Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “bistability”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,081 records · Page 60Linked to original sources
PubMed2001

Oscillatory dynamics protect enzymes and possibly cells against toxic substances.

We have used the oscillating peroxidase-oxidase (PO) reaction as a model system to study how oscillatory dynamics may affect the influence of toxic reaction intermediates on enzyme stability. In the peroxidase-oxidase reaction reactive intermediates, such as hydrogen peroxide, superoxide, and hydroxyl radical are formed. Such intermediates inactivate many cellular macromolecules such as proteins and nucleic acids. These reaction intermediates also react with peroxidase itself to form an inactive enzyme. The fact that the PO reaction shows bistability between an oscillatory and a steady state gives us a unique possibility to compare such inactivation when the system is in one of these two states. We show that inactivation of peroxidase is slower when the system is in an oscillatory state, and using numerical simulations we provide evidence that oscillatory dynamics lower the average concentration of the reactive intermediates.

Cells↗
PubMed2001

Excitability in chemical and biochemical pH-autocatalytic systems.

Using two different kinds of pH systems--the papain catalyzed hydrolysis of N-benzoyl-L-arginine ethyl ester in a membrane reactor and the bromate-sulfite-ferrocyanide (BSF) reaction in the CSTR--we study the relation among excitability, oscillations and bistability, and the ability of the system to respond to external periodic perturbations. Excitable properties of dynamical systems are examined in terms of a threshold set which is used to characterise dynamics in the reactor subject to external periodic stimuli. A precise definition and a method of calculating the threshold set are formulated. Two kinds of excitability distinguished by either direct or indirect initiation of the activatory process are found in both pH systems. Periodic pulsed perturbations of the BSF system display a nontrivial dependence of an excitation number on the forcing period. We examined this system also in oscillatory mode by looking at the phase shifts caused by single-pulse perturbations and constructing the phase transition curves (PTCs).

Algorithms↗
PubMed2004

A copper-complexed rotaxane in motion: pirouetting of the ring on the millisecond timescale.

A new bistable rotaxane, consisting of a 2,2'-bipyridine-containing thread and a ring incorporating both a bidentate chelate and a tridentate fragment, has been prepared; this complex undergoes an electrochemically driven pirouetting motion of the ring around the axis which takes place on the millisecond timescale, i.e. several orders of magnitude faster than the other copper-based machines previously described.

Journal Article↗
PubMed2006

Spiers Memorial Lecture. Molecular mechanics and molecular electronics.

We describe our research into building integrated molecular electronics circuitry for a diverse set of functions, and with a focus on the fundamental scientific issues that surround this project. In particular, we discuss experiments aimed at understanding the function of bistable rotaxane molecular electronic switches by correlating the switching kinetics and ground state thermodynamic properties of those switches in various environments, ranging from the solution phase to a Langmuir monolayer of the switching molecules sandwiched between two electrodes. We discuss various devices, low bit-density memory circuits, and ultra-high density memory circuits that utilize the electrochemical switching characteristics of these molecules in conjunction with novel patterning methods. We also discuss interconnect schemes that are capable of bridging the micrometre to submicrometre length scales of conventional patterning approaches to the near-molecular length scales of the ultra-dense memory circuits. Finally, we discuss some of the challenges associated with fabricated ultra-dense molecular electronic integrated circuits.

Computers, Molecular↗
PubMed2006

Photo-driven molecular devices.

In this critical review, we discuss switching of the light-powered bistable rotaxanes and catenanes and highlight the practical applications of some of these systems. Photoactive molecular and supramolecular machines are comprised of two parts-1) a switching element, based on noncovalent interactions within the recognition units, which is responsible for executing mechanical movement, and 2) a light-harvesting unit which utilizes light to control the competitive interactions between the recognition sites. We also survey another class of molecular devices, namely molecular rotary motors--i.e., those that behave like their macroscopic counterparts--in which photochemically and thermally induced mechanical movement relies on isomerizations of a pivotal C=C bond, leading to a rotation of the top propeller part with respect to the stationary bottom part of the helical shaped chiral molecule. (146 references.).

Journal Article↗
PubMed2006

Amplification of chirality in liquid crystals.

The amplification of molecular chirality by liquid crystalline systems is widely applied in investigations towards enantioselective solvent-solute interactions, chiral supramolecular assemblies, smart materials, and the development of liquid crystal displays. Here we present an overview of recent achievements in the development of new chiral dopant systems for the generation of cholesteric liquid crystalline phases. Based on a distinction between shape-persistent and bistable dopants, several dopant classes will be discussed.

Journal Article↗
PubMed1996

Prion diseases and the 'protein only' hypothesis: a theoretical dynamic study.

In the 'protein only' hypothesis, prion diseases are thought to result from the conformational change of a normal isoform of a prion protein (PrPC) to a protease-resistant, pathogenic form called PrPSc. This conversion rests on an autocatalytic process requiring the presence of pre-existing PrPSc. Theoretical kinetic analysis of the dynamic process, including the turnover of the normal prion protein, shows that the system exhibits bistability properties, indicating that the very slow accumulation of the abnormal form of the protein in the brain could in fact be the consequence and not the cause of the disorders. The cause would be a transition between two alternative steady states of the system. The presence of a small amount of the PrPSc protein in lymphocytes does not necessarily constitute any indication of a non-symptomatic but infectious pathogenic state. Moreover, infectious prion particles should not be seen as necessarily composed of the abnormal isoform of the protein, as usually stated. Particles containing only an excess of the normal form of the protein might also be pathogenic. Compounds that can act on the turnover rate of the normal PrPC protein could be a therapeutic strategy against prion diseases.

Animals↗
PubMed2001

Cell type proportioning in Dictyostelium slugs: lack of regulation within a 2.5-fold tolerance range.

The proportion of prestalk and prespore cells in Dictyostelium discoideum slugs is often cited as an example of "almost perfect" regulation. The pattern is similar over a very wide range of cell number; furthermore, removal of either of the cell types leads to compensatory transdifferentiation. Several studies of Dictyostelium fruiting bodies, however, have suggested that proportioning in Dictyostelium differs systematically from true constancy. We have confirmed this in the slug stage using a short-lived beta-galactosidase as a reporter of the prestalk specific ecmA gene expression: the prestalk proportion decreases from 24+/-5% in slugs of 10(3) cells to 10+/-3% when 10(5) cells are present. Regeneration experiments suggest that this difference is not due to a modulation of the proportioning set-point by size, as one might have expected; instead there appears to be a regulatory "tolerance zone" at all sizes. After amputation of the whole posterior region, transdifferentiation stops after the fraction of prestalk has been reduced from 100% to 28+/-20%, well above the initial value of 10+/-3%, while after anterior removal the transdifferentiation endpoint is about 10%. Most strikingly, we find no regulation at all after partial amputations of the prespore region. It seems that any prestalk proportion is stable between a approximately 10% lower threshold and a approximately 30% upper threshold. To explain this, we propose a regulation mechanism based on a negative feedback plus cell type bistability. In both intact and regenerating slugs we find that the slug morphology is regulated so that the length-to-width ratio of the anterior region is constant.

Amputation, Surgical↗
PubMed2003

Mechanism of protection of peroxidase activity by oscillatory dynamics.

The peroxidase-oxidase reaction is known to involve reactive oxygen species as intermediates. These intermediates inactivate many types of biomolecules, including peroxidase itself. Previously, we have shown that oscillatory dynamics in the peroxidase-oxidase reaction seem to protect the enzyme from inactivation. It was suggested that this is due to a lower average concentration of reactive oxygen species in the oscillatory state compared to the steady state. Here, we studied the peroxidase-oxidase reaction with either 4-hydroxybenzoic acid or melatonin as cofactors. We show that the protective effect of oscillatory dynamics is present in both cases. We also found that the enzyme degradation depends on the concentration of the cofactor and on the pH of the reaction mixture. We simulated the oscillatory behaviour, including the oscillation/steady state bistability observed experimentally, using a detailed reaction scheme. The computational results confirm the hypothesis that protection is due to lower average concentrations of superoxide radical during oscillations. They also show that the shape of the oscillations changes with increasing cofactor concentration resulting in a further decrease in the average concentration of radicals. We therefore hypothesize that the protective effect of oscillatory dynamics is a general effect in this system.

Animals↗
PubMed2001

Computer modelling and experimental evidence for two steady states in the photosynthetic Calvin cycle.

We present observations of photosynthetic carbon dioxide assimilation, and leaf starch content from genetically modified tobacco (Nicotiana tabacum) plants in which the activity of the Calvin cycle enzyme, sedoheptulose-1,7-bisphosphatase, is reduced by an antisense construct. The measurements were made on leaves of varying ages and used to calculate the flux control coefficients of sedoheptulose-1,7-bisphosphatase over photosynthetic assimilation and starch synthesis. These calculations suggest that control coefficients for both are negative in young leaves, and positive in mature leaves. This behaviour is compared to control coefficients obtained from a detailed computer model of the Calvin cycle. The comparison demonstrates that the experimental observations are consistent with bistable behaviour exhibited by the model, and provides the first experimental evidence that such behaviour in the Calvin cycle occurs in vivo as well as in silico.

Carbon Dioxide↗
PubMed1998

Nociceptive integration in the rat spinal cord: role of non-linear membrane properties of deep dorsal horn neurons.

Deep dorsal horn neurons (DHNs) involved in nociception can relay long-lasting inputs and generate prolonged afterdischarges believed to enhance the transfer of nociceptive responses to the brain. We addressed the role of neuronal membrane properties in shaping these responses, by recording lamina V DHNs in a slice preparation of the rat cervical spinal cord. Of 256 neurons, 102 produced accelerating discharges in response to depolarizing current pulses, whereas the other neurons showed spike frequency adaptation. Two mechanisms mediated the firing acceleration: a slow inactivation of a K+ current expressed upon activation of the neuron from hyperpolarized holding potentials, and the expression of a regenerative plateau potential activating around resting membrane potential. The increase in firing frequency was much stronger when sustained by the plateau potential (71 DHNs, 28%). A few neurons produced adaptation and both types of acceleration, in different membrane potential domains, showing that the firing pattern of a deep DHN is not a rigid characteristic. Plateau potentials could be elicited by stimulation of nociceptive primary afferent fibres. The bistability associated with plateau potentials permitted afterdischarges. Because plateau potentials had slow activation kinetics and were voltage-dependent, the neurons had non-linear input-output relationships in both the amplitude and time domains. Nociceptive primary afferent stimulation elicited intense and prolonged responses in plateau-generating DHNs, while brief bursts of spikes were evoked otherwise. These results indicate that in a population of deep DHNs, intense firing and prolonged afterdischarges in response to nociceptive stimulation depend on non-linear intrinsic membrane properties.

4-Aminopyridine↗
PubMed2006

In silico evolution of functional modules in biochemical networks.

Understanding the large reaction networks found in biological systems is a daunting task. One approach is to divide a network into more manageable smaller modules, thus simplifying the problem. This is a common strategy used in engineering. However, the process of identifying biological modules is still in its infancy and very little is understood about the range and capabilities of motif structures found in biological modules. In order to delineate these modules, a library of functional motifs has been generated via in silico evolution techniques. On the basis of their functional forms, networks were evolved from four broad areas: oscillators, bistable switches, homeostatic systems and frequency filters. Some of these motifs were constructed from simple mass action kinetics, others were based on Michaelis-Menten kinetics as found in protein/protein networks and the remainder were based on Hill equations as found in gene/protein interaction networks. The purpose of the study is to explore the capabilities of different network architectures and the rich variety of functional forms that can be generated. Ultimately, the library may be used to delineate functional motifs in real biological networks.

Algorithms↗
PubMed2001

Designer gene networks: Towards fundamental cellular control.

The engineered control of cellular function through the design of synthetic genetic networks is becoming plausible. Here we show how a naturally occurring network can be used as a parts list for artificial network design, and how model formulation leads to computational and analytical approaches relevant to nonlinear dynamics and statistical physics. We first review the relevant work on synthetic gene networks, highlighting the important experimental findings with regard to genetic switches and oscillators. We then present the derivation of a deterministic model describing the temporal evolution of the concentration of protein in a single-gene network. Bistability in the steady-state protein concentration arises naturally as a consequence of autoregulatory feedback, and we focus on the hysteretic properties of the protein concentration as a function of the degradation rate. We then formulate the effect of an external noise source which interacts with the protein degradation rate. We demonstrate the utility of such a formulation by constructing a protein switch, whereby external noise pulses are used to switch the protein concentration between two values. Following the lead of earlier work, we show how the addition of a second network component can be used to construct a relaxation oscillator, whereby the system is driven around the hysteresis loop. We highlight the frequency dependence on the tunable parameter values, and discuss design plausibility. We emphasize how the model equations can be used to develop design criteria for robust oscillations, and illustrate this point with parameter plots illuminating the oscillatory regions for given parameter values. We then turn to the utilization of an intrinsic cellular process as a means of controlling the oscillations. We consider a network design which exhibits self-sustained oscillations, and discuss the driving of the oscillator in the context of synchronization. Then, as a second design, we consider a synthetic network with parameter values near, but outside, the oscillatory boundary. In this case, we show how resonance can lead to the induction of oscillations and amplification of a cellular signal. Finally, we construct a toggle switch from positive regulatory elements, and compare the switching properties for this network with those of a network constructed using negative regulation. Our results demonstrate the utility of model analysis in the construction of synthetic gene regulatory networks. (c) 2001 American Institute of Physics.

Journal Article↗
PubMed2001

Additive noise in noise-induced nonequilibrium transitions.

We study different nonlinear systems which possess noise-induced nonequlibrium transitions and shed light on the role of additive noise in these effects. We find that the influence of additive noise can be very nontrivial: it can induce first- and second-order phase transitions, can change properties of on-off intermittency, or stabilize oscillations. For the Swift-Hohenberg coupling, that is a paradigm in the study of pattern formation, we show that additive noise can cause the formation of ordered spatial patterns in distributed systems. We show also the effect of doubly stochastic resonance, which differs from stochastic resonance, because the influence of noise is twofold: multiplicative noise and coupling induce a bistability of a system, and additive noise changes a response of this noise-induced structure to the periodic driving. Despite the close similarity, we point out several important distinctions between conventional stochastic resonance and doubly stochastic resonance. Finally, we discuss open questions and possible experimental implementations. (c) 2001 American Institute of Physics.

Journal Article↗
PubMed2002

The effect of reactor geometry on frontal polymerization spin modes.

Using reactors of different sizes and geometries the dynamics of the frontal polymerization of 1,6-hexanediol diacrylate (HDDA) and pentaerythritol tetraacrylate (PETAC), with ammonium persulfate as the initiator were studied. For this system, the frontal polymerization exhibits complex behavior that depends on the ratio of the monomers. For a particular range of monomers concentration, the polymerization front becomes nonplanar, and spin modes appear. By varying the reactor diameter, we experimentally confirmed the expected shift of the system to a greater number of "hot spots" for larger diameters. For square test tubes a "zig-zag" mode was observed for the first time in frontal polymerization. We confirmed the viscosity-dependence of the spin mode instabilities. We also observed novel modes in cylinder-inside-cylinder reactors. Lastly, using a conical reactor with a continuously varying diameter, we observed what may be evidence for bistability depending on the direction of propagation. We discuss these finding in terms of the standard linear stability analysis for propagating fronts. (c) 2002 American Institute of Physics.

Journal Article↗
PubMed2002

Theory of electrochemical pattern formation.

The spatial coupling in electrochemical systems is mediated by ion migration under the influence of the electric field. Since field effects spread very rapidly, every point of an electrode can communicate with every other one practically instantaneously through migration coupling. Based on mathematical potential theory we present the derivation of a generally applicable reaction-migration equation, which describes the coupling via an integral over the whole electrode area. The corresponding coupling function depends only on the geometry of the electrode setup and has been computed for commonly used electrode shapes (such as ring, disk, ribbon or rectangle). The pattern formation observed in electrochemical systems in the bistable, excitable and oscillatory regime can be reproduced in computer simulations, and the types of patterns occurring under different geometries can be rationalized. (c) 2002 American Institute of Physics.

Journal Article↗
PubMed2002

Pattern formation on anisotropic and heterogeneous catalytic surfaces.

We review experimental and theoretical work addressing pattern formation on anisotropic and heterogeneous catalytic surfaces. These systems are typically modeled by reaction-diffusion equations reflecting the kinetics and transport of the involved chemical species. Here, we demonstrate the influence of anisotropy and heterogeneity in a simplified model, the FitzHugh-Nagumo equations. Anisotropy causes stratification of labyrinthine patterns and spiral defect chaos in bistable media. For heterogeneous media, we study the situation where the heterogeneity appears on a length scale shorter than the typical pattern length scale. Homogenization, i.e., computation of effective medium properties, is applied to an example and illustrated with simulations in one (fronts) and two dimensions (spirals). We conclude with a discussion of open questions and promising directions that comprise the coupling of the microscopic structure of the surface to the macroscopic concentration patterns and the fabrication of nanostructures with heterogeneous surfaces as templates. (c) 2002 American Institute of Physics.

Journal Article↗
PubMed2003

Frequency and phase synchronization in stochastic systems.

The phenomenon of frequency and phase synchronization in stochastic systems requires a revision of concepts originally phrased in the context of purely deterministic systems. Various definitions of an instantaneous phase are presented and compared with each other with special attention paid to their robustness with respect to noise. We review the results of an analytic approach describing noise-induced phase synchronization in a thermal two-state system. In this context exact expressions for the mean frequency and the phase diffusivity are obtained that together determine the average length of locking episodes. A recently proposed method to quantify frequency synchronization in noisy potential systems is presented and exemplified by applying it to the periodically driven noisy harmonic oscillator. Since this method is based on a threshold crossing rate pioneered by Rice the related phase velocity is termed the Rice frequency. Finally, we discuss the relation between the phenomenon of stochastic resonance and noise-enhanced phase coherence by applying the developed concepts to the periodically driven bistable Kramers oscillator.

Models, Theoretical↗