Electronic couplings and on-site energies for hole transfer in DNA: systematic quantum mechanical/molecular dynamic study

The electron hole transfer (HT) properties of DNA are substantially affected by thermal fluctuations of the π stack structure. Depending on the mutual position of neighboring nucleobases, electronic coupling V may change by several orders of magnitude. In the present paper, we report the results of systematic QM/molecular dynamic (MD) calculations of the electronic couplings and on-site energies for the hole transfer. Based on 15 ns MD trajectories for several DNA oligomers, we calculate the average coupling squares 〈 V2 〉 and the energies of basepair triplets X G+ Y and X A+ Y, where X, Y=G, A, T, and C. For each of the 32 systems, 15 000 conformations separated by 1 ps are considered. The three-state generalized Mulliken-Hush method is used to derive electronic couplings for HT between neighboring basepairs. The adiabatic energies and dipole moment matrix elements are computed within the INDO/S method. We compare the rms values of V with the couplings estimated for the idealized B -DNA structure and show that in several important cases the couplings calculated for the idealized B -DNA structure are considerably underestimated. The rms values for intrastrand couplings G-G, A-A, G-A, and A-G are found to be similar, ∼0.07 eV, while the interstrand couplings are quite different. The energies of hole states G+ and A+ in the stack depend on the nature of the neighboring pairs. The X G+ Y are by 0.5 eV more stable than X A+ Y. The thermal fluctuations of the DNA structure facilitate the HT process from guanine to adenine. The tabulated couplings and on-site energies can be used as reference parameters in theoretical and computational studies of HT processes in DNA

Studies in stoichiometry with compositional data

Geochemical data that is derived from the whole or partial analysis of various geologic materials represent a composition of mineralogies or solute species. Minerals are composed of structured relationships between cations and anions which, through atomic and molecular forces, keep the elements bound in specific configurations. The chemical compositions of minerals have specific relationships that are governed by these molecular controls. In the case of olivine, there is a well-defined relationship between Mn-Fe-Mg with Si. Balances between the principal elements defining olivine composition and other significant constituents in the composition (Al, Ti) have been defined, resulting in a near-linear relationship between the logarithmic relative proportion of Si versus (MgMnFe) and Mg versus (MnFe), which is typically described but poorly illustrated in the simplex. The present contribution corresponds to ongoing research, which attempts to relate stoichiometry and geochemical data using compositional geometry. We describe here the approach by which stoichiometric relationships based on mineralogical constraints can be accounted for in the space of simplicial coordinates using olivines as an example. Further examples for other mineral types (plagioclases and more complex minerals such as clays) are needed. Issues that remain to be dealt with include the reduction of a bulk chemical composition of a rock comprised of several minerals from which appropriate balances can be used to describe the composition in a realistic mineralogical framework. The overall objective of our research is to answer the question: In the cases where the mineralogy is unknown, are there suitable proxies that can be substituted? Kew words: Aitchison geometry, balances, mineral composition, oxides

Recerca versus docència en una experiència d'internalització dels estudis de Geografia a la Universitat de Girona: The faces of landscape, Catalonia and North Karelia = Research versus teaching in one experience of internationalization of the Geography degree studies in the University of Girona: The faces of landscape, Catalonia and North Karelia

Un dels reptes cabdals de la Universitat és enllaçar l’experiència de recerca amb la docència, així com promoure la internacionalització dels estudis, especialment a escala europea, tenint present que ambdues poden actuar com a catalitzadores de la millora de la qualitat docent. Una de les fórmules d’internacionalització és la realització d’assignatures compartides entre universitats de diferents països, fet que suposa l’oportunitat d’implementar noves metodologies docents. En aquesta comunicació es presenta una experiència en aquesta línia desenvolupada entre la Universitat de Girona i la Universitat de Joensuu (Finlàndia) en el marc dels estudis de Geografia amb la realització de l’assignatura 'The faces of landscape: Catalonia and North Karelia'. Aquesta es desenvolupa al llarg de dues setmanes intensives, una en cadascuna de les Universitats. L’objectiu és presentar i analitzar diferents significats del concepte paisatge aportant també metodologies d’estudi tant dels aspectes físics i ecològics com culturals que s’hi poden vincular i que són les que empren els grups de recerca dels professors responsables de l’assignatura. Aquesta part teòrica es completa amb una presentació de les característiques i dinàmiques pròpies dels paisatges finlandesos i catalans i una sortida de camp. Per a la part pràctica es constitueixen grups d’estudi multinacionals que treballen a escala local algun dels aspectes en els dos països, es comparen i es realitza una presentació i defensa davant del conjunt d’estudiants i professorat. La llengua vehicular de l’assignatura és l’anglès

Evaluating the probability and the impact of a failure in GMPLS based networks

In this paper, we define a new scheme to develop and evaluate protection strategies for building reliable GMPLS networks. This is based on what we have called the network protection degree (NPD). The NPD consists of an a priori evaluation, the failure sensibility degree (FSD), which provides the failure probability, and an a posteriori evaluation, the failure impact degree (FID), which determines the impact on the network in case of failure, in terms of packet loss and recovery time. Having mathematical formulated these components, experimental results demonstrate the benefits of the utilization of the NPD, when used to enhance some current QoS routing algorithms in order to offer a certain degree of protection

Perspectives of auto-correcting lens distortions in mosaic-based underwater navigation

When unmanned underwater vehicles (UUVs) perform missions near the ocean floor, optical sensors can be used to improve local navigation. Video mosaics allow to efficiently process the images acquired by the vehicle, and also to obtain position estimates. We discuss in this paper the role of lens distortions in this context, proving that degenerate mosaics have their origin not only in the selected motion model or in registration errors, but also in the cumulative effect of radial distortion residuals. Additionally, we present results on the accuracy of different feature-based approaches for self-correction of lens distortions that may guide the choice of appropriate techniques for correcting distortions

Correction of shading effects in vision-based UUV localization

This paper describes the improvements achieved in our mosaicking system to assist unmanned underwater vehicle navigation. A major advance has been attained in the processing of images of the ocean floor when light absorption effects are evident. Due to the absorption of natural light, underwater vehicles often require artificial light sources attached to them to provide the adequate illumination for processing underwater images. Unfortunately, these flashlights tend to illuminate the scene in a nonuniform fashion. In this paper a technique to correct non-uniform lighting is proposed. The acquired frames are compensated through a point-by-point division of the image by an estimation of the illumination field. Then, the gray-levels of the obtained image remapped to enhance image contrast. Experiments with real images are presented

Internal test sets studies in a group of antimalarials

Topological indices have been applied to build QSAR models for a set of 20 antimalarial cyclic peroxy cetals. In order to evaluate the reliability of the proposed linear models leave-n-out and Internal Test Sets (ITS) approaches have been considered. The proposed procedure resulted in a robust and consensued prediction equation and here it is shown why it is superior to the employed standard cross-validation algorithms involving multilinear regression models

Admission control schemes for TCP elastic traffic in class-based networks

En aquesta tesi proposem dos esquemes de xarxa amb control d'admissió per al trànsit elàstic TCP amb mecanismes senzills. Ambdós esquemes són capaços de proporcionar throughputs diferents i aïllament entre fluxos, on un "flux" es defineix com una seqüència de paquets relacionats dins d'una connexió TCP. Quant a l'arquitectura, ambdós fan servir classes de paquets amb diferents prioritats de descart, i un control d'admissió implícit, edge-to-edge i basat en mesures. En el primer esquema, les mesures són per flux, mentre que en el segon, les mesures són per agregat. El primer esquema aconsegueix un bon rendiment fent servir una modificació especial de les fonts TCP, mentre que el segon aconsegueix un bon rendiment amb fonts TCP estàndard. Ambdós esquemes han estat avaluats satisfactòriament a través de simulació en diferents topologies de xarxa i càrregues de trànsit.

Simulation of interlaminar and intralaminar damage in polymer-based composites for aeronautical applications under impact loading

La aplicación de materiales compuestos de matriz polimérica reforzados mediante fibras largas (FRP, Fiber Reinforced Plastic), está en gradual crecimiento debido a las buenas propiedades específicas y a la flexibilidad en el diseño. Uno de los mayores consumidores es la industria aeroespacial, dado que la aplicación de estos materiales tiene claros beneficios económicos y medioambientales. Cuando los materiales compuestos se aplican en componentes estructurales, se inicia un programa de diseño donde se combinan ensayos reales y técnicas de análisis. El desarrollo de herramientas de análisis fiables que permiten comprender el comportamiento mecánico de la estructura, así como reemplazar muchos, pero no todos, los ensayos reales, es de claro interés. Susceptibilidad al daño debido a cargas de impacto fuera del plano es uno de los aspectos de más importancia que se tienen en cuenta durante el proceso de diseño de estructuras de material compuesto. La falta de conocimiento de los efectos del impacto en estas estructuras es un factor que limita el uso de estos materiales. Por lo tanto, el desarrollo de modelos de ensayo virtual mecánico para analizar la resistencia a impacto de una estructura es de gran interés, pero aún más, la predicción de la resistencia residual después del impacto. En este sentido, el presente trabajo abarca un amplio rango de análisis de eventos de impacto a baja velocidad en placas laminadas de material compuesto, monolíticas, planas, rectangulares, y con secuencias de apilamiento convencionales. Teniendo en cuenta que el principal objetivo del presente trabajo es la predicción de la resistencia residual a compresión, diferentes tareas se llevan a cabo para favorecer el adecuado análisis del problema. Los temas que se desarrollan son: la descripción analítica del impacto, el diseño y la realización de un plan de ensayos experimentales, la formulación e implementación de modelos constitutivos para la descripción del comportamiento del material, y el desarrollo de ensayos virtuales basados en modelos de elementos finitos en los que se usan los modelos constitutivos implementados.