A simple model for DNA denaturation

Following Poland and Scheraga, we consider a simplified model for the denaturation transition of DNA. The two strands are modeled as interacting polymer chains. The attractive interactions, which mimic the pairing between the four bases, are reduced to a single short range binding term. Furthermore, base-pair misalignments are forbidden, implying that this binding term exists only for corresponding (same curvilinear abscissae) monomers of the two chains. We take into account the excluded volume repulsion between monomers of the two chains, but neglect intra-chain repulsion. We find that the excluded volume term generates an effective repulsive interaction between the chains, which decays as $1/r^{d-2}$. Due to this long-range repulsion between the chains, the denaturation transition is first order in any dimension, in agreement with previous studies.Comment: 10 page

X-ray rocking curve study of Si-implanted GaAs, Si, and Ge

Crystalline properties of Si-implanted GaAs, Si, and Ge have been studied by Bragg case double-crystal x-ray diffraction. Sharp qualitative and quantitative differences were found between the damage in GaAs on one hand and Si and Ge on the other. In Si and Ge the number of defects and the strain increase linearly with dose up to the amorphous threshold. In GaAs the increase in these quantities is neither linear nor monotonic with dose. At a moderate damage level the GaAs crystal undergoes a transition from elastic to plastic behavior. This transition is accompanied by the creation of extended defects, which are not detected in Si or Ge

Noise Effects on the Complex Patterns of Abnormal Heartbeats

Patients at high risk for sudden death often exhibit complex heart rhythms in which abnormal heartbeats are interspersed with normal heartbeats. We analyze such a complex rhythm in a single patient over a 12-hour period and show that the rhythm can be described by a theoretical model consisting of two interacting oscillators with stochastic elements. By varying the magnitude of the noise, we show that for an intermediate level of noise, the model gives best agreement with key statistical features of the dynamics.Comment: 4 pages, 4 figures, RevTe

Regulatory Dynamics on Random Networks: Asymptotic Periodicity and Modularity

We study the dynamics of discrete-time regulatory networks on random digraphs. For this we define ensembles of deterministic orbits of random regulatory networks, and introduce some statistical indicators related to the long-term dynamics of the system. We prove that, in a random regulatory network, initial conditions converge almost surely to a periodic attractor. We study the subnetworks, which we call modules, where the periodic asymptotic oscillations are concentrated. We proof that those modules are dynamically equivalent to independent regulatory networks.Comment: 23 pages, 3 figure

Theoretical Isochrones with Extinction in the K Band. II. J - K versus K

We calculate theoretical isochrones in a consistent way for five filter pairs near the J and K band atmospheric windows (J-K, J-K', J-Ks, F110W-F205W, and F110W-F222M) using the Padova stellar evolutionary models of Girardi et al. We present magnitude transformations between various K-band filters as a function of color. Isochrones with extinction of up to 6 mag in the K band are also presented. As found for the filter pairs composed of H & K band filters, we find that the reddened isochrones of different filter pairs behave as if they follow different extinction laws, and that the extinction curves of Hubble Space Telescope NICMOS filter pairs in the color-magnitude diagram are considerably nonlinear. Because of these problems, extinction values estimated with NICMOS filters can be in error by up to 1.3 mag. Our calculation suggests that the extinction law implied by the observations of Rieke et al for wavelengths between the J and K bands is better described by a power-law function with an exponent of 1.66 instead of 1.59, which is commonly used with an assumption that the transmission functions of J and K filters are Dirac delta functions.Comment: Published in PASP, 118, 62 (Jan. 2006

Investigation of single crystal ferrite thin films

Materials suitable for use in magnetic bubble domain memories were developed for aerospace applications. Practical techniques for the preparation of such materials in forms required for fabrication of computer memory devices were considered. The materials studied were epitaxial films of various compositions of the gallium-substituted yttrium gadolinium iron garnet system. The major emphasis was to determine their bubble properties and the conditions necessary for growing uncracked, high quality films

Optimal synchronization of directed complex networks

We study optimal synchronization of networks of coupled phase oscillators. We extend previous theory for optimizing the synchronization properties of undirected networks to the important case of directed networks. We derive a generalized synchrony alignment function that encodes the interplay between network structure and the oscillators' natural frequencies and serves as an objective measure for the network's degree of synchronization. Using the generalized synchrony alignment function, we show that a network's synchronization properties can be systematically optimized. This framework also allows us to study the properties of synchrony-optimized networks, and in particular, investigate the role of directed network properties such as nodal in- and out-degrees. For instance, we find that in optimally rewired networks the heterogeneity of the in-degree distribution roughly matches the heterogeneity of the natural frequency distribution, but no such relationship emerges for out-degrees. We also observe that a network's synchronization properties are promoted by a strong correlation between the nodal in-degrees and the natural frequencies of oscillators, whereas the relationship between the nodal out-degrees and the natural frequencies has comparatively little effect. This result is supported by our theory, which indicates that synchronization is promoted by a strong alignment of the natural frequencies with the left singular vectors corresponding to the largest singular values of the Laplacian matrix

A core genetic module : the Mixed Feedback Loop

The so-called Mixed Feedback Loop (MFL) is a small two-gene network where protein A regulates the transcription of protein B and the two proteins form a heterodimer. It has been found to be statistically over-represented in statistical analyses of gene and protein interaction databases and to lie at the core of several computer-generated genetic networks. Here, we propose and mathematically study a model of the MFL and show that, by itself, it can serve both as a bistable switch and as a clock (an oscillator) depending on kinetic parameters. The MFL phase diagram as well as a detailed description of the nonlinear oscillation regime are presented and some biological examples are discussed. The results emphasize the role of protein interactions in the function of genetic modules and the usefulness of modelling RNA dynamics explicitly.Comment: To be published in Physical Review

Non-invertible transformations and spatiotemporal randomness

We generalize the exact solution to the Bernoulli shift map. Under certain conditions, the generalized functions can produce unpredictable dynamics. We use the properties of the generalized functions to show that certain dynamical systems can generate random dynamics. For instance, the chaotic Chua's circuit coupled to a circuit with a non-invertible I-V characteristic can generate unpredictable dynamics. In general, a nonperiodic time-series with truncated exponential behavior can be converted into unpredictable dynamics using non-invertible transformations. Using a new theoretical framework for chaos and randomness, we investigate some classes of coupled map lattices. We show that, in some cases, these systems can produce completely unpredictable dynamics. In a similar fashion, we explain why some wellknown spatiotemporal systems have been found to produce very complex dynamics in numerical simulations. We discuss real physical systems that can generate random dynamics.Comment: Accepted in International Journal of Bifurcation and Chao

Robustness and Enhancement of Neural Synchronization by Activity-Dependent Coupling

We study the synchronization of two model neurons coupled through a synapse having an activity-dependent strength. Our synapse follows the rules of Spike-Timing Dependent Plasticity (STDP). We show that this plasticity of the coupling between neurons produces enlarged frequency locking zones and results in synchronization that is more rapid and much more robust against noise than classical synchronization arising from connections with constant strength. We also present a simple discrete map model that demonstrates the generality of the phenomenon.Comment: 4 pages, accepted for publication in PR