Theoretical and experimental analysis of arrayed imaging reflectometry as a sensitive proteomics technique

Arrayed imaging reflectometry (AIR) is a newly developed label-free optical biosensing technique based on the creation and perturbation of a condition of zero reflectance on a silicon substrate. The antireflective coating is formed by covalently immobilizing arrayed probes on a silicon dioxide film. Probe-target complex formation causes a localized increase in optical thickness and a measurable reflectance change. To evaluate the performance of AIR, we have employed two proteins, intimin and tir, from enteropathogenic E. coli that are critical to the bacterium's mechanism of host infection. Using substrates functionalized with the intimin-binding domain of tir, we demonstrate detection of the extracellular domain of intimin at concentrations as low as 10 pM. Through the use of a diffusion-limited model for the intimin-tir binding interaction at this concentration, we estimate the detected intimin surface concentration to be 0.33 pg/mm2.     

Self-organization and complexity: a new age for theory,computation and experiment

I first describe the notion of self-organization as a property of far-from-equilibrium nonlinear dissipative dynamical systems. Rather than describing such complex systems at a purely phenomenological level, however, I focus attention on the emergent nature of this complexity, by analysing a few examples of physical and physicochemical systems with simple underlying microscopic dynamics yet complex, self-organizing macroscopic properties. These include several mesoscopic models of fluid dynamics as well as a modern approach to nucleation and growth phenomena. Finally, I discuss how the advent of computational grids is set to provide a major boost to the study of such complex, self-organizing systems.     

Scientometrics,theory of experiment and optimization of research

An approach to optimization of research based on the theory of experiment and scientometrics is proposed. Research is treated as an experiment aimed at attainment of optimal conditions. The following successive phases of optimization have been singled out: selection of optimisation parameters and factors, carrying out the experiment, and processing and interpreting the results obtained. Methods of multidimensional classification and screening are recommended for selection of optimization parameters and factors. Evolutionary operation representations are used at the optimization stage. Problems of optimization research should be tackled in centres of scientific information where data on advances made in various scientific fields are accumulated.     

Polarization properties of corner-cube retroreflectors: theory and experiment

Polarization properties of the corner-cube retroreflector are discussed theoretically by use of ray tracing and analytical geometry. The Jones matrices and eigenpolarizations of the six propagation trips of the corner-cube retroreflector are derived. An experiment is also set up for the determination of the linear eigenpolarizations and the output states of polarization for incident linearly polarized light. The experimental results are consistent with theoretical expectations.     

Tomographic imaging of an ultrasonic field in a plane by use of a linear array: theory and experiment

Quantitative ultrasonic characterization of in-homogeneous and anisotropic materials is often difficult due to undesired phenomena such as beam steering and phase aberration of the insonifying field. We introduce a method based on tomographic reconstruction techniques for the visualization of an ultrasonic field using a linear array rotated in a plane. Tomographic reconstruction of the ultrasonic field is made possible through the phase-sensitive nature of the tall, narrow piezoelectric elements of a linear array that act as parallel line integrators of the pressure field. We validate the proposed imaging method through numerical simulations of propagated ultrasonic fields based upon the angular spectrum decomposition technique. We then demonstrate the technique with experimental measurements of two textile composites and a reference water path. We reconstruct images of the real and imaginary parts of a transmitted 2 MHz ultrasonic field that are then combined to reconstruct images of the power and unwrapped phase. We also construct images of the attenuation and phase shift for several regions of the composites. Our results demonstrate that tomographic imaging of an ultrasonic field in a plane using a rotated linear array can potentially improve ultrasonic characterization of complex materials.     

Buoyancy driven convection in vertically shaken granular matter: experiment, numerics, and theory

Buoyancy driven granular convection is studied for a shallow, vertically shaken granular bed in a quasi 2D container. Starting from the granular Leidenfrost state, in which a dense particle cluster floats on top of a dilute gaseous layer of fast particles (Meerson et al. in Phys Rev Lett 91:024301, 2003; Eshuis et al. in Phys Rev Lett 95:258001, 2005), we witness the emergence of counter-rotating convection rolls when the shaking strength is increased above a critical level. This resembles the classical onset of convection—at a critical value of the Rayleigh number—in a fluid heated from below. The same transition, even quantitatively, is seen in molecular dynamics simulations, and explained by a hydrodynamic-like model in which the granular material is treated as a continuum. The critical shaking strength for the onset of granular convection is accurately reproduced by a linear stability analysis of the model. The results from experiment, simulation, and theory are in good agreement. The present paper extends and completes our earlier analysis (Eshuis et al. in Phys Rev Lett 104:038001, 2010).     

The feedback loop between theory,simulation and experiment for plasticity and property modeling

Recent advances in theory, simulation and experiment are leading to new capabilities for understanding and characterizing the relation between dislocation substructure evolution and materials properties and performance. With the emergence of large-scale computational capabilities, techniques such as three-dimensional discrete dislocation dynamics simulations are providing new insights to a range of materials deformation phenomena. Such simulations provide direct measures of dislocation motion and substructure development at small and continuously increasing length scales and time scales. Concurrently, the advent of new experimental techniques promises to revolutionize our ability to directly characterize dislocation substructures and their relationship to the microstructure of a range of material systems. Taken by themselves, the simulations and experiments will greatly advance our understanding of materials behavior. We argue, however, that close linkage of the two will provide critically needed validation and enable progress in solving some of the most challenging problems of plasticity, thereby profoundly impacting our ability to predict properties and performance of materials in engineered systems.     

Design of a compliant-cylinder-type fiber-optic accelerometer: theory and experiment

Experimental and theoretical research was carried out in order to establish the dependence of the performance of a compliant-cylinder-based fiber-optic accelerometer on the geometry and elastic properties of the transducer cylinders. The sensitivity and the natural frequency of the sensor were measured as a function of the ratio ε = (inner cylinder diameter)/(outer cylinder diameter). Two transducer materials with different elastic properties, a silicone rubber (Ecosil) and a polyetheretherketone polymer (PEEK 450G), were examined. It was found that with decreasing ε the sensitivity increases in the case of Ecosil and decreases in the case of PEEK. In both cases the natural frequency increases with decreasing ε. A simple analytical model was developed in order to explain this behavior qualitatively. The model takes into account the contributions to the effective stiffness from both the cylinder material and the fiber wrapped around the cylinder. The model is useful for the design of such types of accelerometer.     

The Materials Genome Initiative,the interplay of experiment,theory and computation

Advances in theoretical, computational and experimental materials science and engineering offer not only the promise to accelerate the pace at which new materials are discovered, but also to reduce the time required to bring new products to market. The so-called Materials Genome Initiative seeks to capitalize on that promise by identifying innovative research paradigms that integrate theory, computation, synthesis, and characterization in manners that, until recently, were not possible. A workshop was held at the National Science Foundation in December of 2013 to identify some of the central challenges and opportunities facing materials research within the context of that initiative. This article summarizes the findings of the workshop, and presents a series of concrete recommendations with the potential to facilitate its implementation. It also provides an overview of timely fundamental, technical and logistical challenges, organized according to distinct classes of materials, whose solution could have significant practical and societal benefits.     

Virtual experiments,physical validation: dental morphology at the intersection of experiment and theory

Computational models such as finite-element analysis offer biologists a means of exploring the structural mechanics of biological systems that cannot be directly observed. Validated against experimental data, a model can be manipulated to perform virtual experiments, testing variables that are hard to control in physical experiments. The relationship between tooth form and the ability to break down prey is key to understanding the evolution of dentition. Recent experimental work has quantified how tooth shape promotes fracture in biological materials. We present a validated finite-element model derived from physical compression experiments. The model shows close agreement with strain patterns observed in photoelastic test materials and reaction forces measured during these experiments. We use the model to measure strain energy within the test material when different tooth shapes are used. Results show that notched blades deform materials for less strain energy cost than straight blades, giving insights into the energetic relationship between tooth form and prey materials. We identify a hypothetical ‘optimal’ blade angle that minimizes strain energy costs and test alternative prey materials via virtual experiments. Using experimental data and computational models offers an integrative approach to understand the mechanics of tooth morphology.     

Spatial beam shaping of ultrashort laser pulses: theory and experiment

We studied the spatial intensity profile of an ultrashort laser pulse passing through a laser beam shaping system, which uses diffractive optical elements to reshape a Gaussian beam profile into a flat-topped distribution. Both dispersion and nonlinear self-phase modulation are included in the theoretical model. Our calculation shows that this system works well for ultrashort pulses (approximately 100 fs) when the pulse peak intensity is less than 5 x 10(11) W/cm2. Experimental results are presented for 136 fs pulses at 800 nm wavelength from a Ti:sapphire laser with a 6 nJ pulse energy. We also studied the effects of lateral misalignment, beam-size deviation, and defocusing on the energy fluence profile.     

Designing techniques for systemic impact: lessons from C-K theory and matroid structures

As underlined in Arthur’s book “the nature of technology”, we are very knowledgeable on the design of objects, services or technical systems, but we don’t know much on the dynamics of technologies. Still contemporary innovation often consists in designing techniques with systemic impact. They are pervasive—both invasive and perturbing—and they recompose the family of techniques. Can we model the impact and the design of such techniques? More specifically: how can one design generic technology, i.e. a single technology that provokes a complete reordering of families of techniques? Advances in design theories open new possibilities to answer these questions. In this paper, we use C-K design theory and a matroid-based model of the set of techniques to propose a new model (C-K/Ma) of the dynamics of techniques, accounting for the design of generic technologies. We show that: (1) C-K/Ma accounts for basic phenomena in the design of pervasive (and non-pervasive) techniques, in particular for generic techniques. (2) C-K/Ma, when applied iteratively, helps to propose new laws for the dynamics of techniques and helps to build strategic alternatives in the design of techniques. Moreover, C-K/Ma contributes to design theory since it provides some basic quantifiers and operations that could lead to a computational model of the process of designing techniques with systemic impact.     

Angular spectrum of light transmitted through turbid media: theory and experiment

Measurements of the angular spectrum of light transmitted through turbid slabs with monodispersions of polystyrene spheres have been performed. The results obtained are compared with theoretical calculations, based on the small-angle approximation of the radiative transfer theory. The experimental data and the theoretical results coincide with a high accuracy, which allows us to develop the laser diffraction spectroscopy of optically thick light-scattering layers.     

Using magnetic levitation to produce cryogenic targets for inertial fusion energy: experiment and theory

We present experimental and theoretical studies of magnetic levitation of hydrogen gas bubble surrounded by liquid hydrogen confined in a semi-transparent spherical shell of 3 mm internal diameter. Such shells are used as targets for the inertial confinement fusion (ICF), for which a homogeneous (within a few percent) layer of a hydrogen isotope should be deposited on the internal walls of the shells. The gravity does not allow the hydrogen layer thickness to be homogeneous. To compensate this gravity effect, we have used a non-homogeneous magnetic field created by a 10 T superconductive solenoid. Our experiments show that the magnetic levitation homogenizes the thickness of liquid hydrogen layer. However, the variation of the layer thickness is very difficult to measure experimentally. Our theoretical model allows the exact shape of the layer to be predicted. The model takes into account the surface tension, gravity, van der Waals, and magnetic forces. The numerical calculation shows that the homogeneity of the layer thickness is satisfactory for the ICF purposes.     

Spatially offset Raman microspectroscopy of highly scattering tissue: theory and experiment

Spatially Offset Raman Spectroscopy (SORS) has seen considerable interest in recent years as a tool for noninvasively acquiring Raman spectra from beneath the surface of a sample. One of the major limitations of the SORS technique is that accurate knowledge of the optical properties of the medium is required to translate an offset into a sample depth. We report on the benefits of preforming SORS using micron offset distances as opposed to the more typical millimeter offsets used. Monte Carlo simulations are used to demonstrate that at these small offsets, the results depend less on the scattering coefficient of the material. These results provide new insights into the SORS technique and will improve the practical application of SORS in the future.     

Optical characterisation of SiOxCyHz thin films non-uniform in thickness using spectroscopic ellipsometry, spectroscopic reflectometry and spectroscopic imaging reflectometry

The combined optical method enabling us to perform the complete optical characterisation of weakly absorbing non-uniform thin films is described. This method is based on the combination of standard variable angle spectroscopic ellipsometry, standard spectroscopic reflectometry at near normal incidence and spectroscopic imaging reflectometry applied at normal incidence. The spectral dependences of the optical constants are determined using the non-imaging methods by using the dispersion model based on parametrisation of the density of electronic states. The local thickness distribution is then determined by imaging reflectometry. The method is illustrated by means of the complete optical characterisation of SiO_xC_yH_z thin films.     

Nonlinear optimisation techniques for accelerator performance improvement on-line: recent trials and experiment for the CERN antiproton accumulator

The use of function minimisation techniques for optimum design according to given performance criteria is well-known. Given a well-defined criterion and a means of evaluating it precisely, the problem reduces to choosing the best optimisation procedure to suit the problem. Direct search techniques which do not generally rely on the computation of derivatives of the error function are ideal for on-line improvement of the global accelerator performance since the error function is not known analytically, e.g. the number of antiprotons stored in the antiproton accumulator ring on a pulse-to-pulse basis as a function of all the antiproton production and stochastic cooling system parameters.The user-friendliness of the NODAL interpreter at the man-machine interaction level, its capability to easily control and manipulate equipment as well as its capability to synchronise with respect to time events on a cycle-to-cycle basis makes it suitable for an on-line accelerator performance optimisation type of application. A modular procedure, based on the Simplex technique [1] has been implemented recently which allows function minimisation depending on the error function definition module. This enables an easy manipulation of variables and synchronization with machine events.For the antiproton accumulator (AA), while the circulating beam current transformer lacks the resolution to measure the exact number of antiprotons stored on a pulse-to-pulse basis, there are a large number of electrons produced in the production process [2] and a signal emanating from these can be adapted to provide the performance criterion and appropriate parameters used as function variables in the optimisation process. First trials based on optimisation of injection of antiprotons in the AA look promising, but further work is necessary in the direct definition of the error functions.     

Macroscopic fracture surface energy of unidirectional metal matrix composites: experiment and theory

A method of measuring the macroscopic frature surface energyγ _F is studied and its verification is made compared with the theoretical prediction. Metal matrix composites used in the experiment are unidirectional graphite fibre-reinforced 6061 aluminium. A good agreement between the experimental and theoretical results is obtained.     

Bandwidth dependence of pulse duration in intra-cavity frequency-doubled lasers: theory and experiment

A model is presented of pulse evolution in broadband intra-cavity frequency-doubled lasers. The model utilizes normalized coupled rate equations for each mode, including terms that represent the loss due to nonlinear mixing between longitudinal modes. The pulse energy, shape, peak power and duration are calculated by numerical solution of these equations. The model shows that the pulse duration depends not only on the initial population inversion, photon lifetime and the effective nonlinear coupling coefficient, as is the case for narrowband lasers, but also on the fundamental bandwidth. A gain-switched Ti:sapphire laser, pumped by a Q-switched Nd-doped yttrium aluminium garnet laser at 532?nm, was frequency doubled using an intra-cavity β-barium borate crystal. The bandwidth was reduced from about 25?nm to about 1.5?nm in two steps using a series of prisms, and the resulting changes in experimental pulse durations and energies agree well with the model.