Microscopic and macroscopic polarization within a combined quantum mechanics and molecular mechanics model

A polarizable quantum mechanics and molecular mechanics model has been extended to account for the difference between the macroscopic electric field and the actual electric field felt by the solute molecule. This enables the calculation of effective microscopic properties which can be related to macroscopic susceptibilities directly comparable with experimental results. By seperating the discrete local field into two distinct contribution we define two different microscopic properties, the so-called solute and effective properties. The solute properties account for the pure solvent effects, i.e., effects even when the macroscopic electric field is zero, and the effective properties account for both the pure solvent effects and the effect from the induced dipoles in the solvent due to the macroscopic electric field. We present results for the linear and nonlinear polarizabilities of water and acetonitrile both in the gas phase and in the liquid phase. For all the properties we find that the pure solvent effect increases the properties whereas the induced electric field decreases the properties. Furthermore, we present results for the refractive index, third-harmonic generation (THG), and electric field induced second-harmonic generation (EFISH) for liquid water and acetonitrile. We find in general good agreement between the calculated and experimental results for the refractive index and the THG susceptibility. For the EFISH susceptibility, however, the difference between experiment and theory is larger since the orientational effect arising from the static electric field is not accurately described

Polydispersity index from linear viscoelastic data: Unimodal and bimodal linear polymer melts

This article describes a method for determining the polydispersity index Ip2=Mz/Mw of the molecular weight distribution (MWD) of linear polymeric materials from linear viscoelastic data. The method uses the Mellin transform of the relaxation modulus of a simple molecular rheological model. One of the main features of this technique is that it enables interesting MWD information to be obtained directly from dynamic shear experiments. It is not necessary to achieve the relaxation spectrum, so the ill-posed problem is avoided. Furthermore, a determinate shape of the continuous MWD does not have to be assumed in order to obtain the polydispersity index. The technique has been developed to deal with entangled linear polymers, whatever the form of the MWD is. The rheological information required to obtain the polydispersity index is the storage G′(ω) and loss G″(ω) moduli, extending from the terminal zone to the plateau region. The method provides a good agreement between the proposed theoretical approach and the experimental polydispersity indices of several linear polymers for a wide range of average molecular weights and polydispersity indices. It is also applicable to binary blends.

Oscillations in a molecular structured cell population model

We consider a nonlinear cyclin content structured model of a cell population divided into proliferative and quiescent cells. We show, for particular values of the parameters, existence of solutions that do not depend on the cyclin content. We make numerical simulations for the general case obtaining, for some values of the parameters convergence to the steady state but also oscillations of the population for others.

Structural and optical properties of dilute InAsN grown by molecular beam epitaxy

We perform a structural and optical characterization of InAs1¿xNx epilayers grown by molecular beam epitaxy on InAs substrates x 2.2% . High-resolution x-ray diffraction HRXRD is used to obtain information about the crystal quality and the strain state of the samples and to determine the N content of the films. The composition of two of the samples investigated is also obtained with time-of-flight secondary ion mass spectroscopy ToF-SIMS measurements. The combined analysis of the HRXRD and ToF-SIMS data suggests that the lattice parameter of InAsN might significantly deviate from Vegard"s law. Raman scattering and far-infrared reflectivity measurements have been carried out to investigate the incorporation of N into the InAsN alloy. N-related local vibrational modes are detected in the samples with higher N content. The origin of the observed features is discussed. We study the compositional dependence of the room-temperature band gap energy of the InAsN alloy. For this purpose, photoluminescence and optical absorption measurements are presented. The results are analyzed in terms of the band-anticrossing BAC model. We find that the room-temperature coupling parameter for InAsN within the BAC model is CNM=2.0 0.1 eV.

Estudi de la reactivitat respecte l'oxigen molecular d'una nova família de complexos dinuclears de coure(I) amb lligands hexaazamacrocíclics. Estudis preliminars d'oxidacions de fenols i sulfurs

Projecte de recerca elaborat a partir d’una estada a la Università degli Studi di Pavia entre setembre i desembre del 2007. Els lligands macrocíclics són sistemes que han estat àmpliament utilitzats per mimetitzar els centres actius de proteïnes dinuclears de coure com ara oxigenases (per exemple la tirosinasa). S’ha observat que la reactivitat del complex model depèn de les característiques del lligand com ara la geometria, la cavitat o la distància intermetàl•lica. En aquest sentit, es van sintetitzar dues noves famílies de lligands hexaazamacrocíclics ditòpics, una amb braços laterals tipus piridil i l’altra amb braços laterals tipus fenol. Dintre de cada família, els lligands es diferencien en la cavitat macrocíclica. En aquest treball s’han realitzat estudis de ractivitat respecte de l’oxigen molecular dels complexos dinuclears de coure(I) amb els lligands sintetitzats. Quan es deixen reaccionar els complexos amb oxigen molecular a baixa temperatura, no s’ha observat l’acumulació de cap espècie intermèdia, però si una diferència de reactivitat entre les dues famílies, essent els complexos amb els lligands fenolics molt més reactius que els complexos amb els lligands piridina. També s’han realitzat estudis per comprovar l’activitat oxigenasa dels complexos amb substrats externs. S’han assajat el para-clorofenol i la tioanisole. En el cas del p-clorofenol no s’ha observat en cap cas el producte d’oxigenació corresponent (p-clorocatecol). Quan s’han realitzat els experiments amb la tioanisole, en tots tres casos s’ha observat l’aparició del producte d’oxigenació corresponent (metilfenilsulfòxid), però amb una marcada diferència en el rendiment, mostrant-se molt més actius de nou els complexos amb el lligand fenòlic que el complex amb el lligand piridina.

Anàlisi genètica i molecular de les malalties Niemann-Pick tipus A/B i tipus C. Estratègies terapèutiques.

Aquest treball es basa en l’estudi de dues malalties lisosòmiques: la malaltia de Niemann-Pick A/B (NPAB) i la malaltia de Niemann-Pick tipus C (NPC). En relació a la malaltia de NPAB, s’ha realitzat l’expressió in vitro d’algunes de les mutacions de canvi d’aminoàcid trobades en pacients espanyols per tal de detectar les activitats enzimàtiques residuals. Totes les mutacions presenten una activitat molt baixa, gairebé nul•la, excepte la p.L225P i la R608del que tenen un 11% i 20% d’activitat respectivament. Els resultats obtinguts són coherents amb la severitat del fenotip que presenten els pacients. D’altra banda, s’ha caracteritzat un al•lel amb una mutació que afecta a una posició poc conservada d’un donador de splicing i que produeix la generació de trànscrits aberrants corresponents a trànscrits minoritaris de SMPD1, prèviament descrits, que no codifiquen per proteïna funcional. Respecte a malaltia de NPC, s’ha realitzat una anàlisi molecular de pacients espanyols prèviament estudiats identificant, en la majoria dels casos, la segona mutació responsable de la patologia. S’ha descrit per primer cop per aquesta malaltia una gran deleció que inclou el gen NPC1 i altres gens flanquejants i s’ha estudiat l’efecte que tenen les mutacions de splicing trobades a nivell de RNA. Per una d’aquestes mutacions, c.1554-1009G&A, s’ha assajat amb èxit una estratègia terapèutica basada en la utilització d’oligonuclèotids antisentit. D’altra banda, s’està desenvolupant un model cel•lular neuronal de la malaltia de Niemann-Pick tipus C, basat en la utilització de RNAs d’interferència, sobre el qual es podran assajar possibles estratègies terapèutiques en un futur.

Extensional flow of nematic liquid crystal under electric field gradient

Systematic asymptotic methods are used to formulate a model for the extensional flow of a thin sheet of nematic liquid crystal. With no external body forces applied, the model is found to be equivalent to the so-called Trouton model for Newtonian sheets (and fi bers), albeit with a modi fied "Trouton ratio". However, with a symmetry-breaking electric field gradient applied, behavior deviates from the Newtonian case, and the sheet can undergo fi nite-time breakup if a suitable destabilizing field is applied. Some simple exact solutions are presented to illustrate the results in certain idealized limits, as well as sample numerical results to the full model equations.

A Log-linear model of grain size influence on the geochemistry of sediments

Sediment composition is mainly controlled by the nature of the source rock(s), and chemical (weathering) and physical processes (mechanical crushing, abrasion, hydrodynamic sorting) during alteration and transport. Although the factors controlling these processes are conceptually well understood, detailed quantification of compositional changes induced by a single process are rare, as are examples where the effects of several processes can be distinguished. The present study was designed to characterize the role of mechanical crushing and sorting in the absence of chemical weathering. Twenty sediment samples were taken from Alpine glaciers that erode almost pure granitoid lithologies. For each sample, 11 grain-size fractions from granules to clay (ø grades &-1 to &9) were separated, and each fraction was analysed for its chemical composition.The presence of clear steps in the box-plots of all parts (in adequate ilr and clr scales) against ø is assumed to be explained by typical crystal size ranges for the relevant mineral phases. These scatter plots and the biplot suggest a splitting of the full grain size range into three groups: coarser than ø=4 (comparatively rich in SiO2, Na2O, K2O, Al2O3, and dominated by “felsic” minerals like quartz and feldspar), finer than ø=8 (comparatively rich in TiO2, MnO, MgO, Fe2O3, mostly related to “mafic” sheet silicates like biotite and chlorite), and intermediate grains sizes (4≤ø &8; comparatively rich in P2O5 and CaO, related to apatite, some feldspar).To further test the absence of chemical weathering, the observed compositions were regressed against three explanatory variables: a trend on grain size in ø scale, a step function for ø≥4, and another for ø≥8. The original hypothesis was that the trend could be identified with weathering effects, whereas each step function would highlight those minerals with biggest characteristic size at its lower end. Results suggest that this assumption is reasonable for the step function, but that besides weathering some other factors (different mechanical behavior of minerals) have also an important contribution to the trend.Key words: sediment, geochemistry, grain size, regression, step function

Ab initio absorption spectrum of NiO combining molecular dynamics with the embedded cluster approach in a discrete reaction field

We developed a procedure that combines three complementary computational methodologies to improve the theoretical description of the electronic structure of nickel oxide. The starting point is a Car-Parrinello molecular dynamics simulation to incorporate vibrorotational degrees of freedom into the material model. By means ofcomplete active space self-consistent field second-order perturbation theory (CASPT2) calculations on embedded clusters extracted from the resulting trajectory, we describe localized spectroscopic phenomena on NiO with an efficient treatment of electron correlation. The inclusion of thermal motion into the theoretical description allowsus to study electronic transitions that, otherwise, would be dipole forbidden in the ideal structure and results in a natural reproduction of the band broadening. Moreover, we improved the embedded cluster model by incorporating self-consistently at the complete active space self-consistent field (CASSCF) level a discrete (or direct) reaction field (DRF) in the cluster surroundings. The DRF approach offers an efficient treatment ofelectric response effects of the crystalline embedding to the electronic transitions localized in the cluster. We offer accurate theoretical estimates of the absorption spectrum and the density of states around the Fermi level of NiO, and a comprehensive explanation of the source of the broadening and the relaxation of the charge transferstates due to the adaptation of the environment

Nuclear magnetic resonance chemical shifts with the statistical average of orbital-dependent model potentials in Kohn-Sham density functional theory

The performance of the SAOP potential for the calculation of NMR chemical shifts was evaluated. SAOP results show considerable improvement with respect to previous potentials, like VWN or BP86, at least for the carbon, nitrogen, oxygen, and fluorine chemical shifts. Furthermore, a few NMR calculations carried out on third period atoms (S, P, and Cl) improved when using the SAOP potential

Estimation of electronic coupling in π -stacked donor-bridge-acceptor systems: correction of the two-state model

Comparison of donor-acceptor electronic couplings calculated within two-state and three-state models suggests that the two-state treatment can provide unreliable estimates of Vda because of neglecting the multistate effects. We show that in most cases accurate values of the electronic coupling in a π stack, where donor and acceptor are separated by a bridging unit, can be obtained as Ṽ da = (E2 - E1) μ12 Rda + (2 E3 - E1 - E2) 2 μ13 μ23 Rda2, where E1, E2, and E3 are adiabatic energies of the ground, charge-transfer, and bridge states, respectively, μij is the transition dipole moments between the states i and j, and Rda is the distance between the planes of donor and acceptor. In this expression based on the generalized Mulliken-Hush approach, the first term corresponds to the coupling derived within a two-state model, whereas the second term is the superexchange correction accounting for the bridge effect. The formula is extended to bridges consisting of several subunits. The influence of the donor-acceptor energy mismatch on the excess charge distribution, adiabatic dipole and transition moments, and electronic couplings is examined. A diagnostic is developed to determine whether the two-state approach can be applied. Based on numerical results, we showed that the superexchange correction considerably improves estimates of the donor-acceptor coupling derived within a two-state approach. In most cases when the two-state scheme fails, the formula gives reliable results which are in good agreement (within 5%) with the data of the three-state generalized Mulliken-Hush model

Growth, optical characterization, and laser operation of a stoichiometric crystal KYb(WO4)(2)

We present our recent achievements in the growing and optical characterization of KYb(WO4)2 (hereafter KYbW) crystals and demonstrate laser operation in this stoichiometric material. Single crystals of KYbW with optimal crystalline quality have been grown by the top-seeded-solution growth slow-cooling method. The optical anisotropy of this monoclinic crystal has been characterized, locating the tensor of the optical indicatrix and measuring the dispersion of the principal values of the refractive indices as well as the thermo-optic coefficients. Sellmeier equations have been constructed valid in the visible and near-IR spectral range. Raman scattering has been used to determine the phonon energies of KYbW and a simple physical model is applied for classification of the lattice vibration modes. Spectroscopic studies (absorption and emission measurements at room and low temperature) have been carried out in the spectral region near 1 µm characteristic for the ytterbium transition. Energy positions of the Stark sublevels of the ground and the excited state manifolds have been determined and the vibronic substructure has been identified. The intrinsic lifetime of the upper laser level has been measured taking care to suppress the effect of reabsorption and the intrinsic quantum efficiency has been estimated. Lasing has been demonstrated near 1074 nm with 41% slope efficiency at room temperature using a 0.5 mm thin plate of KYbW. This laser material holds great promise for diode pumped high-power lasers, thin disk and waveguide designs as well as for ultrashort (ps/fs) pulse laser systems.

Modeling a processive molecular motor: the conventional kinesin

We present a model that allows for the derivation of the experimentally accesible observables: spatial steps, mean velocity, stall force, useful power, efficiency and randomness, etc. as a function of the [adenosine triphosphate] concentration and an external load F. The model presents a minimum of adjustable parameters and the theoretical predictions compare well with the available experimental results.

Modelization of surface diffusion of a molecular dimer

A simple model for a dimer molecular diffusion on a crystalline surface, as a function of temperature, is presented. The dimer is formed by two particles coupled by a quadratic potential. The dimer diffusion is modeled by an overdamped Langevin equation in the presence of a two-dimensional periodic potential. Numerical simulation¿s results exhibit some dynamical properties observed, for example, in Si2 diffusion on a silicon [100] surface. They can be used to predict the value of the effective friction parameter. Comparison between our model and experimental measurements is presented.