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PubMed2006

Dynamics of semiflexible polymers in a flow field.

We present a method to investigate the dynamics of a single semiflexible polymer, subject to anisotropic friction in a viscous fluid. In contrast to previous approaches, we do not rely on a discrete bead-rod model, but introduce a suitable normal mode decomposition of a continuous space curve. By means of a perturbation expansion for stiff filaments, we derive a closed set of coupled Langevin equations in mode space for the nonlinear dynamics in two dimensions, taking into account exactly the local constraint of inextensibility. The stochastic differential equations obtained this way are solved numerically, with parameters adjusted to describe the motion of actin filaments. As an example, we show results for the tumbling motion in shear flow.

Biopolymers↗
PubMed2003

Influence of mutational and sampling factors on the estimation of demographic parameters in a "continuous" population under isolation by distance.

In numerous species, individual dispersal is restricted in space so that "continuous" populations evolve under isolation by distance. A method based on individual genotypes assuming a lattice population model was recently developed to estimate the product Dsigma2, where D is the population density and sigma2 is the average squared parent-offspring distance. We evaluated the influence on this method of both mutation rate and mutation model, with a particular reference to microsatellite markers, as well as that of the spatial scale of sampling. Moreover, we developed and tested a nonparametric bootstrap procedure allowing the construction of confidence intervals for the estimation of Dsigma2. These two objectives prompted us to develop a computer simulation algorithm based on the coalescent theory giving individual genotypes for a continuous population under isolation by distance. Our results show that the characteristics of mutational processes at microsatellite loci, namely the allele size homoplasy generated by stepwise mutations, constraints on allele size, and change of slippage rate with repeat number, have little influence on the estimation of Dsigma2. In contrast, a high genetic diversity (approximately 0.7-0.8), as is commonly observed for microsatellite markers, substantially increases the precision of the estimation. However, very high levels of genetic diversity (>0.85) were found to bias the estimation. We also show that statistics taking into account allele size differences give unreliable estimations (i.e., high variance of Dsigma2 estimation) even under a strict stepwise mutation model. Finally, although we show that this method is reasonably robust with respect to the sampling scale, sampling individuals at a local geographical scale gives more precise estimations of Dsigma2.

Animals↗
PubMedDate not supplied

[Effect of rotation and vibration on orientation in man in relation to the gravitational vertical].

The man's ability to get oriented in relation to the gravitational vector was investigated. The test subjects were exposed either to rotation in 1 m arm centrifuge or tilting in a chair. They were simultaneously exposed to total-body vertical vibration of 20 Hz. As the exposure continued, the ratio of the perceived vertical (in the absence of visual keys) and the apparent body position changed significantly. It is concluded that the tests used to evaluate the pilot ability for spatial orientation should include evaluations of the subjective vertical and body position relative to the gravitational vector. The tests should be performed during exposures to simulated dynamic flight factors.

Aerospace Medicine↗
PubMed2005

Discovery of gradient pattern in dominant frequency maps during fibrillation: implication of rotor drift and epicardial conduction velocity changes.

Dominant frequency (DF) maps for mapping epicardial activations of ventricular fibrillation (VF) have been studied mainly using fast Fourier transform (FFT). Small and discrete DF domains exhibited in these DF maps have undermined the hypothesis of mother rotor for VF maintenance. We applied continuous Fourier transform (CFT) to generate high-precision DF maps and studied characteristics of these high-precision DF maps. Optical epicardial activations were recorded in isolated rabbit hearts (n=10). Continuous Fourier transform of 1-second segments was performed in VF (n=188) and ventricular tachycardia (n=189) at 0.1 Hz precisions. Banded gradient patterns of gradual change in DF values were observed in 136 of 188 VF segments, but not in ventricular tachycardia. These gradients were not observed when FFT was used. Gradients were observed along the conduction path of reentrant-like waves with decreasing DF values along the path. Spectra in the gradients did not exhibit bimodal spectra as is usually observed in traditional DF domain boundaries. Time-space plots revealed clear association between gradient pattern and epicardial conduction velocity changes. Prior simulation studies predicted a gradient in activation rate during rotor drift. This gradient pattern has been observed for the first time experimentally by only using CFT, but not FFT. High-precision DF videos indicated the existence of gradient movement from one spatial location to another, smoothly instead of randomly disappearing from one location and appearing in another. The discovery of associated pseudoconduction velocity changes, and gradient patterns might suggest that dominant rotor (mother rotor) drifting plays a maintenance role only detectable by CFT and not FFT.

Animals↗
PubMed2000

Experimental and computational flow evaluation of coronary stents.

Local flow alterations created by a metallic stent in a simulated coronary artery were studied to compare the hemodynamic effects of two different stent geometries. Dye injection flow visualization and computational fluid dynamics were used. Resting and exercise conditions were studied. Flow visualization using the dye injection method provided a qualitative picture of stent hemodynamics while the computational approach provided detailed quantitative information on the flow next to the vessel wall near the intersections of stent wires. Dye injection visualization revealed that more dye became entrapped between the wires where the wire spacing was smallest. The dye washout times were shorter under exercise conditions for both wire spacings tested. The computational results showed that stagnation zones were continuous from one wire to the next when the wire spacing was small. Results from greater wire spacing (more than six wire diameters) showed that the stagnation zones were separate for at least part of the cardiac cycle. The sizes of the stagnation zones were larger under exercise conditions, and the largest stagnation zones were observed distal to the stent. These studies demonstrate that stent geometry has a significant effect on local hemodynamics. The observation that fluid stagnation is continuous in stents with wire spacings of less than six wire diameters may provide a criterion for future stent design.

Biomechanical Phenomena↗
PubMed1998

Spatial changes in the transmembrane potential during extracellular electric stimulation.

The purpose of this study was to determine the spatial changes in the transmembrane potential caused by extracellular electric field stimulation. The transmembrane potential was recorded in 10 guinea pig papillary muscles in a tissue bath using a double-barrel microelectrode. After 20 S1 stimuli, a 10-ms square wave S2 shock field with a 30-ms S1-S2 coupling interval was given via patch shock electrodes 1 cm on either side of the tissue during the action potential plateau. Two shock strengths (2.1+/-0.2 and 6.5+/-0.6 V/cm) were tested with both shock polarities. The recording site was moved across the tissue along fibers with either 200 micrometer (macroscopic group [n=5], 12 consecutive recording sites over a 2. 2-mm tissue length in each muscle) or 20 micrometer (microscopic group [n=5], 21 consecutive recording sites over a 0.4-mm tissue length in each muscle) between adjacent recording sites. In the macroscopic group, the portion of the tissue toward the anode was hyperpolarized, whereas the portion toward the cathode was depolarized, with 1 zero-potential crossing from hyperpolarization to depolarization present near the center of the tissue. In the microscopic group, only 1 zero-potential crossing was observed in the center region of the tissue, whereas, away from the center, only hyperpolarization was observed toward the anode and depolarization toward the cathode. Although these results are consistent with predictions from field stimulation of continuous representations of myocardial structure, ie, the bidomain and cable equation models, they are not consistent with the prediction of depolarization-hyperpolarization oscillation from representations based on cellular-level resistive discontinuities associated with gap junctions, ie, the sawtooth model.

Animals↗
PubMedDate not supplied

Postoperative lumbar epiduro-arachnoiditis. Diagnostic and therapeutic aspects.

Thirty-eight patients with the diagnosis of postoperative epiduro-arachnoiditis are reported upon. All had had previous surgery for disc herniation, and the diagnosis of epiduro-arachnoiditis was confirmed at repeat surgery. Massive epidural scarring with no coexistent pathologic condition was found in every patient, and adhesive arachnoiditis was noted in three. The common clinical presentation consisted of low-back pain and sciatica, and radicular pain was usually a continuation or a recurrence of the preoperative sciatic pain. Neurologic deficits were mild, and no patients with the classic picture of adhesive arachnoiditis were found. Myelographic patterns did not disclose any correlation with the clinical symptoms. Five myelograms were normal, while six others simulated a recurrent disc herniation. The results of scar excision were good in 13 patients, fair in eight, and a failure in 17.

Adult↗
PubMed2005

Providing visualisation support for the analysis of anatomy ontology data.

BACKGROUND: Improvements in technology have been accompanied by the generation of large amounts of complex data. This same technology must be harnessed effectively if the knowledge stored within the data is to be retrieved. Storing data in ontologies aids its management; ontologies serve as controlled vocabularies that promote data exchange and re-use, improving analysis. The Edinburgh Mouse Atlas Project stores the developmental stages of the mouse embryo in anatomy ontologies. This project is looking at the use of visual data overviews for intuitive analysis of the ontology data. RESULTS: A prototype has been developed that visualises the ontologies using directed acyclic graphs in two dimensions, with the ability to study detail in regions of interest in isolation or within the context of the overview. This is followed by the development of a technique that layers individual anatomy ontologies in three-dimensional space, so that relationships across multiple data sets may be mapped using physical links drawn along the third axis. CONCLUSION: Usability evaluations of the applications confirmed advantages in visual analysis of complex data. This project will look next at data input from multiple sources, and continue to develop the techniques presented to provide intuitive identification of relationships that span multiple ontologies.

Anatomy↗
PubMed2005

Turing pattern formation in fractional activator-inhibitor systems.

Activator-inhibitor systems of reaction-diffusion equations have been used to describe pattern formation in numerous applications in biology, chemistry, and physics. The rate of diffusion in these applications is manifest in the single parameter of the diffusion constant, and stationary Turing patterns occur above a critical value of d representing the ratio of the diffusion constants of the inhibitor to the activator. Here we consider activator-inhibitor systems in which the diffusion is anomalous subdiffusion; the diffusion rates are manifest in both a diffusion constant and a diffusion exponent. A consideration of this problem in terms of continuous-time random walks with sources and sinks leads to a reaction-diffusion system with fractional order temporal derivatives operating on the spatial Laplacian. We have carried out an algebraic stability analysis of the homogeneous steady-state solution in fractional activator-inhibitor systems, with Gierer-Meinhardt reaction kinetics and with Brusselator reaction kinetics. For each class of reaction kinetics we identify a Turing instability bifurcation curve in the two-dimensional diffusion parameter space. The critical value of d , for Turing instabilities, decreases monotonically with the anomalous diffusion exponent between unity (standard diffusion) and zero (extreme subdiffusion). We have also carried out numerical simulations of the governing fractional activator-inhibitor equations and we show that the Turing instability precipitates the formation of complex spatiotemporal patterns. If the diffusion of the activator and inhibitor have the same anomalous scaling properties, then the surface profiles of these patterns for values of d slightly above the critical value varies from smooth stationary patterns to increasingly rough and nonstationary patterns as the anomalous diffusion exponent varies from unity towards zero. If the diffusion of the activator is anomalous subdiffusion but the diffusion of the inhibitor is standard diffusion, we find stable stationary Turing patterns for values of d well below the threshold values for pattern formation in standard activator-inhibitor systems.

Journal Article↗
PubMed2006

Payoff-monotonic game dynamics and the maximum clique problem.

Evolutionary game-theoretic models and, in particular, the so-called replicator equations have recently proven to be remarkably effective at approximately solving the maximum clique and related problems. The approach is centered around a classic result from graph theory that formulates the maximum clique problem as a standard (continuous) quadratic program and exploits the dynamical properties of these models, which, under a certain symmetry assumption, possess a Lyapunov function. In this letter, we generalize previous work along these lines in several respects. We introduce a wide family of game-dynamic equations known as payoff-monotonic dynamics, of which replicator dynamics are a special instance, and show that they enjoy precisely the same dynamical properties as standard replicator equations. These properties make any member of this family a potential heuristic for solving standard quadratic programs and, in particular, the maximum clique problem. Extensive simulations, performed on random as well as DIMACS benchmark graphs, show that this class contains dynamics that are considerably faster than and at least as accurate as replicator equations. One problem associated with these models, however, relates to their inability to escape from poor local solutions. To overcome this drawback, we focus on a particular subclass of payoff-monotonic dynamics used to model the evolution of behavior via imitation processes and study the stability of their equilibria when a regularization parameter is allowed to take on negative values. A detailed analysis of these properties suggests a whole class of annealed imitation heuristics for the maximum clique problem, which are based on the idea of varying the parameter during the imitation optimization process in a principled way, so as to avoid unwanted inefficient solutions. Experiments show that the proposed annealing procedure does help to avoid poor local optima by initially driving the dynamics toward promising regions in state space. Furthermore, the models outperform state-of-the-art neural network algorithms for maximum clique, such as mean field annealing, and compare well with powerful continuous-based heuristics.

Journal Article↗
PubMed2026

Quantifying the peripheral surface information entropy from conformational ensembles of globular protein-peptide complexes.

Predicting favorable protein-peptide binding events remains a central challenge in biophysics, with continued uncertainty surrounding how nonlocal effects shape the global energy landscape. Here, we introduce peripheral surface information entropy, SΨ, a quantitative measure of the statistical variability in apolar and charged non-interacting surface (NIS) proportions across conformational ensembles. Within the Gibbs free-energy relation ΔG = ΔH - TΔS, SΨ is proposed as a computationally tractable entropic proxy rather than a direct thermodynamic observable or stand-alone estimator of binding affinity. Using energy-directed molecular docking via HADDOCK3 and explicit-solvent molecular dynamics simulations, it is demonstrated that favorable binding partners exhibit emergent, low-entropy N-states (discrete macrostates in NIS state space) indicative of preferential apolar/charged surface configurations. Across dozens of peptides and multiple receptor systems (WW, PDZ, and MDM2 domains), dominant N-states persisted under varied docking parameters and initial conditions. A meta-ensemble of 657 complexes from 36 experiments over 15 years confirmed the presence of dominant NIS modes independent of in silico methodology, suggesting an evolutionary selection pressure toward specific NIS fingerprints. These findings establish SΨ as a thermoinformatic descriptor that encodes favorable binding constraints into unique statistical signatures of the NIS.

Entropy↗
PubMed1997

The intrinsic electrophysiological characteristics of fly lobula plate tangential cells: II. Active membrane properties.

The voltage-gated currents in the fly lobula plate tangential cells were examined using the switched electrode voltage clamp technique. In CH cells, two currents were identified (Figs. 1, 2): a slow calcium inward current and a delayed rectifying, noninactivating potassium outward current. HS and VS cells appear to possess similar currents to CH cells, but in addition, exhibit a fast-activating sodium inward current and a sodium-activated potassium outward current (Figs. 3, 4). While the delayed rectifying potassium current in all three cell classes is responsible for the observed outward rectification described previously (Borst and Haag, 1996), the sodium inward current produced the fast and irregular spikelike depolarizations found in HS and VS cells but not in CH cells: When the sodium current is blocked by either. TTX or intracellular QX314, no more action potentials can be elicited in HS cells under current-clamp conditions (Fig. 5). As is demonstrated in HS cells, space clamp conditions are sufficient to suppress synaptically induced action potentials (Fig. 6). The currents described above were incorporated with the appropriate characteristics into compartmental models of the cells (Fig. 7, 8). The anatomical and electrically passive membrane parameters of these cells were determined in a preceding paper (Borst and Haag, 1996). After fitting the current parameters to the voltage-clamp data (Fig. 9), the model cells qualitatively mimicked the fly tangential cells under current clamp conditions in response to current injection (Fig. 10). The simulations demonstrated that the electrical compactness seen in the HS and VS cells, either in passive models or in active models during continuous hyperpolarization, decreased significantly in the active models during continuous depolarization (Fig. 11). Active HS models reproduce the frequency-dependent amplification of current injected into their axon (Fig. 12).

Animals↗
PubMed2001

Constrained global optimization for estimating molecular structure from atomic distances.

Finding optimal three-dimensional molecular configurations based on a limited amount of experimental and/or theoretical data requires efficient nonlinear optimization algorithms. Optimization methods must be able to find atomic configurations that are close to the absolute, or global, minimum error and also satisfy known physical constraints such as minimum separation distances between atoms (based on van der Waals interactions). The most difficult obstacles in these types of problems are that 1) using a limited amount of input data leads to many possible local optima and 2) introducing physical constraints, such as minimum separation distances, helps to limit the search space but often makes convergence to a global minimum more difficult. We introduce a constrained global optimization algorithm that is robust and efficient in yielding near-optimal three-dimensional configurations that are guaranteed to satisfy known separation constraints. The algorithm uses an atom-based approach that reduces the dimensionality and allows for tractable enforcement of constraints while maintaining good global convergence properties. We evaluate the new optimization algorithm using synthetic data from the yeast phenylalanine tRNA and several proteins, all with known crystal structure taken from the Protein Data Bank. We compare the results to commonly applied optimization methods, such as distance geometry, simulated annealing, continuation, and smoothing. We show that compared to other optimization approaches, our algorithm is able combine sparse input data with physical constraints in an efficient manner to yield structures with lower root mean squared deviation.

Algorithms↗
PubMed1988

The effects of feedback lighting on the circadian drinking rhythm in the diurnal new world primate Saimiri sciureus.

Feedback lighting provides illumination primarily during the subjective night (i.e., the photosensitive portion of the circadian cycle) in response to a given behavior. This technique has previously been used to test the nonparametric model of entrainment in nocturnal rodents. In three species (Rattus norvegicus, Mesocricetus auratus, and Mus musculus), the free-running period of the locomotor activity rhythm was similar whether the animals were exposed to continuous light or discrete light pulses occurring essentially only during the subjective night (i.e., feedback lighting). In the current experiments, feedback lighting was presented to squirrel monkeys so that light fell predominantly during the subjective night. Feedback lighting was linked to the drinking behavior in this diurnal primate so that when the animal drank, the lights went out. Despite the seemingly adverse predicament, the monkeys maintained regular circadian drinking rhythms. Furthermore, just as the period of the free-running activity rhythms of nocturnal rodents exposed to continuous light or feedback lighting were similar, the period of the drinking rhythms of the squirrel monkeys in continuous light and feedback lighting were comparable (25.6 +/- 0.1 and 25.9 +/- 0.1 hours, respectively), despite a substantial decrease in the total amount of light exposure associated with feedback lighting. The free-running period of monkeys exposed to continuous dark (24.5 +/- 0.1 hours) was significantly shorter than either of the two lighting conditions (P < 0.001). The results presented for the drinking rhythm were confirmed by examination of the temperature and activity rhythms. Therefore, discrete light pulses given predominately during the subjective night are capable of simulating the effects of continuous light on the free-running period of the circadian rhythms of a diurnal primate. The response of squirrel monkeys to feedback lighting thus lends further support for the model and suggests that the major entrainment mechanisms are similar in nocturnal rodents and diurnal primates.

Animals↗
PubMed1971

The permeation of several materials into the fluids of the rabbit's brain.

1. (24)Na, (36)Cl and (35)S thiourea were infused I.V. in rabbits according to schedules designed to yield approximately level activity in plasma for periods up to 5 hr. Cerebrospinal fluid was sampled before ending the experiment by decapitation and the radioactivities in cerebrospinal fluid and in homogenized brain were compared in each case to a time weighted mean value for plasma.2. The results are considered in terms of a simplified model which specifically acknowledges the continuity of the extracellular and cerebrospinal fluids and thus the coupling between processes which occur at the interfaces bordering those fluids.3. From the rate constants for exchange across the blood-brain interface that were necessary for simulation of the observed behaviours, permeability coefficients for that interface were estimated for the materials studied and, from experiments of others, for (42)K.

Animals↗
PubMed1990

Simulation of motion on the skin. IV. Responses of Pacinian corpuscle afferents innervating the primate hand to stripe patterns on the OPTACON.

1. To measure spatial acuity of Pacinian corpuscle (PC) afferents in the median and ulnar nerves of macaque monkeys, we displayed horizontal bar patterns spaced 1-13 mm apart on a computer-controlled OPTACON stimulator contacting the hand. Two-point resolution was measured by simultaneously pulsing pairs of rows at rates of 100, 50, and 25 Hz; each pair was shifted in tandem across the skin in 1.2-mm steps to simulate tangential motion at speeds of 30-120 mm/s. Single-fiber responses are reported from eight physiologically identified PC afferents innervating the fingers and palm in anesthetized monkeys. 2. Pacinian afferents differ in their sensitivity to stripe patterns moved across the hand. Bursting PCs fire bursts of two or three spikes/pulse when one of the bars is close to the field center and one spike/pulse when adjacent bars straddle the center. These bursts result in double-peaked response profiles at stripe spacings greater than or equal to 2.4 mm. The passage of individual stripes over the field center is therefore represented by bursts of impulses superimposed on a continuous spike train. Unfortunately, many of these fibers also demonstrate fluctuations in firing that appear unrelated to the stripe pattern and therefore obscure its clear representation. 3. The remainder of the PC population displays uniform-sensitivity responses that resemble those previously reported for rapidly adapting (RA) afferents. They fire one spike/pulse as long as at least one of the bars is contained within the field. They merge individual stripes spaced less than one field diameter apart and show a pause in firing at wider spacing. Spatial resolution of gaps in the stripe pattern is therefore determined by receptive-field diameters, which extend up to 9.6 mm when tested with the OPTACON. 4. PCs display poorer spatial resolution than RAs, because of their larger receptive fields and less regular firing patterns. Only two of eight PCs tested demonstrated a pause in activity representing the gap between bars spaced 4.8 mm apart, whereas 11 of 14 RAs ceased firing briefly between stripes. Resolution of the individual stripes by all of the PCs tested was observed only at bar spacings of 1 cm (8 rows) or more. Spatial resolution of stripes is further impeded by the tendency of PC afferents to summate inputs from stripes spaced less than 2.4 mm apart; this results in response profiles with a single, large-amplitude broad peak.(ABSTRACT TRUNCATED AT 400 WORDS)

Action Potentials↗
PubMed2004

Maintaining spatial body alignment on a rotating platform by means of active counter-circling: role of vestibular and podokinesthetic afferents.

We investigated the behaviour of vision-deprived human subjects who try to maintain their horizontal alignment in space on a rotating platform by stepping about their own axis in counter-direction ('podomotor counter-rotation'), and we ask which of two alternative hypotheses best explains this behaviour. (1) The feedback hypothesis assumes that the podomotor counter-rotation is controlled by negative feedback of vestibular signals from the horizontal canals. (2) The reconstruction hypothesis holds that the vestibular cue first is combined with leg proprioceptive afferents signalling the individual's rotation on the platform ('podokinesthetic cue') in a way that reconstructs the platform's motion in space for internal representation; a negative (direction-inverted) copy of this representation then would drive the counter-rotation. Subjects were exposed to three different velocity profiles of platform rotation: VC, constant velocity rotation with sudden onset and offset; VS, sinusoidal rotation; VN, pseudorandom noise sequences. The subjects' response (i.show $132#e., their active self-rotation on the platform) to the onset and offset of VC rotations was reminiscent of a first-order lead system. Specifically, after rotation onset subjects immediately began to step on the platform in opposite direction; initially, the velocity of this response matched that of platform rotation, leading to a fairly good stabilisation of subjects' alignment in space. However, this response declined exponentially; consequently, subjects began to increasingly rotate in space along with the platform, ultimately stepping in place on the platform. After rotation offset, subjects immediately began to step around on the now stationary platform so as to continue their previous rotation in space; this response again declined exponentially until subjects became gradually stable again with respect to space. Within subjects, the time constant (tau) of these responses was similar for onset and offset. Across subjects it exhibited a conspicuous variability, ranging from 7 s to virtually infinity. The responses to VS and VN rotations were closely correlated to what could be predicted for each individual from his tau during VC on the assumption of a first-order lead system. We conclude that the mechanism stabilising body orientation basically is linear (no prediction with sinusoidal rotation, no extrapolation of constant velocity rotation). A comparison of the experimental results with simulations of the feedback hypothesis and of the reconstruction hypothesis suggests that the reconstruction hypothesis is a more likely description of the underlying processing of the vestibular and podokinesthetic cues.

Adult↗
PubMed2002

Mode-I fracture in a nonlinear lattice with viscoelastic forces.

We study mode-I fracture in a viscoelastic lattice model with a nonlinear force law, with a focus on the velocity and linear stability of the steady-state propagating solution. This study is a continuation both of the study of the piecewise-linear model in mode I, and the study of more general nonlinear force laws in mode-III fracture. At small driving, there is a strong dependency of the velocity curve on the dissipation and a strong sensitivity to the smoothness of the force law at large dissipation. At large driving we calculate, via a linear stability analysis, the critical velocity for the onset of instability as a function of the smoothness, the dissipation and the ratio of lattice spacing to critical extension. This critical velocity is seen to be very sensitive to these parameters. We confirm our calculations via direct numerical simulations of the initial value problem.

Journal Article↗