Centrifuge Modeling of Cadmium Migration in Saturated and Unsaturated Soils

Researchers recently have come to recognize that geotechnical centrifuge can provide a powerful experimental tool for investigating the flow and transport of inorganic contaminants in soils. Inert, non-adsorptive inorganic compounds (e.g., sodium ions) rather than adsorptive heavy metals are often used as the chemical for the investigation of pollutant transport behavior in most centrifuge modeling. To overcome the shortcomings of this approach, centrifuge tests for the study of one-dimensional pollutant migration in both saturated and unsaturated soils were designed using an adsorptive pollutant (i.e., cadmium) and conducted at two centrifugal accelerations. In this study, the concentration profile of adsorptive cadmium along the depth of soil, the moisture content varying with the soil depth and the transport behavior of the cadmium in soils were investigated. The centrifuge results show that the cadmium concentration profiles are found to be similar for the centrifuge models performed at 15 g and 20 g and the one-dimensional moisture movement in the unsaturated soil can be reproducible. The validity of centrifuge modeling of adsorptive pollutants might be affected by the g-level that, in turn, determines the centrifuge testing time and affects the sorption equilibrium.     

Cadmium removal from contaminated soil by thermally responsive elastin (ELPEC20) biopolymers

Cadmium contamination of soil is a major concern in the biosphere. Beyond the suite of available physico-chemical treatment methods, green and more efficient technologies are desired to reduce cadmium and other heavy metal contaminants to acceptable levels. Elastin-like polypeptides (ELP) composed of a polyhistidine domain (ELPH12) can be used as an environmentally benign chelating agent for ex situ soil washing. However, ELPH12 is relatively non-selective. A biopolymer with metal-binding domains that have stronger affinity, capacity, and selectivity would have distinct advantages. The aim of this work is to investigate the use of a new generation of ELP biopolymer, ELPEC20, containing synthetic phytochelatin (EC) as the metal-binding domain for ex situ soil washing. ELPEC20 was shown to bind cadmium more effectively and selectively than ELPH12. The binding constant of ELPEC20 is an order of magnitude higher and the binding capacity is fivefold higher than ELPH12. In contrast to ELPH12, no decrease in cadmium binding was observed in the presence of other competing metal ions. The improved selectivity and binding capacity provided by ELPEC20 were directly reflected in the enhanced cadmium extraction efficiency from contaminated soil. In batch washing studies up to 62% of the bound cadmium was removed by ELPEC20 while less than 12% was removed by ELPH12. Cadmium was removed not only from the exchangeable fraction but also the oxidizable fraction. The high-affinity binding sites of ELPEC20 also results in very rapid extraction with complete removal achieved within 1 h, suggesting that ELPEC20 could be used as part of a rapid (short retention time) technology with minimum possibility for the biodegradation of biopolymers.     

A reduced-dimensional model for near-wall transport in cardiovascular flows

Near-wall mass transport plays an important role in many cardiovascular processes, including the initiation of atherosclerosis, endothelial cell vasoregulation, and thrombogenesis. These problems are characterized by large Péclet and Schmidt numbers as well as a wide range of spatial and temporal scales, all of which impose computational difficulties. In this work, we develop an analytical relationship between the flow field and near-wall mass transport for high-Schmidt-number flows. This allows for the development of a wall-shear-stress-driven transport equation that lies on a codimension-one vessel-wall surface, significantly reducing computational cost in solving the transport problem. Separate versions of this equation are developed for the reaction-rate-limited and transport-limited cases, and numerical results in an idealized abdominal aortic aneurysm are compared to those obtained by solving the full transport equations over the entire domain. The reaction-rate-limited model matches the expected results well. The transport-limited model is accurate in the developed flow regions, but overpredicts wall flux at entry regions and reattachment points in the flow.     

Transport of iodide in structured soil under spring barley during irrigation experiment analyzed using dual-continuum model

Transport of radioactive iodide ¹³¹I^? in a black clay loam soil under spring barley in an early ontogenesis phase was monitored during controlled field irrigation experiment. It was found that iodide bound in the soil matrix could be mobilized by the surface leaching enhanced by mechanical impact of water drops and transported below the root zone of crops via soil cracks. The iodide transport through structured soil profile was simulated by the one-dimensional dual-continuum model, which assumes the existence of two inter-connected flow domains: the soil matrix domain and the preferential flow domain. The model predicted relatively deep percolation of iodide within a short time, in a good agreement with the observed vertical iodide distribution in soil. The dual-continuum approach proved to be an adequate tool for evaluation of field irrigation experiments conducted in structured soils.     

Structure of the translocator domain of a bacterial autotransporter

Autotransporters are virulence-related proteins of Gram-negative bacteria that are secreted via an outer-membrane-based C-terminal extension, the translocator domain. This domain supposedly is sufficient for the transport of the N-terminal passenger domain across the outer membrane. We present here the crystal structure of the in vitro-folded translocator domain of the autotransporter NalP from Neisseria meningitidis, which reveals a 12-stranded beta-barrel with a hydrophilic pore of 10 x 12.5 A that is filled by an N-terminal alpha-helix. The domain has pore activity in vivo and in vitro. Our data are consistent with the model of passenger-domain transport through the hydrophilic channel within the beta-barrel, and inconsistent with a model for transport through a central channel formed by an oligomer of translocator domains. However, the dimensions of the pore imply translocation of the secreted domain in an unfolded form. An alternative model, possibly covering the transport of folded domains, is that passenger-domain transport involves the Omp85 complex, the machinery required for membrane insertion of outer-membrane proteins, on which autotransporters are dependent.     

Numerical models for the simulation of flexible artificial heart valves: part I--computational methods

A numerical model of the coupled motion of a flexing surface in a high Reynolds number flow is presented for the simulation of flexible polyurethane heart valves in the aortic position. This is achieved by matching a Lagrangian dynamic leaflet model with a panel method based flow solver. The two models are coupled via the time-dependent pressure field using the unsteady Bernoulli equation. Incorporation of sub-cycling in the dynamic model equations and fast pre conditioning techniques in the panel method solver yields efficient convergence and near real-time simulations of valve motion. The generality of dynamic model allows different material properties and/or geometries to be studied easily and interactively. This interactivity is realized by embedding the models within a design environment created using the software IRIS Explorer. Two flow domains are developed, an infinite domain and an internal domain using conformal mapping theory. In addition bending stress on the valve is computed using a simple stress model based on spline and circle equation techniques.     

Reconstitution of a disulfide isomerization system

Isomerization of disulfide bonds is vital for the proper folding of proteins that possess multiple disulfides. In prokaryotes, the catalytic pathway responsible for disulfide isomerization involves thioredoxin, thioredoxin reductase, and the DsbC, DsbG, and DsbD proteins. To be active as isomerases, DsbC and DsbG must be kept reduced. This task is performed by the cytoplasmic membrane protein DsbD. DsbD in turn is reduced by the cytoplasmic thioredoxin and is composed of three domains. The beta domain is membrane-embedded, whereas the alpha and gamma domains are localized to the periplasm. It had been proposed that electrons are transferred within DsbD by a succession of disulfide exchange reactions between the three domains. To test this model using biochemical methods, we purified to homogeneity different polypeptides corresponding to the alpha, beta, gamma, and betagamma domains. Using these domains, we could reconstitute a DsbD activity and, for the first time, reconstitute in vitro the electron transport pathway from NADPH and thioredoxin to DsbC and DsbG. We showed that electrons are transferred from thioredoxin to the beta domain then successively to the gamma domain, the alpha domain, and finally on to DsbC or DsbG. We also determined the redox potential of the gamma domain to be -241 mV, and that of the alpha domain was found to be -229 mV. This shows that the direction of electron flow within DsbD is thermodynamically driven.     

A one-dimensional model of water flow in soil-plant systems based on plant architecture

The estimation of root water uptake and water flow in plants is crucial to quantify transpiration and hence the water exchange between land surface and atmosphere. In particular the soil water extraction by plant roots which provides the water supply of plants is a highly dynamic and non-linear process interacting with soil transport processes that are mainly determined by the natural soil variability at different scales. To better consider this root-soil interaction we extended and further developed a finite element tree hydro-dynamics model based on the one-dimensional (1D) porous media equation. This is achieved by including in addition to the explicit three-dimensional (3D) architectural representation of the tree crown a corresponding 3D characterisation of the root system. This 1D xylem water flow model was then coupled to a soil water flow model derived also from the 1D porous media equation. We apply the new model to conduct sensitivity analysis of root water uptake and transpiration dynamics and compare the results to simulation results obtained by using a 3D model of soil water flow and root water uptake. Based on data from lysimeter experiments with young European beech trees (Fagus silvatica L.) is shown, that the model is able to correctly describe transpiration and soil water flow. In conclusion, compared to a fully 3D model the 1D porous media approach provides a computationally efficient alternative, able to reproduce the main mechanisms of plant hydro-dynamics including root water uptake from soil.     

Routes to and from the plasma membrane: bulk flow versus signal mediated endocytosis

Transport of proteins via the secretory pathway is controlled by a combination of signal dependent cargo selection as well as unspecific bulk flow of membranes and aqueous lumen. Using the plant vacuolar sorting receptor as model for membrane spanning proteins, we have distinguished bulk flow from signal mediated protein targeting in biosynthetic and endocytic transport routes and investigated the influence of transmembrane domain length. More specifically, long transmembrane domains seem to prevent ER retention, either by stimulating export or preventing recycling from post ER compartments. Long transmembrane domains also seem to prevent endocytic bulk flow from the plasma membrane, but the presence of specific endocytosis signals overrules this in a dominant manner.     

Ponded infiltration into soil with biopores — field experiment and modeling

Preferential movement of water in macropores plays an important role when the process of ponded infiltration in natural porous systems is studied. For example, the detailed knowledge of water flow through macropores is of a major importance when predicting runoff responses to rainfall events. The main objectives of this study are to detect preferential movement of water in Chernozem soil and to employ numerical modeling to describe the variably saturated flow during a field ponded infiltration experiment. The infiltration experiment was performed at the Macov experimental station (Calcari-Haplic Chernozem in Danubian Lowland, Slovakia). The experiment involved single ring ponded infiltration. At the quasi steady state phase of the experiment dye tracer was added to the infiltrating water. Then the soil profile was excavated and the penetration pattern of the applied tracer was recorded. The abundance of biopores as a product of fauna and flora was found. To quantify the preferential flow effects during the infiltration experiment, three-dimensional axisymmetric simulations were carried out by a two-dimensional dual-continuum numerical model. The water flow simulations based on measured hydraulic characteristics without consideration of preferential flow effects failed to describe the infiltration experiment adequately. The 3D axisymmetric simulation based on dual-permeability approach provided relatively realistic space-time distribution of soil water pressure below the infiltration ring.     

Numerical Models for the Simulation of Flexible Artificial Heart Valves: Part I - Computational Methods

Abstract

A numerical model of the coupled motion of a flexing surface in a high Reynolds number flow is presented for the simulation of flexible polyurethane heart valves in the aortic position. This is achieved by matching a Lagrangian dynamic leaflet model with a panel method based flow solver. The two models are coupled via the time-dependent pressure field using the unsteady Bernoulli equation.

Incorporation of sub-cycling in the dynamic model equations and fast pre conditioning techniques in the panel method solver yields efficient convergence and near real-time simulations of valve motion. The generality of dynamic model allows different material properties and/or geometries to be studied easily and interactively. This interactivity is realized by embedding the models within a design environment created using the software IRIS Explorer ^TM.

Two flow domains are developed, an infinite domain and an internal domain using conformal mapping theory. In addition bending stress on the valve is computed using a simple stress model based on spline and circle equation techniques.     

YodA from Escherichia coli is a metal-binding,lipocalin-like protein

We have determined the crystal structure of YodA, an Escherichia coli protein of unknown function. YodA had been identified under conditions of cadmium stress, and we confirm that it binds metals such as cadmium and zinc. We have also found nickel bound in one of the crystal forms. YodA is composed of two domains: a main lipocalin/calycin-like domain and a helical domain. The principal metal-binding site lies on one side of the calycin domain, thus making YodA the first metal-binding lipocalin known. Our experiments suggest that YodA expression may be part of a more general stress response. From sequence analogy with the C-terminal domain of a metal-binding receptor of a member of bacterial ATP-binding cassette transporters, we propose a three-dimensional model for this receptor and suggest that YodA may have a receptor-type partner in E. coli.     

Is low rooting density of faba beans a cause of high residual nitrate content of soil at harvest ?

It was the aim of this study was to evaluate the hypothesis that low rooting density of faba beans is the major reason for the comparable low depletion of N_min-nitrogen from the rooted soil volume during the vegetation period. Therefore a simulation study was carried out using data from a two-year field experiment with faba beans and the reference crop oats. Since the nitrate dynamics in the soil is closely coupled with the water budget, the model simulated also the water uptake by plants, movement and content in the soil applying a numerical solution of the Richard's equation. The nitrogen budget part of the model includes calculation of vertical nitrate movement in the soil, mineralisation of nitrate from organic matter and nitrate uptake by the crop. Vertical nitrate movement was simulated with the convection-dispersion equation. Mineralisation was computed from a simple first order kinetic approach using only one fraction of mineralisable organic matter. Nitrate uptake was assumed to be determined either by the nitrogen demand of the crop, which was estimated from a logistic growth equation that was fitted to measured data of N-accumulation, or by the maximum nitrate transport rate towards the root surface. The latter was computed from a steady state solution of the diffusion - mass flow equation for cylindrical co-ordinates.For oats the model calculated a maximum nitrate transport rate towards roots that was quite close to the measured N-uptake of that crop. For faba beans, however, the calculated maximum nitrate transport towards roots was much lower than total N-uptake and lower than for oats. Consequently, simulated N_min-contents below faba beans were during the growing season about 20-30 kg N ha^–1 higher than below oats. This difference matches quite close with the observed differences between the two crops. Therefore it was concluded that low nitrate uptake resulting from low rooting density is the main reason for higher residual nitrate contents below faba beans at harvest time.     

Cadmium binding to metallothioneins. Domain specificity in reactions of alpha and beta fragments, apometallothionein, and zinc metallothionein with Cd2+

The cadmium-binding properties of rabbit liver Zn7-metallothionein (MT) 2 and apo-MT, rat liver apo-alpha MT and Zn4-alpha MT, and calf liver apo-beta MT, have been studied using circular dichroism (CD) and magnetic circular dichroism (MCD) spectroscopies. Both sets of spectra recorded during the titration of Zn7-MT 2 with Cd2+ exhibit a complicated pattern that is quite unexpected. Such behavior is not found at all in sets of spectra recorded during titrations of the apo-species (apo-MT, apo-alpha MT, and apo-beta MT), and is observed to a much lesser extent in the titration of Zn-alpha MT. Comparison between the band centers of the Cd-alpha MT and Cd-beta MT indicates that the CD spectrum of Cd7-MT is dominated by intensity from transitions that originate on Cd-S chromophores in the alpha domain, with little direct contribution from the beta domain. Analysis of the spectra recorded during titrations of Zn7-MT 2 with Cd2+ suggests: (i) that Cd2+ replaces Zn2+ in Zn7-MT isomorphously; (ii) that cadmium binds in a nonspecific, "distributed" manner across both domains; (iii) that cluster formation in the alpha domain only occurs after 4 mol eq of cadmium have been added and is indicated by the presence of a cluster-sensitive, CD spectral feature; (iv) that the characteristic derivative CD spectrum of native Cd4,Zn3-MT is only obtained from "synthetic" Cd4,Zn3-MT following a treatment cycle that allows the redistribution of cadmium into the alpha domain; warming the synthetic "native," Cd4,Zn3-MT, to 65 degrees C results in cadmium being preferentially bound in the alpha domain; and (v) Zn7-MT will bind Cd2+ quite normally at up to 65 degrees C but with greater specificity for the alpha domain compared with titrations carried out at 25 degrees C. These results suggest that the initial presence of zinc in both domains is an important factor in the lack of any domain specificity during cadmium binding to Zn-MT which contrasts the domain specific manner observed for cadmium binding to apo-MT.     

The relation between local and global transport parameters in an epithelial membrane having an asymmetric transport mechanism

The relationship between local and global transport parameters is derived for an epithelial membrane having series-parallel topology and an asymmetric transport mechanism at its apical and/or basolateral cell membranes. The result shows that the difference in the local forward and backward solute permeability coefficients is manifest in the global volume flow equation as distinct forward and backward reflection coefficients. The analytical result is applicable to the first order (low concentration) domain of Michaelis-Menten kinetics and a procedure is given for simulating the remainder of the domain on SPICE2.     

TheEscherichia coli mannitol permease as a model for transport via the bacterial phosphotransferase system

The bacterial phosphoenolpyruvate-dependent carbohydrate phosphotransferase system (PTS) consists of several proteins whose primary functions are to transport and phosphorylate their substrates. The complexity of the PTS undoubtedly reflects its additional roles in chemotaxis to PTS substrates and in regulation of other metabolic processes in the cell. The PTS permeases (Enzymes II) are the membrane-associated proteins of the PTS that sequentially recognize, transport, and phosphorylate their specific substrates in separate steps, and theEscherichia coli mannitol permease is one of the best studied of these proteins. It consists of two cytoplasmic domains (EIIA and EIIB) involved in mannitol phosphorylation and an integral membrane domain (EIIC) which is sufficient to bind mannitol, but which transports mannitol at a rate that is dependent on phosphorylation of the EIIA and EIIB domains. Recent results show that several residues in a hydrophilic, 85-residue segment of the EIIC domain are important for the binding, transport, and phosphorylation of mannitol. This segment may be at least partially exposed to the cytoplasm of the cell. A model is proposed in which this region of the EIIC domain is crucial in coupling phosphorylation of the EIIB domain to transport through the EIIC domain of the mannitol permease.     

Modeling a dehalogenase fold into the 8-A density map for Ca(2+)-ATPase defines a new domain structure

Members of the large family of P-type pumps use active transport to maintain gradients of a wide variety of cations across cellular membranes. Recent structures of two P-type pumps at 8-A resolution have revealed the arrangement of transmembrane helices but were insufficient to reveal the architecture of the cytoplasmic domains. However, recent proposals of a structural homology with a superfamily of hydrolases offer a new basis for modeling these domains. In the current work, we have extended the sequence comparison for the superfamily and delineated domains in the 8-A density map of Ca(2+)-ATPase. The homology suggests a new domain structure for Ca(2+)-ATPase and, specifically, that the phosphorylation domain adopts a Rossman fold. Accordingly, the atomic structure of L-2 haloacid dehalogenase has been fitted into the relevant domain of Ca(2+)-ATPase. The resulting model suggests the existence of two ATP sites at the interface between two domains. Based on this new model, we are able to reconcile numerous results of mutagenesis and chemical cross-linking within the catalytic domains. Furthermore, we have used the model to predict the configuration of Mg.ATP at its binding site. Based on this prediction, we propose a mechanism, involving a change in Mg(2+) liganding, for initiating the domain movements that couple sites of ion transport to ATP hydrolysis.     

Membrane cholesterol dynamics: cholesterol domains and kinetic pools

Nonreceptor mediated cholesterol uptake and reverse cholesterol transport in cells occur through cellular membranes. Thus, elucidation of cholesterol dynamics in membranes is essential to understanding cellular cholesterol accumulation and loss. To this end, it has become increasingly evident that cholesterol is not randomly distributed in either model or biologic membranes. Instead, membrane cholesterol appears to be organized into structural and kinetic domains or pools. Cholesterol-rich and poor domains can even be observed histochemically and physically isolated from epithelial cell surface membranes. The physiologic importance of these domains is 2-fold: (i) Select membrane proteins (receptors, transporters, etc.) are localized in either cholesterol-rich or cholesterol-poor domains. Consequently, the structure and properties of the domains rather than of the bulk lipid may selectively affect the function of proteins residing therein. (ii) Kinetic evidence suggests that cholesterol transport through and between membranes may occur through specific domains or pools. Regulation of the size and properties of such domains may be controlling factors of cholesterol transport or accumulation in cells. Recent technologic advances in the use of fluorescent sterols have allowed examination of cholesterol domain structure in model and biologic membranes. These techniques have been applied to examine the role of high-density lipoprotein, cholesterol lowering drugs, and intracellular lipid transfer proteins in membrane sterol domain structure and sterol movement between membranes.     

Numerical Modeling of Interstitial Fluid Flow Coupled with Blood Flow through a Remodeled Solid Tumor Microvascular Network

Modeling of interstitial fluid flow involves processes such as fluid diffusion, convective transport in extracellular matrix, and extravasation from blood vessels. To date, majority of microvascular flow modeling has been done at different levels and scales mostly on simple tumor shapes with their capillaries. However, with our proposed numerical model, more complex and realistic tumor shapes and capillary networks can be studied. Both blood flow through a capillary network, which is induced by a solid tumor, and fluid flow in tumor’s surrounding tissue are formulated. First, governing equations of angiogenesis are implemented to specify the different domains for the network and interstitium. Then, governing equations for flow modeling are introduced for different domains. The conservation laws for mass and momentum (including continuity equation, Darcy’s law for tissue, and simplified Navier–Stokes equation for blood flow through capillaries) are used for simulating interstitial and intravascular flows and Starling’s law is used for closing this system of equations and coupling the intravascular and extravascular flows. This is the first study of flow modeling in solid tumors to naturalistically couple intravascular and extravascular flow through a network. This network is generated by sprouting angiogenesis and consisting of one parent vessel connected to the network while taking into account the non-continuous behavior of blood, adaptability of capillary diameter to hemodynamics and metabolic stimuli, non-Newtonian blood flow, and phase separation of blood flow in capillary bifurcation. The incorporation of the outlined components beyond the previous models provides a more realistic prediction of interstitial fluid flow pattern in solid tumors and surrounding tissues. Results predict higher interstitial pressure, almost two times, for realistic model compared to the simplified model.