Corresponding states vapour–liquid phase equilibria of confined square–well fluid

Corresponding states vapour–liquid phase equilibria of confined square-well fluid are studied by means of grand-canonical transition-matrix Monte Carlo simulation and histogram reweighting method. In this study, square-well fluid is considered under hard and attractive slit pore confinements ranging from 1.5 to 40 molecular diameters. Corresponding states vapour–liquid phase coexistence envelopes display insignificant effect of wall?fluid interaction for slit pore confinements ranging from 1.5 to 3 molecular diameters. On the other hand, significant effect of wall?fluid interaction on the corresponding state coexistence envelope is observed for slit pore confinements ranging from 4 to 40 molecular diameters. Moreover, at a given slit width, shrinking in corresponding state coexistence envelope is observed with increase in the wall?fluid interaction. However, in the larger slit pore width of 30 to 40 molecular diameters, shrinking in the corresponding state vapour–liquid coexistence envelopes become indifferent with the stronger wall?fluid interactions studied in this work. Structural behaviour of coexisting phases in slit pores are also investigated through local density profiles, to understand the overall behaviour of corresponding states coexistence envelopes. Fluctuating positive and negative deviations in the corresponding state spreading pressure with respect to corresponding bulk value is observed for studied wall?fluid interactions and slit pore confinements.     

Critical temperature estimation of bulk and confined atomic fluid using vapour−liquid interfacial free energy

The critical temperatures of bulk and confined atomic fluids are investigated using values of the vapour?liquid interfacial free energy of coexistence obtained from grand-canonical transition-matrix Monte Carlo simulations using a histogram reweighting technique. The temperature corresponding to zero interfacial free energy of coexistence is the estimated critical temperature for the system under investigation. Slit width of confined atomic fluid for this investigation is varied from 40 to 1 fluid particle diameter. The obtained critical temperatures have shown nonlinear monotonic trend with inverse of slit width. Moreover, five different linear regimes of critical temperature are observed in the studied range of slit width. Interestingly, in the slit width range of less than two fluid particle diameters, the critical temperature approaches two-dimensional value and remains approximately indifferent with a decrease in slit width up to one fluid particle diameter. This investigation also reveals that the critical temperature of bulk and confined atomic fluid estimated using the vapour?liquid interfacial free energy of coexistence is within reasonable accuracy with that obtained using the simplified form of scaling law.     

Monte Carlo simulations of vapour–liquid phase equilibrium and microstructure for the system containing azeotropes

Abstract

Phase equilibrium data of the mixtures including alcohols, esters and organic acids are of first interest particularly to design and optimise biodiesel production and reactive distillation processes. In this work, vapour–liquid phase equilibrium of these systems was simulated at low pressure using Gibbs ensemble Monte Carlo method. All Lennard–Jones parameters of pseudo-atoms involved in the systems were derived from previous parametrisations of TraPPE-UA force field. The Fourier coefficients of dihedrals encountered in ethyl acetate molecule have been obtained from the quantum calculations. Using this force field, temperature-composition diagrams are well reproduced for ethyl acetate + ethanol, ethyl acetate + methanol at 70.00 kPa and ethyl acetate + acetic acid mixtures at 77.33 kPa. The transferability of this force field to mixtures in these systems is noticeable. Analysis of the microstructure for the ethyl acetate + ethanol and ethyl acetate + acetic acid mixtures was presented. We found that the hydrogen bond networks consist of autoassociation and cross-association and autoassociation occupies the main position as compared with cross association in the ethyl acetate + ethanol mixture. OC_HAc–H_HAc and OC_EtOAc–H_HAc hydrogen bond interactions play a significant role in the phase behaviours or structures of ethyl acetate + acetic acid mixture.     

Effect of airway surface liquid on the forces on the pharyngeal wall: Experimental fluid–structure interaction study

Obstructive sleep apnoea syndrome (OSAS) is a breathing disorder with a multifactorial etiology. The respiratory epithelium is lined with a thin layer of airway surface liquid preventing interactions between the airflow and epithelium. The effect of the liquid lining in OSAS pathogenesis remains poorly understood despite clinical research. Previous studies have shown that the physical properties of the airway surface liquid or altered stimulation of the airway mechanoreceptors could alleviate or intensify OSAS; however, these studies do not provide a clear physical interpretation. To study the forces transmitted from the airflow to the liquid-lined compliant wall and to discuss the effects of the airway surface liquid properties on the stimulation of the mechanoreceptors, a novel and simplified experimental system mimicking the upper airway fundamental characteristics (i.e., liquid-lined compliant wall and complex unsteady airflow features) was constructed. The fluctuating force on the compliant wall was reduced through a damping mechanism when the liquid film thickness and/or the viscosity were increased. Conversely, the liquid film damping was reduced when the surface tension decreased. Based on the experimental data, empirical correlations were developed to predict the damping potential of the liquid film. In the future, this will enable us to extend the existing computational fluid–structure interaction simulations of airflow in the human upper airway by incorporating the airway surface liquid effect without adopting two-phase flow interface tracking methods. Furthermore, the experimental system developed in this study could be used to investigate the fundamental principles of the complex once/twice-coupled physical phenomena.     

Simulating the vapour–liquid equilibria of 1,4-dioxane

1,4-dioxane, a cyclic ether, is an emerging contaminant which is difficult to remove from water with conventional water treatment methods and resistant to biodegradation. Once a reliable force field is developed for 1,4-dioxane, molecular simulation techniques can be useful to study alternative adsorbents for its removal. For this purpose, we carried out Monte Carlo simulations in a constant volume Gibbs Ensemble to generate a force field which is capable of predicting the vapour–liquid coexistence curve and critical data of 1,4-dioxane. Results are given in comparison with experimental data and results from simulations with other force fields. Liquid densities and critical temperature are predicted in excellent agreement with experimental data using the new force field. At high temperatures, predicted vapour densities are in good agreement with experimental data, however, at lower temperatures the predicted vapour densities deviate about an order of magnitude from the experimental values. The critical density is slightly underestimated with our new force field. However, overall, the results of simulations with the new parameters give much better agreement with experimental data compared to the results obtained using other force fields.     

Liquid–vapour interface varying the softness and range of the interaction potential

Molecular dynamics simulations in a canonical ensemble were carried out for simple fluids. The inter-particles interaction law is described by the Morse function plus a repulsive term. This kind of combination allows to tune the repulsive term of the interaction function by fitting the range of the attractive well and vice versa. As a relevant result, we show that for an inhomogeneous system the particle softness affects the vapour pressure, the surface tension and also the equilibrium densities of a simple fluid. Lower numerical values for these same properties were obtained by using a more repulsive interaction potential. The differences among these same interfacial properties are bigger when the range of the attractive interaction is longer. The surface tension written in terms of the corresponding critical parameters, such as scaled surface tension, was plotted for different softness degrees. And from this comparison, a unique master curve was not found.     

Vapour–liquid phase equilibria of simple fluids confined in patterned slit pores

We present the influence of surface heterogeneity on the vapour–liquid phase behaviour of square-well fluids in slit pores using grand-canonical transition-matrix Monte Carlo simulations along with the histogram-reweighting method. Properties such as phase coexistence envelopes, critical properties and local density profiles of the confined SW fluid are reported for chemically and physically patterned slit surfaces. It is observed that in the chemically patterned pores, fluid–fluid and surface attraction parameters along with the width of attractive and inert stripes play fundamentally different roles in the phase coexistence and critical properties. On the other hand, pillar gap and height significantly affect the vapour–liquid equilibria in the physically patterned slit pores. We also present the effect of chemically and physically patterned slit surfaces on the spreading pressure.     

A molecular dynamics simulation study of the effect of water–graphene interaction on the properties of confined water

The role of water in determining the structure and stability of biomacromolecules has been well studied. In this work, molecular dynamics simulations have been applied to investigate the effect of surface hydrophobicity on the structure and dynamics of water confined between graphene surfaces. In order to evaluate this effect, we apply various attractive/repulsive water–graphene interaction potentials (hydrophobicity). The properties of confined water are studied by applying a purely repulsive interaction potential between water–graphene (modelled as a repulsive r^?12 potential) and repulsive–attractive forces (modelled as an LJ(12-6) potential). Compared to the case of a purely repulsive graphene–water potential, the inclusion of repulsive–attractive forces leads to formation of sharp peaks for density and the number of hydrogen bonds. Also, it was found that repulsive–attractive graphene–water potential caused slower hydrogen bonds dynamics and restricted the diffusion coefficient of water. Consequently, it was found that hydrogen bond breakage and formation rate with the repulsive r^?12 potential model, will increase compared to the corresponding water confined with the LJ(12-6) potential.     

Atomistic simulations of liquid–liquid coexistence in confinement: comparison of thermodynamics and kinetics with bulk

We review a few simulation methods and results related to the structure and non-equilibrium dynamics in the coexistence region of immiscible symmetric binary fluids, in bulk as well as under confinement, with special emphasis on the latter. Monte Carlo methods to estimate interfacial tensions for flat and curved interfaces have been discussed. The latter, combined with a thermodynamic integration technique, provides contact angles for coexisting fluids attached to the wall. For such three-phase coexistence, results for the line tension are also presented. For the kinetics of phase separation, various mechanisms and corresponding theoretical expectations have been discussed. A comparative picture between the domain growth in bulk and confinement (including thin-film and semi-infinite geometry) has been presented from molecular dynamics simulations. Applications of finite-size scaling technique have been discussed in both equilibrium and non-equilibrium contexts.     

Effect of aluminum on the binding properties of α-chymotrypsin

 The effect of aluminum ions on the binding properties of α-chymotrypsin has been studied. The results show that aluminum does not affect the catalytic rate constant k _cat, but it acts as an enzyme activator favoring the binding of the substrate to the catalytic site (i.e. decreasing K _m). Furthermore, aluminum binding to α-chymotrypsin displays about a threefold decrease in its affinity for the macromolecular inhibitor bovine pancreatic trypsin inhibitor (BPTI). Altogether, the different effect of aluminum on the binding of synthetic substrates (e.g. N-α-benzoyl-l-tyrosine ethyl ester, BTEE) and macromolecular inhibitors (e.g. BPTI) to α-chymotrypsin suggests the occurrence of an aluminum-linked conformational change in the enzyme molecule which brings about a marked structural change at the primary and secondary recognition sites for substrates and inhibitors. The modulative effect exerted by aluminum on the enzyme hydrolytic activity has been investigated also as a function of pH. The ion-linked effect appears to be dependent on the pH in a complex fashion, which suggests that aluminum binding is controlled by the protonation of at least two classes of residues on the enzyme molecule. Received: 5 December 1996 / Accepted: 11 March 1997     

Biophysics of endocytic vesicle formation: A focus on liquid–liquid phase separation

Endocytosis is a fine-tuned mechanism of cellular communication through which cells internalize molecules on the plasma membrane, such as receptors and their bound ligands. Through receptor clustering in endocytic pits, recruitment of active receptors to different endocytic routes and their trafficking towards different fates, endocytosis modulates cell signaling and ultimately leads to a variety of biological responses. Many studies have focused their attention on specialized endocytic mechanisms depending on the nature of the internalizing cargo and cellular context, distinct sets of coat proteins, endocytic adaptors and membrane lipids. Here, we review recent advances in our understanding of the principles underlying endocytic vesicle formation, integrating both biochemical and biophysical factors, with a particular focus on intrinsically disordered regions (IDRs) creating weakly interconnected protein networks assembled through liquid–liquid phase separation (LLPS) and driving membrane bending especially in clathrin-mediated endocytosis (CME). We finally discuss how these properties impinge on receptor fate and signaling.     

Application of kinetic Monte Carlo method to the vapour–liquid equilibria of associating fluids and their mixtures

Canonical kinetic Monte Carlo (C-kMC) simulations have been carried out to assess their feasibility and potential for calculating the vapour–liquid equilibria of various pure components with increasingly strong electrostatic interactions (carbon dioxide, methanol, ammonia and water) over a wide range of temperatures and for methanol/water mixtures at 298 K. The simulation results show that C-kMC is successful as a method for studying phase equilibria and thermodynamic properties. For all the examples investigated, the performance of the C-kMC method is at least as good as that of the conventional Monte Carlo (MC) methods and is efficient at low temperature where these fail. It also provides a route that is superior to the Widom method for the calculation of chemical potential. We recommend this method for this purpose and as an alternative to conventional MC for simulations of strongly associating fluids and at low temperatures.     

Plant–soil feedbacks and the coexistence of competing plants

Plant–soil feedbacks can have important implications for the interactions among plants. Understanding these effects is a major challenge since it is inherently difficult to measure and manipulate highly diverse soil communities. Mathematical models may advance this understanding by making the interplay of the various processes affecting plant–soil interaction explicit and by quantifying the relative importance of the factors involved. The aim of this paper is to provide a complete analysis of a pioneering plant–soil feedback model developed by Bever and colleagues (J Ecol 85: 561–573, 1997; Ecol Lett 2: 52–62, 1999; New Phytol 157: 465–473, 2003) to fully understand the range of possible impacts of plant–soil feedbacks on plant communities within this framework. We analyze this model by means of a new graphical method that provides a complete classification of the potential effects of soil communities on plant competition. Due to the graphical character of the method, the results are relatively easy to obtain and understand. We show that plant diversity depends crucially on two key parameters that may be viewed as measures of the intensity of plant competition and the direction and strength of plant–soil feedback, respectively. Our analysis provides a formal underpinning of earlier claims that plant–soil feedbacks, especially when they are negative, may enhance the diversity of plant communities. In particular, negative plant–soil feedbacks can enhance the range of plant coexistence by inducing competitive oscillations. However, these oscillations can also destabilize plant coexistence, leading to low population densities and extinctions. In addition, positive feedbacks can allow locally stable forms of plant coexistence by inducing alternative stable states. Our findings highlight that the inclusion of plant–soil interactions may fundamentally alter the predictions on the structure and functioning of above-ground ecosystems. The scenarios presented in this study can be used to formulate hypotheses about the ways soil community effects may influence plant competition that can be tested with empirical studies. This will advance our understanding of the role of plant–soil feedback in ecological communities.     

Effect of nutrients on the accumulation of glutamyl endopeptidase in the culture liquid ofBacillus intermedius 3–19

The effect of nutrients and growth conditions on the accumulation of glutamyl endopeptidase in the culture liquid ofBacillus intermedius 3–19 was studied. Glucose and other readily metabolizable carbon sources were found to suppress the production of the enzyme, whereas inorganic phosphate and ammonium cations enhanced it. Protein substrates, such as casein, gelatin, and hemoglobin, did not affect enzyme production. Some bivalent cations (Ca²⁺, Mg²⁺, Co²⁺) increased the production of glutamyl endopeptidase, but others (Zn²⁺, Fe²⁺, Cu²⁺) acted in the opposite way. The rate of enzyme accumulation in the culture liquid increased as the growth rate of the bacterium decreased, so that the maximum enzyme activity was observed in the stationary growth phase. Based on the results of this investigation, an optimal medium for the maximum production of glutamyl endopeptidase byB. intermedius 3–19 was elaborated.     

Vapor–liquid equilibria and thermophysical behavior of the SPC-HW model for heavy water

The vapor–liquid coexistence curve of the simple point charge heavy-water model (SPC-HW), [J. Chem. Phys., 114, 8064–8067 (2001)] is determined by Gibbs Ensemble Monte-Carlo (GEMC) simulation. The estimated critical conditions of the model based on the Wegner-type expansion for the order parameters and the rectilinear diameter are ρ_c = 0.300 g/cc, T _c = 661 K and P _c = 156 bars. The dielectric constant determined by isothermal–isochoric molecular dynamics is underpredicted along the coexistence curve by 29–44% in comparison with the experimental values. The analysis of the orthobaric temperature dependence of the system microstructure, in terms of the three site–site radial distribution functions, indicates that the first coordination numbers for the oxygen–oxygen and the oxygen–deuterium interactions are ～4.3 ± 0.1 and ～1.9 ± 0.1 at T = 300 K, and decrease by 15 and 55%, respectively, at criticality. The dipole–dipole correlation functions show that the orientational order in heavy water is quickly lost beyond the first oxygen–oxygen coordination shell. The model's second virial coefficient is determined by Monte-Carlo integration and used to aid the interpretation of the predicted phase equilibrium results.