Experimental and theoretical studies of sequence effects on the fluctuation and melting of short DNA molecules

Understanding the melting of short DNA sequences probes DNA at the scale of the genetic code and raises questions which are very different from those posed by very long sequences, which have been extensively studied. We investigate this problem by combining experiments and theory. A new experimental method allows us to make a mapping of the opening of the guanines along the sequence as a function of temperature. The results indicate that non-local effects may be important in DNA because an AT-rich region is able to influence the opening of a base pair which is about 10 base pairs away. An earlier mesoscopic model of DNA is modified to correctly describe the time scales associated to the opening of individual base pairs well below melting, and to properly take into account the sequence. Using this model to analyze some characteristic sequences for which detailed experimental data on the melting is available [Montrichok et al. 2003 Europhys. Lett. {\bf 62} 452], we show that we have to introduce non-local effects of AT-rich regions to get acceptable results. This brings a second indication that the influence of these highly fluctuating regions of DNA on their neighborhood can extend to some distance.Comment: To be published in J. Phys. Condensed Matte

Continuous phase transition in polydisperse hard-sphere mixture

In a previous paper (J. Zhang {\it et al.}, J. Chem. Phys. {\bf 110}, 5318 (1999)) we introduced a model for polydisperse hard sphere mixtures that is able to adjust its particle-size distribution. Here we give the explanation of the questions that arose in the previous description and present a consistent theory of the phase transition in this system, based on the Percus-Yevick equation of state. The transition is continuous, and like Bose-Einstein condensation a macroscopic aggregate is formed due to the microscopic interactions. A BMCSL-like treatment leads to the same conclusion with slightly more accurate predictions.Comment: 7 pages including 5 figures in revte

Experiences with a simplified microsimulation for the Dallas/Fort Worth area

We describe a simple framework for micro simulation of city traffic. A medium sized excerpt of Dallas was used to examine different levels of simulation fidelity of a cellular automaton method for the traffic flow simulation and a simple intersection model. We point out problems arising with the granular structure of the underlying rules of motion.Comment: accepted by Int.J.Mod.Phys.C, 20 pages, 14 figure

A Cellular Automaton Model for Bi-Directionnal Traffic

We investigate a cellular automaton (CA) model of traffic on a bi-directional two-lane road. Our model is an extension of the one-lane CA model of {Nagel and Schreckenberg 1992}, modified to account for interactions mediated by passing, and for a distribution of vehicle speeds. We chose values for the various parameters to approximate the behavior of real traffic. The density-flow diagram for the bi-directional model is compared to that of a one-lane model, showing the interaction of the two lanes. Results were also compared to experimental data, showing close agreement. This model helps bridge the gap between simplified cellular automata models and the complexity of real-world traffic.Comment: 4 pages 6 figures. Accepted Phys Rev

Non-scattering Metasurface-bound Cavities for Field Localization, Enhancement, and Suppression

We propose and analyse metasurface-bound invisible (non-scattering) partially open cavities where the inside field distribution can be engineered. It is demonstrated both theoretically and experimentally that the cavities exhibit unidirectional invisibility at the operating frequency with enhanced or suppressed field at different positions inside the cavity volume. Several examples of applications of the designed cavities are proposed and analyzed, in particular, cloaking sensors and obstacles, enhancement of emission, and "invisible waveguides". The non-scattering mode excited in the proposed cavity is driven by the incident wave and resembles an ideal bound state in the continuum of electromagnetic frequency spectrum. In contrast to known bound states in the continuum, the mode can stay localized in the cavity infinitely long, provided that the incident wave illuminates the cavity

Cluster density functional theory for lattice models based on the theory of Mobius functions

Rosenfeld's fundamental measure theory for lattice models is given a rigorous formulation in terms of the theory of Mobius functions of partially ordered sets. The free-energy density functional is expressed as an expansion in a finite set of lattice clusters. This set is endowed a partial order, so that the coefficients of the cluster expansion are connected to its Mobius function. Because of this, it is rigorously proven that a unique such expansion exists for any lattice model. The low-density analysis of the free-energy functional motivates a redefinition of the basic clusters (zero-dimensional cavities) which guarantees a correct zero-density limit of the pair and triplet direct correlation functions. This new definition extends Rosenfeld's theory to lattice model with any kind of short-range interaction (repulsive or attractive, hard or soft, one- or multi-component...). Finally, a proof is given that these functionals have a consistent dimensional reduction, i.e. the functional for dimension d' can be obtained from that for dimension d (d'<d) if the latter is evaluated at a density profile confined to a d'-dimensional subset.Comment: 21 pages, 2 figures, uses iopart.cls, as well as diagrams.sty (included

Coherent Retroreflective Metasurfaces

Inhomogeneous metasurfaces have shown possibilities for unprecedented control of wave propagation and scattering. While it is conventional to shine a single incident plane wave from one side of these metastructures, illuminating by several waves simultaneously from both sides may enhance possibilities to control scattered waves, which results in additional functionalities and novel applications. Here, we unveil how using coherent plane-wave illumination of a properly designed inhomogeneous metasurface sheet it is possible to realize controllable retroreflection. We call these metasurfaces as "coherent retroreflectors" and explain the method for realizing them both in theory and practice. We show that coherent retroreflectors can be used for filtering undesired modes and creation of field-localization regions in waveguides. The latter application is in resemblance to bound states in the radiation continuum.Comment: 6 pages, 4 figure

Effects of CPT and Lorentz Invariance Violation on Pulsar Kicks

The breakdown of Lorentz's and CPT invariance, as described by the Extension of the Standard Model, gives rise to a modification of the dispersion relation of particles. Consequences of such a modification are reviewed in the framework of pulsar kicks induced by neutrino oscillations (active-sterile conversion). A peculiar feature of the modified energy-momentum relations is the occurrence of terms of the form \delta {\bbox \Pi}\cdot {\bf {\hat p}}, where \delta {\bbox \Pi} accounts for the difference of spatial components of flavor depending coefficients which lead to the departure of the Lorentz symmetry, and ${\bf {\hat p}}={\bf p}/p$, being ${\bf p}$ the neutrino momentum. Owing to the relative orientation of ${\bf p}$ with respect to \delta {\bbox \Pi}, the {\it coupling} \delta {\bbox \Pi}\cdot {\bf {\hat p}} may induce the mechanism to generate the observed pulsar velocities. Topics related to the velocity distribution of pulsars are also discussed.Comment: 10 pages, 1 figur