Compressive Sensing DNA Microarrays

Compressive sensing microarrays (CSMs) are DNA-based sensors that operate using group testing and compressive sensing (CS) principles. In contrast to conventional DNA microarrays, in which each genetic sensor is designed to respond to a single target, in a CSM, each sensor responds to a set of targets. We study the problem of designing CSMs that simultaneously account for both the constraints from CS theory and the biochemistry of probe-target DNA hybridization. An appropriate cross-hybridization model is proposed for CSMs, and several methods are developed for probe design and CS signal recovery based on the new model. Lab experiments suggest that in order to achieve accurate hybridization profiling, consensus probe sequences are required to have sequence homology of at least 80% with all targets to be detected. Furthermore, out-of-equilibrium datasets are usually as accurate as those obtained from equilibrium conditions. Consequently, one can use CSMs in applications in which only short hybridization times are allowed

Synthesis for Constrained Nonlinear Systems using Hybridization and Robust Controllers on Simplices

In this paper, we propose an approach to controller synthesis for a class of constrained nonlinear systems. It is based on the use of a hybridization, that is a hybrid abstraction of the nonlinear dynamics. This abstraction is defined on a triangulation of the state-space where on each simplex of the triangulation, the nonlinear dynamics is conservatively approximated by an affine system subject to disturbances. Except for the disturbances, this hybridization can be seen as a piecewise affine hybrid system on simplices for which appealing control synthesis techniques have been developed in the past decade. We extend these techniques to handle systems subject to disturbances by synthesizing and coordinating local robust affine controllers defined on the simplices of the triangulation. We show that the resulting hybrid controller can be used to control successfully the original constrained nonlinear system. Our approach, though conservative, can be fully automated and is computationally tractable. To show its effectiveness in practical applications, we apply our method to control a pendulum mounted on a cart

Real-time DNA microarray analysis

We present a quantification method for affinity-based DNA microarrays which is based on the real-time measurements of hybridization kinetics. This method, i.e. real-time DNA microarrays, enhances the detection dynamic range of conventional systems by being impervious to probe saturation in the capturing spots, washing artifacts, microarray spot-to-spot variations, and other signal amplitude-affecting non-idealities. We demonstrate in both theory and practice that the time-constant of target capturing in microarrays, similar to all affinity-based biosensors, is inversely proportional to the concentration of the target analyte, which we subsequently use as the fundamental parameter to estimate the concentration of the analytes. Furthermore, to empirically validate the capabilities of this method in practical applications, we present a FRET-based assay which enables the real-time detection in gene expression DNA microarrays

Adjoint-Based Error Estimation and Mesh Adaptation for Hybridized Discontinuous Galerkin Methods

We present a robust and efficient target-based mesh adaptation methodology, building on hybridized discontinuous Galerkin schemes for (nonlinear) convection-diffusion problems, including the compressible Euler and Navier-Stokes equations. Hybridization of finite element discretizations has the main advantage, that the resulting set of algebraic equations has globally coupled degrees of freedom only on the skeleton of the computational mesh. Consequently, solving for these degrees of freedom involves the solution of a potentially much smaller system. This not only reduces storage requirements, but also allows for a faster solution with iterative solvers. The mesh adaptation is driven by an error estimate obtained via a discrete adjoint approach. Furthermore, the computed target functional can be corrected with this error estimate to obtain an even more accurate value. The aim of this paper is twofold: Firstly, to show the superiority of adjoint-based mesh adaptation over uniform and residual-based mesh refinement, and secondly to investigate the efficiency of the global error estimate

A nested hybridizable discontinuous Galerkin method for computing second-harmonic generation in three-dimensional metallic nanostructures

In this paper, we develop a nested hybridizable discontinuous Galerkin (HDG) method to numerically solve the Maxwell's equations coupled with the hydrodynamic model for the conduction-band electrons in metals. By means of a static condensation to eliminate the degrees of freedom of the approximate solution defined in the elements, the HDG method yields a linear system in terms of the degrees of freedom of the approximate trace defined on the element boundaries. Furthermore, we propose to reorder these degrees of freedom so that the linear system accommodates a second static condensation to eliminate a large portion of the degrees of freedom of the approximate trace, thereby yielding a much smaller linear system. For the particular metallic structures considered in this paper, the resulting linear system obtained by means of nested static condensations is a block tridiagonal system, which can be solved efficiently. We apply the nested HDG method to compute the second harmonic generation (SHG) on a triangular coaxial periodic nanogap structure. This nonlinear optics phenomenon features rapid field variations and extreme boundary-layer structures that span multiple length scales. Numerical results show that the ability to identify structures which exhibit resonances at $\omega$ and $2\omega$ is paramount to excite the second harmonic response.Comment: 31 pages, 7 figure

Spectral Densities from Dynamic Density-Matrix Renormalization

Dynamic density-matrix renormalization provides valuable numerical information on dynamic correlations by computing convolutions of the corresponding spectral densities. Here we discuss and illustrate how and to which extent such data can be deconvolved to retrieve the wanted spectral densities. We advocate a nonlinear deconvolution scheme which minimizes the bias in the ansatz for the spectral density. The procedure is illustrated for the line shape and width of the Kondo peak (low energy feature) and for the line shape of the Hubbard satellites (high energy feature) of the single impurity Anderson model. It is found that the Hubbard satellites are strongly asymmetric.Comment: RevTeX 4, 11 pages, 7 eps figures; published versio

Dynamical structure factor of a nonlinear Klein-Gordon lattice

The quantum modes of a nonlinear Klein-Gordon lattice have been computed numerically [L. Proville, Phys. Rev. B 71, 104306 (2005)]. The on-site nonlinearity has been found to lead to phonon bound states. In the present paper, we compute numerically the dynamical structure factor so as to simulate the coherent scattering cross section at low temperature. The inelastic contribution is studied as a function of the on-site anharmonicity. Interestingly, our numerical method is not limited to the weak anharmonicity and permits one to study thoroughly the spectra of nonlinear phonons