Rigorous elimination of fast stochastic variables from the linear noise approximation using projection operators

The linear noise approximation (LNA) offers a simple means by which one can study intrinsic noise in monostable biochemical networks. Using simple physical arguments, we have recently introduced the slow-scale LNA (ssLNA) which is a reduced version of the LNA under conditions of timescale separation. In this paper, we present the first rigorous derivation of the ssLNA using the projection operator technique and show that the ssLNA follows uniquely from the standard LNA under the same conditions of timescale separation as those required for the deterministic quasi-steady state approximation. We also show that the large molecule number limit of several common stochastic model reduction techniques under timescale separation conditions constitutes a special case of the ssLNA.Comment: 10 pages, 1 figure, submitted to Physical Review E; see also BMC Systems Biology 6, 39 (2012

Scale-Free topologies and Activatory-Inhibitory interactions

A simple model of activatory-inhibitory interactions controlling the activity of agents (substrates) through a "saturated response" dynamical rule in a scale-free network is thoroughly studied. After discussing the most remarkable dynamical features of the model, namely fragmentation and multistability, we present a characterization of the temporal (periodic and chaotic) fluctuations of the quasi-stasis asymptotic states of network activity. The double (both structural and dynamical) source of entangled complexity of the system temporal fluctuations, as an important partial aspect of the Correlation Structure-Function problem, is further discussed to the light of the numerical results, with a view on potential applications of these general results.Comment: Revtex style, 12 pages and 12 figures. Enlarged manuscript with major revision and new results incorporated. To appear in Chaos (2006

Systematic derivation of a rotationally covariant extension of the 2-dimensional Newell-Whitehead-Segel equation

An extension of the Newell-Whitehead-Segel amplitude equation covariant under abritrary rotations is derived systematically by the renormalization group method.Comment: 8 pages, to appear in Phys. Rev. Letters, March 18, 199

Longitudinal response functions of 3H and 3He

Trinucleon longitudinal response functions R_L(q,omega) are calculated for q values up to 500 MeV/c. These are the first calculations beyond the threshold region in which both three-nucleon (3N) and Coulomb forces are fully included. We employ two realistic NN potentials (configuration space BonnA, AV18) and two 3N potentials (UrbanaIX, Tucson-Melbourne). Complete final state interactions are taken into account via the Lorentz integral transform technique. We study relativistic corrections arising from first order corrections to the nuclear charge operator. In addition the reference frame dependence due to our non-relativistic framework is investigated. For q less equal 350 MeV/c we find a 3N force effect between 5 and 15 %, while the dependence on other theoretical ingredients is small. At q greater equal 400 MeV/c relativistic corrections to the charge operator and effects of frame dependence, especially for large omega, become more important. In comparison with experimental data there is generally a rather good agreement. Exceptions are the responses at excitation energies close to threshold, where there exists a large discrepancy with experiment at higher q. Concerning the effect of 3N forces there are a few cases, in particular for the R_L of 3He, where one finds a much improved agreement with experiment if 3N forces are included.Comment: 26 pages, 9 figure

Period Stabilization in the Busse-Heikes Model of the Kuppers-Lortz Instability

The Busse-Heikes dynamical model is described in terms of relaxational and nonrelaxational dynamics. Within this dynamical picture a diverging alternating period is calculated in a reduced dynamics given by a time-dependent Hamiltonian with decreasing energy. A mean period is calculated which results from noise stabilization of a mean energy. The consideration of spatial-dependent amplitudes leads to vertex formation. The competition of front motion around the vertices and the Kuppers-Lortz instability in determining an alternating period is discussed.Comment: 28 pages, 11 figure

Generalized Haldane Equation and Fluctuation Theorem in the Steady State Cycle Kinetics of Single Enzymes

Enyzme kinetics are cyclic. We study a Markov renewal process model of single-enzyme turnover in nonequilibrium steady-state (NESS) with sustained concentrations for substrates and products. We show that the forward and backward cycle times have idential non-exponential distributions: \QQ_+(t)=\QQ_-(t). This equation generalizes the Haldane relation in reversible enzyme kinetics. In terms of the probabilities for the forward ($p_+$) and backward ($p_-$) cycles, $k_BT\ln(p_+/p_-)$ is shown to be the chemical driving force of the NESS, $\Delta\mu$. More interestingly, the moment generating function of the stochastic number of substrate cycle $\nu(t)$, follows the fluctuation theorem in the form of Kurchan-Lebowitz-Spohn-type symmetry. When $\lambda$ = $\Delta\mu/k_BT$, we obtain the Jarzynski-Hatano-Sasa-type equality: $\equiv$ 1 for all $t$, where $\nu\Delta\mu$ is the fluctuating chemical work done for sustaining the NESS. This theory suggests possible methods to experimentally determine the nonequilibrium driving force {\it in situ} from turnover data via single-molecule enzymology.Comment: 4 pages, 3 figure

Mode transitions in a model reaction-diffusion system driven by domain growth and noise

Pattern formation in many biological systems takes place during growth of the underlying domain. We study a specific example of a reaction–diffusion (Turing) model in which peak splitting, driven by domain growth, generates a sequence of patterns. We have previously shown that the pattern sequences which are presented when the domain growth rate is sufficiently rapid exhibit a mode-doubling phenomenon. Such pattern sequences afford reliable selection of certain final patterns, thus addressing the robustness problem inherent of the Turing mechanism. At slower domain growth rates this regular mode doubling breaks down in the presence of small perturbations to the dynamics. In this paper we examine the breaking down of the mode doubling sequence and consider the implications of this behaviour in increasing the range of reliably selectable final patterns

Square Patterns and Quasi-patterns in Weakly Damped Faraday Waves

Pattern formation in parametric surface waves is studied in the limit of weak viscous dissipation. A set of quasi-potential equations (QPEs) is introduced that admits a closed representation in terms of surface variables alone. A multiscale expansion of the QPEs reveals the importance of triad resonant interactions, and the saturating effect of the driving force leading to a gradient amplitude equation. Minimization of the associated Lyapunov function yields standing wave patterns of square symmetry for capillary waves, and hexagonal patterns and a sequence of quasi-patterns for mixed capillary-gravity waves. Numerical integration of the QPEs reveals a quasi-pattern of eight-fold symmetry in the range of parameters predicted by the multiscale expansion.Comment: RevTeX, 11 pages, 8 figure

Shear induced grain boundary motion for lamellar phases in the weakly nonlinear regime

We study the effect of an externally imposed oscillatory shear on the motion of a grain boundary that separates differently oriented domains of the lamellar phase of a diblock copolymer. A direct numerical solution of the Swift-Hohenberg equation in shear flow is used for the case of a transverse/parallel grain boundary in the limits of weak nonlinearity and low shear frequency. We focus on the region of parameters in which both transverse and parallel lamellae are linearly stable. Shearing leads to excess free energy in the transverse region relative to the parallel region, which is in turn dissipated by net motion of the boundary toward the transverse region. The observed boundary motion is a combination of rigid advection by the flow and order parameter diffusion. The latter includes break up and reconnection of lamellae, as well as a weak Eckhaus instability in the boundary region for sufficiently large strain amplitude that leads to slow wavenumber readjustment. The net average velocity is seen to increase with frequency and strain amplitude, and can be obtained by a multiple scale expansion of the governing equations