Effects of potential models on the adsorption of ethane and ethylene on graphitized thermal carbon black. Study of two-dimensional critical temperature and isosteric heat versus loading

Adsorption of ethylene and ethane on graphitized thermal carbon black and in slit pores whose walls are composed of graphene layers is studied in detail to investigate the packing efficiency, the two-dimensional critical temperature, and the variation of the isosteric heat of adsorption with loading and temperature. Here we used a Monte Carlo simulation method with a grand canonical Monte Carlo ensemble. A number of two-center Lennard-Jones (LJ) potential models are investigated to study the impact of the choice of potential models in the description of adsorption behavior. We chose two 2C-LJ potential models in our investigation of the (i) UA-TraPPE-LJ model of Martin and Siepmann (J. Phys. Chem. B 1998,102, 25692577) for ethane and Wick et al. (J. Phys. Chem. B 2000,104, 8008-8016) for ethylene and (ii) AUA4-LJ model of Ungerer et al. (J. Chem. Phys. 2000,112, 5499-5510) for ethane and Bourasseau et al. (J. Chem. Phys. 2003, 118, 3020-3034) for ethylene. These models are used to study the adsorption of ethane and ethylene on graphitized thermal carbon black. It is found that the solid-fluid binary interaction parameter is a function of adsorbate and temperature, and the adsorption isotherms and heat of adsorption are well described by both the UA-TraPPE and AUA models, although the UA-TraPPE model performs slightly better. However, the local distributions predicted by these two models are slightly different. These two models are used to explore the two-dimensional condensation for the graphitized thermal carbon black, and these values are 110 K for ethylene and 120 K for ethane.

PVT behaviour of fluids with potential models optimised for phase equilibria

NPT and NVT Monte Carlo simulations are applied to models for methane and water to predict the PVT behaviour of these fluids over a wide range of temperatures and pressures. The potential models examined in this paper have previously been presented in the literature with their specific parameters optimised to fit phase coexistence data. The exponential-6 potential for methane gives generally good prediction of PVT behaviour over the full range of temperature and pressures studied with the only significant deviation from experimental data seen at high temperatures and pressures. The NSPCE water model shows very poor prediction of PVT behaviour, particularly at dense conditions. To improve this. the charge separation in the NSPCE model is varied with density. Improvements for vapour and liquid phase PVT predictions are achieved with this variation. No improvement was found in the prediction of the oxygen-oxygen radial distribution by varying charge separation under dense phase conditions. (C) 2004 Elsevier B.V. All rights reserved.

Impact of potential models on adsorption of linear molecules on carbon black

In this paper, we investigate the effects of potential models on the description of equilibria of linear molecules (ethylene and ethane) adsorption on graphitized thermal carbon black. GCMC simulation is used as a tool to give adsorption isotherms, isosteric heat of adsorption and the microscopic configurations of these molecules. At the heart of the GCMC are the potential models, describing fluid-fluid interaction and solid-fluid interaction. Here we studied the two potential models recently proposed in the literature, the UA-TraPPE and AUA4. Their impact in the description of adsorption behavior of pure components will be discussed. Mixtures of these components with nitrogen and argon are also studied. Nitrogen is modeled a two-site plus discrete charges while argon as a spherical particle. GCMC simulation is also used for generating simulation mixture isotherms. It is found that co-operation between species occurs when the surface is fractionally covered while competition is important when surface is fully loaded.

Effects of potential models in the vapor-liquid equilibria and adsorption of simple gases on graphitized thermal carbon black

In this paper, we investigate the effects of various potential models in the description of vapor–liquid equilibria (VLE) and adsorption of simple gases on highly graphitized thermal carbon black. It is found that some potential models proposed in the literature are not suitable for the description of VLE (saturated gas and liquid densities and the vapor pressure with temperature). Simple gases, such as neon, argon, krypton, xenon, nitrogen, and methane are studied in this paper. To describe the isotherms on graphitized thermal carbon black correctly, the surface mediation damping factor introduced in our recent publication should be used to calculate correctly the fluid–fluid interaction energy between particles close to the surface. It is found that the damping constant for the noble gases family is linearly dependent on the polarizability, suggesting that the electric field of the graphite surface has a direct induction effect on the induced dipole of these molecules. As a result of this polarization by the graphite surface, the fluid–fluid interaction energy is reduced whenever two particles are near the surface. In the case of methane, we found that the damping constant is less than that of a noble gas having the similar polarizability, while in the case of nitrogen the damping factor is much greater and this could most likely be due to the quadrupolar nature of nitrogen.

Adsorption of carbon tetrachloride on graphitized thermal carbon black and in slit graphitic pores: Five-site versus one-site potential models

The performance of intermolecular potential models on the adsorption of carbon tetrachloride on graphitized thermal carbon black at various temperatures is investigated. This is made possible with the extensive experimental data of Machin and Ross(1), Avgul et al.,(2) and Pierce(3) that cover a wide range of temperatures. The description of all experimental data is only possible with the allowance for the surface mediation. If this were ignored, the grand canonical Monte Carlo (GCMC) simulation results would predict a two-dimensional (2D) transition even at high temperatures, while experimental data shows gradual change in adsorption density with pressure. In general, we find that the intermolecular interaction has to be reduced by 4% whenever particles are within the first layer close to the surface. We also find that this degree of surface mediation is independent of temperature. To understand the packing of carbon tetrachloride in slit pores, we compared the performance of the potential models that model carbon tetrachloride as either five interaction sites or one site. It was found that the five-site model performs better and describes the imperfect packing in small pores better. This is so because most of the strength of fluid-fluid interaction between two carbon tetrachloride molecules comes from the interactions among chlorine atoms. Methane, although having tetrahedral shape as carbon tetrachloride, can be effectively modeled as a pseudospherical particle because most of the interactions come from carbon-carbon interaction and hydrogen negligibly contributes to this.

Thermal diffusion in molecular dynamics simulations of thin film diamond deposition

Molecular dynamics simulations of carbon atom depositions are used to investigate energy diffusion from the impact zone. A modified Stillinger-Weber potential models the carbon interactions for both sp2 and sp3 bonding. Simulations were performed on 50 eV carbon atom depositions onto the (111) surface of a 3.8 x 3.4 x 1.0 nm diamond slab containing 2816 atoms in 11 layers of 256 atoms each. The bottom layer was thermostated to 300 K. At every 100th simulation time step (27 fs), the average local kinetic energy, and hence local temperature, is calculated. To do this the substrate is divided into a set of 15 concentric hemispherical zones, each of thickness one atomic diameter (0.14 nm) and centered on the impact point. A 50-eV incident atom heats the local impact zone above 10 000 K. After the initial large transient (200 fs) the impact zone has cooled below 3000 K, then near 1000 K by 1 ps. Thereafter the temperature profile decays approximately as described by diffusion theory, perturbed by atomic scale fluctuations. A continuum model of classical energy transfer is provided by the traditional thermal diffusion equation. The results show that continuum diffusion theory describes well energy diffusion in low energy atomic deposition processes, at distance and time scales larger than 1.5 nm and 1-2 ps, beyond which the energy decays essentially exponentially. (C) 1998 Published by Elsevier Science S.A. All rights reserved.

Adsorption of ethylene on graphitized thermal carbon black and in slit pores: A computer simulation study

In this paper, we studied vapor-liquid equilibria (VLE) and adsorption of ethylene on graphitized thermal carbon black and in slit pores whose walls are composed of graphene layers. Simple models of a one-center Lennard-Jones (LJ) potential and a two-center united atom (UA)-LJ potential are investigated to study the impact of the choice of potential models in the description of VLE and adsorption behavior. Here, we used a Monte Carlo simulation method with grand canonical Monte Carlo (GCMC) and Gibbs ensemble Monte Carlo ensembles. The one-center potential model cannot describe adequately the VLE over the practical range of temperature from the triple point to the critical point. On the other hand, the two-center potential model (Wick et al. J. Phys. Chem. B 2000, 104, 8008-8016) performs well in the description of VLE (saturated vapor and liquid densities and vapor pressure) over the wide range of temperature. This UA-LJ model is then used in the study of adsorption of ethylene on graphitized thermal carbon black and in slit pores. Agreement between the GCMC simulation results and the experimental data on graphitized thermal carbon black for moderate temperatures is excellent, demonstrating that the potential of the GCMC method and the proper choice of potential model are essential to investigate adsorption. For slit pores of various sizes, we have found that the behavior of ethylene exhibits a number of features that are not manifested in the study of spherical LJ particles. In particular, the singlet density distribution versus distance across the pore and the angle between the molecular axis and the z direction provide rich information about the way molecules arrange themselves when the pore width is varied. Such an arrangement has been found to be very sensitive to the pore width.

Adsorption of benzene on graphitized thermal carbon black: Reduction of the quadrupole moment in the adsorbed phase

The performance of intermolecular potential models on the adsorption of benzene on graphitized thermal carbon black at various temperatures is investigated. Two models contain only dispersive sites, whereas the other two models account explicitly for the dispersive and electrostatic sites. Using numerous data in the literature on benzene adsorption on graphitized thermal carbon black at various temperatures, we have found that the effect of surface mediation on interaction between adsorbed benzene molecules must be accounted for to describe correctly the adsorption isotherm as well as the isosteric heat. Among the two models with partial charges tested, the WSKS model of Wick et at. I that has only six dispersive sites and three discrete partial charges is better than the very expensive all-atom model of Jorgensen and Severance.(2) Adsorbed benzene molecules on graphitized thermal carbon black have a complex orientation with respect to distance from the surface and also with respect to loading. At low loadings, they adopt the parallel configuration relative to the graphene surface, whereas at higher loadings (still less than monolayer coverage) some molecules adopt a slant orientation to maximize the fluid-fluid interaction. For loadings in the multilayer region, the orientation of molecules in the first layer is influenced by the presence of molecules in the second layer. The data that are used in this article come from the work of Isirikyan and Kiselev,(3) Pierotti and Smallwood,(4) Pierce and Ewing,(5) Belyakova, Kiselev, and Kovaleva,(6) and Carrott et al.(7)

The potential of virulent Wolbachia to modulate disease transmission by insects

A virulent strain of Wolbachia has recently been identified in Drosophila that drastically reduces adult lifespan. It has been proposed that this phenotype might be introduced into insect disease vector populations to reduce pathogen transmission. Here we model the requirements for spread of such an agent and the associated reduction in disease transmission. First, a simulation of mosquito population age structure was used to describe the age distribution of mosquitoes transmitting dengue virus. Second, given varying levels of cytoplasmic incompatibility and fecundity effect, the maximum possible longevity reduction that would allow Wolbachia to invade was obtained. Finally, the two models were combined to estimate the reduction in disease transmission according to different introduction frequencies. With strong CI and limited effect of fecundity, an introduction of Wolbachia with an initial frequency of 0.4 could result in a 60–80% reduction of transmitting mosquitoes. Greater reductions are possible at higher initial release rates.

Prediction of rock alteration patterns: a potential tool in mineral exploration

Hydrothermal alteration of a quartz-K-feldspar rock is simulated numerically by coupling fluid flow and chemical reactions. Introduction of CO2 gas generates an acidic fluid and produces secondary quartz, muscovite and/or pyrophyllite at constant temperature and pressure of 300 degrees C and 200 MPa. The precipitation and/or dissolution of the secondary minerals is controlled by either mass-action relations or rate laws. In our simulations the mass of the primary elements are conserved and the mass-balance equations are solved sequentially using an implicit scheme in a finite-element code. The pore-fluid velocity is assumed to be constant. The change of rock volume due to the dissolution or precipitation of the minerals, which is directly related to their molar volume, is taken into account. Feedback into the rock porosity and the reaction rates is included in the model. The model produces zones of pyrophyllite quartz and muscovite due to the dissolution of K-feldspar. Our model simulates, in a simplified way, the acid-induced alteration assemblages observed in various guises in many significant mineral deposits. The particular aluminosilicate minerals produced in these experiments are associated with the gold deposits of the Witwatersrand Basin.

Efficient discovery of immune response targets by cyclical refinement of QSAR models of peptide binding

Peptides that induce and recall T-cell responses are called T-cell epitopes. T-cell epitopes may be useful in a subunit vaccine against malaria. Computer models that simulate peptide binding to MHC are useful for selecting candidate T-cell epitopes since they minimize the number of experiments required for their identification. We applied a combination of computational and immunological strategies to select candidate T-cell epitopes. A total of 86 experimental binding assays were performed in three rounds of identification of HLA-All binding peptides from the six preerythrocytic malaria antigens. Thirty-six peptides were experimentally confirmed as binders. We show that the cyclical refinement of the ANN models results in a significant improvement of the efficiency of identifying potential T-cell epitopes. (C) 2001 by Elsevier Science Inc.

Ecosystem process models at multiple scales for mapping tropical forest productivity

Quantifying mass and energy exchanges within tropical forests is essential for understanding their role in the global carbon budget and how they will respond to perturbations in climate. This study reviews ecosystem process models designed to predict the growth and productivity of temperate and tropical forest ecosystems. Temperate forest models were included because of the minimal number of tropical forest models. The review provides a multiscale assessment enabling potential users to select a model suited to the scale and type of information they require in tropical forests. Process models are reviewed in relation to their input and output parameters, minimum spatial and temporal units of operation, maximum spatial extent and time period of application for each organization level of modelling. Organizational levels included leaf-tree, plot-stand, regional and ecosystem levels, with model complexity decreasing as the time-step and spatial extent of model operation increases. All ecosystem models are simplified versions of reality and are typically aspatial. Remotely sensed data sets and derived products may be used to initialize, drive and validate ecosystem process models. At the simplest level, remotely sensed data are used to delimit location, extent and changes over time of vegetation communities. At a more advanced level, remotely sensed data products have been used to estimate key structural and biophysical properties associated with ecosystem processes in tropical and temperate forests. Combining ecological models and image data enables the development of carbon accounting systems that will contribute to understanding greenhouse gas budgets at biome and global scales.

Virtual models of the HLA class I antigen processing pathway

Antigen recognition by cytotoxic CD8 T cells is dependent upon a number of critical steps in MHC class I antigen processing including proteosomal cleavage, TAP transport into the endoplasmic reticulum, and MHC class 1 binding. Based on extensive experimental data relating to each of these steps there is now the capacity to model individual antigen processing steps with a high degree of accuracy. This paper demonstrates the potential to bring together models of individual antigen processing steps, for example proteosome cleavage, TAP transport, and MHC binding, to build highly informative models of functional pathways. In particular, we demonstrate how an artificial neural network model of TAP transport was used to mine a HLA-binding database so as to identify H LA-binding peptides transported by TAP. This integrated model of antigen processing provided the unique insight that HLA class I alleles apparently constitute two separate classes: those that are TAP-efficient for peptide loading (HLA-B27, -A3, and -A24) and those that are TAP-inefficient (HLA-A2, -B7, and -B8). Hence, using this integrated model we were able to generate novel hypotheses regarding antigen processing, and these hypotheses are now capable of being tested experimentally. This model confirms the feasibility of constructing a virtual immune system, whereby each additional step in antigen processing is incorporated into a single modular model. Accurate models of antigen processing have implications for the study of basic immunology as well as for the design of peptide-based vaccines and other immunotherapies. (C) 2004 Elsevier Inc. All rights reserved.

Fluid-mobile trace element constraints on the role of slab melting and implications for Archaean crustal growth models

We use published and new trace element data to identify element ratios which discriminate between arc magmas from the supra-subduction zone mantle wedge and those formed by direct melting of subducted crust (i.e. adakites). The clearest distinction is obtained with those element ratios which are strongly fractionated during refertilisation of the depleted mantle wedge, ultimately reflecting slab dehydration. Hence, adakites have significantly lower Pb/Nd and B/Be but higher Nb/Ta than typical arc magmas and continental crust as a whole. Although Li and Be are also overenriched in continental crust, behaviour of Li/Yb and Be/Nd is more complex and these ratios do not provide unique signatures of slab melting. Archaean tonalite-trondhjemite-granodiorites (TTGs) strongly resemble ordinary mantle wedge-derived arc magmas in terms of fluid-mobile trace element content, implying that they-did not form by slab melting but that they originated from mantle which was hydrated and enriched in elements lost from slabs during prograde dehydration. We suggest that Archaean TTGs formed by extensive fractional crystallisation from a mafic precursor. It is widely claimed that the time between the creation and subduction of oceanic lithosphere was significantly shorter in the Archaean (i.e. 20 Ma) than it is today. This difference was seen as an attractive explanation for the presumed preponderance of adakitic magmas during the first half of Earth's history. However, when we consider the effects of a higher potential mantle temperature on the thickness of oceanic crust, it follows that the mean age of oceanic lithosphere has remained virtually constant. Formation of adakites has therefore always depended on local plate geometry and not on potential mantle temperature.

Therapeutic potential of selective superoxide dismutase mimetics

Selective superoxide dismutase (SOD) mimetics are potentially useful in pathological conditions in which there is an overproduction of the superoxide anion O-2.(-). These pathological conditions include inflammation, ischemia/reperfusion, shock, various cardiovascular disorders, amyotrophic lateral sclerosis (ALS) and other neurodegenerative disorders. A major step forward in this field was the development of small-molecule selective SOD mimetics that penetrate cell membranes, These selective SOD mimetics catalytically remove O-2.(-) without interfering with nitric oxide (NO), peroxynitrite (ONOO-) or other radicals such as hydroxyl radical or hydrogen peroxide (H2O2). These selective SOD mimetics (SC-52608, SC-55858, M-40403 and M-40401) have been shown to have benefits in animal models of inflammation, ischemia/reperfusion, shock, thrombosis and diabetes. The next challenge with selective SOD mimetics is to develop therapeutic potential into therapeutic agents.