltd.

Tailoring the temperature and strain coefficients of Type I and Type IA dual grating sensors:the impact of hydrogenation conditions

We report experimental findings for tailoring the temperature and strain coefficients of Type I and Type IA fibre Bragg gratings by influencing the photosensitivity presensitization of the host optical fibre. It is shown that by controlling the level of hydrogen saturation, via hot and cold hydrogenation, it is possible to produce gratings with lower thermal coefficients. Furthermore, there is a larger difference between the Type I and Type IA thermal coefficients and a significant improvement in the matrix condition number, which impacts the ability to recover accurate temperature and strain data using the Type 1-1A dual grating sensor. © 2006 IOP Publishing Ltd.

Empirical prediction of peptide octanol-water partition coefficients

Peptides are of great therapeutic potential as vaccines and drugs. Knowledge of physicochemical descriptors, including the partition coefficient P (commonly expressed in logarithm form: logP), is useful for screening out unsuitable molecules and also for the development of predictive Quantitative Structure-Activity Relationships (QSARs). In this paper we develop a new approach to the prediction of LogP values for peptides based on an empirical relationship between global molecular properties and measured physical properties. Our method was successful in terms of peptide prediction (total r2 = 0.641). The final model consisted of 5 physicochemical descriptors (molecular weight, number of single bonds, 2D-VDW volume, 2D-VSA hydrophobic and 2D-VSA polar). The approach is peptide specific and its predictive accuracy was high. Overall, 67% of the peptides were able to be predicted within +/-0.5 log units from the experimental values. Our method thus represents a novel prediction method with proven predictive ability.

Quadratic behavior of fiber Bragg grating temperature coefficients

We describe the characterization of the temperature and strain responses of fiber Bragg grating sensors by use of an interferometric interrogation technique to provide an absolute measurement of the grating wavelength. The fiber Bragg grating temperature response was found to be nonlinear over the temperature range -70°C to 80°C. The nonlinearity was observed to be a quadratic function of temperature, arising from the linear dependence on temperature of the thermo-optic coefficient of silica glass over this range, and is in good agreement with a theoretical model.

Fiber grating type dependence of temperature and strain coefficients and application to simultaneous temperature and strain measurement

Although fiber Bragg gratings (FBGs) have been widely used as advanced optical sensors, the cross-sensitivity between temperature and strain has complicated independent measurement procedures for these two measurands. We report here, for the first time to our knowledge, the results of a systematic investigation of the dependence of both temperature and strain sensitivities on the grating type, including the well-known Type I, Type IIA, and a new type which we have designated Type IA, using both hydrogen-free and hydrogenated B/Ge codoped fibers. We have identified distinct sensitivity characteristics for each grating type, and we have utilised them to implement a novel dual-grating, dual-parameter sensor device with performance superior to that of previously reported grating-based structures.

Quadratic behaviour of fibre Bragg grating temperature coefficients

We describe the characterization of the temperature and strain responses of fiber Bragg grating sensors by use of an interferometric interrogation technique to provide an absolute measurement of the grating wavelength. The fiber Bragg grating temperature response was found to be nonlinear over the temperature range -70 °C to 80 °C. The nonlinearity was observed to be a quadratic function of temperature, arising from the linear dependence on temperature of the thermo-optic coefficient of silica glass over this range, and is in good agreement with a theoretical model.

The Localization Procedures of the Vector of Weighting Coefficients for Fuzzy Models of Choice

The author analyzes the localization procedures of the vector of weighting coefficients which are based on presenting the function of value by additive reduction adapted to fuzzy models of choice.

Perturbed Proximal Point Algorithm with Nonquadratic Kernel

Let H be a real Hilbert space and T be a maximal monotone operator on H. A well-known algorithm, developed by R. T. Rockafellar [16], for solving the problem (P) ”To find x ∈ H such that 0 ∈ T x” is the proximal point algorithm. Several generalizations have been considered by several authors: introduction of a perturbation, introduction of a variable metric in the perturbed algorithm, introduction of a pseudo-metric in place of the classical regularization, . . . We summarize some of these extensions by taking simultaneously into account a pseudo-metric as regularization and a perturbation in an inexact version of the algorithm.

Boundary-Value Problems for almost Nonlinear Singularly Perturbed Systems of Ordinary Differential Equations

A boundary-value problems for almost nonlinear singularly perturbed systems of ordinary differential equations are considered. An asymptotic solution is constructed under some assumption and using boundary functions and generalized inverse matrix and projectors.

The Perturbed Generalized Tikhonov's Algorithm

We work on the research of a zero of a maximal monotone operator on a real Hilbert space. Following the recent progress made in the context of the proximal point algorithm devoted to this problem, we introduce simultaneously a variable metric and a kind of relaxation in the perturbed Tikhonov’s algorithm studied by P. Tossings. So, we are led to work in the context of the variational convergence theory.

Null Condition for Semilinear Wave Equation with Variable Coefficients

∗The author was partially supported by M.U.R.S.T. Progr. Nazionale “Problemi Non Lineari...”

Integral Manifolds and Bounded Solutions of Singularly Perturbed Systems of Impulsive Differential Equations

Sufficient conditions for the existence of bounded solutions of singularly perturbed impulsive differential equations are obtained. For this purpose integral manifolds are used.