Shear viscosity and thermal conductivity of quadrupolar real fluids from molecular simulation

In the present work, equilibrium molecular dynamics was used with the Green-Kubo formalism to simultaneously calculate shear viscosity and thermal conductivity of ten real fluids, i.e. F₂, N₂, O₂, CO₂, C₂H₆, C₂H₄, C₂F₆, C₃H₄, C₃H₆ and SF₆. The fluids were consistently described by the two-center Lennard–Jones plus point quadrupole (2CLJQ) pair potential, whose parameters were adjusted to vapor–liquid equilibria only [J. Phys. Chem. B, 2001, 105, 12126–12133]. The predicted shear viscosities and thermal conductivities show an overall average deviation of only about 10% from correlations of experimental data where comparison was possible.

At low temperature and high density state points, the Green–Kubo integral for shear viscosity shows slow convergence. This problem can be overcome by a new approach developed in the present work. It is based on the adjustment of a suitable function describing the long time behavior of the autocorrelation function and yields reliable results without the need of excessively long simulation runs.     

Predicted melt curve and liquid-state transport properties of TATB from molecular dynamics simulations

The melt curve and the liquid-state transport properties shear viscosity, self-diffusion coefficient and thermal conductivity of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) were predicted using all-atom molecular dynamics simulations. The TATB melt curve was obtained using solid–liquid coexistence simulations and is in good accord with the Simon–Glatzel equation. The temperature dependencies of the shear viscosity and self-diffusion coefficient are predicted to obey Arrhenius behaviour for pressures up to P = 20 kbar. The thermal conductivity has a linear temperature dependence for P < 15 kbar and a linear density (ρ) dependence for ρ > 1200 kg m^?3. At similar densities the shear viscosity of liquid TATB is close to the predictions for liquid nitromethane [58] but lower than the predictions for liquid HMX [24] and RDX [59]. The self-diffusion coefficient for TATB is predicted to be higher than predictions for nitromethane, HMX and RDX at similar densities. The conductivity of TATB is ≈20% greater than the conductivity of liquid HMX at a given density.     

Tracking of single fluorescent particles in three dimensions: use of cylindrical optics to encode particle position.

We present a novel optical technique for three-dimensional tracking of single fluorescent particles using a modified epifluorescence microscope containing a weak cylindrical lens in the detection optics and a microstepper-controlled fine focus. Images of small, fluorescent particles were circular in focus but ellipsoidal above and below focus; the major axis of the ellipsoid shifted by 90 degrees in going through focus. Particle z position was determined from the image shape and orientation by applying a peak detection algorithm to image projections along the x and y axes; x, y position was determined from the centroid of the particle image. Typical spatial resolution was 12 nm along the optical axis and 5 nm in the image plane with a maximum sampling rate of 3-4 Hz. The method was applied to track fluorescent particles in artificial solutions and living cells. In a solution of viscosity 30 cP, the mean squared distance (MSD) traveled by a 264 nm diameter rhodamine-labeled bead was linear with time to 20 s. The measured diffusion coefficient, 0.0558 +/- 0.001 micron2/s (SE, n = 4), agreed with the theoretical value of 0.0556 micron2/s. Statistical variability of MSD curves for a freely diffusing bead was in quantitative agreement with Monte Carlo simulations of three-dimensional random walks. In a porous glass matrix, the MSD data was curvilinear and showed reduced bead diffusion. In cytoplasm of Swiss 3T3 fibroblasts, bead diffusion was restricted. The water permeability in individual Chinese Hamster Ovary cells was measured from the z movement of a fluorescent bead fixed at the cell surface in response osmotic gradients; water permeability was increased by > threefold in cells expressing CHIP28 water channels. The simplicity and precision of this tracking method may be useful to quantify the complex trajectories of fluorescent particles in living cells.     

Determination of rarefaction effects on transport properties of nanoscale gas flows using Green–Kubo molecular dynamic simulation

This study aimed to investigate the rarefaction effects on thermal conductivity, viscosity, and density of Argon, Neon and Xenon gas flows in a Platinum nanochannel. Green–Kubo approach with Lenard Jones potential function are used for molecular dynamic simulation. Simulations showed that with decrease in number of atoms, density, viscosity and thermal conductivity decreases, while decrease in nanochannel width in same number of gas atoms leads to increase in viscosity and thermal conductivity.     

Viscosity of heptane-toluene mixtures. Comparison of molecular dynamics and group contribution methods

Three methods of molecular dynamics simulation [Green–Kubo (G–K), non-equilibrium molecular dynamics (NEMD) and reversed non-equilibrium molecular dynamics (RNEMD)], and two group contribution methods [UNIFAC–VISCO and Grunberg–Nissan (G–N)] were used to calculate the viscosity of mixtures of n-heptane and toluene (known as heptol). The results obtained for the viscosity and density of heptol were compared with reported experimental data, and the advantages and disadvantages of each method are discussed. Overall, the five methods showed good agreement between calculated and experimental viscosities. In all cases, the deviation was lower than 9%. It was found that, as the concentration of toluene increases, the deviation of the density of the mixture (as calculated with molecular dynamics methods) also increases, which directly affects the viscosity result obtained. Among the molecular simulation techniques evaluated here, G–K produced the best results, and represents the optimal balance between quality of result and time required for simulation. The NEMD method produced acceptable results for the viscosity of the system but required more simulation time as well as the determination of an appropriate shear rate. The RNEMD method was fast and eliminated the need to determine a set of values for shear rate, but introduced large fluctuations in measurements of shear rate and viscosity. The two group contribution methods were accurate and fast when used to calculate viscosity, but require knowledge of the viscosity of the pure compounds, which is a serious limitation for applications in complex multicomponent systems.     

Molecular Dynamics Studies of Diffusion in Model Cylindrical Pores at Very Low Densities

Abstract

Molecular dynamics simulation has been used to study diffusion of methane at ambient temperature in cylindrical pores at very low densities. The cylinders were modelled as a continuum solid which interacts with the methane in the radial direction only. At the lowest densities, the VACF method does not yield reliable values of the self diffusion coefficient, D_s , but a suitable choice of time step and run length enables values of D_s to be found from MSD plots that are below the classical Knudsen diffusion coefficients. When density is increased, D_s passes through a maximum although the adsorption isotherm remains inside the Henry law region. Maxima are found for two cylinder radii and for two adsorbent field strengths. The existence of a maximum is attributed to transient intermolecular interactions. Analysis of a molecular trajectory demonstrates that long diffusion paths can be triggered by the rare event of an intermolecular encounter which forces a molecule into the repulsive part of the wall potential. At sufficiently high density, subsequent collisions quench the tendency towards long paths, and D_s decreases again. The issue of simulation artefact as a source of these observations is discussed.     

Intermonolayer friction and surface shear viscosity of lipid bilayer membranes

The flow behavior of lipid bilayer membranes is characterized by a surface viscosity for in-plane shear deformations, and an intermonolayer friction coefficient for slip between the two leaflets of the bilayer. Both properties have been studied for a variety of coarse-grained double-tailed model lipids, using equilibrium and nonequilibrium molecular dynamics simulations. For lipids with two identical tails, the surface shear viscosity rises rapidly with tail length, while the intermonolayer friction coefficient is less sensitive to the tail length. Interdigitation of lipid tails across the bilayer midsurface, as observed for lipids with two distinct tails, strongly enhances the intermonolayer friction coefficient, but hardly affects the surface shear viscosity. The simulation results are compared against the available experimental data.     

Optimization of bilayer floating tablet containing metoprolol tartrate as a model drug for gastric retention

The purpose of the present study was to develop an optimized gastric floating drug delivery system (GFDDS) containing metoprolol tartrate (MT) as a model drug by the optimization technique. A 2³ factorial design was employed in formulating the GFDDS with total polymer content-to-drug ratio (X₁), polymer-to-polymer ratio (X₂), and different viscosity grades of hydroxypropyl methyl cellulose (HPMC) (X₃) as independent variables. Four dependent variables were considered: percentage of MT release at 8 hours, T_50%, diffusion coefficient, and floating time. The main effect and interaction terms were quantitatively evaluated using a mathematical model. The results indicate that X₁ and X₂ significantly affected the floating time and release properties, but the effect of different viscosity grades of HPMC (K4M and K10M) was nonsignificant. Regression analysis and numerical optimization were performed to identify the best formulation. Fickian release transport was confirmed as the release mechanism from the optimized formulation. The predicted values agreed well with the experimental values, and the results demonstrate the feasibility of the model in the development of GFDDS.     

Rapid characterization of protein molecular weights and hydrodynamic structures by quasielastic laser-light scattering

Two methods for the characterization of protein molecular weights from their diffusion coefficients are discussed. These measurements can be made quickly and reliably at low concentrations using quasielastic light-scattering techniques. First, an empirical calibration of the diffusion coefficient at infinite dilution of denatured random coils against molecular weight is reported. The second method combines the measurement of D₀ with the intrinsic viscosity [η]. This D₀–[η] relationship proves to be very insensitive to polymers structure or solvent type. The data indicate that the ratio of the hydrodynamic radius measured by viscosity to the hydrodynamic radius measured by diffusion is about 15% smaller than that predicted by theoretical models. The nature of the molecular-weight average obtained for polydisperse systems is defined for a Schulz distribution. These hydrodynamic methods have also been used to demonstrate the presence of chain branching in the glycoprotein ovomucoid. In addition, a method is proposed by which the effective segment length and an excluded volume parameter for random coils may be evaluated for diffusion measurements.     

Feasibility of setting up generic alert levels for maximum skin dose in fluoroscopically guided procedures

PurposeThe feasibility of setting-up generic, hospital-independent dose alert levels to initiate vigilance on possible skin injuries in interventional procedures was studied for three high-dose procedures (chemoembolization (TACE) of the liver, neuro-embolization (NE) and percutaneous coronary intervention (PCI)) in 9 European countries.MethodsGafchromic® films and thermoluminescent dosimeters (TLD) were used to determine the Maximum Skin Dose (MSD). Correlation of the online dose indicators (fluoroscopy time, kerma- or dose-area product (KAP or DAP) and cumulative air kerma at interventional reference point (K_a,r)) with MSD was evaluated and used to establish the alert levels corresponding to a MSD of 2 Gy and 5 Gy. The uncertainties of alert levels in terms of DAP and K_a,r, and uncertainty of MSD were calculated.ResultsAbout 20–30% of all MSD values exceeded 2 Gy while only 2–6% exceeded 5 Gy. The correlations suggest that both DAP and K_a,r can be used as a dose indicator for alert levels (Pearson correlation coefficient p mostly >0.8), while fluoroscopy time is not suitable (p mostly <0.6). Generic alert levels based on DAP (Gy cm²) were suggested for MSD of both 2 Gy and 5 Gy (for 5 Gy: TACE 750, PCI 250 and NE 400). The suggested levels are close to the lowest values published in several other studies. The uncertainty of the MSD was estimated to be around 10–15% and of hospital-specific skin dose alert levels about 20–30% (with coverage factor k = 1).ConclusionsThe generic alert levels are feasible for some cases but should be used with caution, only as the first approximation, while hospital-specific alert levels are preferred as the final approach.     

Simulation of protein diffusion: a sensitive probe of protein–solvent interactions

Aqueous solutions of Candida antarctica lipase B (CALB) were simulated considering three different water models (SPC/E, TIP3P, TIP4P) by a series of molecular dynamics (MD) simulations of three different box sizes (L = 9, 14, and 19 nm) to determine the diffusion coefficient, the water viscosity and the protein density. The protein–water systems were equilibrated for 500 ns, followed by 100 ns production runs which were analysed. The diffusional properties of CALB were characterized by the Stokes radius (R_S), which was derived from the diffusion coefficient and the viscosity. R_S was compared to the geometric radius (R_G) of CALB, which was derived from the protein density. R_S and R_G differed by 0.27 nm for SPC/E and by 0.40 and 0.39 nm for TIP3P and TIP4P, respectively, which characterizes the thickness of the diffusive hydration layer on the protein surface. The simulated hydration layer of CALB resulted in agreement with those experimentally determined for other seven different proteins of comparable size. By avoiding the most common pitfalls, protein diffusion can be reliably simulated: simulating different box sizes to account for the finite size effect, equilibrating the protein–water system sufficiently, and using the complete production run for the determination of the diffusion coefficient.     

The Investigation of Protein Diffusion via H-Cell Microfluidics

In this study, we developed a microfluidics method, using a so-called H-cell microfluidics device, for the determination of protein diffusion coefficients at different concentrations, pHs, ionic strengths, and solvent viscosities. Protein transfer takes place in the H-cell channels between two laminarly flowing streams with each containing a different initial protein concentration. The protein diffusion coefficients are calculated based on the measured protein mass transfer, the channel dimensions, and the contact time between the two streams. The diffusion rates of lysozyme, cytochrome c, myoglobin, ovalbumin, bovine serum albumin, and etanercept were investigated. The accuracy of the presented methodology was demonstrated by comparing the measured diffusion coefficients with literature values measured under similar solvent conditions using other techniques. At low pH and ionic strength, the measured lysozyme diffusion coefficient increased with the protein concentration gradient, suggesting stronger and more frequent intermolecular interactions. At comparable concentration gradients, the measured lysozyme diffusion coefficient decreased drastically as a function of increasing ionic strength (from zero onwards) and increasing medium viscosity. Additionally, a particle tracing numerical simulation was performed to achieve a better understanding of the macromolecular displacement in the H-cell microchannels. It was found that particle transfer between the two channels tends to speed up at low ionic strength and high concentration gradient. This confirms the corresponding experimental observation of protein diffusion measured via the H-cell microfluidics.     

Oxygen Ion Diffusion and Surface Exchange Properties of the α‐ and δ‐phases of Bi2O3

Fast oxide ion conduction is a highly desirable property for materials in a wide range of applications. The fastest reported ionic conductor, representing the current state of the art and an oft‐proposed effective limit of oxide ion conductivity, is the high temperature fluorite‐structured δ phase of Bi₂O₃. Here, the ionic nature of this conduction is, for the first time, directly determined through oxygen tracer diffusion measurements. This phase also presents a remarkably high oxygen surface exchange coefficient, competitive with the highest performance solid oxide fuel cell (SOFC) cathodes yet counterintuitively in a material with negligible electronic conduction. The low temperature α‐Bi₂O₃ polymorph is also investigated, revealing a remarkable drop in diffusivity of over 7 orders of magnitude with a temperature drop of just ≈150 °C. Surprisingly, the diffusion studies also reveal a secondary, significantly faster migration pathway in the α phase. This is attributed to grain boundary conduction and shown to be 3–4 orders of magnitude higher than in the bulk. This previously unobserved property could present an exciting opportunity to tailor ionic conductivity levels through manipulating microstructure down to the nanoscale.     

How to model the local interaction in the predator–prey system at slow diffusion in a heterogeneous environment?

We examine the nonlinear reaction–diffusion–advection equations to modeling of the predator–prey system under heterogeneous carrying capacity of the prey, and Holling type II functional response. When advection and diffusion fluxes are absent or small, we detect the discrepancy between the resource (carrying capacity) and species distributions. The large diffusion eliminates this effect. We propose a modification of the functional response coefficients to provide the correlation between species distribution and resource in both cases. The numerical simulation of several models both under small and moderate advection–diffusion fluxes is carried out.     

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.     

Effects of shear rate and suspending viscosity on deformation and frequency of red blood cells tank-treading in shear flows

The tank-treading rotation of red blood cells (RBCs) in shear flows has been studied extensively with experimental, analytical, and numerical methods. Even for this relatively simple system, complicated motion and deformation behaviors have been observed, and some of the underlying mechanisms are still not well understood. In this study, we attempt to advance our knowledge of the relationship among cell motion, deformation, and flow situations with a numerical model. Our simulation results agree well with experimental data, and confirm the experimental finding of the decrease in frequency/shear-rate ratio with shear rate and the increase of frequency with suspending viscosity. Moreover, based on the detailed information from our simulations, we are able to interpret the frequency dependency on shear rate and suspending viscosity using a simple two-fluid shear model. The information obtained in this study thus is useful for understanding experimental observations of RBCs in shear and other flow situations; the good agreement to experimental measurements also shows the potential usefulness of our model for providing reliable results for microscopic blood flows.     

Molecular dynamics simulations of a lithium/sodium carbonate mixture

The diffusion and ionic conductivity of Li _x Na_1?x CO₃ salt mixtures were studied by means of Molecular Dynamics (MD) simulations, using the Janssen and Tissen model (Janssen and Tissen, Mol Simul 5:83–98; 1990). These salts have received particular attention due to their central role in fuel cells technology, and reliable numerical methods that could perform as important interpretative tool of experimental data are thus required but still lacking. The chosen computational model nicely reproduces the main structural behaviour of the pure Li₂CO₃, Na₂CO₃ and K₂CO₃ carbonates, but also of their Li/K and Li/Na mixtures. However, it fails to accurately describe dynamic properties such as activation energies of diffusion and conduction processes, outlining the need to develop more accurate models for the simulation of molten salt carbonates.     

Effect of Geometrical and Chemical Constraints on Water Flux across Artificial Membranes

Studies have been made on the temperature dependence of both the hydraulic conductivity, L_p, and the THO diffusion coefficient, ω, for a series of cellulose acetate membranes (CA) of varying porosity. A similar study was also made of a much less polar cellulose triacetate membrane (CTA). The apparent activation energies, E_a, for diffusion across CA membranes vary with porosity, being 7.8 kcal/mole for the nonporous membrane and 5.5 kcal/mole for the most porous one. E_a for diffusion across the less polar CTA membrane is smaller than E_a for the CA membrane of equivalent porosity. Classical viscous flow, in which the hydraulic conductivity is inversely related to bulk water viscosity, has been demonstrated across membranes with very small equivalent pores. Water-membrane interactions, which depend upon both chemical and geometrical factors are of particular importance in diffusion. The implication of these findings for the interpretation of water permeability experiments across biological membranes is discussed.     

In situ effective diffusion coefficient profiles in live biofilms using pulsed‐field gradient nuclear magnetic resonance

Diffusive mass transfer in biofilms is characterized by the effective diffusion coefficient. It is well documented that the effective diffusion coefficient can vary by location in a biofilm. The current literature is dominated by effective diffusion coefficient measurements for distinct cell clusters and stratified biofilms showing this spatial variation. Regardless of whether distinct cell clusters or surface‐averaging methods are used, position‐dependent measurements of the effective diffusion coefficient are currently: (1) invasive to the biofilm, (2) performed under unnatural conditions, (3) lethal to cells, and/or (4) spatially restricted to only certain regions of the biofilm. Invasive measurements can lead to inaccurate results and prohibit further (time‐dependent) measurements which are important for the mathematical modeling of biofilms. In this study our goals were to: (1) measure the effective diffusion coefficient for water in live biofilms, (2) monitor how the effective diffusion coefficient changes over time under growth conditions, and (3) correlate the effective diffusion coefficient with depth in the biofilm. We measured in situ two‐dimensional effective diffusion coefficient maps within Shewanella oneidensis MR‐1 biofilms using pulsed‐field gradient nuclear magnetic resonance methods, and used them to calculate surface‐averaged relative effective diffusion coefficient (D_rs) profiles. We found that (1) D_rs decreased from the top of the biofilm to the bottom, (2) D_rs profiles differed for biofilms of different ages, (3) D_rs profiles changed over time and generally decreased with time, (4) all the biofilms showed very similar D_rs profiles near the top of the biofilm, and (5) the D_rs profile near the bottom of the biofilm was different for each biofilm. Practically, our results demonstrate that advanced biofilm models should use a variable effective diffusivity which changes with time and location in the biofilm. Biotechnol. Bioeng. 2010;106: 928–937. © 2010 Wiley Periodicals, Inc.