Identification of parameters in amplitude equations describing coupled wakes

We study the flow behind an array of equally spaced parallel cylinders. A system of Stuart-Landau equations with complex parameters is used to model the oscillating wakes. Our purpose is to identify the 6 scalar parameters which most accurately reproduce the experimental data of Chauve and Le Gal [{Physica D {\bf 58}}, pp 407--413, (1992)]. To do so, we perform a computational search for the minimum of a distance \calj. We define \calj as the sum-square difference of the data and amplitudes reconstructed using coupled equations. The search algorithm is made more efficient through the use of a partially analytical expression for the gradient $\nabla \cal J$. Indeed $\nabla \cal J$ can be obtained by the integration of a dynamical system propagating backwards in time (a backpropagation equation for the Lagrange multipliers). Using the parameters computed via the backpropagation method, the coupled Stuart-Landau equations accurately predicted the experimental data from Chauve and Le Gal over a correlation time of the system. Our method turns out to be quite robust as evidenced by using noisy synthetic data obtained from integrations of the coupled Stuart-Landau equations. However, a difficulty remains with experimental data: in that case the several sets of identified parameters are shown to yield equivalent predictions. This is due to a strong discretization or ``round-off" error arising from the digitalization of the video images in the experiment. This ambiguity in parameter identification has been reproduced with synthetic data subjected to the same kind of discretization.Comment: 25 pages uuencoded compressed PostScript file (58K) with 13 figures (155K in separated file) Submitted to Physica

On Variational Data Assimilation in Continuous Time

Variational data assimilation in continuous time is revisited. The central techniques applied in this paper are in part adopted from the theory of optimal nonlinear control. Alternatively, the investigated approach can be considered as a continuous time generalisation of what is known as weakly constrained four dimensional variational assimilation (WC--4DVAR) in the geosciences. The technique allows to assimilate trajectories in the case of partial observations and in the presence of model error. Several mathematical aspects of the approach are studied. Computationally, it amounts to solving a two point boundary value problem. For imperfect models, the trade off between small dynamical error (i.e. the trajectory obeys the model dynamics) and small observational error (i.e. the trajectory closely follows the observations) is investigated. For (nearly) perfect models, this trade off turns out to be (nearly) trivial in some sense, yet allowing for some dynamical error is shown to have positive effects even in this situation. The presented formalism is dynamical in character; no assumptions need to be made about the presence (or absence) of dynamical or observational noise, let alone about their statistics.Comment: 28 Pages, 12 Figure

A Robust Method for Detecting Interdependences: Application to Intracranially Recorded EEG

We present a measure for characterizing statistical relationships between two time sequences. In contrast to commonly used measures like cross-correlations, coherence and mutual information, the proposed measure is non-symmetric and provides information about the direction of interdependence. It is closely related to recent attempts to detect generalized synchronization. However, we do not assume a strict functional relationship between the two time sequences and try to define the measure so as to be robust against noise, and to detect also weak interdependences. We apply our measure to intracranially recorded electroencephalograms of patients suffering from severe epilepsies.Comment: 29 pages, 5 figures, paper accepted for publication in Physica

Anticipated synchronization in coupled chaotic maps with delays

We study the synchronization of two chaotic maps with unidirectional (master-slave) coupling. Both maps have an intrinsic delay $n_1$, and coupling acts with a delay $n_2$. Depending on the sign of the difference $n_1-n_2$, the slave map can synchronize to a future or a past state of the master system. The stability properties of the synchronized state are studied analytically, and we find that they are independent of the coupling delay $n_2$. These results are compared with numerical simulations of a delayed map that arises from discretization of the Ikeda delay-differential equation. We show that the critical value of the coupling strength above which synchronization is stable becomes independent of the delay $n_1$ for large delays.Comment: 10 pages, 4 figure

On the Floquet Theory of Delay Differential Equations

We present an analytical approach to deal with nonlinear delay differential equations close to instabilities of time periodic reference states. To this end we start with approximately determining such reference states by extending the Poincar'e Lindstedt and the Shohat expansions which were originally developed for ordinary differential equations. Then we systematically elaborate a linear stability analysis around a time periodic reference state. This allows to approximately calculate the Floquet eigenvalues and their corresponding eigensolutions by using matrix valued continued fractions

Carbon monoxide in the solar atmosphere I. Numerical method and two-dimensional models

The radiation hydrodynamic code CO5BOLD has been supplemented with the time-dependent treatment of chemical reaction networks. Advection of particle densities due to the hydrodynamic flow field is also included. The radiative transfer is treated frequency-independently, i.e. grey, so far. The upgraded code has been applied to two-dimensional simulations of carbon monoxide (CO) in the non-magnetic solar photosphere and low chromosphere. For this purpose a reaction network has been constructed, taking into account the reactions which are most important for the formation and dissociation of CO under the physical conditions of the solar atmosphere. The network has been strongly reduced to 27 reactions, involving the chemical species H, H2, C, O, CO, CH, OH, and a representative metal. The resulting CO number density is highest in the cool regions of the reversed granulation pattern at mid-photospheric heights and decreases strongly above. There, the CO abundance stays close to a value of 8.3 on the usual logarithmic abundance scale with [H]=12 but is reduced in hot shock waves which are a ubiquitous phenomenon of the model atmosphere. For comparison, the corresponding equilibrium densities have been calculated, based on the reaction network but also under assumption of instantaneous chemical equilibrium by applying the Rybicki & Hummer (RH) code by Uitenbroek (2001). Owing to the short chemical timescales, the assumption holds for a large fraction of the atmosphere, in particular the photosphere. In contrast, the CO number density deviates strongly from the corresponding equilibrium value in the vicinity of chromospheric shock waves. Simulations with altered reaction network clearly show that the formation channel via hydroxide (OH) is the most important one under the conditions of the solar atmosphere.Comment: 15 pages, 6 figures, final version will contain online materia

What is Life Worth? A Rough Guide to Valuation

In this speculative article, the aim is to elaborate a definition of life that is not biological, and a valuation of it that is not commodified. This is undertaken by the development of an understanding of death as a process which is embedded in the life of a community. The idea is that we can best understand what life is worth by first understanding what death means

The origin of large molecules in primordial autocatalytic reaction networks

Large molecules such as proteins and nucleic acids are crucial for life, yet their primordial origin remains a major puzzle. The production of large molecules, as we know it today, requires good catalysts, and the only good catalysts we know that can accomplish this task consist of large molecules. Thus the origin of large molecules is a chicken and egg problem in chemistry. Here we present a mechanism, based on autocatalytic sets (ACSs), that is a possible solution to this problem. We discuss a mathematical model describing the population dynamics of molecules in a stylized but prebiotically plausible chemistry. Large molecules can be produced in this chemistry by the coalescing of smaller ones, with the smallest molecules, the `food set', being buffered. Some of the reactions can be catalyzed by molecules within the chemistry with varying catalytic strengths. Normally the concentrations of large molecules in such a scenario are very small, diminishing exponentially with their size. ACSs, if present in the catalytic network, can focus the resources of the system into a sparse set of molecules. ACSs can produce a bistability in the population dynamics and, in particular, steady states wherein the ACS molecules dominate the population. However to reach these steady states from initial conditions that contain only the food set typically requires very large catalytic strengths, growing exponentially with the size of the catalyst molecule. We present a solution to this problem by studying `nested ACSs', a structure in which a small ACS is connected to a larger one and reinforces it. We show that when the network contains a cascade of nested ACSs with the catalytic strengths of molecules increasing gradually with their size (e.g., as a power law), a sparse subset of molecules including some very large molecules can come to dominate the system.Comment: 49 pages, 17 figures including supporting informatio

PARP-3 and APLF function together to accelerate nonhomologous end joining

PARP-3 is a member of the ADP-ribosyl transferase superfamily of unknown function. We show that PARP-3 is stimulated by DNA double-strand breaks (DSBs) in vitro and functions in the same pathway as the poly (ADP-ribose)-binding protein APLF to accelerate chromosomal DNA DSB repair. We implicate PARP-3 in the accumulation of APLF at DSBs and demonstrate that APLF promotes the retention of XRCC4/DNA ligase IV complex in chromatin, suggesting that PARP-3 and APLF accelerate DNA ligation during nonhomologous end-joining (NHEJ). Consistent with this, we show that class switch recombination in Aplf−/− B cells is biased toward microhomology-mediated end-joining, a pathway that operates in the absence of XRCC4/DNA ligase IV, and that the requirement for PARP-3 and APLF for NHEJ is circumvented by overexpression of XRCC4/DNA ligase IV. These data identify molecular roles for PARP-3 and APLF in chromosomal DNA double-strand break repair reactions