Logic Integer Programming Models for Signaling Networks

We propose a static and a dynamic approach to model biological signaling networks, and show how each can be used to answer relevant biological questions. For this we use the two different mathematical tools of Propositional Logic and Integer Programming. The power of discrete mathematics for handling qualitative as well as quantitative data has so far not been exploited in Molecular Biology, which is mostly driven by experimental research, relying on first-order or statistical models. The arising logic statements and integer programs are analyzed and can be solved with standard software. For a restricted class of problems the logic models reduce to a polynomial-time solvable satisfiability algorithm. Additionally, a more dynamic model enables enumeration of possible time resolutions in poly-logarithmic time. Computational experiments are included

Optical Lenses for Atomic Beams

Superpositions of paraxial laser beam modes to generate atom-optical lenses based on the optical dipole force are investigated theoretically. Thin, wide, parabolic, cylindrical and circular atom lenses with numerical apertures much greater than those reported in the literature to date can be synthesized. This superposition approach promises to make high quality atom beam imaging and nano-deposition feasible.Comment: 10 figure

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

Noise in Electron Devices

Contains a report on a research project

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

Letters between Jos. B. Haus and W. J. Kerr

Letters concerning a student position at the Utah Agricultural College

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

Electromagnetics from a quasistatic perspective

Quasistatics is introduced so that it fits smoothly into the standard textbook presentation of electrodynamics. The usual path from statics to general electrodynamics is rather short and surprisingly simple. A closer look reveals however that it is not without confusing issues as has been illustrated by many contributions to this Journal. Quasistatic theory is conceptually useful by providing an intermediate level in between statics and the full set of Maxwell's equations. Quasistatics is easier than general electrodynamics and in some ways more similar to statics. It is however, in terms of interesting physics and important applications, far richer than statics. Quasistatics is much used in electromagnetic modeling, an activity that today is possible on a PC and which also has great pedagogical potential. The use of electromagnetic simulations in teaching gives additional support for the importance of quasistatics. This activity may also motivate some change of focus in the presentation of basic electrodynamics

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