Bubble propagation in a helicoidal molecular chain

We study the propagation of very large amplitude localized excitations in a model of DNA that takes explicitly into account the helicoidal structure. These excitations represent the ``transcription bubble'', where the hydrogen bonds between complementary bases are disrupted, allowing access to the genetic code. We propose these kind of excitations in alternative to kinks and breathers. The model has been introduced by Barbi et al. [Phys. Lett. A 253, 358 (1999)], and up to now it has been used to study on the one hand low amplitude breather solutions, and on the other hand the DNA melting transition. We extend the model to include the case of heterogeneous chains, in order to get closer to a description of real DNA; in fact, the Morse potential representing the interaction between complementary bases has two possible depths, one for A-T and one for G-C base pairs. We first compute the equilibrium configurations of a chain with a degree of uncoiling, and we find that a static bubble is among them; then we show, by molecular dynamics simulations, that these bubbles, once generated, can move along the chain. We find that also in the most unfavourable case, that of a heterogeneous DNA in the presence of thermal noise, the excitation can travel for well more 1000 base pairs.Comment: 25 pages, 7 figures. Submitted to Phys. Rev.

Reconstruction from blind experimental data for an inverse problem for a hyperbolic equation

We consider the problem of reconstruction of dielectrics from blind backscattered experimental data. Experimental data were collected by a device, which was built at University of North Carolina at Charlotte. This device sends electrical pulses into the medium and collects the time resolved backscattered data on a part of a plane. The spatially distributed dielectric constant $\varepsilon_{r}(\mathbf{x}),\mathbf{x}\in \mathbb{R}^{3}$ is the unknown coefficient of a wave-like PDE. This coefficient is reconstructed from those data in blind cases. To do this, a globally convergent numerical method is used.Comment: 27 page

Barrier Functions for Multiagent-POMDPs with DTL Specifications

Multi-agent partially observable Markov decision processes (MPOMDPs) provide a framework to represent heterogeneous autonomous agents subject to uncertainty and partial observation. In this paper, given a nominal policy provided by a human operator or a conventional planning method, we propose a technique based on barrier functions to design a minimally interfering safety-shield ensuring satisfaction of high-level specifications in terms of linear distribution temporal logic (LDTL). To this end, we use sufficient and necessary conditions for the invariance of a given set based on discrete-time barrier functions (DTBFs) and formulate sufficient conditions for finite time DTBF to study finite time convergence to a set. We then show that different LDTL mission/safety specifications can be cast as a set of invariance or finite time reachability problems. We demonstrate that the proposed method for safety-shield synthesis can be implemented online by a sequence of one-step greedy algorithms. We demonstrate the efficacy of the proposed method using experiments involving a team of robots