Molecular simulation of volume of mixing,Helmholtz free energy of mixing and entropy of mixing in bulk fluid mixtures

We describe a kinetic Monte Carlo molecular simulation procedure to calculate the Helmholtz free energy, the entropy and the chemical potentials of all components in a bulk fluid mixture. This allows us to derive the excess properties (volume, free energy and entropy) resulting from the mixing of homogeneous fluids of pure components at constant temperature and pressure. We have chosen neon–xenon mixtures to illustrate our method because of the large difference in collision diameter and well-depth of the interaction energy. When xenon is predominant in the mixture, the volume of mixing is larger. The excess entropy of mixing correlates with the volume of mixing, since a positive excess volume enables more configurations (more possible molecular distributions). The excess thermodynamic quantities as functions of the total density were found to be insensitive to temperature. To investigate the effects of the molecular parameters, we also studied argon–nitrogen and argon–krypton mixtures. The effect of the difference in molecular parameters is in the order: argon–nitrogen < argon–krypton < neon–xenon. A large difference in the well-depth of the interaction energies results in an increase in the excess thermodynamic variables, which is in agreement with the literature McDonald IR. NpT-ensemble Monte Carlo calculations for binary liquid mixtures. Mol Phys. 1972;23(1):41–58; Singer JVL, Singer K. Monte Carlo calculation of thermodynamic properties of binary mixtures of Lennard-Jones (12-6) liquids. Mol Phys. 1972;24(2):357–390.     

Effects of helium and other inert gases on Echinosphaerium nucleofilium (protozoa, heliozoa).

The effects of helium, nitrogen, argon and krypton on Echinosphaerium nucleofilum (Heliozoa) have been studied at partial pressures of 10-130 atm. Additional experiments have been carried out with hydrostatic pressure alone. Helium causes shortening of the axopods over the whole range of pressures, and damage to the cell body at pressures of 60-90 atm, both with a maximum at 80 atm. These effects cannot be explained in terms of hydrostatic pressure alone; a 'pressure reversal' effect may be operating, causing the peak at 80 atm. Nitrogen also causes both cell damage and axopod shortening, the severity increasing with increasing pressure. Argon and krypton cause cell damage but no shortening. The order of potency for cell damage is krypton greater than argon greater than nitrogen greater than helium. It is suggested that there may be tuo sites of action, possibly the microtubules (for axopod shortening) and the cell membrane (for cell damage). In appropriate mixtures of helium and argon, both the cell damage usually caused by argon, and the axopod shortening usually caused by helium, are prevented. Possible mechanisms include the effects of hydrostatic pressure on gas solubility coefficients, reversal of the effects of the gases by the increase in total pressure, and competition for sites of action.     

Molecular dynamics simulation of helium–argon gas mixture under various wall conditions

As computational capabilities increase, molecular dynamics (MD) simulations become important tools of simulating reality. These simulations are especially useful for compressible gas mixture problems. In this study, binary diffusion of helium and argon was examined using a hard-sphere MD simulation method. For the sake of computational speed, low spacing ratios were chosen. Binary mass diffusion of gases in two equally sized halves of a box was simulated for identical initial kinetic energies and number densities. It has been noted that a purely mass diffusion mechanism of different gases is not physically possible. The resultant gas mixtures of several diffusion simulations were used as initial conditions for combined heat transfer – Couette flow, and heating and cooling experiments. The results showed the interesting behaviour of the mixture, which was subjected to various wall conditions. Energy of heavier molecules is found to be more sensitive to the wall velocities and less sensitive to the wall temperatures than lighter molecules. Diffusion, heat transfer, viscosity and heat capacity coefficients are deduced as well.     

Bipartite expressions for diffusional mass transport in biomembranes

Analytical expressions for solute diffusion through a membrane barrier for different initial and boundary conditions are available in the literature. The three commonest initial and boundary conditions are for a membrane without solute respectively immersed in a solution of constant concentration, immersed in such a solution for one side but with the other side isolated, and immersed in such a solution for one side and with the other side kept at zero concentration. The physical quantities for the first two initial and boundary conditions are concentration and average concentration (the total solute entering the membrane) with amperometric current (flux) and solute that permeates through the membrane (charge passed) for the third initial and boundary condition. Expressions for these methods in the literature are inconvenient for practical applications because of the infinite mathematical series required. An investigation of convergence of these expressions was therefore carried out. Simple but accurate bipartite expressions for these methods were constructed and provided theoretical support for studies on mass transport characterization of biomembranes. As a specific application, these expressions enabled a direct fit of the simulated observables to experimental values to obtain diffusion coefficients. For these initial and boundary conditions and corresponding physical quantities, simple one point methods for diffusion coefficient estimation are also suggested. These latter diffusion coefficients can be initial values for numerical fit methods.     

Conceptual, methodological and computational issues concerning the compartmental modeling of a complex biological system: Postprandial inter-organ metabolism of dietary nitrogen in humans

A multi-compartmental model has been developed to describe dietary nitrogen (N) postprandial distribution and metabolism in humans. This paper details the entire process of model development, including the successive steps of its construction, parameter estimation and validation. The model was built using experimental data on dietary N kinetics in certain accessible pools of the intestine, blood and urine in healthy adults fed a [15N]-labeled protein meal. A 13-compartment, 21-parameter model was selected from candidate models of increasing order as being the minimum structure able to properly fit experimental data for all sampled compartments. Problems of theoretical identifiability and numerical identification of the model both constituted mathematical challenges that were difficult to solve because of the large number of unknown parameters and the few experimental data available. For this reason, new robust and reliable methods were applied, which enabled (i) a check that all model parameters could theoretically uniquely be determined and (ii) an estimation of their numerical values with satisfactory precision from the experimental data. Finally, model validation was completed by first verifying its a posteriori identifiability and then carrying out external validation.     

Estimation of diffusion coefficients of proteins

A correlation for estimating the diffusion coefficients of protein molecules is presented. The correlation is based upon literature values of the protein diffusion coefficients and molal volumes for 143 proteins. The correlation can be used for the estimation of diffusion coefficients using only molecular weight. Accuracy is such that a linear regression on 301 proteins showed 75% of the diffusion coefficients estimated fell within 20% of the experimental values. The relationship between this correlation, the Stokes–Einstein equation, and the Wilke–Chang correlation is discussed.     

Viscosity of supercooled aqueous glycerol solutions, validity of the Stokes-Einstein relationship, and implications for cryopreservation

The viscosity of supercooled glycerol aqueous solutions, with glycerol mass fractions between 0.70 and 0.90, have been determined to confirm that the Avramov-Milchev equation describes very well the temperature dependence of the viscosity of the binary mixtures including the supercooled regime. On the contrary, it is shown that the free volume model of viscosity, with the parameters proposed in a recent work (He, Fowler, Toner, J. Appl. Phys. 100 (2006) 074702), overestimates the viscosity of the glycerol-rich mixtures at low temperatures by several orders of magnitude. Moreover, the free volume model for the water diffusion leads to predictions of the Stokes-Einstein product, which are incompatible with the experimental findings. We conclude that the use of these free volume models, with parameters obtained by fitting experimental data far from the supercooled and glassy regions, lead to incorrect predictions of the deterioration rates of biomolecules, overestimating their life times in these cryopreservation media.     

Antiapoptotic activity of argon and xenon

Although chemically non-reactive, inert noble gases may influence multiple physiological and pathological processes via hitherto uncharacterized physical effects. Here we report a cell-based detection system for assessing the effects of pre-defined gas mixtures on the induction of apoptotic cell death. In this setting, the conventional atmosphere for cell culture was substituted with gas combinations, including the same amount of oxygen (20%) and carbon dioxide (5%) but 75% helium, neon, argon, krypton, or xenon instead of nitrogen. The replacement of nitrogen with noble gases per se had no effects on the viability of cultured human osteosarcoma cells in vitro. Conversely, argon and xenon (but not helium, neon, and krypton) significantly limited cell loss induced by the broad-spectrum tyrosine kinase inhibitor staurosporine, the DNA-damaging agent mitoxantrone and several mitochondrial toxins. Such cytoprotective effects were coupled to the maintenance of mitochondrial integrity, as demonstrated by means of a mitochondrial transmembrane potential-sensitive dye and by assessing the release of cytochrome c into the cytosol. In line with this notion, argon and xenon inhibited the apoptotic activation of caspase-3, as determined by immunofluorescence microscopy coupled to automated image analysis. The antiapoptotic activity of argon and xenon may explain their clinically relevant cytoprotective effects.     

Binding of cationic surfactants to DNA, protein and DNA-protein mixtures

Extent of binding (gamma 2(1)) of cationic surfactants cetyltrimethyl ammonium bromide (CTAB), myristyltrimethyl ammonium bromide (MTAB) and dodecyl trimethyl ammonium bromide (DTAB) to calf-thymus DNA, bovine serum albumin (BSA) and to their binary mixture respectively have been measured as function of bulk concentration of the surfactant by using equilibrium dialysis technique. Binding of CTAB has been studied at different pH, ionic strength (mu), temperature and biopolymer composition and with native and denatured states of the biopolymers. The chain-length of different long chain amines plays a significant role in the extent of binding under identical solution condition. The binding ratios for CTAB to collagen, gelatin, DNA-collagen and DNA-gelatin mixtures respectively have also been determined. The conformational structures of different biopolymers are observed to play significant role in macromolecular interactions between protein and DNA in the presence of CTAB. From the experimental values of the maximum binding ratio (gamma 2m) at the saturation level for each individual biopolymer, ideal values (gamma 2m)id have been theoretically calculated for binary mixtures of biopolymers using additivity rule. The protein-DNA-CTAB interaction in mixture has been explained in terms of the deviation (delta) of (gamma 2m) from (gamma 2m)id in the presence of a surfactant in bulk. The binding of surfactants to biopolymers and to their binary mixtures are compared more precisely in terms of the Gibbs' free energy decrease (-delta G degree) for the saturation of the binding sites in the biopolymers or biopolymer mixtures with the change of the bulk surfactant activity from zero to unity in the rational mole fraction scale.     

Determination of Antioxidant Activity of Various Bioantioxidants and Their Mixtures by the Amperometric Method

To date, simple and operative electrochemical methods are widely used to study antioxidant properties of various biological objects. One of them is the amperometric method, which is used in various fields of science, technology and medicine to determine the antioxidant activity (AOA) of various beverages, extracts and biological fluids, as well as the total content of antioxidants (AOs) present in them. Measurements of AOA (electrochemical oxidability) of some known individual AO and their mixtures by the amperometric method was performed in the present work. The coefficients of their oxidability were determined. The AOA values obtained correlate well with the AOA of these compounds measured by other methods. The coincidence of the experimental values of AOA and the values calculated with the use of the coefficients of oxidability for each component of the mixture was observed for most combinations of binary mixtures of used AOs. This indicates the absence of interaction between them (synergism or antagonism) during the oxidation. Several mixtures with a lower value of the measured AOA compared with the calculated value (antagonism) represented the exception. During the electrochemical oxidation of the “oxidized glutathione + ascorbic acid” mixture, partial reduction of glutathione by ascorbic acid is likely to proceed, which results in an excess of the measured AOA value over the calculated value. The results obtained may be useful when working with devices based on the amperometric method.     

Estimation of the mean distance of closest approach of some heavy metal ions in aqueous solutions: some experimental and theoretical calculations

The estimation of numerical values of the mean distance of closest approach of ions, a, of heavy metal ion salts in aqueous solutions, determined from activity coefficients, as well as from different theoretical approaches, is presented and discussed.     

Bestimmung von Substratverbrauchskoeffizienten für Paraffinkohlenwasserstoffe

The empirical determined constant of 3.14 gram biomass per available electron is a good base for the calculation of minimum substrate consumption coefficients in the aerobic fermentation of paraffins by yeasts. The analysis of experimental determined specific substrate consumption coefficients and their comparison with the corresponding theoretical values show that the theoretical ones can be reached only if the substrate composition referring to carbon and hydrogen is of optimal composition for all syntheses.     

Diffusion of Ions in Myelinated Nerve Fibers

The diffusion of ions towards or away from the inner side of the nodal membrane in preparations, the cut ends of which are placed in various media, was investigated. The ion concentration changes were calculated by numerical solution of the unidimensional electrodiffusion equation under a variety of media compositions, axoplasmic diffusion coefficients, and internal anionic compositions. The potassium and cesium ion diffusion along the axon towards the node was determined experimentally by two different electrophysiological methods. On the basis of comparison between the experimental data and the computational predictions the axoplasmic potassium ion diffusion coefficient was determined to be almost equal to that in free aqueous solution, while that of cesium ion was close to one half of that in aqueous solution. Utilizing the values of diffusion parameters thus determined, we solved the electrodiffusion equation for a number of common experimental procedures. We found that in short fibers, cut 0.1-0.2 cm at each side of the node, the concentration approached values close to the new steady-state values within 5-30 min. In long fibers (over 1 cm long) steady-state concentrations were obtained only after a few hours. Under some conditions the internal concentrations transiently overshot the steady-state values. The diffusion potentials generated in the system were also evaluated. The ion concentration changes and generation of diffusion potential cannot be prevented by using side pools with cation content identical to that of the axoplasm.     

Recommended gas transport properties of argon at low density using ab initio potential

The most important transport properties of argon have been calculated using classical kinetic theory expressions in conjunction with high-quality ab initio potential energy values computed by Patkowski and Szalewicz. Dilute gas transport properties have been calculated for the viscosity, thermal conductivity, self-diffusion coefficient and thermal diffusion factor from 83 to 10,000 K. Comparisons between experimental transport property data and values presently calculated indicate that the present theoretical predictions may be employed as recommended values for this set of transport properties over a wide temperature range.     

Separation of amino acids by simulated moving bed using competitive Langmuir isotherm

The separation of two amino acids, phenylalanine and tryptophan, was carried out using laboratory simulated moving bed (SMB) chromatography. The SMB process consisted of four zones, with each zone having 2 columns. The triangle theory was used to obtain the operating conditions for the SMB. The mass transfer coefficients of the two amino acids were obtained from the best-fit values by comparing simulated and experimental pulse data. The competitive adsorption isotherms of the two amino acids were obtained by single and binary frontal analyses, taking into consideration the competition between the two components. A competitive Langmuir isotherm, obtained from single-component frontal chromatography, was used in the first run, and the isotherm from binary frontal chromatography in the second, with the flow rate of zone I modified to improve the purity. Compared to the first and second runs, the competitive Langmuir isotherm from the binary frontal chromatography showed good agreement with the experimental results. Also, adjusting the flow rate in zone I increased the purity of the products. The purities of the phenylalanine in the raffinate and the tryptophan in the extract were 99.84 and 99.99%, respectively.     

A simple and rapid orientation procedure for the estimation of affinities (1/Kd) and maximum binding capacities (Bmax) of ligand binding to two receptor subpopulations

This paper describes a simple and rapid procedure for the estimation of specific parameters (dissociation constants, Kd and maximum binding capacities, Bmax) of ligand binding to two receptor subpopulations. This procedure provides, in a few minutes, the investigator, performing the actual binding studies, the necessary information about receptor heterogeneity, enabling the investigator to plan further experiments. The procedure is based on the graphical comparison of experimental binding data (ligand binding to one or two receptor subpopulations) with the theoretical values of ligand binding to one receptor population at four levels). The values of Kd and Bmax for high- and low-affinity receptors are derived from 4 horizontal deviations of experimental data from a theoretical data plot at these levels by their comparison with tabulated deviations. The correctness of the estimated parameters can be confirmed by the comparison of experimental data with those simulated on the basis of applying the values of Kd and Bmax found in the formula for ligand binding to two receptor subpopulations. The practical applicability of this procedure was demonstrated both on simulated and experimental data, and confirmed by the well known computer programs for evaluating receptor heterogeneity, namely "LIGAND" and "Affinity spectra".     

A Model of Isotope Separation in Plants

A model representing isotope separation during water evaporation in plants was constructed. The model accounts for substance diffusion, convective transfer and evaporation from the surface of the leaves. The dependence of the system’s separation and enrichment coefficients on various parameters (liquid velocity, diffusion coefficient, and potential barriers for molecules and their thermal velocities) was determined. A comparison was made between the enrichment coefficients calculated from experimental data from different plants and those based on the model. Qualitative agreement between the experimental and theoretical values was obtained for the case of \(\frac{uh}{D} {\gg} 1\), where u is the average velocity of water in the plant, h is the height of the plant, and D is the diffusion coefficient of the substance.     

Deterministic and stochastic features of rhythmic human movement

The dynamics of rhythmic movement has both deterministic and stochastic features. We advocate a recently established analysis method that allows for an unbiased identification of both types of system components. The deterministic components are revealed in terms of drift coefficients and vector fields, while the stochastic components are assessed in terms of diffusion coefficients and ellipse fields. The general principles of the procedure and its application are explained and illustrated using simulated data from known dynamical systems. Subsequently, we exemplify the method’s merits in extracting deterministic and stochastic aspects of various instances of rhythmic movement, including tapping, wrist cycling and forearm oscillations. In particular, it is shown how the extracted numerical forms can be analysed to gain insight into the dependence of dynamical properties on experimental conditions.     

The mechanism of action of pressure on intramolecular protein dynamics]

The physical mechanisms of pressure influence on the protein dynamics and parameters of Mossbauer spectra were investigated. The pressure effects measured for human serum albumin using Rayleigh Scattering of Mossbauer Radiation techniques were described using the model of local diffusion. Parameters of this model were determined by analysing the experimental data. As a result an estimation of approximate values for activation volumes was performed. It was shown that the obtained values are well consistent with the previous experimental results.     

Diffusion-ordered NMR spectroscopy: a versatile tool for the molecular weight determination of uncharged polysaccharides

Diffusion-ordered NMR spectroscopy (DOSY) experiments have been carried out on dilute aqueous solutions of uncharged saccharide systems and, in particular, on six well characterized pullulan fractions of different molecular weights. The values of diffusion coefficients and hydrodynamic radii determined for the pullulan fractions are in good agreement with the results obtained with other methodologies such as light scattering. Fitting the diffusion coefficients data as a function of the molecular weight allows for the determination of a calibration curve that can be applied to a wide range of mono-, oligo-, and polysaccharides. Therefore, DOSY is proposed as a versatile tool for achieving a simple estimation of the molecular weight of uncharged polysaccharides. Mixtures of homopolymers of different molecular weight can be nicely separated. An advantage of the method is that the same sample used for the NMR characterization can be used for the molecular weight determination without any further manipulation. Other water soluble polymers, such as poly(ethylene oxide) and poly(vinylpyrrolidone), can be roughly characterized using the same calibration curve.