The effect of shape on the margination dynamics of non-neutrally buoyant particles in two-dimensional shear flows

The margination dynamics of microparticles with different shapes has been analyzed within a laminar flow mimicking the hydrodynamic conditions in the microcirculation. Silica spherical particles, quasi-hemispherical and discoidal silicon particles have been perfused in a parallel plate flow chamber. The effect of the shape and density on their margination propensity has been investigated at different physiologically relevant shear rates S. Simple scaling laws have been derived showing that the number n of marginating particles scales as S(-0.63) for the spheres; S(-0.85) for discoidal and S(-1) for quasi-hemispherical particles, regardless of their density and size. Within the range considered for the shear rate, discoidal particles marginate in a larger number compared to quasi-hemispherical and spherical particles. These results may be of interest in drug delivery and bio-imaging applications, where particles are expected to drift towards and interact with the walls of the blood vessels.     

Universality classes in folding times of proteins

Molecular dynamics simulations in simplified models allow one to study the scaling properties of folding times for many proteins together under a controlled setting. We consider three variants of the Go models with different contact potentials and demonstrate scaling described by power laws and no correlation with the relative contact order parameter. We demonstrate existence of at least three kinetic universality classes that are correlated with the types of structure: the alpha-, alpha-beta-, and beta- proteins have the scaling exponents of approximately 1.7, 2.5, and 3.2, respectively. The three classes merge into one when the contact range is truncated at a reasonable value. We elucidate the role of the potential associated with the chirality of a protein.     

Internal transport properties of macroporous sugar polyacrylate hydrogels: microsphere diffusion described by phenomenological laws

We have determined the internal transport properties of heterogeneous, macroporous hydrogels based on the regioregular sugar polyacrylate poly(6-acryloyl-beta-O-methyl-galactopyranoside). This was accomplished by measuring the diffusive flux of variously sized polystyrene microspheres and combining these results with solutions of phenomenological transport laws (the Navier-Stokes equations and Fick's Law with an assumption of first-order irreversible sphere capture by the gel polymer). This enabled calculation of gel properties such as average pore diameters (ca. 11.76 microm) and the diffusivities of the polystyrene spheres in the gel. These values range from 76% to 83% of that in free solution and correlate closely with the equilibrium solution content of the gel (82.3%). This approach has also enabled calculation of the sphere capture rates (2.4 x 10(-3) to 9.6 x 10(-5) s(-1)). These low capture rates indicate that the gel is extremely non-adhesive towards the spheres, and a linear correlation with sphere form drag area (r(2) = 1) was found. The pore sizes of the hydrated gel were observed via DIC light microscopy and the visible effective diameters corresponded very closely to the calculated values (11.66 vs. 11.76 microm). The diffusion/capture of inert spheres in the hydrogel can thus be described in a non-destructive manner by straightforward application of phenomenological transport laws. This result is significant in that these laws were intended to describe macroscopic ensembles of very large numbers of particles in continuous media, not small numbers (i.e., hundreds) in discontinuous media.     

Allometries and scaling laws interpreted as laws: a reply to Elgin

I analyze here biological regression equations known in the literature as allometries and scaling laws. My focus is on the alleged lawlike status of these equations. In particular I argue against recent views that regard allometries and scaling laws as representing universal, non-continent, and/or strict biological laws. Although allometries and scaling laws appear to be generalizations applying to many taxa, they are neither universal nor exceptionless. In fact there appear to be exceptions to all of them. Nor are the constants in allometries and scaling laws truly constant, stable, or universal in character, but vary in value across different taxa and background conditions. Moreover, these equations represent evolutionary, strongly contingent generalizations, which threatens their lawlike status. Lastly, allometries and scaling laws do not offer stable probabilities to which they hold in different backgrounds. I further suggest that many allometries and scaling laws function to elucidate explananda rather than explanantia or covering laws.     

Percolation theory suggests some general features in range margins across environmental gradients

The margins within the geographic range of species are often specific in terms of ecological and evolutionary processes, and can strongly influence the species’ reaction to climate change. One of the frequently observed features at range margins is fragmentation, caused internally by population dynamics or externally by the limited availability of suitable habitat sites. We study both causes, and describe the transition from a connected to a fragmented state across space using a gradient metapopulation model. Our approach is characterized by the following features. 1) Inhomogeneities can occur at two spatial scales: there is a broad-scale gradient, which can be patterned by fine-scale heterogeneities. 2) We study the occupancy of this terrain in a steady-state on two temporal scales: in snapshots and by long-term averages. The simulations reveal some general scaling laws that are applicable in various environments, independently of the mechanism of fragmentation. The edge of the connected region (the hull) is a fractal with dimension 7/4. Its width and length changes with the gradient according to universal scaling laws, that are characteristic for the percolation transition. The results suggest that percolation theory is a powerful tool for understanding the structure of range margins in a broad variety of real-life scenarios, including those in which the environmental gradient is combined with fine-scale heterogeneity. This provides a new method for comparing the range margins of different species in various geographic regions, and monitoring range shifts under climate change.     

Liquid circulation velocity and overall gas holdup in a modified jet loop bioreactor with low density particles

Effect of low density particles on the apparent liquid circulation velocity and overall gas holdup was studied in a modified reversed flow jet loop bioreactor. Experiments were conducted using polyurethane beads, polystyrene particles which are comparable to bioparticles found in biological applications and glass beads. Influence of gas and liquid flow rates, draft tube to reactor diameter ratio and solids loading on these hydrodynamic properties were studied. The liquid circulation velocity was found to increase with an increase in liquid flow rate but decrease with an increase in gas flow rate or solids loading. The overall gas holdup increased with an increase in gas or liquid flow rate but decreased with an increase in solids loading. The range of optimum draft tube to reactor diameter ratio was found to be 04–0.5. The results obtained with low density particles were comparatively better than those with glass beads. Correlations were proposed to evaluate liquid circulation velocity and overall gas holdup in terms of operational and geometrical variables.     

Flow cytometric measurement of rates of particle uptake from dilute suspensions by a ciliated protozoan

Flow cytometry is used to measure rates of ingestion of particles from dilute monodisperse suspensions by the ciliate Tetrahymena pyriformis. The particles used are polystyrene microspheres containing a fluorescent dye. Measurements were made directly, that is, by determining the fluorescence intensities from microspheres ingested by cells in samples collected from the experimental feeding apparatus. The fact that fluorescence intensities from individual cells can be grouped into discrete classes based on the numbers of fluorescent particles associated with the cells makes it possible to calibrate the flow cytometer and convert fluorescence measurements into numbers of particles ingested by average cells. At low particle concentration or high ciliate concentration, ingestion data must be corrected for depletion of particles during the assay, and a method for doing this is described. Experiments at various ciliate concentrations show that ingestion rates are not affected by this concentration. The methods developed should allow measurements of rates of ingestion of particles from concentrated and polydisperse suspensions. For such measurements, nonfluorescent particles together with a fraction of fluorescent tracer particles would be used.     

Genetic mapping of allometric scaling laws

Many biological processes, from cellular metabolism to population dynamics, are characterized by particular allometric scaling relationships between rate and size (power laws). A statistical model for mapping specific quantitative trait loci (QTLs) that are responsible for allometric scaling laws has been developed. We present an improved model for allometric mapping of QTLs based on a more general allometry equation. This improved model includes two steps: (1) use model II regression analysis to estimate the parameters underlying universal allometric scaling laws, and (2) substitute the estimated allometric parameters in the mixture-based mapping model to obtain the estimation of QTL position and effects. This model has been validated by a real example for a mouse F2 progeny, in which two QTLs were detected on different chromosomes that determine the allometric relationship between growth rate and body weight.     

Micro-thermal focusing field-flow fractionation

Focusing mechanism was effectively exploited to separate large (micrometer-size) particles by using new micro-thermal field-flow fractionation (micro-TFFF). It has been shown that the retention order of micrometer-size particles at high field strength can be explained by the mechanism of steric exclusion only at lowest flow rates of the carrier liquid. A simplistic, purely mechanical model of steric exclusion is not accurate to describe the retention at higher flow rates where the focusing phenomenon appears. Despite the fact that the thickness of the channel for micro-FFF cannot be reduced without taking into account a possible deterioration of the separation due to the contribution of "steric exclusion" mechanism, this paper demonstrates, in agreement with our previous results, that if the operational conditions were conveniently chosen, namely a low flow rate, a reasonable fit of the experimental retention data with the theory of steric exclusion mechanism in FFF was found and the separation of micron-size particles can be accomplished. However, high selectivity and resolution and high-speed separation were achieved if the focusing effect has clearly dominated the FFF mechanism. As a result, it seems that the micro-TFFF is the most universal technique which can be applied for the separation of the synthetic and natural macromolecules within an extended range of molar masses up to ultra-high molar masses and for the particles of various chemical nature and origin in a nano-size range as well as for large (micrometers) particles. Until nowadays, only sedimentation and flow field-flow fractionation techniques in so called "steric" modes were applied for the separations of large size particles. This application of micro-TFFF in focusing mode for the separation of large size particles is the first one described in the literature.     

The fractal nature of nature: power laws,ecological complexity and biodiversity

Underlying the diversity of life and the complexity of ecology is order that reflects the operation of fundamental physical and biological processes. Power laws describe empirical scaling relationships that are emergent quantitative features of biodiversity. These features are patterns of structure or dynamics that are self-similar or fractal-like over many orders of magnitude. Power laws allow extrapolation and prediction over a wide range of scales. Some appear to be universal, occurring in virtually all taxa of organisms and types of environments. They offer clues to underlying mechanisms that powerfully constrain biodiversity. We describe recent progress and future prospects for understanding the mechanisms that generate these power laws, and for explaining the diversity of species and complexity of ecosystems in terms of fundamental principles of physical and biological science.     

Low Reynolds number turbulence modeling of blood flow in arterial stenoses.

Moderate and severe arterial stenoses can produce highly disturbed flow regions with transitional and or turbulent flow characteristics. Neither laminar flow modeling nor standard two-equation models such as the kappa-epsilon turbulence ones are suitable for this kind of blood flow. In order to analyze the transitional or turbulent flow distal to an arterial stenosis, authors of this study have used the Wilcox low-Re turbulence model. Flow simulations were carried out on stenoses with 50, 75 and 86% reductions in cross-sectional area over a range of physiologically relevant Reynolds numbers. The results obtained with this low-Re turbulence model were compared with experimental measurements and with the results obtained by the standard kappa-epsilon model in terms of velocity profile, vortex length, wall shear stress, wall static pressure, and turbulence intensity. The comparisons show that results predicted by the low-Re model are in good agreement with the experimental measurements. This model accurately predicts the critical Reynolds number at which blood flow becomes transitional or turbulent distal an arterial stenosis. Most interestingly, over the Re range of laminar flow, the vortex length calculated with the low-Re model also closely matches the vortex length predicted by laminar flow modeling. In conclusion, the study strongly suggests that the proposed model is suitable for blood flow studies in certain areas of the arterial tree where both laminar and transitional/turbulent flows coexist.     

PIV measurements of flow in a centrifugal blood pump: steady flow

Magnetically suspended left ventricular assist devices have only one moving part, the impeller. The impeller has absolutely no contact with any of the fixed parts, thus greatly reducing the regions of stagnant or high shear stress that surround a mechanical or fluid bearing. Measurements of the mean flow patterns as well as viscous and turbulent stresses were made in a shaft-driven prototype of a magnetically suspended centrifugal blood pump at several constant flow rates (3-9 L/min) using particle image velocimetry (PIV). The chosen range of flow rates is representative of the range over which the pump may operate while implanted. Measurements on a three-dimensional measurement grid within several regions of the pump, including the inlet, blade passage, exit volute, and diffuser are reported. The measurements are used to identify regions of potential blood damage due to high shear stress and/or stagnation of the blood, both of which have been associated with blood damage within artificial heart valves and diaphragm-type pumps. Levels of turbulence intensity and Reynolds stresses that are comparable to those in artificial heart valves are reported. At the design flow rate (6 L/min), the flow is generally well behaved (no recirculation or stagnant flow) and stress levels are below levels that would be expected to contribute to hemolysis or thrombosis. The flow at both high (9 L/min) and low (3 L/min) flow rates introduces anomalies into the flow, such as recirculation, stagnation, and high stress regions. Levels of viscous and Reynolds shear stresses everywhere within the pump are below reported threshold values for damage to red cells over the entire range of flow rates investigated; however, at both high and low flow rate conditions, the flow field may promote activation of the clotting cascade due to regions of elevated shear stress adjacent to separated or stagnant flow.     

Studies on cell adhesion in tissue culture : XV. Some effects of cycloheximide on cell detachment

Attempts were made to identify positively charged groups at the surfaces of Ehrlich ascites tumour (EAT) cells, and particles of polystyrene polymer which had adsorbed proteins after incubation in serum-containing culture medium. The cells and particles were treated with 2,4,6-trinitrobenzene sulphonic acid (TNBS) or 2,3-dimethylmaleic anhydride (DMA), which react with amino and other cationic groups. The increases in cell and particle anodic electrophoretic mobility were consistent with approx. 5% of the total surface charge of each, being due to positively charged groups. The effects of DMA or TNBS treatment of the cells and/or polystyrene surfaces, on the rates of cell adhesion to these surfaces were then determined. The significantly slower rates of adhesion after some modes of treatment suggest that positively charged groups at the surfaces of EAT cells play a part in their initial contact with and adhesion to, protein-coated plastic surfaces. However, quantitatively the role of cationic groups is a minor one in this part of the adhesion process.     

Blood modeling using polystyrene microspheres

The steady flow viscosity at shear rates 0 to 120 sec-1 and dynamic viscoelasticity at frequencies 0.02 to 0.8 Hz were determined for aqueous suspensions of uniform polystyrene microspheres of 1.0 micron diameter. Rheological properties of the microsphere suspensions were Newtonian for particle concentrations up to 32%. By introducing dextran and calcium chloride into the particle suspensions, non-Newtonian behavior was produced similar to that observed for human blood. The cooperative effects of dextran and calcium ions promoted aggregation of particles at a concentration as low as 12%. Thus, a suspension of uniform sized spherical polystyrene particles in aqueous solution of dextran may be made to mimic blood by controlling the surface charge on the polystyrene spheres using addition of calcium ions to the medium.     

Planktonic encounter rates in homogeneous isotropic turbulence: the case of predators with limited fields of sensory perception

It is a well-established fact that encounter rates between different species of planktonic microorganism, either swimming, or passively advected by the flow, are enhanced in the presence of turbulence. However, due to the complexity of the various calculations involved, current encounter rate theories are based on a number of simplifying approximations, which do not reflect reality. In particular, a typical planktonic predator is usually assumed to have perfect 'all round vision', i.e. it can perceive a prey particle at any relative orientation, provided it lies within some given contact radius R. Unfortunately, there is a wide body of experimental evidence that this is not the case. In this study the encounter problem for a predator with a limited field of sensory perception, swimming in a turbulent flow, is examined from first principles and a number of new modelling ideas proposed. A wide range of kinematic simulations are also undertaken to test these predictions. Particular attention is paid to the swimming strategy such a predator might undertake to enhance its encounter rate. It turns out that the predicted optimum swimming strategies differ radically from the results of previous work. Empirical evidence is also presented which appears to support these new findings.     

Metabolic scaling: a many-splendoured thing

Animals at rest and during exercise display rates of aerobic metabolism, VO2, that represent mainly the sum of mitochondrial respiration rates in various organs. The relative contributions of these organs change with physiological state such that internal organs such as liver, kidney and brain account for most of the whole-body VO2 at rest, while locomotory muscles account for >90% of the maximum rate, VO2max, during maximal aerobic exercise. Mechanisms that regulate VO2 are complex and the relative importance of each step in a series, estimated by metabolic control analysis, depends upon the level of biological organization under consideration as well as physiological state. Despite this complexity, prominent single-cause models propose that metabolic rates are supply-limited and that the scaling of supply systems provides a sufficient explanation for the allometric scaling of metabolism. We argue that some assumptions, as well as current interpretations of the meaning (or consequences) of these constraints are flawed, i.e., elephants do not have lower mass-specific basal or maximal rates of aerobic metabolism because their mitochondria are more supply-limited than those of shrews. Animals do not violate the laws of physics, and the allometric scaling of supply systems would be expected, to some extent, to be matched by capacities for (and rates of) energy expenditure. But life is not so simple. Animals are so diverse that to do justice to metabolic scaling, it is also necessary to consider the scaling of energy expenditure. It is by doing so that models of metabolic scaling can be consistent with current paradigms in metabolic regulation and accommodate the range of inter- and intraspecific exponents found in nature. The "allometric cascade," a first attempt at such an accounting, was a source of great satisfaction to Peter Hochachka. It was the last door that he helped open to comparative physiologists before he said goodbye.     

Emergent Systems Energy Laws for Predicting Myosin Ensemble Processivity

In complex systems with stochastic components, systems laws often emerge that describe higher level behavior regardless of lower level component configurations. In this paper, emergent laws for describing mechanochemical systems are investigated for processive myosin-actin motility systems. On the basis of prior experimental evidence that longer processive lifetimes are enabled by larger myosin ensembles, it is hypothesized that emergent scaling laws could coincide with myosin-actin contact probability or system energy consumption. Because processivity is difficult to predict analytically and measure experimentally, agent-based computational techniques are developed to simulate processive myosin ensembles and produce novel processive lifetime measurements. It is demonstrated that only systems energy relationships hold regardless of isoform configurations or ensemble size, and a unified expression for predicting processive lifetime is revealed. The finding of such laws provides insight for how patterns emerge in stochastic mechanochemical systems, while also informing understanding and engineering of complex biological systems.     

Water pumping and analysis of flow in burrowing zoobenthos: an overview

Burrowing animals maintain contact with the water above the sediment by pumping water through a tube system and therefore measurements of water pumping rate of burrowing animals is of crucial importance for the study of many processes both within and above the sea floor. This review deals with the measuring of water pumping and the analysis of flow generated by burrowing deposit- and filter-feeding zoobenthos in order to determine the type of pump and mechanisms involved, flow rate, pump pressure, and pumping power. The practical use of fluid mechanical principles is examined, and it is stressed that not only the pump pressure that a burrowing animal can apply is of interest for assessing the energy cost of pumping, but also the distribution of excess pressure along its burrow is of importance for assessing the seepage flow of oxygen-rich water into the sediment surrounding the burrow because this bioirrigation exerts a considerable effect on the chemistry and microbiology of sediments. Dense populations of burrowing filter-feeding zoobenthos also interact with the water above the sediment interface and this is reflected in the development of phytoplankton concentration profiles above the filter-feeding animals. In stagnant situations the near-bottom water may be depleted of food particles, depending on the population filtration rate and the intensity of the biomixing induced by the filtering activity. But moderate currents and the biomixing can presumably generate enough turbulence to facilitate mixing of water layers at the sea bed with the layers above where food particle concentrations are relatively higher. Following a brief summary of types of burrowing benthic animals, common methods for measuring pumping rates are described along with examples. For estimating the required pump pressure, biofluid mechanical theory for flow in tube–pump systems is summarised (elaborated in Appendix A). Specific examples are given to illustrate general principles and to give an idea of typical values of flow rate, pressure drop and power involved. Finally, some flow effects generated by burrowing animals in and above the sediment are described.