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PubMed1996

The hydration of proteins in solutions by self-diffusion coefficients. NMR study.

The hydration of the globular (lysozyme, albumin) and fibrillar (fibrinogen) proteins in solution has been determined from the measurements of the self-diffusion coefficient by NMR pulsed gradient method. It has been concluded that the concentration dependencies of the self-diffusion coefficient of water molecules in protein solution are controlled by two additive factors: obstruction effect correlated with the protein dimension and direct hydration effect proportional to the number of the adsorption sites on the protein surface.

Animals↗
PubMed2005

Vapor-phase exchange of perchloroethene between soil and plants.

Tree core concentrations of tetrachloroethylene (perchloroethene, PCE) at the Riverfront Superfund Site in New Haven, MO, were found to mimic the profile of soil phase concentrations. The observed soil-tree core relationship was stronger than that of groundwater PCE to tree core concentrations atthe same site. Earlier research has shown a direct, linear relationship between tree core and groundwater concentrations of chlorinated solvents and other organics. Laboratory-scale experiments were performed to elucidate this phenomenon, including determining partitioning coefficients of PCE between plant tissues and air and between plant tissues and water, measured to be 8.1 and 49 L/kg, respectively. The direct relationship of soil to tree core PCE concentrations was hypothesized to be caused by diffusion between tree roots and the soil vapor phase in the subsurface. The central findings of this research are discovering the importance of subsurface vapor-phase transfer for VOCs and uncovering a direct relationship between soil vapor-phase chlorinated solvents and uptake rates that impact contaminant translocation from the subsurface and transfer into the atmosphere.

Carcinogens↗
PubMed2005

Fluorophore-quencher distance correlation functions from single-molecule photon arrival trajectories.

We generalize and simplify the method of Yang and Xie (J. Chem. Phys. 2002, 117, 10965) to obtain distance correlation functions from photon arrival trajectories of single fluorophores whose lifetime, [k(r)](-1), depends on the distance to a quencher. It is assumed that this distance does not change during the fluorescence lifetime. The experimental trajectory is first transformed by replacing the delay time (i.e., the interval between the photon arrival and the nearest laser pulse) by a certain function of this delay time. This function is the inverse Laplace transform of r(k), which is the solution of k(r) = 1. The correlation function of the transformed data then directly gives the distance correlation function. Illustrative examples include Förster energy transfer and quenching due to electron transfer.

Diffusion↗
PubMed2001

Activation-enhanced alpha(IIb)beta(3)-integrin-cytoskeleton interactions outside of focal contacts require the alpha-subunit.

Integrins link the cell's cytoskeleton to the extracellular matrix, as well as to receptors on other cells. These links occur not only at focal contacts but also at smaller integrin-containing protein complexes outside of focal contacts. We previously demonstrated the importance of focal contact-independent integrin-cytoskeleton interactions of beta(2) integrins: activation of adhesion resulted from a release of integrins from cytoskeletal constraints. To determine whether changes in integrin-cytoskeleton interactions were related to activation of the integrin, we used single particle tracking to examine focal contact-independent cytoskeletal associations of alpha(IIb)beta(3)-integrin, in which activation results in a large conformational change. Direct activation of alpha(IIb)beta(3) by mutation did not mimic activation of lymphocytes with phorbol ester, because it enhanced integrin-cytoskeleton interactions, whereas activation of lymphocytes decreased them. Using additional integrin mutants, we found that both alpha- and beta-cytoplasmic domains were required for these links. This suggests that 1) both beta(2)- and beta(3)-integrins interact with the cytoskeleton outside of focal contacts; 2) activation of a cell and activation of an integrin are distinct processes, and both can affect integrin-cytoskeleton interactions; and 3) the role of the alpha-subunit in integrin-cytoskeleton interactions in at least some circumstances is more direct than generally supposed.

Amino Acid Motifs↗
PubMed2004

Nonperturbative renormalization-group study of reaction-diffusion processes.

We generalize nonperturbative renormalization group methods to nonequilibrium critical phenomena. Within this formalism, reaction-diffusion processes are described by a scale-dependent effective action, the flow of which is derived. We investigate branching and annihilating random walks with an odd number of offspring. Along with recovering their universal physics (described by the directed percolation universality class), we determine their phase diagrams and predict that a transition occurs even in three dimensions, contrarily to what perturbation theory suggests.

Diffusion↗
PubMed2004

Anisotropic thermal conduction in a polymer liquid subjected to shear flow.

Flow-induced anisotropic thermal conduction in a polymer liquid is studied using force Rayleigh scattering. Time-dependent measurements of the complete thermal diffusivity tensor, which includes one off-diagonal and three diagonal components, are reported on an entangled polymer melt subjected to a uniform shear deformation. These data, in conjunction with mechanical measurements of the stress, provide the first direct evidence that the thermal conductivity tensor and the stress tensor are linearly related in a deformed polymer liquid.

Anisotropy↗
PubMed1999

Calculation of NMR relaxation, covolume, and scattering-related properties of bead models using the SOLPRO computer program.

The hydrodynamic properties of macromolecules and bioparticles, represented by bead models, can be calculated using methods implemented in the computer routine HYDRO. Recently, a new computer routine, SOLPRO, has been presented for the calculation of various SOLution PROperties. These include (1) time-dependent electro-optic and spectroscopic properties related to rotational diffusion, (2) non-dynamic properties like scattering curves, and (3) dimensionless quantities that combine two or more solution properties in a form which depends on the shape of the macromolecule but not on its size. In the present work we describe the inclusion of more of those types of properties in a new version of SOLPRO. Particularly, we describe the calculation of relaxation rates in nuclear magnetic resonance (NMR). For dipolar coupling, given the direction of the dipole the program calculates values of the spectral density, from which the NMR relaxation times can be obtained. We also consider scattering-related properties, namely the distribution of distances for the bead model, which is directly related to the angular dependence of scattered intensity, and the particle's longest distance. We have devised and programmed a procedure to calculate the covolume of the bead model, related to the second virial coefficient and, in general, to the concentration dependence of solution properties. Various shape-dependent dimensionless quantities involving the covolume are calculated. In this paper we also discuss some aspects, namely bead overlapping and hydration, that are not explicitly included in SOLPRO, but should be considered by the user.

Mathematical Computing↗
PubMed1991

Direct intraarterial wall injection of microparticles via a catheter: a potential drug delivery strategy following angioplasty.

Local delivery into the arterial wall of medications at high concentrations may evolve as a method to reduce postangioplasty restenosis. However, since the atherosclerotic artery has increased vasa vasorum, medications injected in a fluid state may diffuse out of the arterial wall too quickly to have a therapeutic effect. Thus we evaluated whether microparticles as a model for a particulate microcarrier drug delivery system, injected via a porous balloon catheter, could be retained within the atherosclerotic rabbit femoral arterial wall. Arteries were injected with a 5 microns microparticle suspension for 45 seconds at either 3 or 5 atm of infusion pressure immediately following balloon angioplasty. Arteries were obtained immediately following the procedure or at 1, 3, 7, or 14 days after infusion to evaluate for the presence of retained microparticles. Of 34 arteries, 30 contained retained microparticles, with 21 exhibiting microparticles in the neointimia, 12 in the media, and 25 in the adventitia. Microparticles were retained for as long as 14 days, and there was no difference between the distribution or quantity of microparticles at 3 or 5 atm of infusion pressure. The mode of microparticle distribution probably involved deposition within dissection planes, although evidence for vasa vasorum transport was observed. We hypothesize that biodegradable microparticles could serve as a vehicle for intramural drug delivery in the treatment of restenosis.

Angioplasty, Balloon↗
PubMed2004

Transitions and transport for a spatially periodic stochastic system with locally coupled oscillators.

In this paper, with a special model, we investigate the spatially periodic stochastic system with locally coupled oscillators subject to a constant force F. A nonequilibrium second-order phase transition is found when F=0. This phase transition is reentrant when the additive noise is weak. With varying the constant force F, a continuous or discontinuous transition between the states with positive and negative mean fields (mu>0 and mu<0) is observed, which is not a phase transition. The mean field or current sometimes exhibits hysteresis as a function of F. With the variation of the force F, when hysteresis of the mean field or current versus F appears, a nonzero probability current with definite direction will occur at the point F=0. The correlation between the additive and multiplicative noises has an effect on the transitions and the transport.

Animals↗
PubMed1990

An experimental model of chronic renal disease in dogs by infusion of microspheres into the renal arterial circulation.

The feasibility of renal arterial infusion of nonbiodegradable microspheres as a model of chronic renal disease in dogs was evaluated. Resin-coated, styrene-divinyl benzene copolymer microspheres were infused into the kidneys of healthy adult Beagles by direct injections of both renal arteries in a single surgical procedure. Injections of 25-microns diameter microspheres had minimal effect on either the clinical status or serum values of the dogs. Histologic examination revealed the majority of the microspheres lodged within the capillary beds of the glomeruli, and little change to the kidneys. However, injections of 50-microns diameter microspheres caused significant increases in serum concentrations of urea nitrogen and creatinine. Histologically, the larger microspheres obstructed afferent arterioles and small arteries, which caused diffuse glomerular necrosis and nephron damage. With doses ranging from 1 to 3 million microspheres/dog, a correlation between the quantity of microspheres injected and severity of renal damage was observed. The optimal dose for producing a model of moderate renal disease was determined to be 1.8 million microspheres/dog (0.9 million microspheres/kidney). During long-term studies, microsphere-injected dogs fed a moderately restricted protein ration remained relatively azotemic, compared with control dogs on the identical ration. During the 5-month postsurgical period, the serum urea nitrogen concentration averaged 18.41 +/- 1.59 mg/dl (mean +/- SE) for the microsphere-injected dogs vs 9.31 +/- 0.38 for the control dogs (P less than 0.001). Similarly, the mean serum creatinine value was significantly higher (P = 0.020) for the microsphere-injected dogs, compared with the controls (1.23 +/- 0.12 mg/dl vs 0.94 +/- 0.03).(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed2002

Fabricational morphology of oblique ribs in bivalves.

The formation of oblique ribs of bivalve shells usually has been attributed to processes of reaction-diffusion of morphogens from cell to cell at the mantle margin or neural activation and lateral inhibition in the mantle. In particular, such ribs appear with high rates of lateral diffusion. Nevertheless, theoretical models fail to explain either partially or wholly some varieties of oblique ribs. After surveying the modes of formation of the shell and oblique ribs by the bivalve mantle and associated fabricational defects, I have determined that the mantle is able to develop an elaborate behavior in order to displace the rib in a particular direction during growth. The mantle margin is, therefore, not only the shell-secreting organ, but also the main morphogenetic unit. In particular, there are two main fabricational strategies. In forms with strict contact guidance (SCG) the mantle is able to project far enough beyond the shell margins so as to feel the already formed reliefs and to align new growth increments of the ribs in the appropriate directions. The shell margin is always strongly reflected. In bivalves with reduced contact guidance plus constant lateral shift (RCG), the margin is usually acute and the information about ribs available to the mantle is reduced. During rib construction the mantle extrudes slightly from the shell edge and then pushes laterally by muscular action; in this way, the new growth increment of the rib is displaced laterally on a small scale. The contact-guidance model is supported also by the homogeneous structure of the shell-secreting mantle. From the morphogenetic standpoint, oblique ribs are related to commarginal ones and both differ completely from other ribbing patterns of bivalves.

Animals↗
PubMed2005

Reduction of noise in diffusion tensor images using anisotropic smoothing.

To improve the accuracy of tissue structural and architectural characterization with diffusion tensor imaging, a novel smoothing technique is developed for reducing noise in diffusion tensor images. The technique extends the traditional anisotropic diffusion filtering method by allowing isotropic smoothing within homogeneous regions and anisotropic smoothing along structure boundaries. This is particularly useful for smoothing diffusion tensor images in which direction information contained in the tensor needs to be restored following noise corruption and preserved around tissue boundaries. The effectiveness of this technique is quantitatively studied with experiments on simulated and human in vivo diffusion tensor data. Illustrative results demonstrate that the anisotropic smoothing technique developed can significantly reduce the impact of noise on the direction as well as anisotropy measures of the diffusion tensor images.

Algorithms↗
PubMed1976

Convection, diffusion and cardiogenic mixing of inspired gas in the lung; an experimental approach.

In 8 open-chested dogs, we measured the FN2 within 26 airways, 2.5-8.6 mm in diameter, during constant flow inflations with 0.5 liter of O2. At low flows the FN2 did not fall to zero but reached a plateau, at a value that was inversely related to inspiratory flow. When inspiratory flow is constant, the measured FN2 represents one point on a stationary front separating inspired and alveolar gas. At all points on the front the convective and diffusive transport of N2 is equal and opposite in direction. We quantitated cardiogenic gas mixing by comparing in vivo and post mortem the flow which resulted in a given stable FN2 value within the same airway. In vivo, this flow and therefore the calculated effective diffusion coefficient (D') was more than 5 times greater than that post mortem. Our results confiem some of the predictions made from model analyses of gas transport in the lung. However, calculations based on molecular diffusion as the sole mixing mechanism necessarily overestimate diffusion times and the magnitude of stratification.

Animals↗
PubMed2006

Liquid boundary movements in cylindrical and convex hydrophobic matrix tablets: Effects on tablet cracking and drug release.

The aim of this study was to investigate liquid penetration into both cylindrical and convex hydrophobic matrix tablets and to relate the changes in tablet structure to drug release. Starch acetate with degree of substitution of 2.7 was used as a hydrophobic matrix former and anhydrous caffeine as a freely soluble model drug. Phenolred was used as a colouring agent to enhance the visual detection of the liquid boundary movements, which were examined in axial and radial directions for both types of tablets. The tablets started to expand during the dissolution, resulting in cracking as the liquid boundary penetrated into tablet. The cracking influences drug release by shortening the diffusion path and decreasing the tortuosity. The liquid boundaries proceed differently in cylindrical and convex tablets, this being attributable to differences in pore structure and density distribution. Cylindrical tablets are quite homogeneous in terms of density, but convex tablets have more porous areas at the domes of the tablet.

Algorithms↗
PubMed2006

A unifying theoretical and algorithmic framework for least squares methods of estimation in diffusion tensor imaging.

A unifying theoretical and algorithmic framework for diffusion tensor estimation is presented. Theoretical connections among the least squares (LS) methods, (linear least squares (LLS), weighted linear least squares (WLLS), nonlinear least squares (NLS) and their constrained counterparts), are established through their respective objective functions, and higher order derivatives of these objective functions, i.e., Hessian matrices. These theoretical connections provide new insights in designing efficient algorithms for NLS and constrained NLS (CNLS) estimation. Here, we propose novel algorithms of full Newton-type for the NLS and CNLS estimations, which are evaluated with Monte Carlo simulations and compared with the commonly used Levenberg-Marquardt method. The proposed methods have a lower percent of relative error in estimating the trace and lower reduced chi2 value than those of the Levenberg-Marquardt method. These results also demonstrate that the accuracy of an estimate, particularly in a nonlinear estimation problem, is greatly affected by the Hessian matrix. In other words, the accuracy of a nonlinear estimation is algorithm-dependent. Further, this study shows that the noise variance in diffusion weighted signals is orientation dependent when signal-to-noise ratio (SNR) is low (<or=5). A new experimental design is, therefore, proposed to properly account for the directional dependence in diffusion weighted signal variance.

Algorithms↗
PubMed2003

Confined diffusion without fences of a g-protein-coupled receptor as revealed by single particle tracking.

Single particle tracking is a powerful tool for probing the organization and dynamics of the plasma membrane constituents. We used this technique to study the micro -opioid receptor belonging to the large family of the G-protein-coupled receptors involved with other partners in a signal transduction pathway. The specific labeling of the receptor coupled to a T7-tag at its N-terminus, stably expressed in fibroblastic cells, was achieved by colloidal gold coupled to a monoclonal anti T7-tag antibody. The lateral movements of the particles were followed by nanovideomicroscopy at 40 ms time resolution during 2 min with a spatial precision of 15 nm. The receptors were found to have either a slow or directed diffusion mode (10%) or a walking confined diffusion mode (90%) composed of a long-term random diffusion and a short-term confined diffusion, and corresponding to a diffusion confined within a domain that itself diffuses. The results indicate that the confinement is due to an effective harmonic potential generated by long-range attraction between the membrane proteins. A simple model for interacting membrane proteins diffusion is proposed that explains the variations with the domain size of the short-term and long-term diffusion coefficients.

Bacteriophage T7↗
PubMed2003

Effects of pore volume-transmissivity correlation on transport phenomena.

The relevant velocity that describes transport phenomena in a porous medium is the pore velocity. For this reason, one needs not only to describe the variability of transmissivity, which fully determines the Darcy velocity field for given source terms and boundary conditions, but also any variability of the pore volume. We demonstrate that hydraulically equivalent media with exactly the same transmissivity field can produce dramatic differences in the displacement of a solute if they have different pore volume distributions. In particular, we demonstrate that correlation between pore volume and transmissivity leads to a much smoother and more homogeneous solute distribution. This was observed in a laboratory experiment performed in artificial fractures made of two plexiglass plates into which a space-dependent aperture distribution was milled. Using visualization by a light transmission technique, we observe that the solute behaviour is much smoother and more regular after the fractures are filled with glass powder, which plays the role of a homogeneous fault gouge material. This is due to a perfect correlation between pore volume and transmissivity that causes pore velocity to be not directly dependent on the transmissivity, but only indirectly through the hydraulic gradient, which is a much smoother function due to the diffusive behaviour of the flow equation acting as a filter. This smoothing property of the pore volume-transmissivity correlation is also supported by numerical simulations of tracer tests in a dipole flow field. Three different conceptual models are used: an empty fracture, a rough-walled fracture filled with a homogeneous material and a parallel-plate fracture with a heterogeneous fault gouge. All three models are hydraulically equivalent, yet they have a different pore volume distribution. Even if piezometric heads and specific flow rates are exactly the same at any point of the domain, the transport process differs dramatically. These differences make it important to discriminate in situ among different conceptual models in order to simulate correctly the transport phenomena. For this reason, we study the solute breakthrough and recovery curves at the extraction wells. Our numerical case studies show that discrimination on the basis of such data might be impossible except under very favourable conditions, i.e. the integral scale of the transmissivity field has to be known and small compared to the dipole size. If the latter conditions are satisfied, discrimination between the rough-walled fracture filled with a homogeneous material and the other two models becomes possible, whereas the parallel-plate fracture with a heterogeneous fault gouge and the empty fracture still show identifiability problems. The latter may be solved by inspection of aperture and pressure testing.

Geological Phenomena↗
PubMed2006

Nature of the chemical bond in protonated methane.

Protonated methane, CH(5)(+), is a key reactive intermediate in hydrocarbon chemistry and a borderline case for chemical structure theory, being the simplest example of hypercoordinated carbon. Early quantum mechanical calculations predicted that the properties of this species could not be associated with only one structure, because it presents serious limitations of the Born-Oppenheimer approximation. However, ab initio molecular dynamics and diffusion Monte Carlo calculations showed that the most populated structure could be pictured as a CH(3) tripod linked to a H(2) moiety. Despite this controversy, a model for the chemical bonds involved in this ion still lacks. Here we present a modern valence bond model for the electronic structure of CH(5)(+). The chemical bond scheme derived directly from our calculations pictures this ion as H(3)C...H(2)(+). The fluxionality can be seen as the result of a proton transfer between C-H bonds. A new insight on the vibrational bands at approximately 2400 and approximately 2700 cm(-1) is suggested. Our results show that the chemical bond model can be profitably applied to such intriguing systems.

Journal Article↗