Macromolecular crowding in biological systems: hydrodynamics and NMR methods

Most biologically relevant environments involve highly concentrated macromolecular solutions and most biological processes involve macromolecules that diffuse and interact with other macromolecules. Macromolecular crowding is a general phenomenon that strongly affects the transport properties of macromolecules (rotational and translational diffusion) as well as the position of their equilibria. NMR methods can provide information on molecular interactions, as well as on translational and rotational diffusion. In fact, rotational diffusion, through its determinant role in NMR relaxation, places a practical limit on the systems that can be studied by NMR. While in dilute solutions of non-aggregating macromolecules this limit is set by macromolecular size, in crowded solutions excluded volume effects can have a strong effect on the observed diffusion rates. Hydrodynamic theory offers some insight into the magnitude of crowding effects on NMR observable parameters.     

Effect of cell arrangement and interstitial volume fraction on the diffusivity of monoclonal antibodies in tissue.

We present theoretical calculations relating the effective diffusivity of monoclonal antibodies in tissue (Deff) to the actual diffusivity in the interstitium (Dint) and the interstitial volume fraction phi. Measured diffusivity values are effective values, deduced from concentration profiles with the tissue treated as a continuum. By using homogenization theory, the ratio Deff/Dint is calculated for a range of interstitial volume fractions from 10 to 65%. It is assumed that only diffusion in the interstitial spaces between cells contributes to the effective diffusivity. The geometries considered have cuboidal cells arranged periodically, with uniform gaps between cells. Deff/Dint is found to generally be between (2/3) phi and phi for these geometries. In general, the pathways for diffusion between cells are not straight. The effect of winding pathways on Deff/Dint is examined by varying the arrangement of the cells, and found to be slight. Also, the estimates of Deff/Dint are shown to be insensitive to typical nonuniformities in the widths of gaps between cells. From our calculations and from published experimental measurements of the effective diffusivity of an IgG polyclonal antibody both in water and in tumor tissue, we deduce that the diffusivity of this molecule in the interstitium is one-tenth to one-twentieth its diffusivity in water. We also conclude that exclusion of molecules from cells (an effect independent of molecular weight) contributes as much as interstitial hindrance to the reduction of effective diffusivity, for small interstitial volume fractions (around 20%). This suggests that the increase in the rate of delivery to tissues resulting from the use of smaller molecular-weight molecules (such as antibody fragments or bifunctional antibodies) may be less than expected.     

Water transport through plant tissue: the apoplasm and symplasm pathways

A detailed quantitative analysis of water flow through the apoplasm and symplasm of plant tissue is presented. The analysis results in two coupled diffusion equations which describe water transport in the two pathways. Various parameters entering the analysis identify the physical properties of the tissue which control the transport process as the resistance to water flow per cell in the two parallel pathways, the resistance per cell between pathways, and the water capacity per cell in the two pathways. Values for the several resistances and water capacities are estimated from available data, and a model problem is solved wherein a sheet of tissue at an initial water potential of — δ bars is immersed in a container of water. The resulting solutions show that depending on the values assigned to the controlling parameters, local water potential equilibrium between each cell and its cell wall may or may not obtain. In the special case of local equilibrium (water potential in the symplasm and apoplasm pathways essentially equal), the transport process can be described by a single diffusion equation which is derived along with an expression for the tissue diffusivity. It is concluded that the weakest link in the analysis is the estimated value for the permeability of the plasmodesma membrane, and that a logical extension of the theory would be to include the effects of a diffusable solute.     

A novel technique for measuring solute diffusivities in entrapment matrices used in immobilization

A novel technique has been developed for measuring effective solute diffusivities in entrapment matrices used for cell immobilization. In this technique radiotracers were used to measure effective diffusivities and equilibrium partition coefficients of the solute between the liquid and solid matrix. Ca-alginate was used in this study, because it is one of the most commonly employed matrices for the immobilization of microbial, plant and mammalian cells. The experimental apparatus consisted of a single spherical Ca-alginate bead which was attached to a rotating rod and immersed in water containing C(14)-glucose. The rotational speed of the spherical bead was controlled and resulted in excellent mixing, and negligible external film mass transfer resistance, which allowed the measurement of true effective solute diffusivity within the solid matrix. The rates of C(14)-glucose diffusion within the Ca-alginate sphere were measured using a scintillation spectrometer. A mathematical model of unsteady-state diffusion in a sphere was used with appropriate boundary conditions, and the effective diffusivity of glucose was found from the best fit of the experimental data using a computer regression analysis method. Using 2% (w/v) Ca-alginate beads in this new radiotracer technique the effective diffusivity and partition coefficient of glucose were found to be 6.62 x 10(-10) m(2)/s and 0.98, respectively. The accuracy, advantages, and simplicity of this new method for diffusivity measurements are also compared to other existing methods.     

A Numerical Study of the Hydrodynamic Stable Concentration Boundary Layers in a Membrane System Under Microgravitational Conditions

On the basis of the classic formula of the concentration Rayleigh number and the Kedem–Katchalsky equation for diffusive membrane transport, we derived the equations of sixteenth order which show the dependence of the thicknesses of the concentration boundary layers on the difference of the solution concentrations, the concentration Rayleigh number, the solute permeability coefficient of the membrane and the diffusion coefficients in the solution, the kinematic viscosity of the solution, the density of solutions, the temperature and gravitational acceleration. The obtained equation has numerical solutions in the first, third and fourth quadrant of a co-ordinate system. However, only two solutions from the first quadrant of the co-ordinate system have physical meaning. Confining ourselves to the set of solutions with physical meaning only, the thicknesses of concentration boundary layers for different parameters occurring in the obtained equation were calculated numerically.     

Homogenization of Large-Scale Movement Models in Ecology

A difficulty in using diffusion models to predict large scale animal population dispersal is that individuals move differently based on local information (as opposed to gradients) in differing habitat types. This can be accommodated by using ecological diffusion. However, real environments are often spatially complex, limiting application of a direct approach. Homogenization for partial differential equations has long been applied to Fickian diffusion (in which average individual movement is organized along gradients of habitat and population density). We derive a homogenization procedure for ecological diffusion and apply it to a simple model for chronic wasting disease in mule deer. Homogenization allows us to determine the impact of small scale (10–100 m) habitat variability on large scale (10–100 km) movement. The procedure generates asymptotic equations for solutions on the large scale with parameters defined by small-scale variation. The simplicity of this homogenization procedure is striking when compared to the multi-dimensional homogenization procedure for Fickian diffusion,and the method will be equally straightforward for more complex models.     

A stirred bath technique for diffusivity measurements in cell matrices

A stirred bath technique was developed for determining effective diffusivities in cell matrices. The technique involves cell immobilization in a dilute gel which has negligible effect on solute diffusion. Agar and collagen were tested as immobilizing gels. Agar gel was shown to have minor interactions with the diffusion of various biological molecules, and was used for immobilization of Ehrlich Ascites Tumor (EAT) cells. Diffusivities of glucose and lactic acid were measured in EAT matrices for cell loadings between 20 and 45 vol %. Treatment with glutaraldehyde was effective in quenching the metabolic activity of the cells while preserving their physical properties and diffusive resistance. The measured data agree favorably with predictions based on Maxwell's equation for effective diffusion in a periodic composite material. The stirred bath technique is useful for diffusivity determinations in immobilized matrices or free slurries, and is applicable to both microbial and mammalian cell systems.     

Apparent Diffusivity and Taylor Dispersion of Water and Solutes in Capillary Beds

A physical theory explaining the anisotropic dispersion of water and solutes in biological tissues is introduced based on the phenomena of Taylor dispersion, in which highly diffusive solutes cycle between flowing and stagnant regions in the tissue, enhancing dispersion in the direction of microvascular flow. An effective diffusion equation is derived, for which the coefficient of dispersion in the axial direction (direction of capillary orientation) depends on the molecular diffusion coefficient, tissue perfusion, and vessel density. This analysis provides a homogenization that represents three-dimensional transport in capillary beds as an effectively one-dimensional phenomenon. The derived dispersion equation may be used to simulate the transport of solutes in tissues, such as in pharmacokinetic modeling. In addition, the analysis provides a physically based hypothesis for explaining dispersion anisotropy observed in diffusion-weighted imaging (DWI) and diffusion-tensor magnetic resonance imaging (DTMRI) and suggests the means of obtaining quantitative functional information on capillary vessel density from measurements of dispersion coefficients. It is shown that a failure to account for flow-mediated dispersion in vascular tissues may lead to misinterpretations of imaging data and significant overestimates of directional bias in molecular diffusivity in biological tissues. Measurement of the ratio of axial to transverse diffusivity may be combined with an independent measurement of perfusion to provide an estimate of capillary vessel density in the tissue.     

Continuum heterogeneous biofilm model--a simple and accurate method for effectiveness factor determination

We present a novel analytical approach to describe biofilm processes considering continuum variation of both biofilm density and substrate effective diffusivity. A simple perturbation and matching technique was used to quantify biofilm activity using the steady-state diffusion-reaction equation with continuum variable substrate effective diffusivity and biofilm density, along the coordinate normal to the biofilm surface. The procedure allows prediction of an effectiveness factor, η, defined as the ratio between the observed rate of substrate utilization (reaction rate with diffusion resistance) and the rate of substrate utilization without diffusion limitation. Main assumptions are that (i) the biofilm is a continuum, (ii) substrate is transferred by diffusion only and is consumed only by microorganisms at a rate according to Monod kinetics, (iii) biofilm density and substrate effective diffusivity change in the x direction, (iv) the substrate concentration above the biofilm surface is known, and (v) the substratum is impermeable. With this approach one can evaluate, in a fast and efficient way, the effect of different parameters that characterize a heterogeneous biofilm and the kinetics of the rate of substrate consumption on the behavior of the biological system. Based on a comparison of η profiles the activity of a homogeneous biofilm could be as much as 47.8% higher than that of a heterogeneous biofilm, under the given conditions. A comparison of η values estimated for first order kinetics and η values obtained by numerical techniques showed a maximum deviation of 1.75% in a narrow range of modified Thiele modulus values. When external mass transfer resistance, is also considered, a global effectiveness factor, η(0) , can be calculated. The main advantage of the approach lies in the analytical expression for the calculation of the intrinsic effectiveness factor η and its implementation in a computer program. For the test cases studied convergence was achieved quickly after four or five iterations. Therefore, the simulation and scale-up of heterogeneous biofilm reactors can be easily carried out.     

The effective diffusion coefficient and the distribution constant for small molecules in calcium-alginate gel beads

The effective diffusion coefficient, D(e), and the distribution constant, K(i), for selected mono- and disaccharides and organic acids were determined in homogeneous calcium-alginate gel with and without entrapped bacteria. Results were obtained from transient concentration changes in well-stirred solutions of limited volume, in which the gel beads were suspended. The effective diffusioncoefficients and the distribution constants were estimated by fitting mathematical model predictions to the experimental data using a nonlinear model fitting program (MODFIT). Both single solute diffusion and multiple solute diffusion were performed. A small positive effect was obtained onthe values of D(e) for the system of multiple solute diffusion; however, the values of K(i) were not significantly influenced. For the nine solutes tested, D(e) for 2% Ca-alginate gel beads was found to be approximately 85% of the diffusivity measured in water. The effects on D(e) and K(i), for lactose and lactic acid were determined for variations of alginate concentration, pH, temperature, and biomass content in the beads. D(e) decreased linearly for both lactose and lactic acid with increasing cell concentration in the Ca-alginate gel. K(i), was constant for both lactose and lactic acid with increasing cell concentration. D(e) was significantly lower at pH 4.5 than at pH 5.5 and 6.5 for both lactose and lactic acid. Furthermore, D(e) seemed to decrease with increased alginate concentration in the range of 1% to 4%. The diffusion rate increased with increasing temperature, and the activation energy for the diffusion process for both lactose and lactic acid was constant in the temperature range tested. (c) 1995 John Wiley & Sons Inc.     

Convection and Diffusion in Charged Hydrated Soft Tissues: A Mixture Theory Approach

The extracellular matrix of cartilage is a charged porous fibrous material. Transport phenomena in such a medium are very complex. In this study, solute diffusive flux and convective flux in porous fibrous media were investigated using a continuum mixture theory approach. The intrinsic diffusion coefficient of solute in the mixture was defined and its relation to drag coefficients was presented. The effect of mechanical loading on solute diffusion in cartilage under unconfined compression with a frictionless boundary condition was analyzed numerically using the model developed. Both strain-dependent hydraulic permeability and diffusivity were considered. Analyses and results show that (1) In porous media, the convective velocity for each solute phase is different. (2) The solute convection in tissue is governed by the relative convective velocity (i.e., relative to solid velocity). (3) Under the assumption that all the frictional interactions among solutes are negligible, the relative convective velocity for α-solute phase is equal to the relative solvent velocity multiplied by its convective coefficient (H ^α) which is also known as the hindrance factor in the literature. The relationship between the convective coefficient and the relative diffusivity of solute is presented. (4) Solute concentration profile within the cartilage sample depends on the phase of dynamic compression.     

Simultation of gradient and band propagation in the centrifuge.

A technique is developed for simulating the behavior of both the gradient-forming solute and macromolecular bands in a centrifuge. The change with time of the density gradient due to diffusion and sedimentation of the gradient-forming solute is calculated by a finite difference method, making use of the results of earlier work on the theory of the equilibrium density gradient. Using a perturbation technique, the concentration profiles of dilute bands of macromolecules are then calculated as they sediment and diffuse through the varying supporting gradient. Results of the stimulaion techniques are compared with experiment.     

Uptake of solutes by multiple root systems from soil

Summary The theoretical treatment of diffusion of solutes to a number of parallel, competing roots is difficult, but an electrical analog has been constructed which allows solute uptake by such a system to be simulated easily and rapidly. The construction, theory and operation of the analog are described. Differences in diffusion coefficients, dimensions, root size and uptake properties can all be dealt with. Approximate methods are available for simulating mass flow with diffusion, slow release of nutrients in the soil, the presence of root hairs, and incomplete root-soil contact.     

Temperature affects transport of polysaccharides and proteins in articular cartilage explants

Solute transport phenomena mediate many aspects of the physiology and contrast agent-based clinical imaging of articular cartilage. Temperatures up to 10°C below standard body temperature (37°C) are common in articulating joints during normal activities and clinically (e.g. cold treatment of injuries). Therefore it is of interest to characterize the effects of temperature changes on solute transport parameters in cartilage. A range of fluorescent solutes including fluorescein isothiocyanate, 4 and 40kDa dextrans, myoglobin, insulin and chondroitin sulfate were prepared and used in assays of solute effective partition coefficient and effective diffusivity in bovine intermediate zone articular cartilage explants maintained at 10, 22 or 37°C. Trends for increasing partition coefficient with increasing temperature were evident for all solutes except chondroitin sulfate, with significant changes between 22 and 37°C for 4kDa dextran, insulin and myoglobin. Diffusivities of most solutes tested also tended to increase with increasing temperature, with significant changes between 10 and 22°C for FITC, 40kDa dextran and myoglobin. Oddly, insulin diffusivity decreased significantly as temperature increased from 22 to 37°C while chondroitin sulfate diffusivity exhibited no clear temperature dependence. These results highlight solute-specific temperature dependences of transport phenomena which may depend upon molecular weight, chemical structure, molecular conformation, and solute-matrix and solute-solute interactions. The articular cartilage explants themselves exhibited small but significant changes in water and glycosaminoglycan contents during experiments, underscoring the importance of solute-matrix interactions. Solute transport parameters in cartilage and their temperature dependences are therefore not easily predicted, and case-by-case experimental determination may be essential.     

A Biomechanical Triphasic Approach to the Transport of Nondilute Solutions in Articular Cartilage

Biomechanical models for biological tissues such as articular cartilage generally contain an ideal, dilute solution assumption. In this article, a biomechanical triphasic model of cartilage is described that includes nondilute treatment of concentrated solutions such as those applied in vitrification of biological tissues. The chemical potential equations of the triphasic model are modified and the transport equations are adjusted for the volume fraction and frictional coefficients of the solutes that are not negligible in such solutions. Four transport parameters, i.e., water permeability, solute permeability, diffusion coefficient of solute in solvent within the cartilage, and the cartilage stiffness modulus, are defined as four degrees of freedom for the model. Water and solute transport in cartilage were simulated using the model and predictions of average concentration increase and cartilage weight were fit to experimental data to obtain the values of the four transport parameters. As far as we know, this is the first study to formulate the solvent and solute transport equations of nondilute solutions in the cartilage matrix. It is shown that the values obtained for the transport parameters are within the ranges reported in the available literature, which confirms the proposed model approach.     

A new approximate whole boundary solution of the Lamm differential equation for the analysis of sedimentation velocity experiments

Sedimentation velocity is one of the best-suited physical methods for determining the size and shape of macromolecular substances or their complexes in the range from 1 to several thousand kDa. The moving boundary in sedimentation velocity runs can be described by the Lamm differential equation. Fitting of suitable model functions or solutions of the Lamm equation to the moving boundary is used to obtain directly sedimentation and diffusion coefficients, thus allowing quick determination of size, shape and other parameters of macromolecules. Here we present a new approximate whole boundary solution of the Lamm equation that simultaneously allows the specification of sedimentation and diffusion coefficients with deviations smaller than 1% from the expected values.     

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.     

Ligand accumulation in autocrine cell cultures

Cell-culture assays are routinely used to analyze autocrine signaling systems, but quantitative experiments are rarely possible. To enable the quantitative design and analysis of experiments with autocrine cells, we develop a biophysical theory of ligand accumulation in cell-culture assays. Our theory predicts the ligand concentration as a function of time and measurable parameters of autocrine cells and cell-culture experiments. The key step of our analysis is the derivation of the survival probability of a single ligand released from the surface of an autocrine cell. An expression for this probability is derived using the boundary homogenization approach and tested by stochastic simulations. We use this expression in the integral balance equations, from which we find the Laplace transform of the ligand concentration. We demonstrate how the theory works by analyzing the autocrine epidermal growth factor receptor system and discuss the extension of our methods to other experiments with cultured autocrine cells.     

Diffusion through a membrane: Approach to equilibrium

The transfer of solute through a membrane separating two aqueous solutions is studied with the time-dependent diffusion equation for composite media. By introducing new independent and dependent variables it is shown that the differential equations and boundary conditions can be transformed into a dimensionless form which does not explicitly depend on the diffusivities of the media. Laplace transforms are used to derive explicit solutions for the solute concentration as a function of position and time. It is shown that at large time the concentration approaches the equilibrium distribution exponentially. Explicit results are given for the decay time as a function of the parameters of the system. In addition, an accurate and simplified expression is derived for the decay time for the case of small membrane permeability. The accuracy of the analytic solutions for the concentration profiles is tested by comparing them with numerical results obtained by solving the diffusion equations by the method of finite differences. Excellent agreement is found. Research supported in part by a grant from the National Science Foundation.