Comportamento tribo-mecânico e desgaste adesivo de materiais em nanoescala: análises por dinâmica molecular e mecânica do contínuo.

As formulações baseadas na mecânica do contínuo, embora precisas até certo ponto, por vezes não podem ser utilizadas, ou não são conceitualmente corretas para o entendimento de fenômenos em escalas reduzidas. Estas limitações podem aparecer no estudo dos fenômenos tribológicos em escala nanométrica, que passam a necessitar de novos métodos experimentais, teóricos e computacionais que permitam explorar estes fenômenos com a resolução necessária. Simulações atomísticas são capazes de descrever fenômenos em pequena escala, porém, o número necessário de átomos modelados e, portanto, o custo computacional - geralmente torna-se bastante elevado. Por outro lado, os métodos de simulação associados à mecânica do contínuo são mais interessantes em relação ao custo computacional, mas não são precisos na escala atômica. A combinação entre essas duas abordagens pode, então, permitir uma compreensão mais realista dos fenômenos da tribologia. Neste trabalho, discutem-se os conceitos básicos e modelos de atrito em escala atômica e apresentam-se estudos, por meio de simulação numérica, para a análise e compreensão dos mecanismos de atrito e desgaste no contato entre materiais. O problema é abordado em diferentes escalas, e propõe-se uma abordagem conjunta entre a Mecânica do Contínuo e a Dinâmica Molecular. Para tanto, foram executadas simulações numéricas, com complexidade crescente, do contato entre superfícies, partindo-se de um primeiro modelo que simula o efeito de defeitos cristalinos no fenômeno de escorregamento puro, considerando a Dinâmica Molecular. Posteriormente, inseriu-se, nos modelos da mecânica do contínuo, considerações sobre o fenômeno de adesão. A validação dos resultados é feita pela comparação entre as duas abordagens e com a literatura.

Crystal Structures, Magnetic Structures and Photophysics in Supramolecular Transition-Metal Oxalate Compounds

Polymeric two- and three-dimensional, homo- and heterometallic oxalatebridged coordination compounds offer exciting opportunities, mainly in the fields of molecular magnetism and photophysics. Given that a large variety of magnetic phenomena have been reported so far from these molecular magnets, very limited experience is gained from elastic neutron scattering experiments. Therefore, with two examples, we will address the topic of the elucidation of magnetic structures by means of the neutron scattering technique. In addition, due to the possibility of the variation of different metal ions in varying oxidation states, interesting photophysical processes can be observed within the extended three-dimensional host/guest systems.

Coloramatrix : a thermally controlled liquid crystal alphanumeric display /

"June, 1971."

Tractable molecular theory of transport of Lennard-Jones fluids in nanopores

We present here a tractable theory of transport of simple fluids in cylindrical nanopores, which is applicable over a wide range of densities and pore sizes. In the Henry law low-density region the theory considers the trajectories of molecules oscillating between diffuse wall collisions, while at higher densities beyond this region the contribution from viscous flow becomes significant and is included through our recent approach utilizing a local average density model. The model is validated by means of equilibrium as well nonequilibrium molecular dynamics simulations of supercritical methane transport in cylindrical silica pores over a wide range of temperature, density, and pore size. The model for the Henry law region is exact and found to yield an excellent match with simulations at all conditions, including the single-file region of very small pore size where it is shown to provide the density-independent collective transport coefficient. It is also shown that in the absence of dispersive interactions the model reduces to the classical Knudsen result, but in the presence of such interactions the latter model drastically overpredicts the transport coefficient. For larger micropores beyond the single-file region the transport coefficient is reduced at high density because of intermolecular interactions and hindrance to particle crossings leading to a large decrease in surface slip that is not well represented by the model. However, for mesopores the transport coefficient increases monotonically with density, over the range studied, and is very well predicted by the theory, though at very high density the contribution from surface slip is slightly overpredicted. It is also seen that the concept of activated diffusion, commonly associated with diffusion in small pores, is fundamentally invalid for smooth pores, and the apparent activation energy is not simply related to the minimum pore potential or the adsorption energy as generally assumed. (C) 2004 American Institute of Physics.

Modeling molecular transport in slit pores

We examine the transport of methane in microporous carbon by performing equilibrium and nonequilibrium molecular dynamics simulations over a range of pore sizes, densities, and temperatures. We interpret these simulation results using two models of the transport process. At low densities, we consider a molecular flow model, in which intermolecular interactions are neglected, and find excellent agreement between transport diffusion coefficients determined from simulation, and those predicted by the model. Simulation results indicate that the model can be applied up to fluid densities of the order to 0.1-1 nm(-3). Above these densities, we consider a slip flow model, combining hydrodynamic theory with a slip condition at the solid-fluid interface. As the diffusion coefficient at low densities can be accurately determined by the molecular flow model, we also consider a model where the slip condition is supplied by the molecular flow model. We find that both density-dependent models provide a useful means of estimating the transport coefficient that compares well with simulation. (C) 2004 American Institute of Physics.

Diffusion of n-decane in mesoporous MCM-41 silicas

We investigate here the diffusion of n-decane in nanoporous MCM-41 silicas with pore diameters between 3.0 and 4.3 nm, and at various temperatures and purge flow rates, by the Zero Length Column method. A complete-time-range analysis of desorption curves is used to derive the diffusion coefficient, and the effect of pore size, purge flow rate and temperature on the diffusion character is systematically studied. The results show that the calculated low-coverage diffusivity values are strongly dependent on temperature but only weakly dependent on pore size. The study reveals that transport is controlled by intracrystalline diffusion and dominated by sorbate-sorbent interaction, with the experimental isosteric heat matching the potential energy of flat-lying n-decane molecules on the surface, determined using a united atom model. The diffusion activation energy and adsorption isosteric heat at zero loading for the different pore size MCM-41 samples vary in a narrow range respectively, and their ratio is essentially constant over the pore size range studied. The study shows that the ZLC method is an effective tool to investigate the diffusion kinetics of hydrocarbons in mesoporous MCM-41 materials. (c) 2005 Elsevier Inc. All rights reserved.

Quantum effect induced reverse kinetic molecular sieving in microporous materials

We report kinetic molecular sieving of hydrogen and deuterium in zeolite rho at low temperatures, using atomistic molecular dynamics simulations incorporating quantum effects via the Feynman-Hibbs approach. We find that diffusivities of confined molecules decrease when quantum effects are considered, in contrast with bulk fluids which show an increase. Indeed, at low temperatures, a reverse kinetic sieving effect is demonstrated in which the heavier isotope, deuterium, diffuses faster than hydrogen. At 65 K, the flux selectivity is as high as 46, indicating a good potential for isotope separation.

Application of a generalized thermodynamic approach to characterize mesoporous materials

Equilibrium adsorption and desorption in mesoporous adsorbents is considered on the basis of rigorous thermodynamic analysis, in which the curvature-dependent solid-fluid potential and the compressibility of the adsorbed phase are accounted for. The compressibility of the adsorbed phase is considered for the first time in the literature in the framework of a rigorous thermodynamic approach. Our model is a further development of continuum thermodynamic approaches proposed by Derjaguin and Broekhoff and de Boer, and it is based on a reference isotherm of a non-porous material having the same chemical structure as that of the pore wall. In this improved thermodynamic model, we incorporated a prescription for transforming the solid-fluid potential exerted by the flat reference surface to the potential inside cylindrical and spherical pores. We relax the assumption that the adsorbed film density is constant and equal to that of the saturated liquid. Instead, the density of the adsorbed fluid is allowed to vary over the adsorbed film thickness and is calculated by an equation of state. As a result, the model is capable to describe the adsorption-desorption reversibility in cylindrical pores having diameter less than 2 nm. The generalized thermodynamic model may be applied to the pore size characterization of mesoporous materials instead of much more time-consuming molecular approaches. (c) 2005 Elsevier B.V. All rights reserved.

Periodic mesoporous organosilica hollow spheres with tunable wall thickness

Periodic mesoporous organosilica (PMO) hollow spheres with tunable wall thickness have been successfully synthesized by a new vesicle and a liquid crystal “dual templating” mechanism, which may be applicable for drug and DNA delivery systems, biomolecular encapsulation, as well as nanoreactors for conducting biological reactions at the molecular levels.

Molecular recognition of an RNA trafficking element by heterogeneous nuclear ribonucleoprotein A2

Heterogeneous nuclear ribonucleoprotein (hnRNP) A2 is a multitasking protein involved in RNA packaging, alternative splicing of pre-mRNA. telomere maintenance, cytoplasmic RNA trafficking, and translation. It binds short segments of single-stranded nucleic acids, including the A2RE11 RNA element that is necessary and sufficient for cytoplasmic transport of a subset of rnRNAs in oligodendrocytes and neurons. We have explored the structures of hnRNP A2, its RNA recognition motifs (RRMs) and Gly-rich module, and the RRM complexes with A2RE11. Circular dichroism spectroscopy showed that the secondary structure of the first 189 residues of hnRNP A2 parallels that of the tandem beta alpha beta beta alpha beta RRMs of its paralogue, hnRNP A1, previously deduced from X-ray diffraction studies. The unusual GRD was shown to have substantial beta-sheet and beta-turn structure. Sedimentation equilibrium and circular dichroism results were consistent with the tandem RRM region being monomeric and supported earlier evidence for the binding of two A2RE11 oligoribonucleotides to this domain, in contrast to the protein dimer formed by the complex of hnRNP A1 with the telomeric ssDNA repeat. A three-dimensional structure for the N-terminal, two-RRM-containing segment of hnRNP A2 was derived by homology modeling. This structure was used to derive a model for the complex with A2RE11 using the previously described interaction of pairs of stacked nucleotides with aromatic residues on the RRM beta-sheet platforms, conserved in other RRM-RNA complexes, together with biochemical data and molecular dynamics-based observations of inter-RRM mobility.

Characterization of the structure of RAMP1 by mutagenesis and molecular modeling

Receptor activity modifying proteins (RAMPs) are a family of single-pass transmembrane proteins that dimerize with G-protein-coupled receptors. They may alter the ligand recognition properties of the receptors (particularly for the calcitonin receptor-like receptor, CLR). Very little structural information is available about RAMPs. Here, an ab initio model has been generated for the extracellular domain of RAMP1. The disulfide bond arrangement (Cys 27-Cys82, Cys40-Cys72, and Cys 57-Cys104) was determined by site-directed mutagenesis. The secondary structure (a-helices from residues 29-51, 60-80, and 87-100) was established from a consensus of predictive routines. Using these constraints, an assemblage of 25,000 structures was constructed and these were ranked using an all-atom statistical potential. The best 1000 conformations were energy minimized. The lowest scoring model was refined by molecular dynamics simulation. To validate our strategy, the same methods were applied to three proteins of known structure; PDB:1HP8, PDB:1V54 chain H (residues 21-85), and PDB:1T0P. When compared to the crystal structures, the models had root mean-square deviations of 3.8 Å, 4.1 Å, and 4.0 Å, respectively. The model of RAMP1 suggested that Phe93, Tyr 100, and Phe101 form a binding interface for CLR, whereas Trp74 and Phe92 may interact with ligands that bind to the CLR/RAMP1 heterodimer. © 2006 by the Biophysical Society.

21-residue peptide's dynamics at and between elementary structural transitions

Elementary conformational changes of the backbone of a 21-residue peptide A5(A3RA)3A are studied using molecular dynamics simulations in explicit water. The processes of the conformational transitions and the regimes of stationary fluctuations between them are investigated using minimal perturbations of the system. The perturbations consist of a few degrees rotation of the velocity of one of the systems' atoms and keep the system on the same energy surface. It is found that (i) the system dynamics is insignificantly changed by the perturbations in the regimes between the transitions; (ii) it is very sensitive to the perturbations just before the transitions that prevents the peptide from making the transitions; and (iii) the perturbation of any atom of the system, including distant water molecules is equally effective in preventing the transition. The latter implies strongly collective dynamics of the peptide and water during the transitions.

Identifying and correcting non-Markov states in peptide conformational dynamics

Conformational transitions in proteins define their biological activity and can be investigated in detail using the Markov state model. The fundamental assumption on the transitions between the states, their Markov property, is critical in this framework. We test this assumption by analyzing the transitions obtained directly from the dynamics of a molecular dynamics simulated peptide valine-proline-alanine-leucine and states defined phenomenologically using clustering in dihedral space. We find that the transitions are Markovian at the time scale of ˜ 50 ps and longer. However, at the time scale of 30–40 ps the dynamics loses its Markov property. Our methodology reveals the mechanism that leads to non-Markov behavior. It also provides a way of regrouping the conformations into new states that now possess the required Markov property of their dynamics.

Experiments and analysis of combined diffraction and self diffraction effects in a nematic liquid crystal cell

The potential for nonlinear optical processes in nematic-liquid-crystal cells is great due to the large phase changes resulting from reorientation of the nematic-liquid-crystal director. Here the combination of diffraction and self-diffraction effects are studied simultaneously by the use of a pair of focused laser beams which are coincident on a homeotropically aligned liquid-crystal cell. The result is a complicated diffraction pattern in the far field. This is analyzed in terms of the continuum theory for liquid crystals, using a one-elastic-constant approximation to solve the reorientation profile. Very good comparison between theory and experiment is obtained. An interesting transient grating, existing due to the viscosity of the liquid-crystal material, is observed in theory and practice for large cell-tilt angles.

Ion interactions with the carbon nanotube surface in aqueous solutions:understanding the molecular mechanisms

We study the molecular mechanisms of alkali halide ion interactions with the single-wall carbon nanotube surface in water by means of fully atomistic molecular dynamics simulations. We focus on the basic physical-chemical principles of ion–nanotube interactions in aqueous solutions and discuss them in light of recent experimental findings on selective ion effects on carbon nanotubes.