On the Application of Widom's Test Particle Method to Homogeneous and Inhomogeneous Fluids

Abstract

Chemical potentials of a homogeneous and an inhomogeneous Lennard-Jones fluid have been determined by molecular dynamics simulations on the vector computer CYBER 205 by applying essentially the fictitious test particle method of Widom. For the homogeneous fluid we find, contrary to the previous result of Guillot and Guissani, that the simulated chemical potential is independent of the particle number. The crucial point, however, is a sufficiently large cut-off radius in the evaluation of the Boltzmann factor. Comparing with our WCA-type perturbation theory, we get agreement in the chemical potentials within 0.1 kT up to the density n[sgrave]³ = 0.80 and a difference of 0.2 kT at n[sgrave]³ = 0.85. For the inhomogeneous case we consider a fluid in a cylindrical pore and integrate Widom's equation over a certain probe volume as suggested earlier by us. Chemical potentials are then calculated independently in five different probe volumes, which are cylindrical shells. The results agree well from the second to the fourth shell. Inaccuracies in the innermost cylinder can be easily explained by bad statistics. In the shell close to the wall the extremely high local density is responsible for the inaccuracies. Extending the probe volume over all cylindrical shells besides the one closest to the wall is thought to yield rather reliable results for the chemical potential. As a by-product of the simulations we also obtained diffusion coefficients, which are given in an appendix.     

Editorial

Abstract

Grand canonical molecular dynamics (GCMD) simulations are used to study the adsorption and desorption of Lennard-Jones nitrogen in three slit pore junction models of microporous graphite. These networks consist of two narrow pores separated by a wider (cavity) pore. We report results for cases where the narrow pore has a width of only two or three molecular diameters. Using the GCMD technique, a novel freezing transition is observed which results in pore blocking in the narrow pores of the network, which are less than 1 nm wide. This freezing results from the adsorption energy barrier at the junction between the narrow and wider pores. This type of pore blocking could account for the apparent increase in pore volume with increasing temperature that has been experimentally observed in microporous graphite systems. For networks in which the narrower pores are somewhat larger, with a width of 1.28 nm, this pore blocking effect is much reduced, and adsorbate molecules enter and fill the central cavity. In such cases, however, desorption is incomplete, some residual adsorbate remaining in the central cavity even at the lowest pressures.     

Gas adsorption and diffusion in a highly CO2 selective metal–organic framework: molecular simulations

Grand canonical Monte Carlo and equilibrium molecular dynamics simulations were used to assess the performance of an rht-type metal–organic framework (MOF), Cu-TDPAT, in adsorption-based and membrane-based separation of CH₄/H₂, CO₂/CH₄ and CO₂/H₂ mixtures. Adsorption isotherms and self-diffusivities of pure gases and binary gas mixtures in Cu-TDPAT were computed using detailed molecular simulations. Several properties of Cu-TDPAT such as adsorption selectivity, working capacity, diffusion selectivity, gas permeability and permeation selectivity were computed and compared with well-known zeolites and MOFs. Results showed that Cu-TDPAT is a very promising adsorbent and membrane material especially for separation of CO₂ and it can outperform traditional zeolites and MOFs such as DDR, MFI, CuBTC, IRMOF-1 in adsorption-based CO₂/CH₄ and CO₂/H₂ separations.     

First-principles investigation of the interaction of gold and palladium with armchair carbon nanotube

In this paper, we investigate the adsorption mechanisms at the interface between carbon nanotubes and metal electrodes that can influence the Schottky barrier (SB). We developed a theoretical model based on the first-principles density functional theory for the interaction of an armchair single-wall carbon nanotube (SWNT) with either Au(111) or Pd(111) surface. We considered the side-wall contact by modelling the full SWNT as well as the end-contact geometry using the graphene ribbon model to mimic the contact with very large diameter nanotubes. Strong interaction has been found for the Pd–SWNT interface where the partial density of states (DOS) shows that d-orbitals of palladium are dominant at the Fermi energy so that the hybrid Pd-orbitals have the correct symmetry to overlap with π-electrons and form covalent bonds. The SWNT can only be physisorbed on the gold surface for which the contribution to the DOS of the d-orbitals is very low. Moreover, the filling of antibonding states makes the Au–SWNT bond unstable. The average and ‘atom to atom’ energy barriers at the interface have been evaluated. The matching of open-edge carbon dimers with metal lattice in the end-contact geometry is more likely for large diameter SWNTs and this makes lower the SB at the interface.     

Kinetics of adsorption of extended ligands on DNA at small fillings

In the present work, the adsorption kinetics of extended ligands on DNA duplexes at small fillings when molecules of DNA duplexes are on the underlayer within diffusion layer has been investigated. Both diffusion of ligands in solution (diffusion stage) and adsorption of ligands (kinetic stage) are taken into consideration at adsorption of ligands on DNA duplexes. Nonlinear system of differential equations describing adsorption of ligands where not only diffusion stage but also kinetic stage is taken into account, is obtained, moreover the equations allow localizing duplexes in arbitrary place within diffusion layer. Numeric solution of the equations makes possible to investigate the filling kinetics of DNA duplexes by ligands depending on parameters controlling adsorption process. It has been shown that depending on relation between adsorption parameters different kinetic regimes of adsorption – kinetic, complex, and diffusion regimes may be realized.     

Foreword: Translocation of proteins across membranes: systems,conservation and evolutionary origin

The interactions of mouse thymocytes with unilamellar phospholipid vesicles comprised of dimyristyl lecithin (DML), dipalmitoyl lecithin (DPL), dioleoyl lecithin (DOL), and egg yolk lecithin (EYL) were examined in vitro.

In cells treated with [³H]DML or [³H]DPL vesicles, electron microscope (EM) autoradiographic analysis showed most of the radioactive lipids to be confined to the cell surface. Transmission EM studies showed the presence of intact vesicles (DPL) and collapsed or ruptured vesicle fragments (DML) adsorbed to the surfaces of treated cells. In cells treated with DPL vesicles containing a watersoluble dye (6-carboxyfluorescein; 6-CF), most of the fluorescent vesicles were localized at the periphery of the treated cells. Furthermore, substantial fractions of the cell-associated DPL and DML could be released by a mild trypsinization without damaging the cells. These results suggest that the uptake of DML and DPL is primarily due to vesicle-cell adsorption. Such an adsorption process appears to be enhanced at or below the thermotropic-phase transition temperature of the vesicle lipid. Under certain conditions these adherent vesicles also formed patches or caps on the cell surface.

In cells treated with DOL or EYL vesicles, transmission EM and EM autoradiography showed relatively little exogenous vesicle lipid located at the cell surface. Thymocytes incubated (37°C) with [¹⁴C] EYL vesicles containing a trapped marker, [³H]inulin, incor porated both isotopes at identical rates. In separate experiments it was found that this marker was located inside the treated cells. Thymocytes treated with DOL vesicles containing 6-CF exhibited a uniform and diffuse distribution of dye in the internal volume of the cells. Little cell-associated EYL or DOL could be released by trypsinization. Evidence against endocytosis of intact vesicles as a major pathway of vesicle uptake is also presented. These observations, coupled with the demonstration of vesicle-cell lipid exchange as a minor component of vesicle uptake suggest that incorporation of EYL and DOL vesicles by thymocytes is primarily by vesicle-cell fusion.     

Selection of ceramic fluorapatite‐binding peptides from a phage display combinatorial peptide library: optimum affinity tags for fluorapatite chromatography

Peptide affinity tags have become efficient tools for the purification of recombinant proteins from biological mixtures. The most commonly used ligands in this type of affinity chromatography are immobilized metal ions, proteins, antibodies, and complementary peptides. However, the major bottlenecks of this technique are still related to the ligands, including their low stability, difficulties in immobilization, and leakage into the final products. A model approach is presented here to overcome these bottlenecks by utilizing macroporous ceramic fluorapatite (CFA) as the stationary phase in chromatography and the CFA‐specific short peptides as tags. The CFA chromatographic materials act as both the support matrix and the ligand. Peptides that bind with affinity to CFA were identified from a randomized phage display heptapeptide library. A total of five rounds of phage selection were performed. A common N‐terminal sequence was found in two selected peptides: F4‐2 (KPRSMLH) and F5‐4 (KPRSVSG). The peptide F5‐4, displayed by more than 40% of the phages analyzed in the fifth round of selection, was subjected to further studies. Selectivity of the peptide for the chemical composition and morphology of CFA was assured by the adsorption studies. The dissociation constant, obtained from the F5‐4/CFA adsorption isotherm, was in the micromolar range, and the maximum capacity was 39.4 nmol/mg. The chromatographic behavior of the peptides was characterized on a CFA stationary phase with different buffers. Preferential affinity and specific retention properties suggest the possible application of the phage‐derived peptides as a tag in CFA affinity chromatography for enhancing the selective recovery of proteins. Copyright © 2013 John Wiley & Sons, Ltd.     

Adsorption of Basic violet 16 from aqueous solutions by waste sugar beet pulp: kinetic,thermodynamic, and equilibrium isotherm studies

Waste sugar beet pulp has been used as adsorbent for the removal of a hazardous cationic dye, Basic violet 16, from its aqueous solution. Adsorption of the dye was studied as function of time, pH of the solution, dosage of the adsorbent, sieve size of the particles, concentration of the dye, and temperature. The initial pH of the dye solution did not affect the chemistry of the dye molecule and the surface of beet pulp. Langmuir and Freundlich adsorption isotherms were successfully employed, and on the basis of these models, the thermodynamic parameters were evaluated. Adsorption of Basic violet 16 on beet pulp was found to be an exothermic reaction. Time contact studies showed that more than 80% adsorption of the dye is achieved in less than 1 h. Kinetics investigations confirmed both pseudo-first-order and pseudo-second-order behaviors; on the other hand, it shows that the intraparticle diffusion step is not the only rate-controlling step in all concentrations.     

Chemical speciation and competitive cationic partitioning on a sandy aquifer material

Abstract

Coupled geochemical speciation/transport models are being developed to assess potential transport of metal contaminants in the subsurface environment. In a test of the geochemical speciation portion of the effort, MINTEQA2 model predictions are compared with laboratory data concerning the pH dependent partitioning behavior of eight cationic contaminants (Ba, Be, Cd, Cu, Ni, Pb, Tl and Zn) on a sandy aquifer material in an oxidized environment. MINTEQA2 contains provisions for describing potential attenuation due to both mineral phase precipitation processes and adsorption processes resulting from amorphous iron oxides in aquifer materials (MIT Diffuse Layer Model). In the comparison, several trends were discerned. (1) Adsorptive processes tend to better describe the pH-dependent partitioning behavior of transition metals (especially Pb, Zn and Ni). (2) Cd behavior is better described by precipitation as a cadmium carbonate phase. (3) Cu behavior is not reasonably described by the model. (4) Ba and Be comparisons are poor (although presumably their partitioning behavior results from adsorptive and/or pH sensitive solid solution processes). (5) unlike the other elements, the behavior of Tl is relatively insensitive to pH.     

Effect of Solute Adsorption Properties on Its Separation from Supercritical Carbon Dioxide with a Thin Porous Silica Membrane

A thin porous silica membrane (average pore size of 3.3 mm) was prepared by the sol–gel method and used to separate the solute from supercritical carbon dioxide. The characteristics of solute permeation were investigated in respect of the adsorption properties of the solute, the desorption rate of the solute from the membrane being measured and the potential energy of solute near the silica surface being calculated by the molecular modeling technique. It was found that caffeine was strongly adsorbed to the surface and then slowly desorbed to form an adsorption layer, making the pores narrower and causing a molecular-sieving effect. Therefore, the rejection value was positive. On the other hand, the rejection value of n-octanoic acid, which was well adsorbed and rapidly desorbed, was negative. It is presumed that the molecules filled the pores due to their potential energy and were then forced to flow through the pores by the transmembrane pressure.