Non-exponential decay via tunneling in tight-binding lattices and the optical Zeno effect

An exactly-solvable model for the decay of a metastable state coupled to a semi-infinite tight-binding lattice, showing large deviations from exponential decay in the strong coupling regime, is presented. An optical realization of the lattice model, based on discrete diffraction in a semi-infinite array of tunneling-coupled optical waveguides, is proposed to test non-exponential decay and for the observation of an optical analog of the quantum Zeno effect

Spontaneous and Stimulated Raman Scattering near Metal Nanostructures in the Ultrafast, High-Intensity regime

The inclusion of atomic inversion in Raman scattering can significantly alter field dynamics in plasmonic settings. Our calculations show that large local fields and femtosecond pulses combine to yield: (i) population inversion within hot spots; (ii) gain saturation; and (iii) conversion efficiencies characterized by a switch-like transition to the stimulated regime that spans twelve orders of magnitude. While in Raman scattering atomic inversion is usually neglected, we demonstrate that in some circumstances full accounting of the dynamics of the Bloch vector is required

Solvable glassy system: static versus dynamical transition

A directed polymer is considered on a flat substrate with randomly located parallel ridges. It prefers to lie inside wide regions between the ridges. When the transversel width $W=\exp(\lambda L^{1/3})$ is exponential in the longitudinal length $L$, there can be a large number $\sim \exp L^{1/3}$ of available wide states. This ``complexity'' causes a phase transition from a high temperature phase where the polymer lies in the widest lane, to a glassy low temperature phase where it lies in one of many narrower lanes. Starting from a uniform initial distribution of independent polymers, equilibration up to some exponential time scale induces a sharp dynamical transition. When the temperature is slowly increased with time, this occurs at a tunable temperature. There is an asymmetry between cooling and heating. The structure of phase space in the low temperature non-equilibrium glassy phase is of a one-level tree.Comment: 4 pages revte

A Dynamical Model of Harmonic Generation in Centrosymmetric Semiconductors

We study second and third harmonic generation in centrosymmetric semiconductors at visible and UV wavelengths in bulk and cavity environments. Second harmonic generation is due to a combination of symmetry breaking, the magnetic portion of the Lorentz force, and quadrupolar contributions that impart peculiar features to the angular dependence of the generated signals, in analogy to what occurs in metals. The material is assumed to have a non-zero, third order nonlinearity that gives rise to most of the third harmonic signal. Using the parameters of bulk Silicon we predict that cavity environments can significantly modify second harmonic generation (390nm) with dramatic improvements for third harmonic generation (266nm). This occurs despite the fact that the harmonics may be tuned to a wavelength range where the dielectric function of the material is negative: a phase locking mechanism binds the pump to the generated signals and inhibits their absorption. These results point the way to novel uses and flexibility of materials like Silicon as nonlinear media in the visible and UV ranges

Minimal Conflicting Sets for the Consecutive Ones Property in ancestral genome reconstruction

A binary matrix has the Consecutive Ones Property (C1P) if its columns can be ordered in such a way that all 1's on each row are consecutive. A Minimal Conflicting Set is a set of rows that does not have the C1P, but every proper subset has the C1P. Such submatrices have been considered in comparative genomics applications, but very little is known about their combinatorial structure and efficient algorithms to compute them. We first describe an algorithm that detects rows that belong to Minimal Conflicting Sets. This algorithm has a polynomial time complexity when the number of 1's in each row of the considered matrix is bounded by a constant. Next, we show that the problem of computing all Minimal Conflicting Sets can be reduced to the joint generation of all minimal true clauses and maximal false clauses for some monotone boolean function. We use these methods on simulated data related to ancestral genome reconstruction to show that computing Minimal Conflicting Set is useful in discriminating between true positive and false positive ancestral syntenies. We also study a dataset of yeast genomes and address the reliability of an ancestral genome proposal of the Saccahromycetaceae yeasts.Comment: 20 pages, 3 figure

Generation and manipulation of squeezed states of light in optical networks for quantum communication and computation

We analyze a fiber-optic component which could find multiple uses in novel information-processing systems utilizing squeezed states of light. Our approach is based on the phenomenon of photon-number squeezing of soliton noise after the soliton has propagated through a nonlinear optical fiber. Applications of this component in optical networks for quantum computation and quantum cryptography are discussed.Comment: 12 pages, 2 figures; submitted to Journal of Optics

Consistently Simulating a Wide Range of Atmospheric Scenarios for K2-18b with a Flexible Radiative Transfer Module

The atmospheres of small, potentially rocky exoplanets are expected to cover a diverse range in composition and mass. Studying such objects therefore requires flexible and wide-ranging modeling capabilities. We present in this work the essential development steps that lead to our flexible radiative transfer module, REDFOX, and validate REDFOX for the Solar system planets Earth, Venus and Mars, as well as for steam atmospheres. REDFOX is a k-distribution model using the correlated-k approach with random overlap method for the calculation of opacities used in the $\delta$-two-stream approximation for radiative transfer. Opacity contributions from Rayleigh scattering, UV / visible cross sections and continua can be added selectively. With the improved capabilities of our new model, we calculate various atmospheric scenarios for K2-18b, a super-Earth / sub-Neptune with $\sim$8 M$_\oplus$ orbiting in the temperate zone around an M-star, with recently observed H$_2$O spectral features in the infrared. We model Earth-like, Venus-like, as well as H$_2$-He primary atmospheres of different Solar metallicity and show resulting climates and spectral characteristics, compared to observed data. Our results suggest that K2-18b has an H$_2$-He atmosphere with limited amounts of H$_2$O and CH$_4$. Results do not support the possibility of K2-18b having a water reservoir directly exposed to the atmosphere, which would reduce atmospheric scale heights, hence too the amplitudes of spectral features inconsistent with the observations. We also performed tests for H$_2$-He atmospheres up to 50 times Solar metallicity, all compatible with the observations.Comment: 28 pages, 13 figures, accepted for publication in Ap

Decoherence of Quantum-Enhanced Timing Accuracy

Quantum enhancement of optical pulse timing accuracy is investigated in the Heisenberg picture. Effects of optical loss, group-velocity dispersion, and Kerr nonlinearity on the position and momentum of an optical pulse are studied via Heisenberg equations of motion. Using the developed formalism, the impact of decoherence by optical loss on the use of adiabatic soliton control for beating the timing standard quantum limit [Tsang, Phys. Rev. Lett. 97, 023902 (2006)] is analyzed theoretically and numerically. The analysis shows that an appreciable enhancement can be achieved using current technology, despite an increase in timing jitter mainly due to the Gordon-Haus effect. The decoherence effect of optical loss on the transmission of quantum-enhanced timing information is also studied, in order to identify situations in which the enhancement is able to survive.Comment: 12 pages, 4 figures, submitte

Revisiting the Training of Logic Models of Protein Signaling Networks with a Formal Approach based on Answer Set Programming

A fundamental question in systems biology is the construction and training to data of mathematical models. Logic formalisms have become very popular to model signaling networks because their simplicity allows us to model large systems encompassing hundreds of proteins. An approach to train (Boolean) logic models to high-throughput phospho-proteomics data was recently introduced and solved using optimization heuristics based on stochastic methods. Here we demonstrate how this problem can be solved using Answer Set Programming (ASP), a declarative problem solving paradigm, in which a problem is encoded as a logical program such that its answer sets represent solutions to the problem. ASP has significant improvements over heuristic methods in terms of efficiency and scalability, it guarantees global optimality of solutions as well as provides a complete set of solutions. We illustrate the application of ASP with in silico cases based on realistic networks and data