Serially-regulated biological networks fully realize a constrained set of functions

We show that biological networks with serial regulation (each node regulated by at most one other node) are constrained to {\it direct functionality}, in which the sign of the effect of an environmental input on a target species depends only on the direct path from the input to the target, even when there is a feedback loop allowing for multiple interaction pathways. Using a stochastic model for a set of small transcriptional regulatory networks that have been studied experimentally, we further find that all networks can achieve all functions permitted by this constraint under reasonable settings of biochemical parameters. This underscores the functional versatility of the networks.Comment: 9 pages, 3 figure

Relation between stress heterogeneity and aftershock rate in the rate-and-state model

We estimate the rate of aftershocks triggered by a heterogeneous stress change, using the rate-and-state model of Dieterich [1994].We show that an exponential stress distribution Pt(au) ~exp(-tautau_0) gives an Omori law decay of aftershocks with time ~1/t^p, with an exponent p=1-A sigma_n/tau_0, where A is a parameter of the rate-and-state friction law, and \sigma_n the normal stress. Omori exponent p thus decreases if the stress "heterogeneity" tau_0 decreases. We also invert the stress distribution P(tau) from the seismicity rate R(t), assuming that the stress does not change with time. We apply this method to a synthetic stress map, using the (modified) scale invariant "k^2" slip model [Herrero and Bernard, 1994]. We generate synthetic aftershock catalogs from this stress change.The seismicity rate on the rupture area shows a huge increase at short times, even if the stress decreases on average. Aftershocks are clustered in the regions of low slip, but the spatial distribution is more diffuse than for a simple slip dislocation. Because the stress field is very heterogeneous, there are many patches of positive stress changes everywhere on the fault.This stochastic slip model gives a Gaussian stress distribution, but nevertheless produces an aftershock rate which is very close to Omori's law, with an effective p<=1, which increases slowly with time. We obtain a good estimation of the stress distribution for realistic catalogs, when we constrain the shape of the distribution. However, there are probably other factors which also affect the temporal decay of aftershocks with time. In particular, heterogeneity of A\sigma_n can also modify the parameters p and c of Omori's law. Finally, we show that stress shadows are very difficult to observe in a heterogeneous stress context.Comment: In press in JG

Dynamic Fluctuation Phenomena in Double Membrane Films

Dynamics of double membrane films is investigated in the long-wavelength limit including the overdamped squeezing mode. We demonstrate that thermal fluctuations essentially modify the character of the mode due to its nonlinear coupling to the transversal shear hydrodynamic mode. The corresponding Green function acquires as a function of the frequency a cut along the imaginary semi-axis. Fluctuations lead to increasing the attenuation of the squeezing mode it becomes larger than the `bare' value.Comment: 7 pages, Revte

Efficient LZ78 factorization of grammar compressed text

We present an efficient algorithm for computing the LZ78 factorization of a text, where the text is represented as a straight line program (SLP), which is a context free grammar in the Chomsky normal form that generates a single string. Given an SLP of size $n$ representing a text $S$ of length $N$, our algorithm computes the LZ78 factorization of $T$ in $O(n\sqrt{N}+m\log N)$ time and $O(n\sqrt{N}+m)$ space, where $m$ is the number of resulting LZ78 factors. We also show how to improve the algorithm so that the $n\sqrt{N}$ term in the time and space complexities becomes either $nL$, where $L$ is the length of the longest LZ78 factor, or $(N - \alpha)$ where $\alpha \geq 0$ is a quantity which depends on the amount of redundancy that the SLP captures with respect to substrings of $S$ of a certain length. Since $m = O(N/\log_\sigma N)$ where $\sigma$ is the alphabet size, the latter is asymptotically at least as fast as a linear time algorithm which runs on the uncompressed string when $\sigma$ is constant, and can be more efficient when the text is compressible, i.e. when $m$ and $n$ are small.Comment: SPIRE 201

Traffic jams and ordering far from thermal equilibrium

The recently suggested correspondence between domain dynamics of traffic models and the asymmetric chipping model is reviewed. It is observed that in many cases traffic domains perform the two characteristic dynamical processes of the chipping model, namely chipping and diffusion. This correspondence indicates that jamming in traffic models in which all dynamical rates are non-deterministic takes place as a broad crossover phenomenon, rather than a sharp transition. Two traffic models are studied in detail and analyzed within this picture.Comment: Contribution to the Niels Bohr Summer Institute on Complexity and Criticality; to appear in a Per Bak Memorial Issue of PHYSICA

Factorised Steady States in Mass Transport Models

We study a class of mass transport models where mass is transported in a preferred direction around a one-dimensional periodic lattice and is globally conserved. The model encompasses both discrete and continuous masses and parallel and random sequential dynamics and includes models such as the Zero-range process and Asymmetric random average process as special cases. We derive a necessary and sufficient condition for the steady state to factorise, which takes a rather simple form.Comment: 6 page

Straightening of Thermal Fluctuations in Semi-Flexible Polymers by Applied Tension

We investigate the propagation of a suddenly applied tension along a thermally excited semi-flexible polymer using analytical approximations, scaling arguments and numerical simulation. This problem is inherently non-linear. We find sub-diffusive propagation with a dynamical exponent of 1/4. By generalizing the internal elasticity, we show that tense strings exhibit qualitatively different tension profiles and propagation with an exponent of 1/2.Comment: Latex file; with three postscript figures; .ps available at http://dept.physics.upenn.edu/~nelson/pull.p

Bayesian Bounds on Parameter Estimation Accuracy for Compact Coalescing Binary Gravitational Wave Signals

A global network of laser interferometric gravitational wave detectors is projected to be in operation by around the turn of the century. Here, the noisy output of a single instrument is examined. A gravitational wave is assumed to have been detected in the data and we deal with the subsequent problem of parameter estimation. Specifically, we investigate theoretical lower bounds on the minimum mean-square errors associated with measuring the parameters of the inspiral waveform generated by an orbiting system of neutron stars/black holes. Three theoretical lower bounds on parameter estimation accuracy are considered: the Cramer-Rao bound (CRB); the Weiss-Weinstein bound (WWB); and the Ziv-Zakai bound (ZZB). We obtain the WWB and ZZB for the Newtonian-form of the coalescing binary waveform, and compare them with published CRB and numerical Monte-Carlo results. At large SNR, we find that the theoretical bounds are all identical and are attained by the Monte-Carlo results. As SNR gradually drops below 10, the WWB and ZZB are both found to provide increasingly tighter lower bounds than the CRB. However, at these levels of moderate SNR, there is a significant departure between all the bounds and the numerical Monte-Carlo results.Comment: 17 pages (LaTeX), 4 figures. Submitted to Physical Review