Adsorption of supercritical fluids in non-porous and porous carbons: analysis of adsorbed phase volume and density

In this paper, we revisit the surface mass excess in adsorption studies and investigate the role of the volume of the adsorbed phase and its density in the analysis of supercritical gas adsorption in non-porous as well as microporous solids. For many supercritical fluids tested (krypton, argon, nitrogen, methane) on many different carbonaceous solids, it is found that the volume of the adsorbed phase is confined mostly to a geometrical volume having a thickness of up to a few molecular diameters. At high pressure the adsorbed phase density is also found to be very close to but never equal or greater than the liquid phase density. (C) 2003 Elsevier Science Ltd. All rights reserved.

Phase equilibria and surface tension of pure fluids using a molecular layer structure theory (MLST) model

This paper presents a new model based on thermodynamic and molecular interaction between molecules to describe the vapour-liquid phase equilibria and surface tension of pure component. The model assumes that the bulk fluid can be characterised as set of parallel layers. Because of this molecular structure, we coin the model as the molecular layer structure theory (MLST). Each layer has two energetic components. One is the interaction energy of one molecule of that layer with all surrounding layers. The other component is the intra-layer Helmholtz free energy, which accounts for the internal energy and the entropy of that layer. The equilibrium between two separating phases is derived from the minimum of the grand potential, and the surface tension is calculated as the excess of the Helmholtz energy of the system. We test this model with a number of components, argon, krypton, ethane, n-butane, iso-butane, ethylene and sulphur hexafluoride, and the results are very satisfactory. (C) 2002 Elsevier Science B.V. All rights reserved.

Lower bounds on the complexity of simulating quantum gates

We give a simple proof of a formula for the minimal time required to simulate a two-qubit unitary operation using a fixed two-qubit Hamiltonian together with fast local unitaries. We also note that a related lower bound holds for arbitrary n-qubit gates.

Adsorption of Supercritical fluids on graphitised thermal carbon black: Molecular layer structure theory versus grand canonical Monte Carlo simulation

This paper presents a detailed analysis of adsorption of supercritical fluids on nonporous graphitized thermal carbon black. Two methods are employed in the analysis. One is the molecular layer structure theory (MLST), proposed recently by our group, and the other is the grand canonical Monte Carlo (GCMC) simulation. They were applied to describe the adsorption of argon, krypton, methane, ethylene, and sulfur hexafluoride on graphitized thermal carbon black. It was found that the MLST describes all the experimental data at various temperatures well. Results from GCMC simulations describe well the data at low pressure but show some deviations at higher pressures for all the adsorbates tested. The question of negative surface excess is also discussed in this paper.

Rare earth element fractionation in authigenic illite–smectite from Late Permian clastic rocks, Bowen Basin, Australia: implications for physico-chemical environments of fluids during illitization

REE analyses were performed on authigenic illitic clay. minerals from Late Permian mudrocks, sandstones and bentonites from the Bowen Basin (Australia). The mixed-layer illite-smectite exhibit REE patterns with an obvious fractionation of the HREE from the LREE and MREE, which is an apparent function of degree of illitization reaction. The highly illitic (R greater than or equal to 3) illite-smectite from the northern Bowen Basin show a depletion of LREE relative to the less illitic (R=0 and 1) clays. In contrast, an enrichment of HREE for the illite-rich clays relative to less. illitic clays is evident for the southern Bowen Basin samples. The North American Shale Composite-normalized (La/Lu)(sn) ratios show negative correlations with the illite content in illite-smectite and positive correlations with the delta(18)O values of the clays for both the northern and southern Bowen Basin samples. These correlations indicate that the increasing depletion of LREE in hydrothermal fluids is a function of increasing water/rock ratios in the northern Bowen Basin. Good negative correlations between (La/Lu)(sn) ratios and illite content in illite-smectite from the southern Bowen Basin suggest the involvement of fluids with higher alkalinity and higher pH in low water/ rock ratio conditions. Increasing HREE enrichment with delta(18)O decrease indicates the effect of increasing temperature at low water/rock ratios in the southern Bowen Basin. Results of the present study confirm the conclusions of some earlier studies suggesting that REE in illitic clay minerals are mobile and fractionated during illitization and that this fact should be considered in studies of sedimentary processes and in identifying provenance. Moreover, our results show that REE systematic of illitic clay minerals can be applied as an useful technique to gain information about physico-chemical conditions during thermal and fluid flow events in certain sedimentary basins. (C) 2003 Elsevier Science B.V. All rights reserved.

Simulating the effects of dominance and epistasis on selection response in the CIMMYT wheat breeding program using QuCim

Plant breeders use many different breeding methods to develop superior cultivars. However, it is difficult, cumbersome, and expensive to evaluate the performance of a breeding method or to compare the efficiencies of different breeding methods within an ongoing breeding program. To facilitate comparisons, we developed a QU-GENE module called QuCim that can simulate a large number of breeding strategies for self-pollinated species. The wheat breeding strategy Selected Bulk used by CIMMYT's wheat breeding program was defined in QuCim as an example of how this is done. This selection method was simulated in QuCim to investigate the effects of deviations from the additive genetic model, in the form of dominance and epistasis, on selection outcomes. The simulation results indicate that the partial dominance model does not greatly influence genetic advance compared with the pure additive model. Genetic advance in genetic systems with overdominance and epistasis are slower than when gene effects are purely additive or partially dominant. The additive gene effect is an appropriate indicator of the change in gene frequency following selection when epistasis is absent. In the absence of epistasis, the additive variance decreases rapidly with selection. However, after several cycles of selection it remains relatively fixed when epistasis is present. The variance from partial dominance is relatively small and therefore hard to detect by the covariance among half sibs and the covariance among full sibs. The dominance variance from the overdominance model can be identified successfully, but it does not change significantly, which confirms that overdominance cannot be utilized by an inbred breeding program. QuCim is an effective tool to compare selection strategies and to validate some theories in quantitative genetics.

Binomial leap methods for simulating stochastic chemical kinetics

This paper discusses efficient simulation methods for stochastic chemical kinetics. Based on the tau-leap and midpoint tau-leap methods of Gillespie [D. T. Gillespie, J. Chem. Phys. 115, 1716 (2001)], binomial random variables are used in these leap methods rather than Poisson random variables. The motivation for this approach is to improve the efficiency of the Poisson leap methods by using larger stepsizes. Unlike Poisson random variables whose range of sample values is from zero to infinity, binomial random variables have a finite range of sample values. This probabilistic property has been used to restrict possible reaction numbers and to avoid negative molecular numbers in stochastic simulations when larger stepsize is used. In this approach a binomial random variable is defined for a single reaction channel in order to keep the reaction number of this channel below the numbers of molecules that undergo this reaction channel. A sampling technique is also designed for the total reaction number of a reactant species that undergoes two or more reaction channels. Samples for the total reaction number are not greater than the molecular number of this species. In addition, probability properties of the binomial random variables provide stepsize conditions for restricting reaction numbers in a chosen time interval. These stepsize conditions are important properties of robust leap control strategies. Numerical results indicate that the proposed binomial leap methods can be applied to a wide range of chemical reaction systems with very good accuracy and significant improvement on efficiency over existing approaches. (C) 2004 American Institute of Physics.

Simulating quantum interference in a three-level system with perpendicular transition dipole moments

We consider a three-level V-type atomic system with the ground state coupled by a laser field to only one of the excited states, and with the two excited states coupled together by a dc field. Although the dipole moments of the two dipole-allowed transitions are assumed perpendicular, we demonstrate that this system emulates to a large degree a three-level system with parallel dipole moments-the latter being a system that exhibits quantum interference and displays a number of interesting features. As examples, we show that the system can produce extremely large values for the intensity-intensity correlation function, and that its resonance fluorescence spectrum can display ultranarrow lines. The dressed states for this system are identified, and the spectral features are interpreted in terms of transitions among these dressed states. We also show that this system is capable of exhibiting considerable squeezing.

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.

A multi-scaled approach for simulating chemical reaction systems

In this paper we give an overview of some very recent work, as well as presenting a new approach, on the stochastic simulation of multi-scaled systems involving chemical reactions. In many biological systems (such as genetic regulation and cellular dynamics) there is a mix between small numbers of key regulatory proteins, and medium and large numbers of molecules. In addition, it is important to be able to follow the trajectories of individual molecules by taking proper account of the randomness inherent in such a system. We describe different types of simulation techniques (including the stochastic simulation algorithm, Poisson Runge–Kutta methods and the balanced Euler method) for treating simulations in the three different reaction regimes: slow, medium and fast. We then review some recent techniques on the treatment of coupled slow and fast reactions for stochastic chemical kinetics and present a new approach which couples the three regimes mentioned above. We then apply this approach to a biologically inspired problem involving the expression and activity of LacZ and LacY proteins in E. coli, and conclude with a discussion on the significance of this work.

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.

Effects of the juxtaposition of carbonaceous slit pores on the overall transport behavior of adsorbed fluids

It is a common approximation in the modeling of adsorption in microporous carbons to treat the pores as slit pores, whose walls are considered to consist of an infinite number of graphitic layers. In practice, such an approximation is appropriate as long as the number of graphitic layers in the wall is greater than three. However, it is understood that pore walls in microporous carbons commonly consist of three or fewer layers. As well as affecting the solid-fluid interaction within a pore, such narrow walls permit the interaction of fluid molecules through the wall, with consequences for the adsorption characteristics. We consider the effect that a distributed pore-wall thickness model can have on transport properties. At low density we find that the only significant deviation in the transport properties from the infinite pore-wall thickness model occurs in pores with single-layer walls. For a model of activated carbons with a distribution of pore widths and pore-wall thicknesses, the transport properties are generally insensitive to the effects of finite walls, in terms of both the solid-fluid interaction within a pore and fluid-fluid interaction through the pore walls.

Peptide quantification by matrix-assisted laser desorption ionisation time-of-flight mass spectrometry: Investigations of the cyclotide kalata B1 in biological fluids

A rapid method has been developed for the quantification of the prototypic cyclotide kalata B I in water and plasma utilizing matrix-assisted laser desorption ionisation time-of-flight (MALDI-TOF) mass spectrometry. The unusual structure of the cyclotides means that they do not ionise as readily as linear peptides and as a result of their low ionisation efficiency, traditional LC/MS analyses were not able to reach the levels of detection required for the quantification of cyclotides in plasma for pharmacokinetic studies. MALDI-TOF-MS analysis showed linearity (R-2 > 0.99) in the concentration range 0.05-10 mu g/mL with a limit of detection of 0.05 mu g/mL (9 fmol) in plasma. This paper highlights the applicability of MALDI-TOF mass spectrometry for the rapid and sensitive quantification of peptides in biological samples without the need for extensive extraction procedures. (c) 2005 Elsevier B.V. All rights reserved.

Capillary break-up rheometry of low-viscosity elastic fluids

We investigate the dynamics of the capillary thinning and break-up process for low viscosity elastic fluids such as dilute polymer solutions. Standard measurements of the evolution of the midpoint diameter of the necking fluid filament are augmented by high speed digital video images of the break up dynamics. We show that the successful operation of a capillary thinning device is governed by three important time scales (which characterize the relative importance of inertial, viscous and elastic processes), and also by two important length scales (which specify the initial sample size and the total stretch imposed on the sample). By optimizing the ranges of these geometric parameters, we are able to measure characteristic time scales for tensile stress growth as small as 1 millisecond for a number of model dilute and semi-dilute solutions of polyethylene oxide (PEO) in water and glycerol. If the final aspect ratio of the sample is too small, or the total axial stretch is too great, measurements are limited, respectively, by inertial oscillations of the liquid bridge or by the development of the well-known beads-on-a-string morphology which disrupt the formation of a uniform necking filament. By considering the magnitudes of the natural time scales associated with viscous flow, elastic stress growth and inertial oscillations it is possible to construct an operability diagram characterizing successful operation of a capillary break-up extensional rheometer. For Newtonian fluids, viscosities greater than approximately 70 mPas are required; however for dilute solutions of high molecular weight polymer, the minimum Viscosity is substantially lower due to the additional elastic stresses arising from molecular extension. For PEO of molecular weight 2.10(6) g/mol, it is possible to measure relaxation times of order 1 ms in dilute polymer solutions with zero-shear-rate viscosities on the order of 2-10 mPas.