An axisymmetric boundary integral model for incompressible linear viscoelasticity: application to the micropipette aspiration contact problem

The micropipette aspiration test has been used extensively in recent years as a means of quantifying cellular mechanics and molecular interactions at the microscopic scale. However, previous studies have generally modeled the cell as an infinite half-space in order to develop an analytical solution for a viscoelastic solid cell. In this study, an axisymmetric boundary integral formulation of the governing equations of incompressible linear viscoelasticity is presented and used to simulate the micropipette aspiration contact problem. The cell is idealized as a homogeneous and isotropic continuum with constitutive equation given by three-parameter (E, tau 1, tau 2) standard linear viscoelasticity. The formulation is used to develop a computational model via a "correspondence principle" in which the solution is written as the sum of a homogeneous (elastic) part and a nonhomogeneous part, which depends only on past values of the solution. Via a time-marching scheme, the solution of the viscoelastic problem is obtained by employing an elastic boundary element method with modified boundary conditions. The accuracy and convergence of the time-marching scheme are verified using an analytical solution. An incremental reformulation of the scheme is presented to facilitate the simulation of micropipette aspiration, a nonlinear contact problem. In contrast to the halfspace model (Sato et al., 1990), this computational model accounts for nonlinearities in the cell response that result from a consideration of geometric factors including the finite cell dimension (radius R), curvature of the cell boundary, evolution of the cell-micropipette contact region, and curvature of the edges of the micropipette (inner radius a, edge curvature radius epsilon). Using 60 quadratic boundary elements, a micropipette aspiration creep test with ramp time t* = 0.1 s and ramp pressure p*/E = 0.8 is simulated for the cases a/R = 0.3, 0.4, 0.5 using mean parameter values for primary chondrocytes. Comparisons to the half-space model indicate that the computational model predicts an aspiration length that is less stiff during the initial ramp response (t = 0-1 s) but more stiff at equilibrium (t = 200 s). Overall, the ramp and equilibrium predictions of aspiration length by the computational model are fairly insensitive to aspect ratio a/R but can differ from the half-space model by up to 20 percent. This computational approach may be readily extended to account for more complex geometries or inhomogeneities in cellular properties.     

An immersed boundary method for simulating a single axisymmetric cell growth and division

For an animal cell, cytokinesis is the process by which a cell divides its cytoplasm to produce two daughter cells. We propose a new mathematical model for simulating cytokinesis. The proposed model is robust and realistic in deciding the position of the cleavage furrow and in defining the contractile force leading to cell division. We use an immersed boundary method to track the morphology of cell membrane during cytokinesis. For accurate calculation, we adaptively add and delete the immersed boundary points. We perform numerical simulations on the axisymmetric domain to have sufficient resolution and to incorporate three-dimensional effects such as anisotropic surface tension. Finally, we investigate the effects of each model parameter and compare a numerical result with the experimental data to demonstrate the efficiency and accuracy of our proposed method.     

Comparison of analytical and inverse finite element approaches to estimate cell viscoelastic properties by micropipette aspiration

The viscoelastic properties of cells are important in predicting cell deformation under mechanical loading and may reflect cell phenotype or pathological transition. Previous studies have demonstrated that viscoelastic parameters estimated by finite element (FE) analyses of micropipette aspiration (MA) data differ from those estimated by the analytical half-space model. However, it is unclear whether these differences are statistically significant, as previous studies have been based on average cell properties or parametric analyses that do not reflect the inherent experimental and biological variability of real experimental data. To determine whether cell material parameters estimated by the half-space model are significantly different from those predicted by the FE method, we implemented an inverse FE method to estimate the viscoelastic parameters of a population of primary porcine aortic valve interstitial cells tested by MA. We found that inherent differences between the analytical and inverse FE estimation methods resulted in statistically significant differences in individual cell properties. However, in cases with small pipette to cell radius ratios and short loading periods, model-dependent differences were masked by experimental and cell-to-cell variability. Analytical models that account for finite cell-size and loading rate further relaxed the experimental conditions for which accurate cell material parameter estimates could be obtained. These data provide practical guidelines for analysis of MA data that account for the wide range of conditions encountered in typical experiments.     

Mechanics and deformation of the nucleus in micropipette aspiration experiment

Robust biomechanical models are essential for the study of nuclear mechanics and deformation and can help shed light on the underlying mechanisms of stress transition in nuclear elements. Here, we develop a computational model for an isolated nucleus undergoing micropipette aspiration. Our model includes distinct components representing the nucleoplasm and nuclear envelope. The nuclear envelope itself comprises three layers: inner and outer nuclear membranes and one thicker layer representing the nuclear lamina. The nucleoplasm is modeled as a viscoelastic Maxwell material with a single time constant, while a modified Maxwell model, equivalent to a spring and a dashpot in series and both in parallel with a spring, is adopted for the inner and outer nuclear membranes. The nuclear envelope layer is taken as a linear elastic material. The proposed computational model, validated using experimental observations of Guilak et al. [2000. Viscoelastic properties of the cell nucleus. Biochemical and Biophysical Research Communications 269, 781-786] and Deguchi et al. [2005, Flow-induced hardening of endothelial nucleus as an intracellular stress-bearing organelle. Journal of Biomechanics 38, 1751-1759], is employed to study nuclear mechanics and deformation in micropipette aspiration and to shed light on the contribution of individual nuclear components on the response. The results indicate that the overall response of an isolated nucleus in micropipette aspiration is highly sensitive to the apparent stiffness of the nuclear lamina. This observation suggests that micropipette aspiration is an effective technique for examining the influence of various kinds of alteration in the nuclear lamina, such as mutations in the gene encoding lamin A, and also structural remodeling due to mechanical perturbation.     

An axisymmetric single-path model for gas transport in the conducting airways

In conventional one-dimensional single-path models, radially averaged concentration is calculated as a function of time and longitudinal position in the lungs, and coupled convection and diffusion are accounted for with a dispersion coefficient. The axisymmetric single-path model developed in this paper is a two-dimensional model that incorporates convective-diffusion processes in a more fundamental manner by simultaneously solving the Navier-Stokes and continuity equations with the convection-diffusion equation. A single airway path was represented by a series of straight tube segments interconnected by leaky transition regions that provide for flow loss at the airway bifurcations. As a sample application, the model equations were solved by a finite element method to predict the unsteady state dispersion of an inhaled pulse of inert gas along an airway path having dimensions consistent with Weibel's symmetric airway geometry. Assuming steady, incompressible, and laminar flow, a finite element analysis was used to solve for the axisymmetric pressure, velocity and concentration fields. The dispersion calculated from these numerical solutions exhibited good qualitative agreement with the experimental values, but quantitatively was in error by 20%-30% due to the assumption of axial symmetry and the inability of the model to capture the complex recirculatory flows near bifurcations.     

An integral dynamic model for the UASB reactor

In this article a dynamic model of a continuous working UASB reactor is described. It results from the integration of the fluid flow pattern in the reactor, the kinetic behavior of the bacteria (where inhibition and limitation were taken into account), and the mass transport phenomena between different compartments and different phases. The mathematical equations underlying the model and describing the important mechanisms were programmed and prepared for computations and simulations by computer. The settler efficiency has to be over 99% to prevent the reactor from wash-out. When the settler efficiency is over 99%, the total sludge content of the reactor increases steadily, so the reactor is hardly ever in a steady state. This implies dynamic modeling. The model is able to predict the various observable and nonobservable or difficult to observe state variables, e.g., the sludge bed height, the sludge blanket concentration, the short-circuiting flows over bed and blanket, and the effluent COD concentration as a function of the hydrodynamic load, COD load, pH, and settler efficiency. The optimal pH value is between 6.0 and 8.0; fatty acid shock loadings are difficult to handle outside this optimal pH range.     

An elastic rod model for anguilliform swimming

We develop a model for anguilliform (eel-like) swimming as an elastic rod actuated via time-dependent intrinsic curvature and subject to hydrodynamic drag forces, the latter as proposed by Taylor (in Proc Roy Proc Lond A 214:158–183, 1952). We employ a eometrically exact theory and discretize the resulting nonlinear partial differential evolution both to perform numerical simulations, and to compare with previous models consisting of chains of rigid links or masses connected by springs, dampers, and prescribed force generators representing muscles. We show that muscle activations driven by motoneuronal spike trains via calcium dynamics produce intrinsic curvatures corresponding to near-sinusoidal body shapes in longitudinally-uniform rods, but that passive elasticity causes Taylor’s assumption of prescribed shape to fail, leading to time-periodic motions and lower speeds than those predicted Taylor (in Proc Roy Proc Lond A 214:158–183, 1952). We investigate the effects of bending stiffness, body geometry, and activation patterns on swimming speed, turning behavior, and acceleration to steady swimming. We show that laterally-uniform activation yields stable straight swimming and laterally differential activation levels lead to stable turns, and we argue that tapered bodies with reduced caudal (tail-end) activation (to produce uniform intrinsic curvature) swim faster than ones with uniform activation.     

A nonlinear axisymmetric model with fluid-wall interactions for steady viscous flow in stenotic elastic tubes.

Arteries with high-grade stenoses may compress under physiologic conditions due to negative transmural pressure caused by high-velocity flow passing through the stenoses. To quantify the compressive conditions near the stenosis, a nonlinear axisymmetric model with fluid-wall interactions is introduced to simulate the viscous flow in a compliant stenotic tube. The nonlinear elastic properties of the tube (tube law) are measured experimentally and used in the model. The model is solved using ADINA (Automatic Dynamic Incremental Nonlinear Analysis), which is a finite element package capable of solving problems with fluid-structure interactions. Our results indicate that severe stenoses cause critical flow conditions such as negative pressure and high and low shear stresses, which may be related to artery compression, plaque cap rupture, platelet activation, and thrombus formation. The pressure filed near a stenosis has a complex pattern not seen in one-dimensional models. Negative transmural pressure as low as -24 mmHg for a 78 percent stenosis by diameter is observed at the throat of the stenosis for a downstream pressure of 30 mmHg. Maximum shear stress as a high as 1860 dyn/cm2 occurs at the throat of the stenoses, while low shear stress with reversed direction is observed right distal to the stenosis. Compressive stresses are observed inside the tube wall. The maximal principal stress and hoop stress in the 78 percent stenosis are 80 percent higher than that from the 50 percent stenosis used in our simulation. Flow rates under different pressure drop conditions are calculated and compared with experimental measurements and reasonable agreement is found for the prebuckling stage.     

The application of a homogeneous half-space model in the analysis of endothelial cell micropipette measurements

Experimental studies have shown that endothelial cells which have been exposed to shear stress maintain a flattened and elongated shape after detachment. Their mechanical properties, which are studied using the micropipette experiments, are influenced by the level as well as the duration of the shear stress. In the present paper, we analyze these mechanical properties with the aid of two mathematical models suggested by the micropipette technique and by the geometry peculiar to these cells in their detached post-exposure state. The two models differ in their treatment of the contact zone between the cell and the micropipette. The main results are expressions for an effective Young's modulus for the cells, which are used in conjunction with the micropipette data to determine an effective Young's modulus for bovine endothelial cells, and to discuss the dependence of this modulus upon exposure to shear stress.     

An integral equation model for the control of a smallpox outbreak

An integral equation model of a smallpox epidemic is proposed. The model structures the incidence of infection among the household, the workplace, the wider community and a health-care facility; and incorporates a finite incubation period and plausible infectivity functions. Linearisation of the model is appropriate for small epidemics, and enables analytic expressions to be derived for the basic reproduction number and the size of the epidemic. The effects of control interventions (vaccination, isolation, quarantine and public education) are explored for a smallpox epidemic following an imported case. It is found that the rapid identification and isolation of cases, the quarantine of affected households and a public education campaign to reduce contact would be capable of bringing an epidemic under control. This could be used in conjunction with the vaccination of healthcare workers and contacts. Our results suggest that prior mass vaccination would be an inefficient method of containing an outbreak.     

Application of the micropipette technique to the measurement of cultured porcine aortic endothelial cell viscoelastic properties

The viscoelastic deformation of porcine aortic endothelial cells grown under static culture conditions was measured using the micropipette technique. Experiments were conducted both for control cells (mechanically or trypsin detached from the substrate) and for cells in which cytoskeletal elements were disrupted by cytochalasin B or colchicine. The time course of the aspirated length into the pipette was measured after applying a stepwise increase in aspiration pressure. To analyze the data, a standard linear viscoelastic half-space model of the endothelial cell was used. The aspirated length was expressed as an exponential function of time. The actin microfilaments were found to be the major cytoskeletal component determining the viscoelastic response of endothelial cells grown in static culture.     

A model for passive elastic properties of rat vena cava

A two-dimensional model for the elastic properties of vena cava abdominalis under orthotropic deformation is introduced and tested against the experimental data obtained from six specimen of rat venae cavae by pressurization experiments. The model is based on membrane approximation and suited for vessels where most of the elastic elements are oriented axially, while circumferential contraction is exerted by redirecting axial stress by some network of oblique fibers. For the experimental data considered in this paper, the ratio between axial and circumferential stress depends almost exclusively on the circumferential extension ratio. As a consequence, the mechanical system can be formally decomposed in a kinematic system reacting by axial contraction on circumferential extension without any loss or storage of energy, serially connected to a hyperelastic system acting only in axial direction. Both systems are modeled separately by equations obtained by a purely phenomenological approach with two parameters for each system. This leads to reasonable reproduction of the experimental data. Introducing a correction parameter, which takes into account that the model assumption on the decomposition does not hold exactly, we get better reproduction of data. However, this is paid for by loss of physical rigor and in particular by departing from the assumption of hyperelasticity.     

A theoretical model for the elastic properties of very soft tissues.

A theoretical model is developed to predict the elastic properties of very soft tissues such as glands, tumors and brain. Tissues are represented as regular arrays of polyhedral (cubic or tetrakaidecahedral) cells, surrounded by extracellular spaces of uniform width. Cells are assumed to be incompressible, with very low resistance to shear deformation. Tissue shear rigidity is assumed to result mainly from the extracellular matrix, which is treated as a compressible elastic mesh of interconnected fibers. Small-strain elastic properties of tissue are predicted using a finite-element method and an analytical method. The model can be used to estimate the compressibility of a very soft tissue based on its Young's modulus and extracellular volume fraction.     

An elastic network model based on the structure of the red blood cell membrane skeleton.

A finite element network model has been developed to predict the macroscopic elastic shear modulus and the area expansion modulus of the red blood cell (RBC) membrane skeleton on the basis of its microstructure. The topological organization of connections between spectrin molecules is represented by the edges of a random Delaunay triangulation, and the elasticity of an individual spectrin molecule is represented by the spring constant, K, for a linear spring element. The model network is subjected to deformations by prescribing nodal displacements on the boundary. The positions of internal nodes are computed by the finite element program. The average response of the network is used to compute the shear modulus (mu) and area expansion modulus (kappa) for the corresponding effective continuum. For networks with a moderate degree of randomness, this model predicts mu/K = 0.45 and kappa/K = 0.90 in small deformations. These results are consistent with previous computational models and experimental estimates of the ratio mu/kappa. This model also predicts that the elastic moduli vary by 20% or more in networks with varying degrees of randomness. In large deformations, mu increases as a cubic function of the extension ratio lambda 1, with mu/K = 0.62 when lambda 1 = 1.5.     

An insect model for assessing oxidative stress related to arsenic toxicity

The potential usefulness of an insect model to evaluate oxidative stress induced by environmental pollutants was examined with trivalent arsenic (As³⁺, NaAsO₂) and pentavalent arsenic (As⁵⁺, Na₂HAsO₄) in adult female house flies, Musca domestica, and fourth-instar cabbage loopers, Trichoplusia ni. M. domestica was highly susceptible to both forms of arsenic following 48 h exposure in the drinking water with LC₅₀s of 0.008 and 0.011% w/v for As³⁺ and As⁵⁺, respectively. T. ni larvae were susceptible to dietary As³⁺ with an LC₅₀ of 0.032% w/w but seem to tolerate As⁵⁺ well with an LC₅₀ of 0.794% concentration after 48 h exposure. The minimally acute LC₅ dose of both As³⁺ and As⁵⁺ varied considerably but averaged 0.005% for both insects. The potential of both valencies of arsenic for inducing oxidative stress in the insects exposed ad libitum to approximately LC₅ levels was assessed. The parameters examined were the alterations of the antioxidant enzyme activities of superoxide dismutase (SOD), catalase (CAT), glutathione transferase (GST), the peroxidase activity of glutathione transferase (GSTPX), and glutathione reductase (GR), and increases in lipid peroxidation and protein oxidation. SOD (1.3-fold), GST (1.6-fold), and GR (1.5-fold) were induced by As³⁺ in M. domestica but CAT and GSTPX were not affected. As⁵⁺ had no effect on M. domestica. In T. ni, the antioxidant enzyme activities were not affected by As³⁺ except for SOD which was suppressed by 29.4% and GST which was induced by 1.4-fold. As⁵⁺ had no effect except the suppression of SOD by 41.2%. Lipid peroxidation and protein oxidation, which represent stronger indices of oxidative stress, were elevated in both insects by up to 2.9-fold. However, based on the antioxidant enzyme response to the arsenic anions, the mode of action of arsenic induced oxidative stress may differ between the two insects. Until this aspect is further clarified, evidence at this time favors the prospect of As³⁺ as a pro-oxidant, especially for M. domestica. © 1995 Wiley-Liss, Inc.     

An application of the micropipette technique to the measurement of the mechanical properties of cultured bovine aortic endothelial cells

The mechanical properties of endothelial cells were measured using the micropipette technique. The cells employed were collected from bovine aortic endothelium and cultured in our laboratory. Endothelial cells from confluent monolayers under no-flow conditions were detached from their substrate by trypsin or by a mechanical method and suspended in modified Dulbecco medium (MDM). In the micropipette technique, a part of the cell is aspirated into the tip of the micropipette under a microscope, and the deformation measured from a photograph. In this study, the data obtained were analyzed using a model where the cytoskeletal elements, which are considered to be the primary stress bearing components, are assumed to reside in a submembranous, cortical layer. Detached cells were found to have almost homogeneous mechanical properties based on measurements from different regions of the surface of a single cell. However, a hysteresis loop was observed in the relation between pressure and cell deformation during the loading and unloading processes. The calculated elastic shear moduli obtained for the trypsin-detached cells were as much as 10-20 times larger than those of a red blood cell. Mechanically-detached cells had moduli approximately twice that of the trypsin detached cells. Passage time, i.e., cell culture age, had no influence on the mechanical properties of the trypsin-detached cells, but did have an effect on the mechanically-detached cells, with both the younger and older cells being somewhat stiffer.     

Laboratory methods for assessing the toxicity of contact poisons to slugs

Two techniques for comparing the activity of different contact poisons to slugs in controlled conditions were used to measure the relative toxicities of five substances. A laboratory immersion test rated their median lethal concentrations as follows: ioxynil 8·3 ppm, sodium pentachlorophenate 22·0 ppm, copper sulphate 68·1–75·3 ppm, acetaldehyde 4822·0 ppm. Metaldehyde gave inconsistent results with this method but, using a dry-contact method, metaldehyde (42370 ppm) was much less toxic than copper sulphate (2027 ppm). The materials giving practical control in the field were not the most toxic of those tested.     

Dynamical properties of model gene networks and implications for the inverse problem

We study the inverse problem, or the "reverse-engineering" problem, for two abstract models of gene expression dynamics, discrete-time Boolean networks and continuous-time switching networks. Formally, the inverse problem is similar for both types of networks. For each gene, its regulators and its Boolean dynamics function must be identified. However, differences in the dynamical properties of these two types of networks affect the amount of data that is necessary for solving the inverse problem. We derive estimates for the average amounts of time series data required to solve the inverse problem for randomly generated Boolean and continuous-time switching networks. We also derive a lower bound on the amount of data needed that holds for both types of networks. We find that the amount of data required is logarithmic in the number of genes for Boolean networks, matching the general lower bound and previous theory, but are superlinear in the number of genes for continuous-time switching networks. We also find that the amount of data needed scales as 2(K), where K is the number of regulators per gene, rather than 2(2K), as previous theory suggests.     

The zebrafish as a model system for assessing the reinforcing properties of drugs of abuse

Recent reports make use of the zebrafish to study complex behavior such as addiction, anxiety, or learning and memory. We have established reliable tests and appropriate controls to measure these behavioral parameters in the zebrafish adult. Our assays are robust enough to permit the detection of dominant mutations affecting drug-induced reward, and therefore can be used in forward genetic screens. We provide the reader with the technical details of these tests, as well as their appropriate and crucial, although often overlooked, control assays. In particular, our results make it possible to use the zebrafish as a promising model to identify new genetic components of the reward pathway, or other measurable behaviors.     

An in vivo method for assessing the antimicrobial properties of topical antiseptics using artifically contaminated skin

A method is described for assessing the antimicrobial activity of topical antiseptics on human skin. The test, carried out on the forearms of volunteers, uses an inoculum of Stuphylococcus aureus . Up to four preparations may be tested at one time plus a placebo and untreated control site. The method has been used to compare four proprietary antiseptics and to evaluate their activity for up to one hour and has demonstrated a chloroxylenol, triclosan, EDTA combination product to be the most effective. The method is highly adaptable and may be used to evaluate activity versus other organisms and to examine other factors affecting antiseptic efficacy