Sine-Gordon ratchets with general periodic, additive, and parametric driving forces

We study the soliton ratchets in the damped sine-Gordon equation with periodic nonsinusoidal, additive, and parametric driving forces. By means of symmetry analysis of this system we show that the net motion of the kink is not possible if the frequencies of both forces satisfy a certain relationship. Using a collective coordinate theory with two degrees of freedom, we show that the ratchet motion of kinks appears as a consequence of a resonance between the oscillations of the momentum and the width of the kink. We show that the equations of motion that fulfill these collective coordinates follow from the corresponding symmetry properties of the original systems. As a further application of the collective coordinate technique we obtain another relationship between the frequencies of the parametric and additive drivers that suppresses the ratchetlike motion of the kink. We check all these results by means of numerical simulations of the originaMEC, (Spain) and by DAAD (Germany) through “Acciones Integradas Hispano-Alemanas” HA2004-0034—D/04/39957MEC Grant No. FIS2005-973Junta de Andalucía under Projects No. 00481, No. P06-FQM-01735, and No. FQM-020

Ratchet effect in a damped sine-Gordon system with additive and parametric ac driving forces

We study in detail the damped sine-Gordon equation, driven by two ac forces (one is added as a parametric perturbation and the other one in an additive way), as an example of soliton ratchets. By means of a collective coordinate approach we derive an analytical expression for the average velocity of the soliton, which allows us to show that this mechanism of transport requires certain relationships both between the frequencies and between the initial phases of the two ac forces. The control of the velocity by the damping coefficient and parameters of the ac forces is also presented and discussed. All these results are subsequently checked by means of simulations for the driven and damped sine-Gordon equation that we have studied.Ministerio de Educación y Ciencia (MEC, Spain) Grant No. HA2004-0034-D/04/39957Ministerio de Educación y Ciencia (MEC, Spain) Grant No. FIS2005-973Junta de Andalucía Project No. 00481Junta de Andalucía Project No. FQM-020

Efficient characterization of high-dimensional parameter spaces for systems biology

BACKGROUND: A biological system's robustness to mutations and its evolution are influenced by the structure of its viable space, the region of its space of biochemical parameters where it can exert its function. In systems with a large number of biochemical parameters, viable regions with potentially complex geometries fill a tiny fraction of the whole parameter space. This hampers explorations of the viable space based on "brute force" or Gaussian sampling. RESULTS: We here propose a novel algorithm to characterize viable spaces efficiently. The algorithm combines global and local explorations of a parameter space. The global exploration involves an out-of-equilibrium adaptive Metropolis Monte Carlo method aimed at identifying poorly connected viable regions. The local exploration then samples these regions in detail by a method we call multiple ellipsoid-based sampling. Our algorithm explores efficiently nonconvex and poorly connected viable regions of different test-problems. Most importantly, its computational effort scales linearly with the number of dimensions, in contrast to "brute force" sampling that shows an exponential dependence on the number of dimensions. We also apply this algorithm to a simplified model of a biochemical oscillator with positive and negative feedback loops. A detailed characterization of the model's viable space captures well known structural properties of circadian oscillators. Concretely, we find that model topologies with an essential negative feedback loop and a nonessential positive feedback loop provide the most robust fixed period oscillations. Moreover, the connectedness of the model's viable space suggests that biochemical oscillators with varying topologies can evolve from one another. CONCLUSIONS: Our algorithm permits an efficient analysis of high-dimensional, nonconvex, and poorly connected viable spaces characteristic of complex biological circuitry. It allows a systematic use of robustness as a tool for model discrimination

Domain wall dynamics in expanding spaces

We study the effects on the dynamics of kinks due to expansions and contractions of the space. We show that the propagation velocity of the kink can be adiabatically tuned through slow expansions/contractions, while its width is given as a function of the velocity. We also analyze the case of fast expansions/contractions, where we are no longer on the adiabatic regime. In this case the kink moves more slowly after an expansion-contraction cycle as a consequence of loss of energy through radiation. All these effects are numerically studied in the nonlinear Klein-Gordon equations (both for the sine-Gordon and for the phi^4 potential), and they are also studied within the framework of the collective coordinate evolution equations for the width and the center of mass of the kink. These collective coordinate evolution equations are obtained with a procedure that allows us to consider even the case of large expansions/contractions.Comment: LaTeX, 18 pages, 2 figures, improved version to appear in Phys Rev

Lagrangian Formalism in Perturbed Nonlinear Klein-Gordon Equations

We develop an alternative approach to study the effect of the generic perturbation (in addition to explicitly considering the loss term) in the nonlinear Klein-Gordon equations. By a change of the variables that cancel the dissipation term we are able to write the Lagrangian density and then, calculate the Lagrangian as a function of collective variables. We use the Lagrangian formalism together with the Rice {\it Ansatz} to derive the equations of motion of the collective coordinates (CCs) for the perturbed sine-Gordon (sG) and $\phi^{4}$ systems. For the $N$ collective coordinates, regardless of the {\it Ansatz} used, we show that, for the nonlinear Klein-Gordon equations, this approach is equivalent to the {\it Generalized Traveling Wave Ansatz} ({\it GTWA})Comment: 9 page

Topological augmentation to infer hidden processes in biological systems

Motivation: A common problem in understanding a biochemical system is to infer its correct structure or topology. This topology consists of all relevant state variables—usually molecules and their interactions. Here we present a method called topological augmentation to infer this structure in a statistically rigorous and systematic way from prior knowledge and experimental data. Results: Topological augmentation starts from a simple model that is unable to explain the experimental data and augments its topology by adding new terms that capture the experimental behavior. This process is guided by representing the uncertainty in the model topology through stochastic differential equations whose trajectories contain information about missing model parts. We first apply this semiautomatic procedure to a pharmacokinetic model. This example illustrates that a global sampling of the parameter space is critical for inferring a correct model structure. We also use our method to improve our understanding of glutamine transport in yeast. This analysis shows that transport dynamics is determined by glutamine permeases with two different kinds of kinetics. Topological augmentation can not only be applied to biochemical systems, but also to any system that can be described by ordinary differential equations. Availability and implementation: Matlab code and examples are available at: http://www.csb.ethz.ch/tools/index. Contact: [email protected]; [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin

Directed transient long-range transport in a slowly driven Hamiltonian system of interacting particles

We study the Hamiltonian dynamics of a one-dimensional chain of linearly coupled particles in a spatially periodic potential which is subjected to a time-periodic mono-frequency external field. The average over time and space of the related force vanishes and hence, the system is effectively without bias which excludes any ratchet effect. We pay special attention to the escape of the entire chain when initially all of its units are distributed in a potential well. Moreover for an escaping chain we explore the possibility of the successive generation of a directed flow based on large accelerations. We find that for adiabatic slope-modulations due to the ac-field transient long-range transport dynamics arises whose direction is governed by the initial phase of the modulation. Most strikingly, that for the driven many particle Hamiltonian system directed collective motion is observed provides evidence for the existence of families of transporting invariant tori confining orbits in ballistic channels in the high dimensional phase spaces

Biphasic regulation of the transcription factor ABORTED MICROSPORES (AMS) is essential for tapetum and pollen development in Arabidopsis

Viable pollen is essential for plant reproduction and crop yield. Its production requires coordinated expression at specific stages during anther development, involving early meiosis-associated events and late pollen wall formation. The ABORTED MICROSPORE (AMS) transcription factor is a master regulator of sporopollenin biosynthesis, secretion and pollen wall formation in Arabidopsis. Here we show it has complex regulation and additional essential roles earlier in pollen formation. • An inducible-AMS reporter was created for functional rescue, protein expression pattern analysis and to distinguish between direct and indirect targets. Mathematical modelling was used to create regulatory networks based on wildtype RNA and protein expression. • Dual activity of AMS was defined by biphasic protein expression in anther tapetal cells, with an initial peak around pollen meiosis and then later during pollen wall development. Direct AMS-regulated targets exhibit temporal regulation, indicating additional factors are associated with their regulation. • We demonstrate that AMS biphasic expression is essential for pollen development and defines distinct functional activities during early and late pollen development. Mathematical modelling suggests AMS may competitively form a protein complex with other tapetum-expressed transcription factors, and that biphasic regulation is due to repression of upstream regulators and promotion of AMS protein degradation