Stochastic simulation of time-series models combined with geostatistics to predict water-table scenarios in a Guarani Aquifer System outcrop area, Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Monte Carlo investigations of intermolecular interactions in water-amide mixtures

Monte Carlo simulations of water-amides (amide=fonnamide-FOR, methylfonnamide-NMF and dimethylformamide-DMF) solutions have been carried out in the NpT ensemble at 308 K and 1 atm. The structure and excess enthalpy of the mixtures as a function of the composition have been investigated. The TIP4P model was used for simulating water and six-site models previously optimized in this laboratory were used for simulating the liquid amides. The intermolecular interaction energy was calculated using the classical 6-12 Lennard-Jones potential plus a Coulomb term. The interaction energy between solute and solvent has been partitioned what leads to a better understanding of the behavior of the enthalpy of mixture obtained for the three solutions experimentally. Radial distribution functions for the water-amides correlations permit to explore the intermolecular interactions between the molecules. The results show that three, two and one hydrogen bonds between the water and the amide molecules are formed in the FOR, NMF and DMF-water solutions, respectively. These H-bonds are, respectively, stronger for DMF-water, NMF-water and FOR-water. In the NMF-water solution, the interaction between the methyl group of the NMF and the oxygen of the water plays a role in the stabilization of the aqueous solution quite similar to that of an H-bond in the FOR-water solution. (c) 2005 Elsevier B.V. All rights reserved.

Surface pressure-area isotherms for Langmuir monolayers and a docking molecular orientation of perylene tetracarboxylic derivatives on a water surface

The surface pressure-molecular area (pi-A) isotherms for Langmuir monolayers of four perylenetetracarboxylic (PTCD) derivatives, measured with varying subphase temperatures and compression speeds, are reported. The behavior of these PTCD derivatives at the water-air interface is modeled using the rigid docking method. This approach is the first attempt to model the molecular orientation of PTCD on the water surface to be compared with experimental Langmuir isotherms. Through this methodology, it would be possible to anticipate aggregation and determine if favorable spatial orientations of perylenes are generated on the water surface. The pi-A isotherm experiments show that these molecules can support high surface pressures, indicating strong packing on the water surface and that the isotherms are compression speed independent but temperature dependent. The molecular orientation and stacking was further examined in Langmuir-Blodgett (LB) monolayers deposited onto glass and glass coated with Ag island films using UV-visible absorption and surface-enhanced fluorescence (SEF) measurements.

Distribution of Cr, Ni, Cu, Cd and Pb in different molecular size of humic fractions extracted from water and sediment samples collected at Anhumas reservoir - Araraquara/SP

In this work was studied the distribution of Cr, Ni, Cu, Cd and Pb in humic fractions with different molecular size. The HS were extracted from waters (AHS), surface sediments (HESS), interface water sediment (HSIS) and bottom sediment (HSBS) collected in the Anhumas surface water collection reservoir, located in the district of Araraquara - São Paulo State Brazil. The humic substances were extracted by procedures recommended by International Humic Substances Society (IHSS). After purification by dialysis, the humic substances were fractionated using a multistage tangential flow ultrafiltration system. The fractionation patterns of HS characterized a mass distribution relatively uniform among the fractions with different molecular sizes, with larger values in the fractions F-2 (20.8%) and F-4 (23.8%), Except for the ions Pb(II) and Cu(II), which presented relatively higher concentrations in the fractions F-2 and F-4, respectively. In general, chromium, nickel, cadmium and lead have similar distributions in the five fractions with larger and medium molecular sizes (F-1 to F-5). With relation to the mass distributions in the different humic substances fractions extracted from sediment samples collected at three depth, they presented 42-48% of HS in the fractions with larger molecular sizes (F-1 and F-2), 29-31% in the middle fractions (F-3 and F-4) and 13-20% in the fractions with smaller molecular sizes (F-5 and F-6). In general, the metallic ions presented distributions similar among the respective fractions F-1 to F-6, Exceptions for Pb(II) and M(II) in surface sediment with concentrations relatively smaller in the fractions F-2 and F-4, respectively,

Molecular dynamics simulation on devitrification: Isothermal devitrification and thermodynamics of PbF2 glasses

The vitrification and devitrification features of lead fluoride are investigated by means of molecular dynamic simulations. The influence of heating rate on the devitrification temperature as well as the dependence of the glass properties on its thermal history, i.e., the cooling rate employed, is identified. As expected, different glasses are obtained when the cooling rates differ. Diffusion coefficient analysis during heating of glass and crystal, indicates that the presence of defects on the glassy matrix favors the transition processes from the ionic to a superionic state, with high mobility of fluorine atoms, responsible for the high anionic conduction of lead fluoride. Nonisothermal and isothermal devitrification processes are simulated in glasses obtained at different cooling rates and structural organizations occurring during the heat treatments are clearly observed. When a fast cooling rate is employed during the glass formation, the devitrification of a single crystal (limited by the cell dimensions) is observed, while the glass obtained with slower cooling rate, allowing relaxations and organization of various regions on the glass bulk during the cooling process, devitrifies in more than one crystalline plane. (C) 2004 American Institute of Physics.

Theoretical studies of liquids by computer simulations: the water-acetone mixture.

Monte Carlo simulation results for pure liquid acetone and water-acetone mixtures calculated in the isothermal and isobaric (NPT) ensemble at T=298K and p=1.0atm are presented. The TIP4P model was used for water and optimized potential for liquid simulation (OPLS) force field parameters used for acetone. The results obtained for the average configurational energy as a function of the mole fraction are in good accord with experimental data. Energy partitioning and co-ordination numbers results calculated for equimolar water-acetone solution are compared to similar data obtained for other water-organic liquid mixtures. These results show an increase in water-water interaction energy and co-ordination numbers when the interaction between water and organic liquid molecules decrease. Distribution functions for pure liquid acetone and water-acetone mixtures are presented. Dipole-dipole angular correlation functions obtained for pure liquid acetone show a predominance of dimers with parallel alignment of dipole moments. Radial distribution functions from water-acetone interaction show characteristic features of hydrogen bonded liquids. Radial and angular distribution functions for water-water correlation calculated in pure water and in equimolar water-acetone mixture are compared, showing very similar features in both systems. (C) 1999 Elsevier B.V. B.V. All rights reserved.

Application of a new reverse Monte Carlo algorithm to polyatomic molecular systems. I. Liquid water

Using a new reverse Monte Carlo algorithm, we present simulations that reproduce very well several structural and thermodynamic properties of liquid water. Both Monte Carlo, molecular dynamics simulations and experimental radial distribution functions used as input are accurately reproduced using a small number of molecules and no external constraints. Ad hoc energy and hydrogen bond analysis show the physical consistency and limitations of the generated RMC configurations. (C) 2001 American Institute of Physics.

Solid mass falling into the reservoirs shallow water equations validity from the engineering point of view

Water waves generated by a solid mass is a complex phenomenon discussed in this paper by numerical and experimental approaches. A model based on shallow water equations with shocks (Saint Venant) has developed. It can reproduce the amplitude and the energy of the wave quite well, but because it consistently generates a hydraulic jump, it is able to reproduce the profile, in the case of high relative thickness of slide, but in the case of small relative thickness it is unable to reproduce the amplitude of the wave. As the momentum conservation is not verified during the phase of wave creation, a second technique based on discharge transfer coefficient α, is introduced at the zone of impact. Numerical tests have been performed and validated this technique from the experimental results of the wave's height obtained in a flume.

Study of water and dimethylformamide interaction by computer simulation

Monte Carlo simulations of water-dimethylformamide (DMF) mixtures were performed in the isothermal and isobaric ensemble at 298.15 K and 1 atm. The intermolecular interaction energy was calculated using the classical 6-12 Lennard-Jones pairwise potential plus a Coulomb term. The TIP4P model was used for simulating water molecules, and a six-site model previously optimised by us was used to represent DMF. The potential energy for the water-DMF interaction was obtained via standard geometric combining rules using the original potential parameters for the pure liquids. The radial distribution functions calculated for water-DMF mixtures show well characterised hydrogen bonds between the oxygen site of DMF and hydrogen of water. A structureless correlation curve was observed for the interaction between the hydrogen site of the carbonyl group and the oxygen site of water. Hydration effects on the stabilisation of the DMF molecule in aqueous solution have been investigated using statistical perturbation theory. The results show that energetic changes involved in the hydration process are not strong enough to stabilise another configuration of DMF than the planar one.

The use of molecular spectra simulation for diagnostics of reactive flows

The C 2 * radical is used as a system probe tool to the reactive flow diagnostic, and it was chosen due to its large occurrence in plasma and combustion in aeronautics and aerospace applications. The rotational temperatures of C 2 * species were determined by the comparison between experimental and theoretical data. The simulation code was developed by the authors, using C++ language and the object oriented paradigm, and it includes a set of new tools that increase the efficacy of the C 2 * probe to determine the rotational temperature of the system. A brute force approach for the determination of spectral parameters was adopted in this version of the computer code. The statistical parameter c 2 was used as an objective criterion to determine the better match of experimental and synthesized spectra. The results showed that the program works even with low-quality experimental data, typically collected from in situ airborne compact apparatus. The technique was applied to flames of a Bunsen burner, and the rotational temperature of ca. 2100 K was calculated.

Clinical and molecular study of a new form of hereditary myotonia in Murrah water buffalo

Hereditary myotonia caused by mutations in CLCN1 has been previously described in humans, goats, dogs, mice and horses. The goal of this study was to characterize the clinical, morphological and genetic features of hereditary myotonia in Murrah buffalo. Clinical and laboratory evaluations were performed on affected and normal animals. CLCN1 cDNA and the relevant genomic region from normal and affected animals were sequenced. The affected animals exhibited muscle hypertrophy and stiffness. Myotonic discharges were observed during EMG, and dystrophic changes were not present in skeletal muscle biopsies; the last 43 nucleotides of exon-3 of the CLCN1 mRNA were deleted. Cloning of the genomic fragment revealed that the exclusion of this exonic sequence was caused by aberrant splicing, which was associated with the presence of a synonymous SNP in exon-3 (c.396C>T). The mutant allele triggered the efficient use of an ectopic 5' splice donor site located at nucleotides 90-91 of exon-3. The predicted impact of this aberrant splicing event is the alteration of the CLCN1 translational reading frame, which results in the incorporation of 24 unrelated amino acids followed by a premature stop codon. Copyright © 2012 Elsevier B.V. All rights reserved.

Molecular and serological prevalence of Babesia bovis and Babesia bigemina in water buffaloes in the north region of Brazil

Bovine babesiosis is a tick-borne disease caused mainly by Babesia bovis and Babesia bigemina, which are associated to considerable economic losses in cattle herds worldwide. Approximately 60% of buffalo herds in South America are located in Northern Brazil. Little is known about the impact of babesiosis on buffalo herds in Brazil. The present work aimed to verify the occurrence of B. bovis and B. bigemina in 542 water buffaloes in the state of Pará, Northern Brazil, using molecular and serological techniques. The percentage of seropositive animals for B. bovis and B. bigemina was 41.2% and 19.0%, respectively, by ELISA. B. bovis and B. bigemina DNA were detected in 15 and 16% of sampled buffaloes, respectively. A high correlation (Kappa index of 0.9) between serological and molecular tests suggests that the combination of the utilized techniques in the present study is suitable for babesiosis diagnosis in an endemic unstable area. Significantly difference of positivity for serological and molecular assays was verified to localities and reproductive status of sampled animals, but not between buffalo breeds. The immune status of sampled buffaloes associated to the circulation of babesiosis agents in sampled population suggests that the studied area is at risk to clinical babesiosis outbreaks. Furthermore, this study demonstrated that this region can be classified as endemically unstable. © 2013 Elsevier B.V.

Estudo por dinâmica molecular da estabilidade conformacional de dímeros do peptídeo Eumenine mastoparan-AF em água e mistura TFE-água

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Simulação de poli(etileno glicol) em água por dinâmica molecular

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Estudos conformacionais por dinâmica molecular de peptídeos antimicrobianos da família dos Mastoparanos em misturas de TFE-água

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)