ESTIMATING REACTION CONSTANTS BY AB INITIO MOLECULAR MODELING: A STUDY ON THE OXIDATION OF PHENOL TO CATECHOL AND HYDROQUINONE IN ADVANCED OXIDATION PROCESSES

Molecular modeling is growing as a research tool in Chemical Engineering studies, as can be seen by a simple research on the latest publications in the field. Molecular investigations retrieve information on properties often accessible only by expensive and time-consuming experimental techniques, such as those involved in the study of radical-based chain reactions. In this work, different quantum chemical techniques were used to study phenol oxidation by hydroxyl radicals in Advanced Oxidation Processes used for wastewater treatment. The results obtained by applying a DFT-based model showed good agreement with experimental values available, as well as qualitative insights into the mechanism of the overall reaction chain. Solvation models were also tried, but were found to be limited for this reaction system within the considered theoretical level without further parameterization.

Computation of (3)J(HH) coupling constants with a combination of density functional theory and semiempirical calculations. Application to complex molecules

This work evaluates the efficiency of economic levels of theory for the prediction of (3)J(HH) spin-spin coupling constants, to be used when robust electronic structure methods are prohibitive. To that purpose, DFT methods like mPW1PW91. B3LYP and PBEPBE were used to obtain coupling constants for a test set whose coupling constants are well known. Satisfactory results were obtained in most of cases, with the mPW1PW91/6-31G(d,p)//B3LYP/6-31G(d,p) leading the set. In a second step. B3LYP was replaced by the semiempirical methods PM6 and RM1 in the geometry optimizations. Coupling constants calculated with these latter structures were at least as good as the ones obtained by pure DFT methods. This is a promising result, because some of the main objectives of computational chemistry - low computational cost and time, allied to high performance and precision - were attained together. (C) 2012 Elsevier B.V. All rights reserved.

Modeling the gluon propagator in Landau gauge: Lattice estimates of pole masses and dimension-two condensates

We present an analytic description of numerical results for the Landau-gauge SU(2) gluon propagator D(p(2)), obtained from lattice simulations (in the scaling region) for the largest lattice sizes to date, in d = 2, 3 and 4 space-time dimensions. Fits to the gluon data in 3d and in 4d show very good agreement with the tree-level prediction of the refined Gribov-Zwanziger (RGZ) framework, supporting a massive behavior for D(p(2)) in the infrared limit. In particular, we investigate the propagator's pole structure and provide estimates of the dynamical mass scales that can be associated with dimension-two condensates in the theory. In the 2d case, fitting the data requires a noninteger power of the momentum p in the numerator of the expression for D(p(2)). In this case, an infinite-volume-limit extrapolation gives D(0) = 0. Our analysis suggests that this result is related to a particular symmetry in the complex-pole structure of the propagator and not to purely imaginary poles, as would be expected in the original Gribov-Zwanziger scenario.

Structure and anomalous solubility for hard spheres in an associating lattice gas model

In this paper we investigate the solubility of a hard-sphere gas in a solvent modeled as an associating lattice gas. The solution phase diagram for solute at 5% is compared with the phase diagram of the original solute free model. Model properties are investigated both through Monte Carlo simulations and a cluster approximation. The model solubility is computed via simulations and is shown to exhibit a minimum as a function of temperature. The line of minimum solubility (TmS) coincides with the line of maximum density (TMD) for different solvent chemical potentials, in accordance with the literature on continuous realistic models and on the "cavity" picture. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4743635]

Flux-Line-Lattice Melting and Upper Critical Field of Bi1.65Pb0.35Sr2Ca2Cu3O10+delta Ceramic Samples

We have conducted magnetoresistance measurements rho(T,H) in applied magnetic fields up to 18 T in Bi1.65Pb0.35Sr2Ca2Cu3O10+delta ceramic samples which were subjected to different uniaxial compacting pressures. The anisotropic upper critical fields H (c2)(T) were extracted from the rho(T,H) data, yielding and the out-of-plane superconducting coherence length xi (c) (0)similar to 3 . We have also estimated and xi (ab) (0) similar to 90 . In addition to this, a flux-line-lattice (FLL) melting temperature T (m) has been identified as a second peak in the derivative of the magnetoresistance d rho/dT data close to the superconducting transition temperature. An H (m) vs. T phase diagram was constructed and the FLL boundary lines were found to obey a temperature dependence H (m) ae(T (c) /T-1) (alpha) , where alpha similar to 2 for the sample subjected to the higher compacting pressure. A reasonable value of the Lindemann parameter c (L) similar to 0.29 has been found for all samples studied.

Minimal Landau background gauge on the lattice

We present the first numerical implementation of the minimal Landau background gauge for Yang-Mills theory on the lattice. Our approach is a simple generalization of the usual minimal Landau gauge and is formulated for the general SU(N) gauge group. We also report on preliminary tests of the method in the four-dimensional SU(2) case, using different background fields. Our tests show that the convergence of the numerical minimization process is comparable to the case of a null background. The uniqueness of the minimizing functional employed is briefly discussed.

QUASI-TOPOLOGICAL QUANTUM FIELD THEORIES AND Z(2) LATTICE GAUGE THEORIES

We consider a two-parameter family of Z(2) gauge theories on a lattice discretization T(M) of a three-manifold M and its relation to topological field theories. Familiar models such as the spin-gauge model are curves on a parameter space Gamma. We show that there is a region Gamma(0) subset of Gamma where the partition function and the expectation value h < W-R(gamma)> i of the Wilson loop can be exactly computed. Depending on the point of Gamma(0), the model behaves as topological or quasi-topological. The partition function is, up to a scaling factor, a topological number of M. The Wilson loop on the other hand, does not depend on the topology of gamma. However, for a subset of Gamma(0), < W-R(gamma)> depends on the size of gamma and follows a discrete version of an area law. At the zero temperature limit, the spin-gauge model approaches the topological and the quasi-topological regions depending on the sign of the coupling constant.

Estimating reaction constants by ab initio molecular modeling: a study on the oxidation of phenol to catechol and hydroquinone in advanced oxidation processes

Molecular modeling is growing as a research tool in Chemical Engineering studies, as can be seen by a simple research on the latest publications in the field. Molecular investigations retrieve information on properties often accessible only by expensive and time-consuming experimental techniques, such as those involved in the study of radical-based chain reactions. In this work, different quantum chemical techniques were used to study phenol oxidation by hydroxyl radicals in Advanced Oxidation Processes used for wastewater treatment. The results obtained by applying a DFT-based model showed good agreement with experimental values available, as well as qualitative insights into the mechanism of the overall reaction chain. Solvation models were also tried, but were found to be limited for this reaction system within the considered theoretical level without further parameterization.

Stochastic lattice model describing a vector-borne disease

We employ the approach of stochastic dynamics to describe the dissemination of vector-borne diseases such as dengue, and we focus our attention on the characterization of the threshold of the epidemic. The coexistence space comprises two representative spatial structures for both human and mosquito populations. The human population has its evolution described by a process that is similar to the Susceptible-Infected-Recovered (SIR) dynamics. The population of mosquitoes follows a dynamic of the type of the Susceptible Infected-Susceptible (SIS) model. The coexistence space is a bipartite lattice constituted by two structures representing the human and mosquito populations. We develop a truncation scheme to solve the evolution equations for the densities and the two-site correlations from which we get the threshold of the disease and the reproductive ratio. We present a precise deØnition of the reproductive ratio which reveals the importance of the correlations developed in the early stage of the disease. According to our deØnition, the reproductive rate is directed related to the conditional probability of the occurrence of a susceptible human (mosquito) given the presence in the neighborhood of an infected mosquito (human). The threshold of the epidemic as well as the phase transition between the epidemic and the non-epidemic states are also obtained by performing Monte Carlo simulations. References: [1] David R. de Souza, T^ania Tom∂e, , Suani R. T. Pinho, Florisneide R. Barreto and M∂ario J. de Oliveira, Phys. Rev. E 87, 012709 (2013). [2] D. R. de Souza, T. Tom∂e and R. M. ZiÆ, J. Stat. Mech. P03006 (2011).

Study of surface free energy on a lattice-gas model applied to Liquid bridge

The pulmonary crackling and the formation of liquid bridges are problems that for centuries have been attracting the attention of scientists. In order to study these phenomena, it was developed a canonical cubic lattice-gas­ like model to explain the rupture of liquid bridges in lung airways [A. Alencar et al., 2006, PRE]. Here, we further develop this model and add entropy analysis to study thermodynamic properties, such as free energy and force. The simulations were performed using the Monte Carlo method with Metropolis algorithm. The exchange between gas and liquid particles were performed randomly according to the Kawasaki dynamics and weighted by the Boltzmann factor. Each particle, which can be solid (s), liquid (l) or gas (g), has 26 neighbors: 6 + 12 + 8, with distances 1, √2 and √3, respectively. The energy of a lattice's site m is calculated by the following expression: Em = ∑k=126 Ji(m)j(k) in witch (i, j) = g, l or s. Specifically, it was studied the surface free energy of the liquid bridge, trapped between two planes, when its height is changed. For that, was considered two methods. First, just the internal energy was calculated. Then was considered the entropy. It was fond no difference in the surface free energy between this two methods. We calculate the liquid bridge force between the two planes using the numerical surface free energy. This force is strong for small height, and decreases as the distance between the two planes, height, is increased. The liquid-gas system was also characterized studying the variation of internal energy and heat capacity with the temperature. For that, was performed simulation with the same proportion of liquid and gas particle, but different lattice size. The scale of the liquid-gas system was also studied, for low temperature, using different values to the interaction Jij.

On some Banach space constants arising in nonlinear fixed point and eigenvalue theory

[EN] As is well known, in any infinite-dimensional Banach space one may find fixed point free self-maps of the unit ball, retractions of the unit ball onto its boundary, contractions of the unit sphere, and nonzero maps without positive eigenvalues and normalized eigenvectors. In this paper, we give upper and lower estimates, or even explicit formulas, for the minimal Lipschitz constant and measure of noncompactness of such maps.

Systematic studies of protein immobilization by surface plasmon field-enhanced fluorescence spectroscopy

The research interest of this study is to investigate surface immobilization strategies for proteins and other biomolecules by the surface plasmon field-enhanced fluorescence spectroscopy (SPFS) technique. The recrystallization features of the S-layer proteins and the possibility of combining the S-layer lattice arrays with other functional molecules make this protein a prime candidate for supramolecular architectures. The recrystallization behavior on gold or on the secondary cell wall polymer (SCWP) was recorded by SPR. The optical thicknesses and surface densities for different protein layers were calculated. In DNA hybridization tests performed in order to discriminate different mismatches, recombinant S-layer-streptavidin fusion protein matrices showed their potential for new microarrays. Moreover, SCWPs coated gold chips, covered with a controlled and oriented assembly of S-layer fusion proteins, represent an even more sensitive fluorescence testing platform. Additionally, S-layer fusion proteins as the matrix for LHCII immobilization strongly demonstrate superiority over routine approaches, proving the possibility of utilizing them as a new strategy for biomolecular coupling. In the study of the SPFS hCG immunoassay, the biophysical and immunological characteristics of this glycoprotein hormone were presented first. After the investigation of the effect of the biotin thiol dilution on the coupling efficiently, the interfacial binding model including the appropriate binary SAM structure and the versatile streptavidin-biotin interaction was chosen as the basic supramolecular architecture for the fabrication of a SPFS-based immunoassay. Next, the affinity characteristics between different antibodies and hCG were measured via an equilibrium binding analysis, which is the first example for the titration of such a high affinity interaction by SPFS. The results agree very well with the constants derived from the literature. Finally, a sandwich assay and a competitive assay were selected as templates for SPFS-based hCG detection, and an excellent LOD of 0.15 mIU/ml was attained via the “one step” sandwich method. Such high sensitivity not only fulfills clinical requirements, but is also better than most other biosensors. Fully understanding how LHCII complexes transfer the sunlight energy directionally and efficiently to the reaction center is potentially useful for constructing biomimetic devices as solar cells. After the introduction of the structural and the spectroscopic features of LHCII, different surface immobilization strategies of LHCII were summarized next. Among them the strategy based on the His-tag and the immobilized metal (ion) affinity chromatography (IMAC) technique were of great interest and resulted in different kinds of home-fabricated His-tag chelating chips. Their substantial protein coupling capacity, maintenance of high biological activity and a remarkably repeatable binding ability on the same chip after regeneration was demonstrated. Moreover, different parameters related to the stability of surface coupled reconstituted complexes, including sucrose, detergent, lipid, oligomerization, temperature and circulation rate, were evaluated in order to standardize the most effective immobilization conditions. In addition, partial lipid bilayers obtained from LHCII contained proteo-liposomes fusion on the surface were observed by the QCM technique. Finally, the inter-complex energy transfer between neighboring LHCIIs on a gold protected silver surface by excitation with a blue laser (λ = 473nm) was recorded for the first time, and the factors influencing the energy transfer efficiency were evaluated.

Lattice preferred orientation in omphacite: Examples from the Tauern Window, Austria and the Western Gneiss Region, Norway

It is lively debated how eclogites find their way from deep to mid-crustal levels during exhumation. Different exhumation models for high-pressure and ultrahigh-pressure rocks were suggested in previous studies, based mainly on field observations and less on microstructural studies on the exhumed rocks. The development and improvement of electron microscopy techniques allows it, to focus interest on direct investigations of microstructures and crystallographic properties in eclogites. In this case, it is of importance to study the applicability of crystallographic measurements on eclogites for exhumation processes and to unravel which processes affect eclogite textures. Previous studies suggested a strong relationship between deformation and lattice preferred orientation (LPO) in omphacite but it is still unclear if the deformation is related to the exhumation of eclogites. This study is focused on the questions which processes affect omphacite LPO and if textural investigations of omphacite are applicable for studying eclogite exhumation. Therefore, eclogites from two examples in the Alps and in the Caledonides were collected systematically and investigated with respect to omphacite LPO by using the electron backscattered diffraction (EBSD) technique. Omphacite textures of the Tauern Window (Austria) and the Western Gneiss Region (Norway) were studied to compare lattice preferred orientation with field observations and suggested exhumation models from previous studies. The interpretation of omphacite textures, regarding the deformation regime is mainly based on numerical simulations in previous studies. Omphacite LPO patterns of the Eclogite Zone are clearly independent from any kind of exhumation process. The textures were generated during omphacite growth on the prograde path of eclogite development until metamorphic peak conditions. Field observations in the Eclogite Zone show that kinematics in garnet mica schist, surrounding the eclogites, strongly indicate an extrusion wedge geometry. Stretching lineations show top-N thrusting at the base and a top-S normal faulting with a sinistral shear component at the top of the Eclogite Zone. The different shear sense on both sides of the unit does not affect the omphacite textures in any way. The omphacite lattice preferred orientation patterns of the Western Gneiss Region can not be connected with any exhumation model. The textures were probably generated during the metamorphic peak and reflect the change from subduction to exhumation. Eclogite Zone and Western Gneiss Region differ significantly in size and especially in metamorphic conditions. While the Eclogite Zone is characterized by constant P-T conditions (600-650°C, 20-25 kbar), the Western Gneiss Region contains a wide P-T range from high- to ultrahigh pressure conditions (400-800°C, 20-35 kbar). In contrast to this, the omphacite textures of both units are very similar. This means that omphacite LPO is independent from P-T conditions and therefore from burial depth. Further, in both units, omphacite LPO is independent from grain and subgrain size as well as from any shape preferred orientation (SPO) on grain and subgrain scale. Overall, omphacite lattice preferred orientation are generated on the prograde part of omphacite development. Therefore, textural investigations on omphacite LPO are not applicable to study eclogite exhumation.

Thermal fluctuations and boundary conditions in the lattice Boltzmann method

The lattice Boltzmann method is a popular approach for simulating hydrodynamic interactions in soft matter and complex fluids. The solvent is represented on a discrete lattice whose nodes are populated by particle distributions that propagate on the discrete links between the nodes and undergo local collisions. On large length and time scales, the microdynamics leads to a hydrodynamic flow field that satisfies the Navier-Stokes equation. In this thesis, several extensions to the lattice Boltzmann method are developed. In complex fluids, for example suspensions, Brownian motion of the solutes is of paramount importance. However, it can not be simulated with the original lattice Boltzmann method because the dynamics is completely deterministic. It is possible, though, to introduce thermal fluctuations in order to reproduce the equations of fluctuating hydrodynamics. In this work, a generalized lattice gas model is used to systematically derive the fluctuating lattice Boltzmann equation from statistical mechanics principles. The stochastic part of the dynamics is interpreted as a Monte Carlo process, which is then required to satisfy the condition of detailed balance. This leads to an expression for the thermal fluctuations which implies that it is essential to thermalize all degrees of freedom of the system, including the kinetic modes. The new formalism guarantees that the fluctuating lattice Boltzmann equation is simultaneously consistent with both fluctuating hydrodynamics and statistical mechanics. This establishes a foundation for future extensions, such as the treatment of multi-phase and thermal flows. An important range of applications for the lattice Boltzmann method is formed by microfluidics. Fostered by the "lab-on-a-chip" paradigm, there is an increasing need for computer simulations which are able to complement the achievements of theory and experiment. Microfluidic systems are characterized by a large surface-to-volume ratio and, therefore, boundary conditions are of special relevance. On the microscale, the standard no-slip boundary condition used in hydrodynamics has to be replaced by a slip boundary condition. In this work, a boundary condition for lattice Boltzmann is constructed that allows the slip length to be tuned by a single model parameter. Furthermore, a conceptually new approach for constructing boundary conditions is explored, where the reduced symmetry at the boundary is explicitly incorporated into the lattice model. The lattice Boltzmann method is systematically extended to the reduced symmetry model. In the case of a Poiseuille flow in a plane channel, it is shown that a special choice of the collision operator is required to reproduce the correct flow profile. This systematic approach sheds light on the consequences of the reduced symmetry at the boundary and leads to a deeper understanding of boundary conditions in the lattice Boltzmann method. This can help to develop improved boundary conditions that lead to more accurate simulation results.

Fluid-structure interaction by a coupled lattice Boltzmann-finite element approach

In this thesis, a strategy to model the behavior of fluids and their interaction with deformable bodies is proposed. The fluid domain is modeled by using the lattice Boltzmann method, thus analyzing the fluid dynamics by a mesoscopic point of view. It has been proved that the solution provided by this method is equivalent to solve the Navier-Stokes equations for an incompressible flow with a second-order accuracy. Slender elastic structures idealized through beam finite elements are used. Large displacements are accounted for by using the corotational formulation. Structural dynamics is computed by using the Time Discontinuous Galerkin method. Therefore, two different solution procedures are used, one for the fluid domain and the other for the structural part, respectively. These two solvers need to communicate and to transfer each other several information, i.e. stresses, velocities, displacements. In order to guarantee a continuous, effective, and mutual exchange of information, a coupling strategy, consisting of three different algorithms, has been developed and numerically tested. In particular, the effectiveness of the three algorithms is shown in terms of interface energy artificially produced by the approximate fulfilling of compatibility and equilibrium conditions at the fluid-structure interface. The proposed coupled approach is used in order to solve different fluid-structure interaction problems, i.e. cantilever beams immersed in a viscous fluid, the impact of the hull of the ship on the marine free-surface, blood flow in a deformable vessels, and even flapping wings simulating the take-off of a butterfly. The good results achieved in each application highlight the effectiveness of the proposed methodology and of the C++ developed software to successfully approach several two-dimensional fluid-structure interaction problems.