Non-additivity of attractive potentials in modeling of N-2 and Ar adsorption isotherms on graphitized carbon black and porous carbon by means of density functional theory

We present a new approach accounting for the nonadditivity of attractive parts of solid-fluid and fluidfluid potentials to improve the quality of the description of nitrogen and argon adsorption isotherms on graphitized carbon black in the framework of non-local density functional theory. We show that the strong solid-fluid interaction in the first monolayer decreases the fluid-fluid interaction, which prevents the twodimensional phase transition to occur. This results in smoother isotherm, which agrees much better with experimental data. In the region of multi-layer coverage the conventional non-local density functional theory and grand canonical Monte Carlo simulations are known to over-predict the amount adsorbed against experimental isotherms. Accounting for the non-additivity factor decreases the solid-fluid interaction with the increase of intermolecular interactions in the dense adsorbed fluid, preventing the over-prediction of loading in the region of multi-layer adsorption. Such an improvement of the non-local density functional theory allows us to describe experimental nitrogen and argon isotherms on carbon black quite accurately with mean error of 2.5 to 5.8% instead of 17 to 26% in the conventional technique. With this approach, the local isotherms of model pores can be derived, and consequently a more reliab * le pore size distribution can be obtained. We illustrate this by applying our theory against nitrogen and argon isotherms on a number of activated carbons. The fitting between our model and the data is much better than the conventional NLDFT, suggesting the more reliable PSD obtained with our approach.

Momentum transfer effects in the transport of adsorbate at a nano-patterned surface

Adsorbate molecules scattered in the repulsive field of a surface feature in the form of a semi-cylindrical stripe may be considered as a simple model for a nano-patterned surface. The extent of scattering was conveniently expressed as the tangential momentum accommodation coefficient. An analytical result was obtained using a simple local specular reflection hypothesis in contrast to the more complicated situation of an array of atoms discussed elsewhere, in which screening and secondary reflection may occur (Nicholson and Bhatia 2005). It was also demonstrated that a simple 2D representation leads to the same result for the tangential momentum accommodation coefficient.

Scattering and tangential momentum accommodation at a 2D adsorbate-solid interface

We calculate tangential momentum coefficients for the exchange of momentum between molecules in transport and the internal surface of a membrane pore, modelled as a simple atomic structure. We introduce a local specular reflection (LSR) hypothesis, which states that impinging molecules undergo mirror-like reflection in a plane tangent to a surface atom at the point of impact. As a consequence, the components of the velocity, parallel to the direction of flow will (in general) change on impact. The overall effect is a loss of tangential momentum, since more is lost in the upstream direction than is gained in the downstream direction. The loss of tangential momentum is greater when the size ratio of fluid to solid atom is small, allowing more steeply inclined impact planes to become accessible to the fluid phase molecules. (c) 2005 Elsevier B.V. All rights reserved.

Exponential integrators and a dual-scale model for wood drying

For the timber industry, the ability to simulate the drying of wood is invaluable for manufacturing high quality wood products. Mathematically, however, modelling the drying of a wet porous material, such as wood, is a diffcult task due to its heterogeneous and anisotropic nature, and the complex geometry of the underlying pore structure. The well{ developed macroscopic modelling approach involves writing down classical conservation equations at a length scale where physical quantities (e.g., porosity) can be interpreted as averaged values over a small volume (typically containing hundreds or thousands of pores). This averaging procedure produces balance equations that resemble those of a continuum with the exception that effective coeffcients appear in their deffnitions. Exponential integrators are numerical schemes for initial value problems involving a system of ordinary differential equations. These methods differ from popular Newton{Krylov implicit methods (i.e., those based on the backward differentiation formulae (BDF)) in that they do not require the solution of a system of nonlinear equations at each time step but rather they require computation of matrix{vector products involving the exponential of the Jacobian matrix. Although originally appearing in the 1960s, exponential integrators have recently experienced a resurgence in interest due to a greater undertaking of research in Krylov subspace methods for matrix function approximation. One of the simplest examples of an exponential integrator is the exponential Euler method (EEM), which requires, at each time step, approximation of φ(A)b, where φ(z) = (ez - 1)/z, A E Rnxn and b E Rn. For drying in porous media, the most comprehensive macroscopic formulation is TransPore [Perre and Turner, Chem. Eng. J., 86: 117-131, 2002], which features three coupled, nonlinear partial differential equations. The focus of the first part of this thesis is the use of the exponential Euler method (EEM) for performing the time integration of the macroscopic set of equations featured in TransPore. In particular, a new variable{ stepsize algorithm for EEM is presented within a Krylov subspace framework, which allows control of the error during the integration process. The performance of the new algorithm highlights the great potential of exponential integrators not only for drying applications but across all disciplines of transport phenomena. For example, when applied to well{ known benchmark problems involving single{phase liquid ow in heterogeneous soils, the proposed algorithm requires half the number of function evaluations than that required for an equivalent (sophisticated) Newton{Krylov BDF implementation. Furthermore for all drying configurations tested, the new algorithm always produces, in less computational time, a solution of higher accuracy than the existing backward Euler module featured in TransPore. Some new results relating to Krylov subspace approximation of '(A)b are also developed in this thesis. Most notably, an alternative derivation of the approximation error estimate of Hochbruck, Lubich and Selhofer [SIAM J. Sci. Comput., 19(5): 1552{1574, 1998] is provided, which reveals why it performs well in the error control procedure. Two of the main drawbacks of the macroscopic approach outlined above include the effective coefficients must be supplied to the model, and it fails for some drying configurations, where typical dual{scale mechanisms occur. In the second part of this thesis, a new dual{scale approach for simulating wood drying is proposed that couples the porous medium (macroscale) with the underlying pore structure (microscale). The proposed model is applied to the convective drying of softwood at low temperatures and is valid in the so{called hygroscopic range, where hygroscopically held liquid water is present in the solid phase and water exits only as vapour in the pores. Coupling between scales is achieved by imposing the macroscopic gradient on the microscopic field using suitably defined periodic boundary conditions, which allows the macroscopic ux to be defined as an average of the microscopic ux over the unit cell. This formulation provides a first step for moving from the macroscopic formulation featured in TransPore to a comprehensive dual{scale formulation capable of addressing any drying configuration. Simulation results reported for a sample of spruce highlight the potential and flexibility of the new dual{scale approach. In particular, for a given unit cell configuration it is not necessary to supply the effective coefficients prior to each simulation.

Structure of a cyclic water tetramer in a nucleotide crystal host and a hypothetical model for water cluster growth

Structure of a cyclic water tetramer in channels (pores) formed by self-assembly of N6-methyl-5'-AMP center dot Na-2 molecules is described and a hypothetical model is proposed for growth of water clusters. (C) 2010 Elsevier B.V. All rights reserved.

A numerical model of a liquid-feed solid polymer electrolyte DMFC and its experimental validation

A one-dimensional, biphasic, multicomponent steady-state model based on phenomenological transport equations for the catalyst layer, diffusion layer, and polymeric electrolyte membrane has been developed for a liquid-feed solid polymer electrolyte direct methanol fuel cell (SPE- DMFC). The model employs three important requisites: (i) implementation of analytical treatment of nonlinear terms to obtain a faster numerical solution as also to render the iterative scheme easier to converge, (ii) an appropriate description of two-phase transport phenomena in the diffusive region of the cell to account for flooding and water condensation/evaporation effects, and (iii) treatment of polarization effects due to methanol crossover. An improved numerical solution has been achieved by coupling analytical integration of kinetics and transport equations in the reaction layer, which explicitly include the effect of concentration and pressure gradient on cell polarization within the bulk catalyst layer. In particular, the integrated kinetic treatment explicitly accounts for the nonhomogeneous porous structure of the catalyst layer and the diffusion of reactants within and between the pores in the cathode. At the anode, the analytical integration of electrode kinetics has been obtained within the assumption of macrohomogeneous electrode porous structure, because methanol transport in a liquid-feed SPE- DMFC is essentially a single-phase process because of the high miscibility of methanol with water and its higher concentration in relation to gaseous reactants. A simple empirical model accounts for the effect of capillary forces on liquid-phase saturation in the diffusion layer. Consequently, diffusive and convective flow equations, comprising Nernst-Plank relation for solutes, Darcy law for liquid water, and Stefan-Maxwell equation for gaseous species, have been modified to include the capillary flow contribution to transport. To understand fully the role of model parameters in simulating the performance of the DMCF, we have carried out its parametric study. An experimental validation of model has also been carried out. (C) 2003 The Electrochemical Society.

A generalized model for the effective thermal conductivity of porous media based on self-similarity

A generalized model for the effective thermal conductivity of porous media is derived based on the fact that statistical self-similarity exists in porous media. The proposed model assumes that porous media consist of two portions: randomly distributed non-touching particles and self-similarly distributed particles contacting each other with resistance. The latter are simulated by Sierpinski carpets with side length L = 13 and cutout size C = 3, 5, 7 and 9, respectively, depending upon the porosity concerned. Recursive formulae are presented and expressed as a function of porosity, ratio of areas, ratio of component thermal conductivities and contact resistance, and there is no empirical constant and every parameter has a clear physical meaning. The model predictions are compared with the existing experimental data, and good agreement is found in a wide range of porosity of 0.14-0.80, and this verifies the validity of the proposed model.

Can carbon surface oxidation shift the pore size distribution curve calculated from Ar, N(2) and CO(2) adsorption isotherms? Simulation results for a realistic carbon model

Using the virtual porous carbon model proposed by Harris et al, we study the effect of carbon surface oxidation on the pore size distribution (PSD) curve determined from simulated Ar, N(2) and CO(2) isotherms. It is assumed that surface oxidation is not destructive for the carbon skeleton, and that all pores are accessible for studied molecules (i.e., only the effect of the change of surface chemical composition is studied). The results obtained show two important things, i.e., oxidation of the carbon surface very slightly changes the absolute porosity (calculated from the geometric method of Bhattacharya and Gubbins (BG)); however, PSD curves calculated from simulated isotherms are to a greater or lesser extent affected by the presence of surface oxides. The most reliable results are obtained from Ar adsorption data. Not only is adsorption of this adsorbate practically independent from the presence of surface oxides, but, more importantly, for this molecule one can apply the slit-like model of pores as the first approach to recover the average pore diameter of a real carbon structure. For nitrogen, the effect of carbon surface chemical composition is observed due to the quadrupole moment of this molecule, and this effect shifts the PSD curves compared to Ar. The largest differences are seen for CO2, and it is clearly demonstrated that the PSD curves obtained from adsorption isotherms of this molecule contain artificial peaks and the average pore diameter is strongly influenced by the presence of electrostatic adsorbate-adsorbate as well as adsorbate-adsorbent interactions.

Interactions of mast cell degranulating peptides with model membranes: A comparative biophysical study

In the last decade, there has been renewed interest in biologically active peptides in fields like allergy, autoimmume diseases and antibiotic therapy. Mast cell degranulating peptides mimic G-protein receptors, showing different activity levels even among homologous peptides. Another important feature is their ability to interact directly with membrane phospholipids, in a fast and concentration-dependent way. The mechanism of action of peptide HR1 on model membranes was investigated comparatively to other mast cell degranulating peptides (Mastoparan, Eumenitin and Anoplin) to evidence the features that modulate their selectivity. Using vesicle leakage, single-channel recordings and zeta-potential measurements, we demonstrated that HR1 preferentially binds to anionic bilayers, accumulates, folds, and at very low concentrations, is able to insert and create membrane spanning ion-selective pores. We discuss the ion selectivity character of the pores based on the neutralization or screening of the peptides charges by the bilayer head group charges or dipoles. (C) 2009 Elsevier Inc. All rights reserved.

Melting Regime of the Anionic Phospholipid DMPG: New Lamellar Phase and Porous Bilayer Model

Aqueous dispersions of the anionic phospholipid dimyristoyl phosphatidylglycerol (DMPG) at pH above the apparent pK of DMPG and concentrations in the interval 70-300 mM have been investigated by small (SAXS) and wide-angle X-ray scattering, differential scanning calorimetry, and polarized optical microscopy. The order. disorder transition of the hydrocarbon chains occurs along an interval of about 10 degrees C (between T(m)(on) similar to 20 degrees C and T(m)(off) similar to 30 degrees C). Such melting regime was previously characterized at lower concentrations, up to 70 mM DMPG, when sample transparency was correlated with the presence of pores across the bilayer. At higher concentrations considered here, the melting regime persists but is not transparent. Defined SAXS peaks appear and a new lamellar phase L(p) with pores is proposed to exist above 70 mM DMPG, starting at similar to 23 degrees C (similar to 3 degrees C above T(m)(on)) and losing correlation after T(m)(off). A new model for describing the X-ray scattering of bilayers with pores, presented here, is able to explain the broad band attributed to in-plane correlation between pores. The majority of cell membranes have a net negative charge, and the opening of pores across the membrane tuned by ionic strength, temperature, and lipid composition is likely to have biological relevance.

Interactions of mast cell degranulating peptides with model membranes: A comparative biophysical study

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Model peptides mimic the structure and function of the N-terminus of the pore-forming toxin sticholysin II

To investigate the role of the N-terminal region in the lytic mechanism of the pore-forming toxin sticholysin II (St II), we studied the conformational and functional properties of peptides encompassing the first 30 residues of the protein. Peptides containing residues 1-30 (P1-30) and 11-30 (P11-30) were synthesized and their conformational properties were examined in aqueous solution as a function of peptide concentration, pH, ionic strength, and addition of the secondary structure-inducing solvent trifluoroethanol (TFE). CD spectra showed that increasing concentration, pH, and ionic strength led to aggregation of P1-30; as a consequence, the peptide acquired beta-sheet conformation. In contrast, P11-30 exhibited practically no conformational changes under the same conditions, remaining essentially structureless. Moreover, this peptide did not undergo aggregation. These differences clearly point to the modulating effect of the first 10 hydrophobic residues on the peptides aggregation and conformational properties. In TFE both the first ten hydrophobic peptides acquired alpha-helical conformation, albeit to a different extent, P11-30 displayed lower alpha-helical content. P1-30 presented a larger-fraction of residues in alpha-helical conformation in TFE than that found in St II's crystal structure for that portion of the protein. Since TFE mimics the membrane em,, such increase in helical content could also occur upon toxin binding to membranes and represent a step in the mechanism of pore formation. The peptides conformational properties correlated well with their functional behaviour. Thus, P1-30 exhibited much higher hemolytic activity than P11-30. In addition, P11-30 was able to block the toxin's hemolytic activity. The size of pores formed in red blood cells by P 1-30 was estimated by measuring the permeability PEGs of different molecular mass. The pore radius (0.95 +/- 0.01 nm) was very similar to that of the PEGs of different pore formed by the toxin. The results demonstrate that the synthetic peptide P1-30 is a good model of St 11 conformation and function and emphasize the contribution of the toxin's N-terminal region, and, in particular, the hydrophobic residues 1-10 to pore formation. (c) 2005 Wiley Periodicals, Inc.

Filtration and oxidation characteristics of a diesel oxidation catalyst and a catalyzed particulate filter : development of a 1-D 2-layer model

The emissions, filtration and oxidation characteristics of a diesel oxidation catalyst (DOC) and a catalyzed particulate filter (CPF) in a Johnson Matthey catalyzed continuously regenerating trap (CCRT ®) were studied by using computational models. Experimental data needed to calibrate the models were obtained by characterization experiments with raw exhaust sampling from a Cummins ISM 2002 engine with variable geometry turbocharging (VGT) and programmed exhaust gas recirculation (EGR). The experiments were performed at 20, 40, 60 and 75% of full load (1120 Nm) at rated speed (2100 rpm), with and without the DOC upstream of the CPF. This was done to study the effect of temperature and CPF-inlet NO2 concentrations on particulate matter oxidation in the CCRT ®. A previously developed computational model was used to determine the kinetic parameters describing the oxidation characteristics of HCs, CO and NO in the DOC and the pressure drop across it. The model was calibrated at five temperatures in the range of 280 – 465° C, and exhaust volumetric flow rates of 0.447 – 0.843 act-m3/sec. The downstream HCs, CO and NO concentrations were predicted by the DOC model to within ±3 ppm. The HCs and CO oxidation kinetics in the temperature range of 280 - 465°C and an exhaust volumetric flow rate of 0.447 - 0.843 act-m3/sec can be represented by one ’apparent’ activation energy and pre-exponential factor. The NO oxidation kinetics in the same temperature and exhaust flow rate range can be represented by ’apparent’ activation energies and pre-exponential factors in two regimes. The DOC pressure drop was always predicted within 0.5 kPa by the model. The MTU 1-D 2-layer CPF model was enhanced in several ways to better model the performance of the CCRT ®. A model to simulate the oxidation of particulate inside the filter wall was developed. A particulate cake layer filtration model which describes particle filtration in terms of more fundamental parameters was developed and coupled to the wall oxidation model. To better model the particulate oxidation kinetics, a model to take into account the NO2 produced in the washcoat of the CPF was developed. The overall 1-D 2-layer model can be used to predict the pressure drop of the exhaust gas across the filter, the evolution of particulate mass inside the filter, the particulate mass oxidized, the filtration efficiency and the particle number distribution downstream of the CPF. The model was used to better understand the internal performance of the CCRT®, by determining the components of the total pressure drop across the filter, by classifying the total particulate matter in layer I, layer II, the filter wall, and by the means of oxidation i.e. by O2, NO2 entering the filter and by NO2 being produced in the filter. The CPF model was calibrated at four temperatures in the range of 280 – 465 °C, and exhaust volumetric flow rates of 0.447 – 0.843 act-m3/sec, in CPF-only and CCRT ® (DOC+CPF) configurations. The clean filter wall permeability was determined to be 2.00E-13 m2, which is in agreement with values in the literature for cordierite filters. The particulate packing density in the filter wall had values between 2.92 kg/m3 - 3.95 kg/m3 for all the loads. The mean pore size of the catalyst loaded filter wall was found to be 11.0 µm. The particulate cake packing densities and permeabilities, ranged from 131 kg/m3 - 134 kg/m3, and 0.42E-14 m2 and 2.00E-14 m2 respectively, and are in agreement with the Peclet number correlations in the literature. Particulate cake layer porosities determined from the particulate cake layer filtration model ranged between 0.841 and 0.814 and decreased with load, which is about 0.1 lower than experimental and more complex discrete particle simulations in the literature. The thickness of layer I was kept constant at 20 µm. The model kinetics in the CPF-only and CCRT ® configurations, showed that no ’catalyst effect’ with O2 was present. The kinetic parameters for the NO2-assisted oxidation of particulate in the CPF were determined from the simulation of transient temperature programmed oxidation data in the literature. It was determined that the thermal and NO2 kinetic parameters do not change with temperature, exhaust flow rate or NO2 concentrations. However, different kinetic parameters are used for particulate oxidation in the wall and on the wall. Model results showed that oxidation of particulate in the pores of the filter wall can cause disproportionate decreases in the filter pressure drop with respect to particulate mass. The wall oxidation model along with the particulate cake filtration model were developed to model the sudden and rapid decreases in pressure drop across the CPF. The particulate cake and wall filtration models result in higher particulate filtration efficiencies than with just the wall filtration model, with overall filtration efficiencies of 98-99% being predicted by the model. The pre-exponential factors for oxidation by NO2 did not change with temperature or NO2 concentrations because of the NO2 wall production model. In both CPF-only and CCRT ® configurations, the model showed NO2 and layer I to be the dominant means and dominant physical location of particulate oxidation respectively. However, at temperatures of 280 °C, NO2 is not a significant oxidizer of particulate matter, which is in agreement with studies in the literature. The model showed that 8.6 and 81.6% of the CPF-inlet particulate matter was oxidized after 5 hours at 20 and 75% load in CCRT® configuration. In CPF-only configuration at the same loads, the model showed that after 5 hours, 4.4 and 64.8% of the inlet particulate matter was oxidized. The increase in NO2 concentrations across the DOC contributes significantly to the oxidation of particulate in the CPF and is supplemented by the oxidation of NO to NO2 by the catalyst in the CPF, which increases the particulate oxidation rates. From the model, it was determined that the catalyst in the CPF modeslty increases the particulate oxidation rates in the range of 4.5 – 8.3% in the CCRT® configuration. Hence, the catalyst loading in the CPF of the CCRT® could possibly be reduced without significantly decreasing particulate oxidation rates leading to catalyst cost savings and better engine performance due to lower exhaust backpressures.

Single-molecule force spectroscopy of membrane proteins from membranes freely spanning across nanoscopic pores.

Single-molecule force spectroscopy (SMFS) provides detailed insight into the mechanical (un)folding pathways and structural stability of membrane proteins. So far, SMFS could only be applied to membrane proteins embedded in native or synthetic membranes adsorbed to solid supports. This adsorption causes experimental limitations and raises the question to what extent the support influences the results obtained by SMFS. Therefore, we introduce here SMFS from native purple membrane freely spanning across nanopores. We show that correct analysis of the SMFS data requires extending the worm-like chain model, which describes the mechanical stretching of a polypeptide, by the cubic extension model, which describes the bending of a purple membrane exposed to mechanical stress. This new experimental and theoretical approach allows to characterize the stepwise (un)folding of the membrane protein bacteriorhodopsin and to assign the stability of single and grouped secondary structures. The (un)folding and stability of bacteriorhodopsin shows no significant difference between freely spanning and directly supported purple membranes. Importantly, the novel experimental SMFS setup opens an avenue to characterize any protein from freely spanning cellular or synthetic membranes.

Flickering fusion pores comparable with initial exocytotic pores occur in protein-free phospholipid bilayers

For the act of membrane fusion, there are two competing, mutually exclusive molecular models that differ in the structure of the initial pore, the pathway for ionic continuity between formerly separated volumes. Because biological “fusion pores” can be as small as ionic channels or gap junctions, one model posits a proteinaceous initial fusion pore. Because biological fusion pore conductance varies widely, another model proposes a lipidic initial pore. We have found pore opening and flickering during the fusion of protein-free phospholipid vesicles with planar phospholipid bilayers. Fusion pore formation appears to follow the coalescence of contacting monolayers to create a zone of hemifusion where continuity between the two adherent membranes is lipidic, but not aqueous. Hypotonic stress, causing tension in the vesicle membrane, promotes complete fusion. Pores closed soon after opening (flickering), and the distribution of fusion pore conductance appears similar to the distribution of initial fusion pores in biological fusion. Because small flickering pores can form in the absence of protein, the existence of small pores in biological fusion cannot be an argument in support of models based on proteinaceous pores. Rather, these results support the model of a lipidic fusion pore developing within a hemifused contact site.