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At least 937 records · Page 52Linked to original sources
PubMed2005

Are conformational changes, induced by osmotic pressure variations, the underlying mechanism of controlling the adhesive activity of mussel adhesive proteins?

The mussel adhesive protein Mefp-1, under physiological conditions, presumably has a self-avoiding random walk conformation with helix-like or turned deca-peptide segments. Such a conformation may coil up under osmotic pressure induced by surrounding macromolecules. As a consequence, the orientation of the 3,4-dihydroxy-phenylalanine groups (dopa), essential for the adhesive strength as well as the cohesive strength in Mefp-1, will be altered. Changing the concentration of the protein itself or of different-type surrounding macromolecules may therefore be a tool to control the protein's adhesive activity. The effect of osmotic pressure on the conformation and dopa reactivity of Mefp-1 is studied by the addition of (poly)ethylene oxide (PEO) as a model macromolecule (Mw = 100 kD). From UV-spectroscopy measurements, it can be concluded that dopa reactivity in Mefp-1 changes with increasing PEO concentration. Fitting of the measured absorbance intensity data of the oxidation product dopaquinone versus time with a kinetic model points to the decreased accessibility of dopa groups in the Mefp-1 structure, a faster oxidation, and diminished cross linking under the influence of increasing PEO concentration up to 2.4 g/L, corresponding to an osmotic pressure of approximately 73 Pa. At higher PEO concentrations, the accessibility of the dopa groups for oxidation as well as cross-link formation decreases until about 20% of the dopa groups are oxidized at a PEO concentration of 3.8 g/L, corresponding to an osmotic pressure of approximately 113 Pa. FTIR measurements on the basis of amide I shifts qualitatively point to a transition to a more continuously turned structure of Mefp-1 in the presence of PEO. Therefore, it seems that conformational changes caused by variations of osmotic pressure determine the extent of steric hindrance of the dopa groups and hence the adhesive reactivity of Mefp-1.

Adhesiveness↗
PubMed1999

A heterogeneous tube model of intestinal drug absorption based on probabilistic concepts.

PURPOSE: To develop an approach based on computer simulations for the study of intestinal drug absorption. METHODS: The drug flow in the gastrointestinal tract was simulated with a biased random walk model in the heterogeneous tube model (Pharm. Res. 16, 87-91, 1999), while probability concepts were used to describe the dissolution and absorption processes. An amount of drug was placed into the input end of the tube and allowed to flow, dissolve and absorb along the tube. Various drugs with a diversity in dissolution and permeability characteristics were considered. The fraction of dose absorbed (Fabs) was monitored as a function of time measured in Monte Carlo steps (MCS). The absorption number An was calculated from the mean intestinal transit time and the absorption rate constant adhering to each of the drugs examined. RESULTS: A correspondence between the probability factor used to simulate drug absorption and the conventional absorption rate constant derived from the analysis of data was established. For freely soluble drugs, the estimates for Fabs derived from simulations using as an intestinal transit time 24500 MCS (equivalent to 4.5 h) were in accord with the corresponding data obtained from literature. For sparingly soluble drugs, a comparison of the normalized concentration profiles in the tube derived from the heterogeneous tube model and the classical macroscopic mass balance approach enabled the estimation of the dissolution probability factor for five drugs examined. The prediction of Fabs can be accomplished using estimates for the absorption and the dissolution probability factors. CONCLUSIONS: A fully computerized approach which describes the flow, dissolution and absorption of drug in the gastrointestinal tract in terms of probability concepts was developed. This approach can be used to predict Fabs for drugs with various solubility and permeability characteristics provided that probability factors for dissolution and absorption are available.

Computer Simulation↗
PubMed2002

Photosynthetic exciton theory in the 1960s.

Theoretical developments in the 1960s concerning the migration of chlorophyll electronic excitation energy through a photosynthetic core antenna to a reaction center are reviewed in three parts. These include the first theory paper whose calculated results were consistent with experiment, the first analytic determination of the mean number of steps in the two-dimensional random walk of a dephased exciton to reach the reaction center, and the first theoretical description of the possible effects of true collective excited states (Frenkel excitons) on the rate of trap-limited migration and trapping. The possible relevance of these developments, particularly the last, to current photosynthesis research is briefly discussed.

Journal Article↗
PubMed1998

Application of the dispersion model for description of the outflow dilution profiles of noneliminated reference indicators in rat liver perfusion studies.

The dispersion model (DM) is a stochastic model describing the distribution of blood-borne substances within organ vascular beds. It is based on assumptions of concurrent convective and random-walk (pseudodiffusive) movements in the direction of flow, and is characterized by the mean transit time (t) and the dispersion number (inverse Peclet number), DN. The model is used with either closed (reflective) boundary conditions at the inflow and the outflow point (Danckwerts conditions) or a closed condition at the inflow and an open (transparent) condition at the outflow (mixed conditions). The appropriateness of DM was assessed with outflow data from single-pass perfused rat liver multiple indicator dilution (MID) experiments, with varying lengths of the inflow and outflow catheters. The studies were performed by injection, of bolus doses of 51Crlabeled red blood cells (vascular indicator), 125I-labeled albumin and [14C] sucrose (interstitual indicators), and [3H]2O (whole tissue indicator) into the portal vein at a perfusion rate of 12 ml/ min. The outflow profiles based on the DM were convolved with the transport function of the catheters, then fitted to the data. A fairly good fit was obtained for most of the MID curve, with the exception of the late-in-time data (prolonged tail) beyond 3 x [symbol: see text]. The fitted DNS were found to differ among the indicators, and not with the length of the inflow and outflow catheters. But the differences disappeared when a delay parameter, t0 = 4.1 +/- 0.7 sec (x +/- SD), was included as an additional fitted parameter for all of the indicators except water. Using the short catheters, the average DN for the model with delay was 0.31 +/- 0.13 for closed and 0.22 +/- 0.07 for mixed boundary conditions, for all reference indicators. Mean transit times and the variances of the fitted distributions were always smaller than the experimental ones (on average, by 6.8 +/- 3.7% and 58 +/- 19%, respectively). In conclusion, the DM is a reasonable descriptor of dispersion for the early-in-time data and not the late-in-time data. The existence of a common DN for all noneliminated reference indicators suggests that intrahepatic dispersion depends only on the geometry of the vasculature rather than the diffusional processes. The role of the nonsinusoidal ("large") vessels can be partly represented by a simple delay.

Animals↗
PubMed2002

Nonparametric AUC estimation in population studies with incomplete sampling: a Bayesian approach.

The estimation of the AUC in a population without frequent and/or fixed individual samplings is of interest because the number of plasma samples can often be limited due to technical, ethical and cost reasons. Non-linear mixed effect models can provide both population and individual estimates of AUC based on sparse sampling protocols; however, appropriate structural models for the description of the pharmacokinetics are required. Nonparametric solutions have also been proposed to estimate the population AUC and the associated error when particular sampling protocols are adopted. However, they do not estimate the individual AUCs and lack flexibility. Also a semiparametric method has been proposed for addressing the problem of sparse sampling in reasonably well designed studies. In this work, we propose and evaluate a nonparametric Bayesian scheme for AUC estimation in population studies with arbitrary sampling protocols. In the stochastic model representing the whole population, the individual plasma concentration curves and the "mean" population curve are described by random walk processes, allowing the application of the method to the reconstruction of any kind of "regular" curves. Population and individual AUC estimation are performed by numerically computing the posterior expectation through a Markov chain Monte Carlo algorithm.

Algorithms↗
PubMed2003

A reappraisal of drug release laws using Monte Carlo simulations: the prevalence of the Weibull function.

PURPOSE: To verify the Higuchi law and study the drug release from cylindrical and spherical matrices by means of Monte Carlo computer simulation. METHOD: A one-dimensional matrix, based on the theoretical assumptions of the derivation of the Higuchi law, was simulated and its time evolution was monitored. Cylindrical and spherical three-dimensional lattices were simulated with sites at the boundary of the lattice having been denoted as leak sites. Particles were allowed to move inside it using the random walk model. Excluded volume interactions between the particles was assumed. We have monitored the system time evolution for different lattice sizes and different initial particle concentrations. RESULTS: The Higuchi law was verified using the Monte Carlo technique in a one-dimensional lattice. It was found that Fickian drug release from cylindrical matrices can be approximated nicely with the Weibull function. A simple linear relation between the Weibull function parameters and the specific surface of the system was found. CONCLUSIONS: Drug release from a matrix, as a result of a diffusion process assuming excluded volume interactions between the drug molecules, can be described using a Weibull function. This model, although approximate and semiempirical, has the benefit of providing a simple physical connection between the model parameters and the system geometry, which was something missing from other semiempirical models.

Computer Simulation↗
PubMed2004

Cell membrane fluidity changes and membrane undulations observed using a laser scattering technique.

Local transversal micromotions of cell membranes have been reported. These may provide the physical basis for changes in membrane fluidity. In this study, tissue scattering properties are used to measure the magnitude of transversal micromotions under varying stimuli. Laser light is directed at the cell surface at a low incident angle of 12 degrees so that reflected or refracted light does not enter the microscope objective. Scattered light showed strong low-frequency intensity fluctuations with random-walk behavior. Fluctuations were quantified by the median coefficient of variation over the entire observed cell area. Incubation of the cells with protein crosslinkers (paraformaldehyde) and metabolic suppressors (sodium azide) suppressed these fluctuations by 62 and 44%, respectively. The application of hypoosmotic media caused an increase of fluctuation magnitude by 23% (p < 0.005). Agents that increase membrane fluidity (2% ethanol and xenon) increased fluctuation magnitude by 15 and 31%, respectively (p < 0.05). Cessation of the ethanol and xenon exposure led to partial recovery of the fluctuation magnitude, which was nonsignificant for ethanol. This study shows a strong link between membrane fluidity and transversal membrane undulations and provides an important step in the understanding of the mechanosensing function of the cell membrane.

Cell Line, Tumor↗
PubMed2001

How do indirect measures of evaluation work? Evaluating the inference of prejudice in the Implicit Association Test.

There has been significant interest in indirect measures of attitudes like the Implicit Association Test (IAT), presumably because of the possibility of uncovering implicit prejudices. The authors derived a set of qualitative predictions for people's performance in the IAT on the basis of random walk models. These were supported in 3 experiments comparing clearly positive or negative categories to nonwords. They also provided evidence that participants shift their response criterion when doing the IAT. Because of these criterion shifts, a response pattern in the IAT can have multiple causes. Thus, it is not possible to infer a single cause (such as prejudice) from IAT results. A surprising additional result was that nonwords were treated as though they were evaluated more negatively than obviously negative items like insects, suggesting that low familiarity items may generate the pattern of data previously interpreted as evidence for implicit prejudice.

Attitude↗
PubMed1993

Strategic control of processing in word recognition.

Strategic control of word recognition in a lexical decision task was examined by manipulating the similarity of nonword foils to real words (nonword lexicality). Overall correct reaction times to words and the advantage of high- over low-frequency words were greater when nonword foils were more wordlike. This was true for both illegal (BTESE) versus legal (DEEST) nonword foils and legal nonword versus pseudohomophone (BEEST) foils. The same pattern of results was replicated in a 2nd experiment in which the word targets were always irregular (e.g., HAVE). A 3rd experiment demonstrated a large frequency blocking effect for low-frequency words, given pseudohomophone foils. The results are applied to pathway selection and random-walk frame-works. For both framework, canonical models are developed, which characterize qualitative predictions of broad classes of models within that framework. We argue for a pluralistic approach to theory development that moves from lower to higher order isomorphisms between data and theory.

Adult↗
PubMed2001

Executive control of visual attention in dual-task situations.

A theory of executive control is presented that proposes that executive processes control subordinate processes by manipulating their parameters, reconfiguring them to respond in accord with the current task set. It adopts C. Bundesen's (1990) theory of visual attention (TVA) and R. M. Nosofsky and T. J. Palmeri's (1997) exemplar-based random walk (EBRW) as the theory of subordinate processes. It assumes that a task set is a set of TVA and EBRW parameters sufficient to perform a task and that set switching involves changing those parameters. The theory solves 2 computational problems that emerge in dual-task situations: the binding problem and the serial order problem. It can perform dual tasks in series or in parallel but prefers the serial strategy because it is faster and it solves the binding problem naturally. The theory accounts for concurrence cost, set-switching cost, crosstalk between tasks, and the modulation of crosstalk by task set.

Attention↗
PubMed2006

Speeded old-new recognition of multidimensional perceptual stimuli: modeling performance at the individual-participant and individual-item levels.

Observers made speeded old-new recognition judgments of color stimuli embedded in a multidimensional similarity space. The paradigm used multiple lists but with the underlying similarity structures repeated across lists, to allow for quantitative modeling of the data at the individual-participant and individual-item levels. Correct-rejection response times (RTs) got systematically faster as the similarity of foils to the old study items decreased. There were also intricate patterns of speed-accuracy trade-offs that varied across individual items and participants. An exemplar-based random-walk model provided a good overall quantitative account of the recognition choice probabilities, mean correct RTs, and mean error RTs associated with the individual items on the basis of their positions in multidimensional similarity space. However, the model failed to predict the very long RTs associated with correct rejections of a prototype foil.

Adult↗
PubMedDate not supplied

Persistent, directional motility of cells and cytoplasmic fragments in the absence of microtubules.

Directional cell locomotion is displayed by many cell types both in vivo and in vitro. In many instances, persistency and directionality are imposed by external stimuli such as chemical attractants or substrate properties. Some cell types, such as fibroblasts or leukocytes, are capable of migrating in the absence of known stimuli in a pattern known as persistent random walk, where the direction of movement is maintained for at least one cell diameter before the cell performs a sudden directional change. In many examples of persistent motility, microtubules are believed to have a key role as elements that stabilize or even determine a cell's direction of movement. If disassembled, persistency is reduced or impaired. Despite some reports to the contrary, these and other observations have led to the widely accepted view that microtubules may be the overall organizers of cell geometry, polarity and motile activity. Here we report that rapid, directional locomotion of fish epidermal keratocytes is independent of the presence of microtubules. Moreover, small cytoplasmic fragments derived from the anterior lamella of these cells are capable of locomoting in a pattern indistinguishable from that of intact cells. Since these fragments contain no nucleus, microtubules or centrioles, the persistency-determining component must be sought in some other component(s) of the cytoplasm, possibly the motile machinery of the lamella itself.

Animals↗
PubMed2001

Reproductive pair correlations and the clustering of organisms.

Clustering of organisms can be a consequence of social behaviour, or of the response of individuals to chemical and physical cues. Environmental variability can also cause clustering: for example, marine turbulence transports plankton and produces chlorophyll concentration patterns in the upper ocean. Even in a homogeneous environment, nonlinear interactions between species can result in spontaneous pattern formation. Here we show that a population of independent, random-walking organisms ('brownian bugs'), reproducing by binary division and dying at constant rates, spontaneously aggregates. Using an individual-based model, we show that clusters form out of spatially homogeneous initial conditions without environmental variability, predator-prey interactions, kinesis or taxis. The clustering mechanism is reproductively driven-birth must always be adjacent to a living organism. This clustering can overwhelm diffusion and create non-poissonian correlations between pairs (parent and offspring) or organisms, leading to the emergence of patterns.

Models, Biological↗
PubMed2001

Diffusion of point defects in two-dimensional colloidal crystals.

Uniform colloidal microspheres dispersed in a solvent will, under appropriate conditions, self-assemble into ordered crystalline structures. Using these colloidal crystals as a model system, a great variety of problems of interest to materials science, physical chemistry, and condensed-matter physics have been investigated during the past two decades. Recently, it has been demonstrated that point defects can be created in two-dimensional colloidal crystals by manipulating individual particles with optical tweezers. Direct imaging of these defects verified that their stable configurations have lower symmetry than the underlying triangular lattice, as predicted by numerical simulations for a number of two-dimensional systems. It was also observed that point defects can dissociate into pairs of well-separated dislocations, a topological excitation especially important in two dimensions. Here we use a similar experimental system to study the dynamics of mono- and di-vacancies in two-dimensional colloidal crystals. We see evidence that the excitation of point defects into dislocation pairs enhances the diffusion of di-vacancies. Moreover, the hopping of the defects does not follow a pure random walk, but exhibits surprising memory effects. We expect the results presented in this work to be relevant for explaining the dynamics of other two-dimensional systems.

Journal Article↗
PubMed2005

Escherichia coli swim on the right-hand side.

The motion of peritrichously flagellated bacteria close to surfaces is relevant to understanding the early stages of biofilm formation and of pathogenic infection. This motion differs from the random-walk trajectories of cells in free solution. Individual Escherichia coli cells swim in clockwise, circular trajectories near planar glass surfaces. On a semi-solid agar substrate, cells differentiate into an elongated, hyperflagellated phenotype and migrate cooperatively over the surface, a phenomenon called swarming. We have developed a technique for observing isolated E. coli swarmer cells moving on an agar substrate and confined in shallow, oxidized poly(dimethylsiloxane) (PDMS) microchannels. Here we show that cells in these microchannels preferentially 'drive on the right', swimming preferentially along the right wall of the microchannel (viewed from behind the moving cell, with the agar on the bottom). We propose that when cells are confined between two interfaces--one an agar gel and the second PDMS--they swim closer to the agar surface than to the PDMS surface (and for much longer periods of time), leading to the preferential movement on the right of the microchannel. Thus, the choice of materials guides the motion of cells in microchannels.

Agar↗
PubMed2005

Chaos and threshold for irreversibility in sheared suspensions.

Systems governed by time reversible equations of motion often give rise to irreversible behaviour. The transition from reversible to irreversible behaviour is fundamental to statistical physics, but has not been observed experimentally in many-body systems. The flow of a newtonian fluid at low Reynolds number can be reversible: for example, if the fluid between concentric cylinders is sheared by boundary motion that is subsequently reversed, then all fluid elements return to their starting positions. Similarly, slowly sheared suspensions of solid particles, which occur widely in nature and science, are governed by time reversible equations of motion. Here we report an experiment showing precisely how time reversibility fails for slowly sheared suspensions. We find that there is a concentration dependent threshold for the deformation or strain beyond which particles do not return to their starting configurations after one or more cycles. Instead, their displacements follow the statistics of an anisotropic random walk. By comparing the experimental results with numerical simulations, we demonstrate that the threshold strain is associated with a pronounced growth in the Lyapunov exponent (a measure of the strength of chaotic particle interactions). The comparison illuminates the connections between chaos, reversibility and predictability.

Journal Article↗
PubMed2006

The depolymerizing kinesin MCAK uses lattice diffusion to rapidly target microtubule ends.

The microtubule cytoskeleton is a dynamic structure in which the lengths of the microtubules are tightly regulated. One regulatory mechanism is the depolymerization of microtubules by motor proteins in the kinesin-13 family. These proteins are crucial for the control of microtubule length in cell division, neuronal development and interphase microtubule dynamics. The mechanism by which kinesin-13 proteins depolymerize microtubules is poorly understood. A central question is how these proteins target to microtubule ends at rates exceeding those of standard enzyme-substrate kinetics. To address this question we developed a single-molecule microscopy assay for MCAK, the founding member of the kinesin-13 family. Here we show that MCAK moves along the microtubule lattice in a one-dimensional (1D) random walk. MCAK-microtubule interactions were transient: the average MCAK molecule diffused for 0.83 s with a diffusion coefficient of 0.38 microm2 s(-1). Although the catalytic depolymerization by MCAK requires the hydrolysis of ATP, we found that the diffusion did not. The transient transition from three-dimensional diffusion to 1D diffusion corresponds to a "reduction in dimensionality" that has been proposed as the search strategy by which DNA enzymes find specific binding sites. We show that MCAK uses this strategy to target to both microtubule ends more rapidly than direct binding from solution.

Adenosine Triphosphate↗
PubMed2001

Control systems with stochastic feedback.

In this paper we use the analogy of Parrondo's games to design a second order switched mode circuit which is unstable in either mode but is stable when switched. We do not require any sophisticated control law. The circuit is stable, even if it is switched at random. We use a stochastic form of Lyapunov's second method to prove that the randomly switched system is stable with probability of one. Simulations show that the solution to the randomly switched system is very similar to the analytic solution for the time-averaged system. This is consistent with the standard techniques for switched state-space systems with periodic switching. We perform state-space simulations of our system, with a randomized discrete-time switching policy. We also examine the case where the control variable, the loop gain, is a continuous Gaussian random variable. This gives rise to a matrix stochastic differential equation (SDE). We know that, for a one-dimensional SDE, the difference between solution for the time averaged system and any given sample path for the SDE will be an appropriately scaled and conditioned version of Brownian motion. The simulations show that this is approximately true for the matrix SDE. We examine some numerical solutions to the matrix SDE in the time and frequency domains, for the case where the noise power is very small. We also perform some simulations, without analysis, for the same system with large amounts of noise. In this case, the solution is significantly shifted away from the solution for the time-averaged system. The Brownian motion terms dominate all other aspects of the solution. This gives rise to very erratic and "bursty" behavior. The stored energy in the system takes the form a logarithmic random walk. The simulations of our curious circuit suggest that it is possible to implement a control algorithm that actively uses noise, although too much noise eventually makes the system unusable. (c) 2001 American Institute of Physics.

Journal Article↗