Augmented Sparse Reconstruction of Protein Signaling Networks

The problem of reconstructing and identifying intracellular protein signaling and biochemical networks is of critical importance in biology today. We sought to develop a mathematical approach to this problem using, as a test case, one of the most well-studied and clinically important signaling networks in biology today, the epidermal growth factor receptor (EGFR) driven signaling cascade. More specifically, we suggest a method, augmented sparse reconstruction, for the identification of links among nodes of ordinary differential equation (ODE) networks from a small set of trajectories with different initial conditions. Our method builds a system of representation by using a collection of integrals of all given trajectories and by attenuating block of terms in the representation itself. The system of representation is then augmented with random vectors, and minimization of the 1-norm is used to find sparse representations for the dynamical interactions of each node. Augmentation by random vectors is crucial, since sparsity alone is not able to handle the large error-in-variables in the representation. Augmented sparse reconstruction allows to consider potentially very large spaces of models and it is able to detect with high accuracy the few relevant links among nodes, even when moderate noise is added to the measured trajectories. After showing the performance of our method on a model of the EGFR protein network, we sketch briefly the potential future therapeutic applications of this approach.Comment: 24 pages, 6 figure

Time-Resolved Studies of a Rolled-Up Semiconductor Microtube Laser

We report on lasing in rolled-up microtube resonators. Time-resolved studies on these semiconductor lasers containing GaAs quantum wells as optical gain material reveal particularly fast turn-on-times and short pulse emissions above the threshold. We observe a strong red-shift of the laser mode during the pulse emission which is compared to the time evolution of the charge-carrier density calculated by rate equations

Delay-Coordinates Embeddings as a Data Mining Tool for Denoising Speech Signals

In this paper we utilize techniques from the theory of non-linear dynamical systems to define a notion of embedding threshold estimators. More specifically we use delay-coordinates embeddings of sets of coefficients of the measured signal (in some chosen frame) as a data mining tool to separate structures that are likely to be generated by signals belonging to some predetermined data set. We describe a particular variation of the embedding threshold estimator implemented in a windowed Fourier frame, and we apply it to speech signals heavily corrupted with the addition of several types of white noise. Our experimental work seems to suggest that, after training on the data sets of interest,these estimators perform well for a variety of white noise processes and noise intensity levels. The method is compared, for the case of Gaussian white noise, to a block thresholding estimator

Fluctuations and stability in front propagation

Propagating fronts arising from bistable reaction-diffusion equations are a purely deterministic effect. Stochastic reaction-diffusion processes also show front propagation which coincides with the deterministic effect in the limit of small fluctuations (usually, large populations). However, for larger fluctuations propagation can be affected. We give an example, based on the classic spruce-budworm model, where the direction of wave propagation, i.e., the relative stability of two phases, can be reversed by fluctuations.Comment: 5 pages, 5 figure

Solar sail formation flying for deep-space remote sensing

In this paper we consider how 'near' term solar sails can be used in formation above the ecliptic plane to provide platforms for accurate and continuous remote sensing of the polar regions of the Earth. The dynamics of the solar sail elliptical restricted three-body problem (ERTBP) are exploited for formation flying by identifying a family of periodic orbits above the ecliptic plane. Moreover, we find a family of 1 year periodic orbits where each orbit corresponds to a unique solar sail orientation using a numerical continuation method. It is found through a number of example numerical simulations that this family of orbits can be used for solar sail formation flying. Furthermore, it is illustrated numerically that Solar Sails can provide stable formation keeping platforms that are robust to injection errors. In addition practical trajectories that pass close to the Earth and wind onto these periodic orbits above the ecliptic are identified

Structural Examination of Au/Ge(001) by Surface X-Ray Diffraction and Scanning Tunneling Microscopy

The one-dimensional reconstruction of Au/Ge(001) was investigated by means of autocorrelation functions from surface x-ray diffraction (SXRD) and scanning tunneling microscopy (STM). Interatomic distances found in the SXRD-Patterson map are substantiated by results from STM. The Au coverage, recently determined to be 3/4 of a monolayer of gold, together with SXRD leads to three non-equivalent positions for Au within the c(8x2) unit cell. Combined with structural information from STM topography and line profiling, two building blocks are identified: Au-Ge hetero-dimers within the top wire architecture and Au homo-dimers within the trenches. The incorporation of both components is discussed using density functional theory and model based Patterson maps by substituting Germanium atoms of the reconstructed Ge(001) surface.Comment: 5 pages, 3 figure

Observation of spinor dynamics in optically trapped 87Rb Bose-Einstein Condensates

We measure spin mixing of F=1 and F=2 spinor condensates of 87Rb atoms confined in an optical trap. We determine the spin mixing time to be typically less than 600 ms and observe spin population oscillations. The equilibrium spin configuration in the F=1 manifold is measured for different magnetic fields and found to show ferromagnetic behavior for low field gradients. An F=2 condensate is created by microwave excitation from F=1 manifold, and this spin-2 condensate is observed to decay exponentially with time constant 250 ms. Despite the short lifetime in the F=2 manifold, spin mixing of the condensate is observed within 50 ms.Comment: 4 pages, 6 figure