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PubMed1998

Ocular fixation index and mathematical models.

Ocular fixation test and ocular fixation index (OFI) never have been interpreted in terms of mathematical models, despite their widespread diffusion. However, ocular fixation is a typical case of visual-vestibular interaction, and mathematical models have proven very helpful in interpreting some mechanisms of this interaction, e.g. those of the optokinetic-vestibular interaction. In the present paper, a first attempt is proposed toward a model interpretation of OFI. By using very simple mathematical models, the hypothesis is tested that visual suppression of vestibular nystagmus results from direct action of smooth pursuit system (SPS). The aim is to draw consequences and recognize possible limits of this hypothesis. Dependence of OFI on SPS performance is examined. Although the available experimental data are insufficient for comprehensive validation of the model, the results agree with the current interpretations. In particular, quantitative support is given to the sensitivity of OFI to central vestibular diseases. Although the interpretation of visual suppression and OFI in terms of mathematical models is still at a very preliminary stage, models may provide a theoretical reference framework for the interpretation of new experimental results and/or suggest new test protocols.

Fixation, Ocular↗
PubMed2002

Molecular mechanism of H+ conduction in the single-file water chain of the gramicidin channel.

The conduction of protons in the hydrogen-bonded chain of water molecules (or "proton wire") embedded in the lumen of gramicidin A is studied with molecular dynamics free energy simulations. The process may be described as a "hop-and-turn" or Grotthuss mechanism involving the chemical exchange (hop) of hydrogen nuclei between hydrogen-bonded water molecules arranged in single file in the lumen of the pore, and the subsequent reorganization (turn) of the hydrogen-bonded network. Accordingly, the conduction cycle is modeled by two complementary steps corresponding respectively to the translocation 1) of an ionic defect (H+) and 2) of a bonding defect along the hydrogen-bonded chain of water molecules in the pore interior. The molecular mechanism and the potential of mean force are analyzed for each of these two translocation steps. It is found that the mobility of protons in gramicidin A is essentially determined by the fine structure and the dynamic fluctuations of the hydrogen-bonded network. The translocation of H+ is mediated by spontaneous (thermal) fluctuations in the relative positions of oxygen atoms in the wire. In this diffusive mechanism, a shallow free-energy well slightly favors the presence of the excess proton near the middle of the channel. In the absence of H+, the water chain adopts either one of two polarized configurations, each of which corresponds to an oriented donor-acceptor hydrogen-bond pattern along the channel axis. Interconversion between these two conformations is an activated process that occurs through the sequential and directional reorientation of water molecules of the wire. The effect of hydrogen-bonding interactions between channel and water on proton translocation is analyzed from a comparison to the results obtained previously in a study of model nonpolar channels, in which such interactions were missing. Hydrogen-bond donation from water to the backbone carbonyl oxygen atoms lining the pore interior has a dual effect: it provides a coordination of water molecules well suited both to proton hydration and to high proton mobility, and it facilitates the slower reorientation or turn step of the Grotthuss mechanism by stabilizing intermediate configurations of the hydrogen-bonded network in which water molecules are in the process of flipping between their two preferred, polarized states. This mechanism offers a detailed molecular model for the rapid transport of protons in channels, in energy-transducing membrane proteins, and in enzymes.

Amino Acid Sequence↗
PubMed2006

Two-dimensional indium sulfide framework constructed from pentasupertetrahedral p1 and supertetrahedral t2 clusters.

A new open-framework indium sulfide ([In12S24H2]10-) constructed from pentasupertetrahedral sulfide clusters ([In8S17H],9- P1) and supertetrahedral sulfide clusters ([In4S10H],7-) T2) has been prepared through hydrothermal synthesis. Unlike previously reported P1 clusters that require divalent metal cations, the P1 cluster reported here consists of only trivalent ions (In3+) and is the only known example of tetrahedral clusters with a core sulfur site bonded to four trivalent ions. Each P1 cluster is joined to three T2 clusters (vice versa) to form an infinite two-dimensional sheet stacked along the crystallographic c-axis. In contrast with known three-dimensional open-framework indium sulfides in which locations of extraframework amines are rarely known due to disorder, structure-directing amine molecules are much less disordered as a result of host-guest N-H...S hydrogen bonding. The UV-vis diffuse reflectance spectrum shows that this material is a wide band gap semiconductor.

Crystallography, X-Ray↗
PubMed2005

A simple method for measuring thoron spatial distributions.

A simple but effective method that allows the measurement of the 220Rn spatial distribution in working or living environments using a solid-state detector is presented in this paper. The method is based on measurements of the alpha particles emitted by 216Po (the first 220Rn progeny) directly deposited on the detector surface at different distances from a 220Rn exhalation source. The validity of the method is shown by comparing the results of an experiment, where the 220Rn activity concentration is measured under conditions of diffusion at constant temperature, with finite-element calculations.

Air Pollution, Indoor↗
PubMed1990

The role of the clinical nurse specialist in the research utilization process.

The goal of nursing research is to generate new information for the profession. Ideally, research findings validate clinical practice, and practice provides direction for research. Currently, there is a gap between knowledge generation through research and use of research findings in practice. This paper presents a model of research utilization which identifies the clinical nurse specialist's role in implementing the research utilization process in clinical practice.

Clinical Nursing Research↗
PubMed2004

Identifiability analysis of models for reversible intermolecular two-state excited-state processes coupled with species-dependent rotational diffusion monitored by time-resolved fluorescence depolarization.

A deterministic identifiability analysis of the kinetic model for a reversible intermolecular two-state excited-state process with species-dependent rotational diffusion described by Brownian reorientation is presented. The cases of both spherically and cylindrically symmetric rotors, with no change in the principal axes of rotation on interconversion in the latter case, are specifically considered. The identifiability analysis is carried out in terms of compartmental modeling based on the S(t) identical with I( parallel)(t)+2I( perpendicular)(t) and D(t) identical with I( parallel)(t)-I( perpendicular)(t) functions, where I( parallel)(t) and I( perpendicular)(t) are the delta-response functions for fluorescence, polarized, respectively, parallel and perpendicular to the electric vector of linearly polarized excitation. It is shown that, from polarized time-resolved fluorescence data collected at two concentrations of coreactant and three appropriately chosen emission wavelengths, (a) a unique set of rate constants for the overall excited-state process is always obtained by making use of polarized measurements and (b) the rotational diffusion constants and geometrical factors associated with the different anisotropy decay components can be uniquely determined and assigned to each species. The geometrical factors are determined by the absorption and emission transitions in the two rotating species. For spherical rotors, these factors depend directly on the relative orientations of the transition moments, while for cylindrically symmetric rotors they depend on the orientations with respect to each other and to the symmetry axis.

Algorithms↗
PubMed1998

Role of enzyme-substrate flexibility in catalytic activity: an evolutionary perspective.

Site-directed mutagenesis has proved an effective experimental technique to investigate catalytic mechanisms and to determine relations between enzyme structure and function. This article invokes an analytical model based on evolution by mutation and natural selection-Nature's analogue of site-directed mutagenesis-to derive a set of general rules relating enzyme structure and activity. The catalysts are described in terms of the structural parameters, rigidity and flexibility, and the functional variables, reaction rate and substrate specificity. The evolutionary model predicts the following structure-activity relations: (a) rigid enzyme-flexible substrate: large variation in reaction rates, broad substrate specificity; (b) rigid enzyme-rigid substrate: diffusion controlled rates, absolute specificity; (c) flexible enzyme-rigid substrate: intermediate reaction rates, group specificity; (d) flexible enzyme-flexible substrate: slow rates, absolute specificity. Spectroscopic methods and X-ray crystallography now yield important characteristics of enzyme-substrate complexes such as molecular flexibility. The evolutionary analysis we have exploited provides general principles for inferring catalytic activity from structural studies of enzyme-substrate complexes.

Animals↗
PubMed1995

Molecular dynamics studies of simple membrane-water interfaces: structure and functions in the beginnings of cellular life.

Molecular dynamics computer simulations of the structure and functions of a simple membrane are performed in order to examine whether membranes provide an environment capable of promoting protobiological evolution. Our model membrane is composed of glycerol 1-monooleate. It is found that the bilayer surface fluctuates in time and space, occasionally creating thinning defects in the membrane. These defects are essential for passive transport of simple ions across membranes because they reduce the Born barrier to this process by approximately 40%. Negative ions are transferred across the bilayer more readily than positive ions due to favorable interactions with the electric field at the membrane-water interface. Passive transport of neutral molecules is, in general, more complex than predicted by the solubility-diffusion model. In particular, molecules which exhibit sufficient hydrophilicity and lipophilicity concentrate near membrane surfaces and experience "interfacial resistance" to transport. The membrane-water interface forms an environment suitable for heterogeneous catalysis. Several possible mechanisms leading to an increase of reaction rates at the interface are discussed. We conclude that vesicles have many properties that make them very good candidates for earliest protocells. Some potentially fruitful directions of experimental and theoretical research on this subject are proposed.

Biophysical Phenomena↗
PubMed2001

Echo planar magnetic resonance imaging of anisotropic diffusion in asparagus stems.

MR diffusion-weighted imaging (DWI) uses the signal loss associated with the random thermal motion of water molecules in the presence of magnetic field gradients to derive a number of parameters that reflect the translational mobility of the water molecules in tissues. In highly organized but asymmetric structures, this mobility may be affected by the obstacles present and this in a direction-dependent way. Important examples of this are white brain matter and the stem of certain plants, both containing fibrous components where diffusion of water molecules across fibers is much more restricted than along the fibers. Diffusion that exhibits such directional dependence is said to be anisotropic, and diffusion tensor magnetic resonance imaging allows localized characterization of this behavior. Interpretation of the information obtained in terms of the underlying tissue structure is often hampered by the complexity of factors that can produce the observed behavior. A phantom that exhibits well-defined anisotropic diffusion and yields sufficient signal can help the experimental testing of the relevant methods and models. In this paper, we have used a phantom consisting of asparagus stems as a test object for assessing the value of the acquisition and postprocessing techniques commonly used in the clinic for this kind of investigation. Because of its strongly fibrous and cylindrically symmetric morphology, exhibiting a well-defined sub-classification of cells on the basis of size and shape, asparagus allows a relatively simple interpretation of the results obtained in the diffusion experiments. Our experiments show that the known structural information about the main cell types encountered correlates well with the behavior patterns of the diffusion parameters.

Algorithms↗
PubMed2006

Flexible ex vivo phantoms for validation of diffusion tensor tractography on a clinical scanner.

PURPOSE: The aim of this study was to develop ex vivo diffusion tensor (DT) flexible phantoms. MATERIALS AND METHODS: Materials were bundles of textile threads of cotton, monofilament nylon, rayon, and polyester bunched with spiral wrapping bands and immersed in water. DT images were acquired on a 1.5-Tesla clinical magnetic resonance scanner using echo planar imaging sequences with 15 motion probing gradient directions. DT tractography with seeding and a line-tracking method was carried out by software originally developed on a PC-based workstation. RESULTS: We observed relatively high fractional anisotropy on the polyester phantom and were able to reconstruct tractography. Straight tracts along the bundle were displayed when it was arranged linearly. It was easy to bend arcuately or bifurcate at one end; and tracts followed the course of the bundle, whether it was curved or branched and had good agreement with direct visual observation. Tractography with the other fibers was unsuccessful. CONCLUSION: The polyester phantom revealed a diffusion anisotropic structure according to its shape and would be utilizable repeatedly under the same conditions, differently from living central neuronal system. It would be useful to validate DT sequences and to optimize an algorithm or parameters of DT tractography software. Additionally, the flexibility of the phantom would enable us to model human axonal projections.

Anisotropy↗
PubMed2002

Some kinetic aspects in the immunoradiometric assay of insulin-like growth factor binding protein-3.

In this article the kinetics of the insulin-like growth factor binding protein-3 (IGFBP-3) reaction with its specific antibody immobilised on the inner wall of the reaction tube, and the subsequent binding of the immunocomplex formed with a second (125)I-labelled antibody are described. These reactions are used in the immunoradiometric determination of IGFBP-3. Independent variables were analyte and labelled antibody, temperature, viscosity, and the ionic strength of the medium. For the global process mono-exponential kinetics were found to be dependent on the concentrations, such dependence fitting with the models discussed in this paper. Viscosity results clearly indicate its negative influence on the direct reaction rate. Ionic strength shows noticeable but not too relevant effects, which suggests that the variation caused by the glycerol addition is not due to the influence of the dielectric constant of the solutions used. The effect of temperature shows activation parameters similar to the viscous flow energy of water, which suggests diffusion control for the global process.

Immunoradiometric Assay↗
PubMed1992

Microdialysis sampling for the investigation of dermal drug transport.

Microdialysis perfusion in vivo has the potential to be a powerful sampling technique in dermal and transdermal drug delivery studies. Characterization of a commercially available microdialysis probe in vitro considering relevant physiological parameters is a vital first step in the evaluation of microdialysis as a dermal sampling technique. In previous microdialysis studies, analyte concentration and neutrality have been implicated in altering microdialysis recovery. The recovery of a model compound 5-fluorouracil (5-FU) was investigated at several pH values and donor concentrations. The relative recovery of 5-FU by the microdialysis probe was affected by pH but not by donor concentration. To confirm further that the changing concentration and pH profile presented by the flux of 5-FU was not significantly altering microdialysis recovery, an experiment comparing direct and microdialysis sampling of a Franz diffusion cell receptor compartment was performed. Although the 5-FU concentration (0-686 ng/ml) and pH (7.40-7.24) changed substantially, the recovery of 5-FU was not adversely affected. To demonstrate the feasibility of dermal microdialysis, the flux of a commercial preparation of 5-fluorouracil was monitored utilizing a microdialysis probe implanted in excised rat skin in vitro. The results from the dermally implanted probe demonstrate the potential of the technique while establishing the limitations of the current microdialysis system.

Animals↗
PubMed2006

Model for dynamics of inhomogeneous and bulk fluids.

An accurate model for the density of states (DOS) for strongly inhomogeneous and bulk fluids has been proposed based on gamma distributions. The contribution to the density of states from the collective dynamics is modeled as an incomplete gamma distribution and the high frequency region is obtained from the solution of the memory equation using a sech memory kernel. Using only the frequency moments as input, the model parameters for the collective dynamics are obtained by matching moments of the resulting distribution. The model results in an analytical expression for the self-diffusivity of the fluid. We present results for soft sphere fluids confined in slit-shaped pores as well as bulk soft sphere liquids. Comparisons of the DOS, velocity autocorrelation functions, and memory kernels with molecular dynamics simulations reveal that the model predicts features in the DOS over the entire frequency range and is able to capture changes in the DOS as a function of fluid density and temperature. As a result the predicted VACFs, memory kernels, and self-diffusivities are accurately predicted over a wide range of conditions. Since the frequency moments for bulk liquids can be obtained from pair correlation functions, our method provides a direct route from fluid structure to dynamics. For fluids confined in slit-shaped pores, where the frequency moments are obtained from molecular dynamics simulations, the predicted self-diffusivities capture the resulting oscillations due to variations in the solvation pressure, and in the case of smooth walled pores, the predictions are superior to those obtained using kinetic theory.

Journal Article↗
PubMed1992

2-Deoxyglucose and cytochalasin D modulate aldolase mobility in living 3T3 cells.

Approximately 23% of the glycolytic enzyme aldolase in the perinuclear region of Swiss 3T3 cells is immobile as measured by FRAP. Previous studies suggest that the immobile fraction may be associated with the actin cytoskeleton (Pagliaro, L. and D. L. Taylor. 1988. J. Cell Biol. 107:981-991), and it has been proposed that the association of some glycolytic enzymes with the cytoskeleton could have functional significance, perhaps involving a fundamental relationship between glycolysis, cytoplasmic organization, and cell motility. We have tested the effect of a key glycolytic inhibitor and an actin cytoskeletal modulator on the mobility of aldolase in living cells directly, using fluorescent analog cytochemistry and FRAP. We report here that the competitive hexokinase inhibitor 2-deoxyglucose releases the bound fraction of aldolase in 3T3 cells within 10 min, and that this process is reversible upon washout of the inhibitor. A similar result is produced with the actin-binding agent, cytochalasin D. These results are consistent with models in which glycolytic enzymes are not exclusively diffusion-limited, soluble proteins, but may exist partially in the solid phase of cytoplasm. Such organization has significant implications for both the modulation of cytoplasmic structure and for cellular metabolism.

3T3 Cells↗
PubMed2000

Transport mechanisms of the large neutral amino acid L-phenylalanine in the human intestinal epithelial caco-2 cell line.

The transepithelial transport and the intracellular accumulation of the large neutral amino acid L-phenylalanine (L-Phe) were studied in monolayers of Caco-2 cells, cultivated in a bicameral insert system, to characterize the mechanisms involved in the absorption of this essential amino acid by the human intestinal mucosa. In our model, L-Phe was transported selectively in the apical (AP)-to-basolateral (BL) direction. AP-to-BL transport of L-Phe was temperature dependent and Na(+) independent, increased in the absence of protein synthesis and showed competition with large neutral and cationic amino acids. By contrast, transport in the BL-to-AP direction mainly resulted from passive movement (probably paracellular passage and transcellular diffusion). L-Phe accumulation into Caco-2 cells was higher from the BL pole than from the AP pole and characterized by the incorporation of most of the accumulated molecules into newly synthesized proteins. In addition, L-Phe accumulation was Na(+) dependent from both poles, whereas only accumulation from the AP pole was sensitive to inhibition by both large neutral and cationic amino acids. These results suggest that the processes involved in AP-to-BL transport and AP accumulation of this amino acid are very different from those involved in BL-to-AP transport and BL accumulation.

Biological Transport↗
PubMed2001

Physiological significance of the rate constants in compartmental analysis.

Transfer (rate) constants in compartmental analysis are generally considered solely in operational terms, and little attention has been paid to their physiological interpretation. In this study we have examined the significance of their roles in physiological terms and the implications of this interpretation. When freely diffusible tracers are introduced into the blood stream by bolus injection, the sum of the exit rate constants from the blood compartment gives the number of blood volumes turned over per unit time; when multiplied by the blood volume, this value is the cardiac output. When corrected for body weight, the product yields the cardiac index, a biological constant for large mammals. The ratio of the rate constant supplying an organ to the exit-constant sum gives fractional cardiac output, and when multiplied by the cardiac output the ratio gives organ blood flow, independent of diffusibility. For freely diffusible tracers, organ blood flow can be calculated directly from the product of the organ rate constant and blood volume. At equilibrium and at equal concentration, the ratio of rate constants between adjacent compartments gives their relative volumes; this interpretation is fundamental when partitioning compartments for detailed analysis. These considerations have been validated by testing in both animals and man. Multiple solution sets may occur in mammillary models. Knowledge of the physiological interpretation of intercompartmental rate constants is of importance not only in model interpretation but in model validation, where this information serves as an independent check on model structure and its realization.

Animals↗
PubMed2000

Dynamics and lateral interactions of dipolar chains

The dynamics and lateral interactions of dipolar chains in magnetorheological suspensions determine the long-time microscopic structure and resulting rheological response. In this paper we characterize proposed lateral interaction mechanisms and their implications for long-time coarsening of structure and compare them to direct measurements of the lateral interaction of dipolar chains using optical trap micromanipulation. We observe a long-range far-field attraction between flexible chains, while the near-field interaction can be repulsive or attractive. At high field strengths, we observe the short-range attraction of rigid chains. Chain dynamics measured with videomicroscopy and diffusing wave spectroscopy are described by a local-mode model and are consistent with fluctuation-mediated interaction theories. The subdiffusive behavior at intermediate and long times scales as t(0.75), identical to semiflexible molecules. Finally, we show examples of how defects in chains can create lateral attractions or repulsions.

Journal Article↗
PubMed2001

Dynamics of supercooled water in configuration space.

We study the potential energy surface (PES) sampled by a liquid modeled via the widely studied extended simple point charge (SPC/E) model for water. We characterize the curvature of the PES by calculating the instantaneous normal mode (INM) spectrum for a wide range of densities and temperatures. We discuss the information contained in the INM density of states, which requires additional processing to be unambiguously associated with the long-time dynamics. For the SPC/E model, we find that the slowing down of the dynamics in the supercooled region-where the ideal mode coupling theory has been used to describe the dynamics-is controlled by the reduction in the number of directions in configuration space that allow a structural change. We find that the fraction f(dw) of the double-well directions in configuration space determines the value of the diffusion constant D, thereby relating a property of the PES to a macroscopic dynamic quantity; specifically, it appears that square root D is approximately linear in f(dw). Our findings are consistent with the hypothesis that, at the mode coupling crossover temperature, dynamical processes based on the free exploration of configuration space vanish, and processes requiring activation dominate. Hence, the reduction of the number of directions allowing free exploration of configuration space is the mechanism of diffusion implicitly implemented in the ideal mode coupling theory. Additionally, we find a direct relationship between the number of basins sampled by the system and the number of free directions. In this picture, diffusion appears to be related to geometrical properties of the PES, and to be entropic in origin.

Journal Article↗