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At least 1,099 records · Page 61Linked to original sources
PubMed2003

Intrinsic localized modes in photonic crystal circuits.

A discussion of intrinsic localized modes (ILMs) in photonic crystals is given. Emphasis is placed on ILMs in photonic crystal waveguides formed from Kerr nonlinear materials and photonic crystal circuits formed by joining nonlinear photonic crystal waveguides into networks. Work on stationary and propagating ILMs in nonlinear waveguides and waveguide junctions is reviewed. In addition, some discussion is given on the optical bistability of the barrier and junction geometries and on recent results on two-dimensional ILMs in Kerr nonlinear photonic crystals.

Journal Article↗
PubMed1991

Oscillations and chaos in CO+O(2) combustion.

The gas-phase reaction between carbon monoxide and oxygen (in the presence of small amounts of hydrogen) shows bistability and oscillatory behavior. Typically, the oscillatory ignition has a period-1 relaxation waveform. The limit cycle is born at a saddle-node loop and terminates via a supercritical Hopf bifurcation. For a mean residence time of 8 s there is a period-doubling to a period-2 solution followed by period-halving to quasisinusoidal period-1 oscillations. At longer residence times, more period-doublings forming a full cascade to chaos with subsequent periodic windows are observed. The chaotic attractor has an underlying single-humped next maximum map.

Journal Article↗
PubMed1992

Coupled maps and pattern formation on the Sierpinski gasket.

The bifurcation structure of coupled maps on the Sierpinski gasket is investigated. The fractal character of the underlying lattice gives rise to stability boundaries for the periodic synchronized states with unusual features and spatially inhomogeneous states with a complex structure. The results are illustrated by calculations on coupled quadratic and cubic maps. For the coupled cubic map lattice bistability and domain growth processes are studied.

Journal Article↗
PubMed1994

Chemical turbulence and standing waves in a surface reaction model: The influence of global coupling and wave instabilities.

Among heterogeneously catalyzed chemical reactions, the CO oxidation on the Pt(110) surface under vacuum conditions offers probably the greatest wealth of spontaneous formation of spatial patterns. Spirals, fronts, and solitary pulses were detected at low surface temperatures (T<500 K), in line with the standard phenomenology of bistable, excitable, and oscillatory reaction-diffusion systems. At high temperatures (T greater, similar 540 K), more surprising features like chemical turbulence and standing waves appeared in the experiments. Herein, we study a realistic reaction-diffusion model of this system, with respect to the latter phenomena. In particular, we deal both with the influence of global coupling through the gas phase on the oscillatory reaction and the possibility of wave instabilities under excitable conditions. Gas-phase coupling is shown to either synchronize the oscillations or to yield turbulence and standing structures. The latter findings are closely related to clustering in networks of coupled oscillators and indicate a dominance of the global gas-phase coupling over local coupling via surface diffusion. In the excitable regime wave instabilities in one and two dimensions have been discovered. In one dimension, pulses become unstable due to a vanishing of the refractory zone. In two dimensions, turbulence can also emerge due to spiral breakup, which results from a violation of the dispersion relation.

Journal Article↗
PubMed1995

Multiple time scale analysis of two models for the peroxidase-oxidase reaction.

A multiple time scale analysis of two four-variable models of the peroxidase-oxidase reaction, the DOP, and the Olsen model, is carried out. It is shown that autonomous limit cycle oscillations are exhibited by the fast subsets of these two models, but only in certain regions of parameter space, confirming the prior suggestion that the slow variable (NADH) is not essential for oscillatory behavior. However, it is found that the slow variable is essential for oscillatory behavior over other ranges of parameter values, and is always essential for complex oscillatory and chaotic behavior. This latter conclusion is based on a study involving driving the fast subset with a sinusoidally varying (NADH). This study suggests the level of coupling between fast and slow variables of an autonomous system necessary to cause the chaos observed in the DOP model. Further study of the driven system allows for the identification of a natural period of the nonoscillatory but bistable fast subsystem and a set of rules for applying a parametric driving in such a way as to generate a more complete Farey sequence from a truncated Farey sequence. These conclusions are used to compare the very similar DOP and Olsen models, which, nevertheless, exhibit quite different Farey sequences and routes to chaos. (c) 1995 American Institute of Physics.

Journal Article↗
PubMed2004

Fluctuation theorem for nonequilibrium reactions.

A fluctuation theorem is derived for stochastic nonequilibrium reactions ruled by the chemical master equation. The theorem is expressed in terms of the generating and large-deviation functions characterizing the fluctuations of a quantity which measures the loss of detailed balance out of thermodynamic equilibrium. The relationship to entropy production is established and discussed. The fluctuation theorem is verified in the Schlögl model of far-from-equilibrium bistability.

Journal Article↗
PubMed2004

Biomolecular free energy profiles by a shooting/umbrella sampling protocol, "BOLAS".

We develop an efficient technique for computing free energies corresponding to conformational transitions in complex systems by combining a Monte Carlo ensemble of trajectories generated by the shooting algorithm with umbrella sampling. Motivated by the transition path sampling method, our scheme "BOLAS" (named after a cowboy's lasso) preserves microscopic reversibility and leads to the correct equilibrium distribution. This makes possible computation of free energy profiles along complex reaction coordinates for biomolecular systems with a lower systematic error compared to traditional, force-biased umbrella sampling protocols. We demonstrate the validity of BOLAS for a bistable potential, and illustrate the method's scope with an application to the sugar repuckering transition in a solvated deoxyadenosine molecule.

Algorithms↗
PubMed2004

Bifurcation analysis of a model of the budding yeast cell cycle.

We study the bifurcations of a set of nine nonlinear ordinary differential equations that describe regulation of the cyclin-dependent kinase that triggers DNA synthesis and mitosis in the budding yeast, Saccharomyces cerevisiae. We show that Clb2-dependent kinase exhibits bistability (stable steady states of high or low kinase activity). The transition from low to high Clb2-dependent kinase activity is driven by transient activation of Cln2-dependent kinase, and the reverse transition is driven by transient activation of the Clb2 degradation machinery. We show that a four-variable model retains the main features of the nine-variable model. In a three-variable model exhibiting birhythmicity (two stable oscillatory states), we explore possible effects of extrinsic fluctuations on cell cycle progression.

Cell Cycle↗
PubMed2005

Stochastic resonance: theory and numerics.

We address the phenomenon of stochastic resonance in a noisy bistable system driven by a time-dependent periodic force (not necessarily sinusoidal) and in its two-state approximation. Even for driving forces with subthreshold amplitudes, the behavior of the system response might require a nonlinear description. We introduce analytical and numerical tools to analyze the power spectral amplification and the signal-to-noise ratio in a nonlinear regime. Our analysis shows the importance of the effects of the driving force on the system fluctuations in a nonlinear regime. These effects can be usefully exploited to achieve high quality output signals with gains larger than unity, which is impossible within a linear regime.

Mechanics↗
PubMed2005

Topography of the free-energy landscape probed via mechanical unfolding of proteins.

Single-molecule experiments in which proteins are unfolded by applying mechanical stretching forces generally force unfolding to proceed along a reaction coordinate that is different from that in chemical or thermal denaturation. Here we simulate the mechanical unfolding and refolding of a minimalist off-lattice model of the protein ubiquitin to explore in detail the slice of the multidimensional free-energy landscape that is accessible via mechanical pulling experiments. We find that while the free-energy profile along typical "chemical" reaction coordinates may exhibit two minima, corresponding to the native and denatured states, the free energy G(z) is typically a monotonic function of the mechanical coordinate z equal to the protein extension. Application of a stretching force along z tilts the free-energy landscape resulting in a bistable (or multistable) free energy G(z)-fz probed in mechanical unfolding experiments. We construct a two-dimensional free-energy surface as a function of both chemical and mechanical reaction coordinates and examine the coupling between the two. We further study the refolding trajectories after the protein has been prestretched by a large force, as well as the mechanical unfolding trajectories in the presence of a large stretching force. We demonstrate that the stretching forces required to destabilize the native state thermodynamically are larger than those expected on the basis of previous experimental estimates of G(z). This finding is consistent with the recent experimental studies, indicating that proteins may refold even in the presence of a substantial stretching force. Finally, we show that for certain temperatures the free energy of a polyprotein chain consisting of multiple domains is a linear function of the chain extension. We propose that the recently observed "slow phase" in the refolding of proteins under mechanical tension may be viewed as downhill diffusion in such a linear potential.

Computer Simulation↗
PubMed2005

Transient and steady state CO oxidation kinetics on nanolithographically prepared supported Pd model catalysts: experiments and simulations.

Applying molecular-beam methods to a nanolithographically prepared planar PdSiO2 model catalyst, we have performed a detailed study of the kinetics of CO oxidation. The model catalyst was prepared by electron-beam lithography, allowing individual control of particle size and position. The sample was structurally characterized by atomic force microscopy and scanning electron microscopy before and after reaction. In the kinetic experiments, the O-rich and CO-rich regimes were investigated systematically with respect to their transient and steady-state behaviors, both under bistable and monostable reaction conditions. Separate molecular beams were used in order to supply the reactants, allowing individual control over the reactant fluxes. The desorbing CO2 was detected by both angle-resolved and angle-integrated mass spectrometries. The experimental results were analyzed using different types of microkinetic models, including a detailed reaction-diffusion model, which takes into account the structural parameters of the catalyst as well as scattering of the reactants from the support. The model quantitatively reproduces the results as a function of the reactant fluxes and the surface temperature. Various kinetic effects observed are discussed in detail on the basis of the model. Specifically, it is shown that under conditions of limited oxygen mobility, the switching behavior between the kinetic regimes is largely driven by the surface mobility of CO.

Journal Article↗
PubMed2005

Stationary fronts due to weak thermal effects in models of catalytic oxidation.

We analyze the possible existence of an infinite number of stationary front solutions in a microkinetic model of a catalytic reaction coupled with weak enthalpy effects in the domain of kinetics bistability. The kinetic model incorporates three steps: dissociative oxygen adsorption, reactant adsorption and desorption, and surface reaction. The infinitude of stationary front solutions emerges due to the lack of intercrystallites communication of surface species in supported catalysts; thermal conductions and gas-phase diffusion are the only means of interaction. Incorporation of surface species diffusion leads to a very slow front motion. We complement this analysis with simulations of stationary states on one- (wire and ring) and two-dimensional (disk) systems which may be subject to control or to fluid flow. These results account for certain experimental results and may have implications for various technological problems.

Journal Article↗
PubMed2005

Nonadiabatic quantum-classical reaction rates with quantum equilibrium structure.

Time correlation function expressions for quantum reaction-rate coefficients are computed in a quantum-classical limit. This form for the correlation function retains the full quantum equilibrium structure of the system in the spectral density function but approximates the time evolution of the operator by quantum-classical Liouville dynamics. Approximate analytical expressions for the spectral density function, which incorporate quantum effects in the many-body environment and reaction coordinate, are derived. The results of numerical simulations of the reaction rate are presented for a reaction model in which a two-level system is coupled to a bistable oscillator which is, in turn, coupled to a bath of harmonic oscillators. The nonadiabatic quantum-classical dynamics is simulated in terms of an ensemble of surface-hopping trajectories and the effects of the quantum equilibrium structure on the reaction rate are discussed.

Journal Article↗
PubMed2006

Gene regulatory networks: a coarse-grained, equation-free approach to multiscale computation.

We present computer-assisted methods for analyzing stochastic models of gene regulatory networks. The main idea that underlies this equation-free analysis is the design and execution of appropriately initialized short bursts of stochastic simulations; the results of these are processed to estimate coarse-grained quantities of interest, such as mesoscopic transport coefficients. In particular, using a simple model of a genetic toggle switch, we illustrate the computation of an effective free energy Phi and of a state-dependent effective diffusion coefficient D that characterize an unavailable effective Fokker-Planck equation. Additionally we illustrate the linking of equation-free techniques with continuation methods for performing a form of stochastic "bifurcation analysis"; estimation of mean switching times in the case of a bistable switch is also implemented in this equation-free context. The accuracy of our methods is tested by direct comparison with long-time stochastic simulations. This type of equation-free analysis appears to be a promising approach to computing features of the long-time, coarse-grained behavior of certain classes of complex stochastic models of gene regulatory networks, circumventing the need for long Monte Carlo simulations.

Algorithms↗
PubMed2006

On the calculation of time correlation functions by potential scaling.

We present and analyze a general method to calculate time correlation functions from molecular dynamics on scaled potentials for complex systems for which simulation is affected by broken ergodicity. Depending on the value of the scaling factor, correlations can be calculated for times that can be orders of magnitude longer than those accessible to direct simulations. We show that the exact value of the time correlation functions of the original system (i.e., with unscaled potential) can be obtained, in principle, using an action-reweighting scheme based on a stochastic path-integral formalism. Two tests (involving a bistable potential model and a dipeptide bond-vector orientational relaxation) are exemplified to showcase the strengths, as well as the limitations of the approach, and a procedure for the estimation of the time-dependent standard deviation error is outlined.

Journal Article↗
PubMed2006

Phonon driven proton transfer in crystals with short strong hydrogen bonds.

Recent work on understanding why protons migrate with increasing temperature in short, strong hydrogen bonds is extended here to three more organic, crystalline systems. Inelastic neutron scattering and density functional theory based simulations are used to investigate structure, vibrations, and dynamics of these systems as functions of temperature. The mechanism determined in a previous work on urea phosphoric acid of low frequency vibrations stabilizing average crystal structures, in which the potential energy well of the hydrogen bond has its minimum shifted towards the center of the bond, is found to be valid here. The new feature of the N-H...O hydrogen bonds studied in this work is that the proton is transferred from the donor atom to the acceptor atom. Molecular dynamics simulations show that in an intermediate temperature regime, in which the proton is not completely transferred, the proton is bistable, jumping from one side of the hydrogen bond to the other. In the case of 3,5-pyridine dicarboxylic acid, which has been studied in most detail, specific phonons are identified, which influence the potential energy surface of the proton in the short, strong hydrogen bond.

Journal Article↗
PubMed2006

Feedback loops for Shil'nikov chaos: The peroxidase-oxidase reaction.

Special structures in a chemical reaction network can give rise to bistability, oscillations, and chaos. It has been shown recently [A. Sensse and M. Eiswirth, J. Chem. Phys. 122, 044516 (2005)] that the introduction of an additional species in a supplementary feedback loop to a minimal autocatalytic oscillator gives rise to chaotic dynamics in a certain range of parameters, independent of the particular realization of the additional loop. This provides a possibility to decide if chaos may occur just by analyzing the network structure of an existing model. Here, we apply this concept to analyze the complex dynamics in several essential subsystems of the peroxidase-oxidase reaction system. The aim of the present paper is to determine the nature of the occurring chaos and its location in the parameter space by numerical bifurcation analysis and simulations.

Algorithms↗
PubMed2006

Obtaining reaction coordinates by likelihood maximization.

We present a new approach for calculating reaction coordinates in complex systems. The new method is based on transition path sampling and likelihood maximization. It requires fewer trajectories than a single iteration of existing procedures, and it applies to both low and high friction dynamics. The new method screens a set of candidate collective variables for a good reaction coordinate that depends on a few relevant variables. The Bayesian information criterion determines whether additional variables significantly improve the reaction coordinate. Additionally, we present an advantageous transition path sampling algorithm and an algorithm to generate the most likely transition path in the space of collective variables. The method is demonstrated on two systems: a bistable model potential energy surface and nucleation in the Ising model. For the Ising model of nucleation, we quantify for the first time the role of nuclei surface area in the nucleation reaction coordinate. Surprisingly, increased surface area increases the stability of nuclei in two dimensions but decreases nuclei stability in three dimensions.

Journal Article↗