Predicate Abstraction with Under-approximation Refinement

We propose an abstraction-based model checking method which relies on refinement of an under-approximation of the feasible behaviors of the system under analysis. The method preserves errors to safety properties, since all analyzed behaviors are feasible by definition. The method does not require an abstract transition relation to be generated, but instead executes the concrete transitions while storing abstract versions of the concrete states, as specified by a set of abstraction predicates. For each explored transition the method checks, with the help of a theorem prover, whether there is any loss of precision introduced by abstraction. The results of these checks are used to decide termination or to refine the abstraction by generating new abstraction predicates. If the (possibly infinite) concrete system under analysis has a finite bisimulation quotient, then the method is guaranteed to eventually explore an equivalent finite bisimilar structure. We illustrate the application of the approach for checking concurrent programs.Comment: 22 pages, 3 figures, accepted for publication in Logical Methods in Computer Science journal (special issue CAV 2005

3D spatially-resolved optical energy density enhanced by wavefront shaping

We study the three-dimensional (3D) spatially-resolved distribution of the energy density of light in a 3D scattering medium upon the excitation of open transmission channels. The open transmission channels are excited by spatially shaping the incident optical wavefronts. To probe the local energy density, we excite isolated fluorescent nanospheres distributed inside the medium. From the spatial fluorescent intensity pattern we obtain the position of each nanosphere, while the total fluorescent intensity gauges the energy density. Our 3D spatially-resolved measurements reveal that the local energy density versus depth (z) is enhanced up to 26X at the back surface of the medium, while it strongly depends on the transverse (x; y) position. We successfully interpret our results with a newly developed 3D model that considers the time-reversed diffusion starting from a point source at the back surface. Our results are relevant for white LEDs, random lasers, solar cells, and biomedical optics

Quantitative analysis of directional spontaneous emission spectra from light sources in photonic crystals

We have performed angle-resolved measurements of spontaneous-emission spectra from laser dyes and quantum dots in opal and inverse opal photonic crystals. Pronounced directional dependencies of the emission spectra are observed: angular ranges of strongly reduced emission adjoin with angular ranges of enhanced emission. It appears that emission from embedded light sources is affected both by the periodicity and by the structural imperfections of the crystals: the photons are Bragg diffracted by lattice planes and scattered by unavoidable structural disorder. Using a model comprising diffuse light transport and photonic band structure, we quantitatively explain the directional emission spectra. This provides detailed understanding of the transport of spontaneously emitted light in real photonic crystals, which is essential in the interpretation of quantum-optics in photonic band-gap crystals and for applications wherein directional emission and total emission power are controlled.Comment: 10 pages, 10 figures, corrected pdf, inserted new referenc

A Survey of New Trends in Symbolic Execution for Software Testing and Analysis

Symbolic execution is a well-known program analysis technique which represents values of program inputs with symbolic values instead of concrete (initialized) data and executes the program by manipulating program expressions involving the symbolic values. Symbolic execution has been proposed over three decades ago but recently it has found renewed interest in the research community, due in part to the progress in decision procedures, availability of powerful computers and new algorithmic developments. We provide a survey of some of the new research trends in symbolic execution, with particular emphasis on applications to test generation and program analysis. We first describe an approach that handles complex programming constructs such as input data structures, arrays, as well as multi-threading. We follow with a discussion of abstraction techniques that can be used to limit the (possibly infinite) number of symbolic configurations that need to be analyzed for the symbolic execution of looping programs. Furthermore, we describe recent hybrid techniques that combine concrete and symbolic execution to overcome some of the inherent limitations of symbolic execution, such as handling native code or availability of decision procedures for the application domain. Finally, we give a short survey of interesting new applications, such as predictive testing, invariant inference, program repair, analysis of parallel numerical programs and differential symbolic execution

Engineering Dehydrated Amino Acid Residues in the Antimicrobial Peptide Nisin

The small antimicrobial peptide nisin, produced by Lactococcus lactis, contains the uncommon amino acid residues dehydroalanine and dehydrobutyrine and five thio ether bridges. Since these structures are posttranslationally formed from Ser, Thr, and Cys residues, it is feasible to study their role in nisin function and biosynthesis by protein engineering. Here we report the development of an expression system for mutated nisin Z (nisZ) genes, using nisin A producing L. lactis as a host. Replacement by site-directed mutagenesis of the Ser-5 codon in nisZ by a Thr codon, led to a mutant with a dehydrobutyrine instead of a dehydroalanine residue at position 5, as shown by NMR. Its antimicrobial activity was 2-10-fold lower relative to wild-type nisin Z, depending on the indicator strain used. In another mutagenesis study a double mutation was introduced in the nisZ gene by replacing the codons for Met-17 and Gly-18 by codons for Gln and Thr, respectively, as in the third lanthionine ring of the related antimicrobial peptide subtilin from Bacillus subtilis. This resulted in the simultaneous production of two mutant species, one containing a Thr residue and the other containing a dehydrobutyrine residue at position 18, both having different bacteriocidal properties.

Strongly nonexponential time-resolved fluorescence of quantum-dot ensembles in three-dimensional photonic crystals

We observe experimentally that ensembles of quantum dots in three-dimensional (3D) photonic crystals reveal strongly nonexponential time-resolved emission. These complex emission decay curves are analyzed with a continuous distribution of decay rates. The log-normal distribution describes the decays well for all studied lattice parameters. The distribution width is identified with variations of the radiative emission rates of quantum dots with various positions and dipole orientations in the unit cell. We find a striking sixfold change of the width of the distribution by varying the lattice parameter. This interpretation qualitatively agrees with the calculations of the 3D projected local density of states. We therefore conclude that fluorescence decay of ensembles of quantum dots is highly nonexponential to an extent that is controlled by photonic crystals

Selective coupling of optical energy into the fundamental diffusion mode of a scattering medium

We demonstrate experimentally that optical wavefront shaping selectively couples light into the fundamental diffusion mode of a scattering medium. The total energy density inside a scattering medium of zinc oxide (ZnO) nanoparticles was probed by measuring the emitted fluorescent power of spheres that were randomly positioned inside the medium. The fluorescent power of an optimized incident wave front is observed to be enhanced compared to a non-optimized incident front. The observed enhancement increases with sample thickness. Based on diffusion theory, we derive a model wherein the distribution of energy density of wavefront-shaped light is described by the fundamental diffusion mode. The agreement between our model and the data is striking not in the least since there are no adjustable parameters. Enhanced total energy density is crucial to increase the efficiency of white LEDs, solar cells, and of random lasers, as well as to realize controlled illumination in biomedical optics.Comment: 5 pages, 5 figure

Test Input Generation for Red-Black Trees using Abstraction

We consider the problem of test input generation for code that manipulates complex data structures. Test inputs are sequences of method calls from the data structure interface. We describe test input generation techniques that rely on state matching to avoid generation of redundant tests. Exhaustive techniques use explicit state model checking to explore all the possible test sequences up to predefined input sizes. Lossy techniques rely on abstraction mappings to compute and store abstract versions of the concrete states; they explore under-approximations of all the possible test sequences. We have implemented the techniques on top of the Java PathFinder model checker and we evaluate them using a Java implementation of red-black trees