Molecular dynamics simulation study of the static and dynamic properties of a model colloidal suspension with explicit solvent

Molecular dynamics simulation was used to study a colloidal suspension with explicit solvent to determine how inclusion of the solvent affects the structure and dynamics of the system. The solute was modelled as a hard-core particle enclosed in a Weeks–Chandler–Andersen (WCA) potential shell, while the solvent was modelled as a simple WCA fluid. We found that when the solute–solvent interaction included a hard core equal to half of the solute hard-core diameter, large depletion effects arose, leading to an effective attraction and large deviations from hard-sphere structure for the colloidal component. It was found that these effects could be eliminated by reducing the hard-core distance parameter in the solute–solvent interaction, thus allowing the solvent to penetrate closer to the colloidal particles. Three different values for the solute–solvent hard-core parameter were systematically studied by comparing the static structure factor and radial distribution function to the predictions of the Percus–Yevick theory for hard spheres. When the optimal value of the solute–solvent hard-core interaction parameter was found, this model was then used to study the dynamical behaviour of the colloidal suspension. This was done by first measuring the velocity autocorrelation function (VACF) over a large range of packing fractions. We found that this model predicted the sign of the long-time tail in the VACF in agreement with experimental values, something that single component hard-sphere systems have failed to do. The intermediate scattering functions at low wavevector were briefly studied to determine their behaviour in a dilute system. It was found that they could be modelled using a simple diffusion equation with a wavevector independent diffusion coefficient, making this model an excellent analogue of experimentally studied hard-sphere colloids.     

Release of phospholipids from colloidal particles to polymeric surfaces

This study presents a small-scale polymerization of high molecular weight methyl methacrylate/n-butyl acrylate (MMA/n-BA) colloidal particles that are synthesized in an aqueous environment in the presence of phospholipid hydrogenated soybean phosphatidylcholine (HSPC) molecules that also serve as the particle stabilizing agents. When such particles coalesce to form polymeric films, they release phospholipids, which, in turn, form organized structures near the film-air (F-A) interface. Diffusion and mobility of phospholipid molecules are affected not only by their compatibility with colloidal particles but also by electrolyte environments of colloidal dispersions. When Na(+), K(+), and Ca(2+) counterions are added to MMA/n-BA aqueous colloidal dispersions stabilized with HSPC, and such films are coalesced, different degrees of diffusion of HSPC to the F-A interface exist, depending on the counterion, and conformational changes of HSPC result. For example, in the presence of Ca(2+), HSPC molecules collapse entropically to form random surface layers, as opposed to smaller Na(+) and K(+), which force amphiphilic HSPC ends to align preferentially parallel to the film surface. These studies show that it is possible to design stimuli-response colloidal systems triggered by chemical environments of active molecules on colloidal polymer particles.     

Ultrastructural study of cholestasis induced by longterm treatment with estradiol valerate. I. Tight junctional analysis and tracer experiments

Over a period of 20 weeks estradiol valerate (1.5 mg/kg body weight/week) was administered subcutaneously to male Wistar rats from which the livers were examined at four week intervals employing a freeze-fracture technique and colloidal lanthanum tracer studies. In connection with intrahepatic cholestasis, distinct alterations in the tight junctions were observed, consisting of disorganization, rarification and proliferation. Disruption of the tight junctions was not seen and colloidal lanthanum did not penetrate into the bile canalicular lumen. Holding the view that the term "leakiness" of tight junctions should be defined with reference to the tracer employed, we conclude that in the liver one tight junctional strand is sufficient to prevent the escape of larger bile constituents such as bile acids and that a back diffusion of bile acids over the tight junctional barrier does not play a role in the pathogenesis of the estrogen-induced cholestasis. Interruptions of tight junctions, as described by other authors, are interpreted as a secondary mechanical effect. On the other hand, we consider an increased permeability of the tight junctions to water and small solute molecules as probable; possibly this increased permeability is brought about by alterations in the microfilaments. A model for the pathogenesis of the estrogen-induced intrahepatic cholestasis is proposed.     

Patterns of accumulation resulting from Taxes and changes in motility of micro-organisms

Summary An analysis is made of the development of patterns of accumulation of micro-organisms, as governed by tactic responses, changes in motility, and the effects of diffusion.When a soluble crystal is placed in a suspension of micro-organisms, the first manifestation is the development of a clear zone surrounding the crystal. This effect is a physical one, produced by a transfer of momentum from the solute molecules to the organisms.As the solute spreads and its boundary moves more slowly, the organisms are distributed in patterns which depend upon the occurrence of tactic responses and the influence of the solute upon motility. A congregation in the zone occupied by the solute can correspond either to a positive chemotaxis or to an inhibition of motility by the solute. Conversely, a withdrawal from the solute can signal either a negative chemotaxis or an enhancement of motility by the solute.The proper interpretation of the patterns described in Figs. 10 and 11 requires a microscopic study of individual organisms, in which the effect of the reagent upon motility is noted.     

The effect of hydration of lecithin-water lamellar phases: a comparative study of solute diffusion and ESR spectroscopic measurements

An analysis of the paramagnetic resonance spectra of spin labels in the lipidic region of lecithin-water lamellar phases as a function of phase water content has been carried out. The observed variation of the local organization and mobility of the lipids is consonant with previous results obtained from solute diffusion measurements. The previously observed sudden changes of solute diffusion for hydration of 9 and 18 molecules water per lecithin molecule are compared with the concomitant sudden changes as seen by ESR spectroscopy. The results also indicate that there is a gradient of fluidity across the lipid leaflets which are therefore not homogeneous to diffusing molecules.     

Molecular modeling and simulation of Mycobacterium tuberculosis cell wall permeability

The low permeability of the mycobacterial cell wall is thought to contribute to the intrinsic drug resistance of mycobacteria. In this study, the permeability of the Mycobacterium tuberculosis cell wall is studied by computer simulation. Thirteen known drugs with diverse chemical structures were modeled as solutes undergoing transport across a model for the M. tuberculosis cell wall. The properties of the solute-membrane complexes were investigated by means of molecular dynamics simulation, especially the diffusion coefficients of the solute molecules inside the cell wall. The molecular shape of the solute was found to be an important factor for permeation through the M. tuberculosis cell wall. Predominant lateral diffusion within, as opposed to transverse diffusion across, the membrane/cell wall system was observed for some solutes. The extent of lateral diffusion relative to transverse diffusion of a solute within a biological cell membrane may be an important finding with respect to absorption distribution, metabolism, elimination, and toxicity properties of drug candidates. Molecular similarity measures among the solutes were computed, and the results suggest that compounds having high molecular similarity will display similar transport behavior in a common membrane/cell wall environment. In addition, the diffusion coefficients of the solute molecules across the M. tuberculosis cell wall model were compared to those across the monolayers of dipalmitoylphosphatidylethanolamine and dimyristoylphosphatidylcholine, are two common phospholipids in bacterial and animal membranes. The differences among these three groups of diffusion coefficients were observed and analyzed.     

Porin channels in Escherichia coli: studies with liposomes reconstituted from purified proteins.

Rates of diffusion of uncharged and charged solute molecules through porin channels were determined by using liposomes reconstituted from egg phosphatidylcholine and purified Escherichia coli porins OmpF (protein 1a), OmpC (protein 1b), and PhoE (protein E). All three porin proteins appeared to produce channels of similar size, although the OmpF channel appeared to be 7 to 9% larger than the OmpC and PhoE channels in an equivalent radius. Hydrophobicity of the solute retarded the penetration through all three channels in a similar manner. The presence of one negative charge on the solute resulted in about a threefold reduction in penetration rates through OmpF and OmpC channels, whereas it produced two- to tenfold acceleration of diffusion through the PhoE channel. The addition of the second negatively charged group to the solutes decreased the diffusion rates through OmpF and OmpC channels further, whereas diffusion through the PhoE channel was not affected much. These results suggest that PhoE specializes in the uptake of negatively charged solutes. At the present level of resolution, no sign of true solute specificity was found in OmpF and OmpC channels; peptides, for example, diffused through both of these channels at rates expected from their molecular size, hydrophobicity, and charge. However, the OmpF porin channel allowed influx of more solute molecules per unit time than did the equivalent weight of the OmpC porin when the flux was driven by a concentration gradient of the same size. This apparent difference in "efficiency" became more pronounced with larger solutes, and it is likely to be the consequence of the difference in the sizes of OmpF and OmpC channels.     

A multiscale theoretical model for diffusive mass transfer in cellular biological media

An integrated methodology is developed for the theoretical analysis of solute transport and reaction in cellular biological media, such as tissues, microbial flocs, and biofilms. First, the method of local spatial averaging with a weight function is used to establish the equation which describes solute conservation at the cellular biological medium scale, starting with a continuum-based formulation of solute transport at finer spatial scales. Second, an effective-medium model is developed for the self-consistent calculation of the local diffusion coefficient in the cellular biological medium, including the effects of the structural heterogeneity of the extra-cellular space and the reversible adsorption to extra-cellular polymers. The final expression for the local effective diffusion coefficient is: D(Abeta)=lambda(beta)D(Aupsilon), where D(Aupsilon) is the diffusion coefficient in water, and lambda(beta) is a function of the composition and fundamental geometric and physicochemical system properties, including the size of solute molecules, the size of extra-cellular polymer fibers, and the mass permeability of the cell membrane. Furthermore, the analysis sheds some light on the function of the extra-cellular hydrogel as a diffusive barrier to solute molecules approaching the cell membrane, and its implications on the transport of chemotherapeutic agents within a cellular biological medium. Finally, the model predicts the qualitative trend as well as the quantitative variability of a large number of published experimental data on the diffusion coefficient of oxygen in cell-entrapping gels, microbial flocs, biofilms, and mammalian tissues.     

Permselectivity of the glomerular capillary wall to macromolecules. I. Theoretical considerations.

The transport of macromolecules across the renal glomerular capillary wall has been described theoretically using flux equations based on (a) restricted transport through small pores, and (b) the Kedem-Katchalsky formulation. The various assumptions and limitations inherent in these two approaches are discussed. To examine the coupling between macromolecular solute transport and the determinants of glomerular filtration rate, these flux equations were combined with mass balance relations which allow for variations in the transmembrane driving forces along a glomerular capillary. It was predicted, using both pore theory and the Kedem-Katchalsky equations, that fractional solute clearance should be strongly dependent on the determinants of glomerular filtration rate when convection and diffusion both contribute to solute transport. When convection becomes the sole mechanism for transcapillary solute transport, however, fractional solute clearance is essentially independent of changes in the determinants of glomerular filtration rate. Consequently, unless diffusion is absent, fractional solute clearances alone are insufficient to characterize the permselective properties of the glomerular capillary wall, since these values may be altered by changes in glomerular pressures and flows as well as changes in the properties of the capillary wall per se.     

Dynamic loading of deformable porous media can induce active solute transport

Active solute transport mediated by molecular motors across porous membranes is a well-recognized mechanism for transport across the cell membrane. In contrast, active transport mediated by mechanical loading of porous media is a non-intuitive mechanism that has only been predicted recently from theory, but not yet observed experimentally. This study uses agarose hydrogel and dextran molecules as a model experimental system to explore this mechanism. Results show that dynamic loading can enhance the uptake of dextran by a factor greater than 15 over passive diffusion, for certain combinations of gel concentration and dextran molecular weight. Upon cessation of loading, the concentration reverts back to that achieved under passive diffusion. Thus, active solute transport in porous media can indeed be mediated by cyclical mechanical loading.     

The variance of the distribution of traversal times in a capillary bed

A random walk model of capillary tracer transit times is developed that treats simulataneously: plug flow in the capillary, radial and axial diffusion in the capillary cylinder and tissue annulus, and endothelial barriers to solute transport. The mean transit time is simply the volume of distribution divided by blood flow. Variance of transit times has additive terms for radial, axial, and barrier influences that are reduceable to variances of simpler models of capillary exchange. The dependence of variance on the solute diffusion coefficient is not monotonic, but has a minimum near 0·5 × 10?6 cm²/s for reasonable parameters and no barrier, Small molecules like inert gases are expected to have larger variances with higher diffusion coefficients, while larger molecules and barrier limited solutes will have the reverse dependence. Available literature data indicates that capillary heterogeneity will have a major influence on whole-body variance of transit times.     

Fractionation of macromolecules in an alternating transverse electric field: simulation of the method

An electric field of alternating polarity applied in a direction transverse to the direction of solute transport is used as the basis of a method for the separation of biological macromolecules. The method derives directly from the ability of an electric field to induce movement of a charged macromolecule and from the physics of laminar fluid flow; no adsorptive immobile phase component is involved.

The method is simulated by computer for the case of solute molecules in a solvent flowing through a narrow chamber of recta generates an electric field orthogonal to the direction of solvent flow. Solute molecules repetitively traverse the solvent channel at rates determined by their electrophoretic mobility. During the transit across the channel, solute molecules are transported in the direction of solvent flow; at the channel wall, solvent velocity is negligible and solute transport is limited to that provided by transient diffusion into a mobile solvent zone. Molecules of different intrinsic electrophoretic mobility are separated.

The computer model was used to illustrate the process and to demonstrate the ‘tunability’ of the method as a function of the oscillation frequency and voltage wave form. Because of this tunability, a single instrument can function as the equivalent of several different chromatographic systems. Because fractionation is effected by direct physicochemical phenomena rather than via interaction with chromatographic sites, variations in fractionation results arising from formation of polymers for gel electrophoresis, packing of chromatography columns, or deterioration of columns with use are avoided. This method may be of particular use for the purification of nucleic acid fragments and for the analysis of protei: nucleic acid interactions.     

Osmosis and solute—Solvent drag

In 1903, George Hulett explained how solute alters water in an aqueous solution to lower the vapor pressure of its water. Hulett also explained how the same altered water causes osmosis and osmotic pressure when the solution is separated from liquid water by a membrane permeable to the water only. Hulett recognized that the solute molecules diffuse toward all boundaries of the solution containing the solute. Solute diffusion is stopped at all boundaries, at an open-unopposed surface of the solution, at a semipermeable membrane, at a container wall, or at the boundary of a solid or gaseous inclusion surrounded by solution but not dissolved in it. At each boundary of the solution, the solute molecules are reflected, they change momentum, and the change of momentum of all reflected molecules is a pressure, a solute pressure (i.e., a force on a unit area of reflecting boundary). When a boundary of the solution is open and unopposed, the solute pressure alters the internal tension in the force bonding the water in its liquid phase, namely, the hydrogen bond. All altered properties of the water in the solution are explained by the altered internal tension of the water in the solution. We acclaim Hulett's explanation of osmosis, osmotic pressure, and lowering of the vapor pressure of water in an aqueous solution. His explanation is self-evident. It is the necessary, sufficient, and inescapable explanation of all altered properties of the water in the solution relative to the same property of pure liquid water at the same externally applied pressure and the same temperature. We extend Hulett's explanation of osmosis to include the osmotic effects of solute diffusing through solvent and dragging on the solvent through which it diffuses. Therein lies the explanations of (1) the extravasation from and return of interstitial fluid to capillaries, (2) the return of luminal fluid in the proximal and distal convoluted tubules of a kidney nephron to their peritubular capillaries, (3) the return of interstitial fluid to the vasa recta, (4) return of aqueous humor to the episcleral veins, and (5) flow of phloem from source to sink in higher plants and many more examples of fluid transport and fluid exchange in animal and plant physiology. When a membrane is permeable to water only and when it separates differing aqueous solutions, the flow of water is from the solution with the lower osmotic pressure to the solution with the higher osmotic pressure.     

Determination of microvessel permeability and tissue diffusion coefficient of solutes by laser scanning confocal microscopy

Interstitium contains a matrix of fibrous molecules that creates considerable resistance to water and solutes in series with the microvessel wall. On the basis of our preliminary studies, by using laser-scanning confocal microscopy and a theoretical model for interstitial transport, we determined both microvessel solute permeability (P) and solute tissue diffusion coefficient (D) of alpha-lactalbumin (Stokes radius 2.01 nm) from the rate of tissue solute accumulation and the radial concentration gradient around individually perfused microvessel in frog mesentery. P(alpha-lactalbumin) is 1.7 +/- 0.7(SD) x 10(-6) cm/s (n = 6). D(t)/D(free) for alpha-lactalbumin is 27% +/- 5% (SD) (n = 6). This value of D(t)/D(free) is comparable to that for small solute sodium fluorescein (Stokes radius 0.45 nm), while p(alpha-lactalbumin) is only 3.4% of p(sodium fluorescein). Our results suggest that frog mesenteric tissue is much less selective to solutes than the microvessel wall.     

Abiotic synthesis of organic molecules from minerals containing traces of dissolved H2O,CO2 and N2 part I: Basic principles

Oxides and silicates which crystallize in the presence of H₂O, CO₂ and N₂, especially at high pressures, are expected to dissolve traces of these fluid components. In doing so atomic and electronic rearrangements occur between the host lattice and the dissolved molecules which lead to different solute species. These may be simply hydroxyl OH^–, carbonate CO₃ ^2– of similar ions, but other species can also form which are chemically reduced such as molecular H₂, CO₂ ^2– and CO^– or oxidized such as peroxy ions, O₂ ^2–. When the minerals containing such solute species are decompressed and cooled, they eventually become supersaturated with respect to their dissolved impurities. If the relative mobilities of the different solute species are different, diffusion and subsurface segregation lead to spatial separation: the surface and subsurface zone become enriched in the reduced species while the oxidized species remain in the bulk. Upon heating or during chemical dissolution (weathering) the reduced species contained in the surface react leading to the formation of a wide variety of H–C–O–N molecules: not only H₂O, CO₂ and possibly N₂ but also organic molecules. No external reduced atmosphere is needed, according to this hypothesis.     

Hydrostatic pressures developed by osmotically swelling vesicles bound to planar membranes

When phospholipid vesicles bound to a planar membrane are osmotically swollen, they develop a hydrostatic pressure (delta P) and fuse with the membrane. We have calculated the steady-state delta P, from the equations of irreversible thermodynamics governing water and solute flows, for two general methods of osmotic swelling. In the first method, vesicles are swollen by adding a solute to the vesicle-containing compartment to make it hyperosmotic. delta P is determined by the vesicle membrane's permeabilities to solute and water. If the vesicle membrane is devoid of open channels, then delta P is zero. When the vesicle membrane contains open channels, then delta P peaks at a channel density unique to the solute permeability properties of both the channel and the membrane. The solute enters the vesicle through the channels but leaks out through the region of vesicle-planar membrane contact. delta P is largest for channels having high permeabilities to the solute and for solutes with low membrane permeabilities in the contact region. The model predicts the following order of solutes producing pressures of decreasing magnitude: KCl greater than urea greater than formamide greater than or equal to ethylene glycol. Differences between osmoticants quantitatively depend on the solute permeability of the channel and the density of channels in the vesicle membrane. The order of effectiveness is the same as that experimentally observed for solutes promoting fusion. Therefore, delta P drives fusion. When channels with small permeabilities are used, coupling between solute and water flows within the channel has a significant effect on delta P. In the second method, an impermeant solute bathing the vesicles is isosmotically replaced by a solute which permeates the channels in the vesicle membrane. delta P resulting from this method is much less sensitive to the permeabilities of the channel and membrane to the solute. delta P approaches the theoretical limit set by the concentration of the impermeant solute.     

THE INFLUENCE OF ELECTROLYTES ON THE ELECTRIFICATION AND THE RATE OF DIFFUSION OF WATER THROUGH COLLODION MEMBRANES

1. When pure water is separated by a collodion membrane from a watery solution of an electrolyte the rate of diffusion of water is influenced not only by the forces of gas pressure but also by electrical forces. 2. Water is in this case attracted by the solute as if the molecules of water were charged electrically, the sign of the charge of the water particles as well as the strength of the attractive force finding expression in the following two rules, (a) Solutions of neutral salts possessing a univalent or bivalent cation influence the rate of diffusion of water through a collodion membrane, as if the water particles were charged positively and were attracted by the anion and repelled by the cation of the electrolyte; the attractive and repulsive action increasing with the number of charges of the ion and diminishing inversely with a quantity which we will designate arbitrarily as the "radius" of the ion. The same rule applies to solutions of alkalies. (b) Solutions of neutral or acid salts possessing a trivalent or tetravalent cation influence the rate of diffusion of water through a collodion membrane as if the particles of water were charged negatively and were attracted by the cation and repelled by the anion of the electrolyte. Solutions of acids obey the same rule, the high electrostatic effect of the hydrogen ion being probably due to its small "ionic radius." 3. The correctness of the assumption made in these rules concerning the sign of the charge of the water particles is proved by experiments on electrical osmose. 4. A method is given by which the strength of the attractive electric force of electrolytes on the molecules of water can be roughly estimated and the results of these measurements are in agreement with the two rules. 5. The electric attraction of water caused by the electrolyte increases with an increase in the concentration of the electrolyte, but at low concentrations more rapidly than at high concentrations. A tentative explanation for this phenomenon is offered. 6. The rate of diffusion of an electrolyte from a solution to pure solvent through a collodion membrane seems to obey largely the kinetic theory inasmuch as the number of molecules of solute diffusing through the unit of area of the membrane in unit time is (as long as the concentration is not too low) approximately proportional to the concentration of the electrolyte and is the same for the same concentrations of LiCl, NaCl, MgCl₂, and CaCl₂.     

Computer simulation of small molecule permeation across a lipid bilayer: dependence on bilayer properties and solute volume, size, and cross-sectional area

Cell membrane permeation is required for most drugs to reach their biological target, and understanding this process is therefore crucial for rational drug design. Recent molecular dynamics simulations have studied the permeation of eight small molecules through a phospholipid bilayer. Unlike experiments, atomistic simulations allow the direct calculation of diffusion and partition coefficients of solutes at different depths inside a lipid membrane. Further analyses of the simulations suggest that solute diffusion is less size-dependent and solute partitioning more size-dependent than was commonly thought.