Mapping and controlling molecular processes: The application of control theory and system identification algorithms to ASOPS and other fast pulse spectroscopies

Asynchronous Optical Sampling (ASOPS) [1,2] and frequency comb spectrometry [3] based on dual Ti:saphire resonators operated in a master/slave mode have the potential to improve signal to noise ratio in THz transient and IR sperctrometry. The multimode Brownian oscillator time-domain response function described by state-space models is a mathematically robust framework that can be used to describe the dispersive phenomena governed by Lorentzian, Debye and Drude responses. In addition, the optical properties of an arbitrary medium can be expressed as a linear combination of simple multimode Brownian oscillator functions. The suitability of a range of signal processing schemes adopted from the Systems Identification and Control Theory community for further processing the recorded THz transients in the time or frequency domain will be outlined [4,5]. Since a femtosecond duration pulse is capable of persistent excitation of the medium within which it propagates, such approach is perfectly justifiable. Several de-noising routines based on system identification will be shown. Furthermore, specifically developed apodization structures will be discussed. These are necessary because due to dispersion issues, the time-domain background and sample interferograms are non-symmetrical [6-8]. These procedures can lead to a more precise estimation of the complex insertion loss function. The algorithms are applicable to femtosecond spectroscopies across the EM spectrum. Finally, a methodology for femtosecond pulse shaping using genetic algorithms aiming to map and control molecular relaxation processes will be mentioned.

Cross-species amplification and phylogenetic reconstruction using fragaria microsatellite primers

Twenty-eight microsatellite primer pairs developed from Fragaria vesca ‘Rügen’ were applied to sixteen accessions representing eight diploid Fragaria species. The number of alleles generated, the power of discrimination and the percentage of accessions where no PCR product could be amplified were calculated for each locus for the thirteen non-F. vesca accessions. A phylogeny was then generated for the species accessions sampled, using the presence or absence of alleles at the polymorphic loci as character states. Despite the problems inherent in phylogeny reconstruction from microsatellite data, the phylogeny showed some congruence with a previously published phylogeny of Fragaria, based on nucleotide sequence data. However, relationships inferred from microsatellite allele data were relatively unresolved and poorly supported. The genetic basis of allelic polymorphisms at specific loci was investigated through direct sequencing of the PCR products amplified by three primer pairs. The potential utility of sequence data generated from microsatellite loci in evolutionary studies of closely related species groups is briefly explored.

A pulse radiolysis study of free radicals formed by one-electron oxidation of the antimalarial drug pyronaridine

Free radicals from one-electron oxidation of the antimalarial drug pyronaridine have been studied by pulse radiolysis. The results show that pyronaridine is readily oxidised to an intermediate semi-iminoquine radical by inorganic and organic free radicals, including those derived from tryptophan and acetaminophen. The pyronaridine radical is rapidly reduced by both ascorbate and caffeic acid. The results indicate that the one-electron reduction potential of the pyronaridine radical at neutral pH lies between those of acetaminophen (707 mV) and caffeic acid (534 mV). The pyronaridine radical decays to produce the iminoquinone, detected by electrospray mass spectrometry, in a second-order process that density functional theory (DFT) calculations (UB3LYP/6-31+G*) suggest is a disproportionation reaction. Important calculated dimensions of pyronaridine, its phenoxyl and aminyl radical, as well as the iminoquinone, are presented.

Pulse shaping using state space algorithms

We discuss the use of pulse shaping for optimal excitation of samples in time-domain THz spectroscopy. Pulse shaping can be performed in a 4f optical system to specifications from state space models of the system's dynamics. Subspace algorithms may be used for the identification of the state space models.

Application of auto regressive models of wavelet sub-bands for classifying Terahertz pulse measurements

This paper presents an approach for automatic classification of pulsed Terahertz (THz), or T-ray, signals highlighting their potential in biomedical, pharmaceutical and security applications. T-ray classification systems supply a wealth of information about test samples and make possible the discrimination of heterogeneous layers within an object. In this paper, a novel technique involving the use of Auto Regressive (AR) and Auto Regressive Moving Average (ARMA) models on the wavelet transforms of measured T-ray pulse data is presented. Two example applications are examined - the classi. cation of normal human bone (NHB) osteoblasts against human osteosarcoma (HOS) cells and the identification of six different powder samples. A variety of model types and orders are used to generate descriptive features for subsequent classification. Wavelet-based de-noising with soft threshold shrinkage is applied to the measured T-ray signals prior to modeling. For classi. cation, a simple Mahalanobis distance classi. er is used. After feature extraction, classi. cation accuracy for cancerous and normal cell types is 93%, whereas for powders, it is 98%.

The importance of friction in mountain wave drag amplification by Scorer parameter resonance

A mechanism for amplification of mountain waves, and their associated drag, by parametric resonance is investigated using linear theory and numerical simulations. This mechanism, which is active when the Scorer parameter oscillates with height, was recently classified by previous authors as intrinsically nonlinear. Here it is shown that, if friction is included in the simplest possible form as a Rayleigh damping, and the solution to the Taylor-Goldstein equation is expanded in a power series of the amplitude of the Scorer parameter oscillation, linear theory can replicate the resonant amplification produced by numerical simulations with some accuracy. The drag is significantly altered by resonance in the vicinity of n/l_0 = 2, where l_0 is the unperturbed value of the Scorer parameter and n is the wave number of its oscillation. Depending on the phase of this oscillation, the drag may be substantially amplified or attenuated relative to its non-resonant value, displaying either single maxima or minima, or double extrema near n/l_0 = 2. Both non-hydrostatic effects and friction tend to reduce the magnitude of the drag extrema. However, in exactly inviscid conditions, the single drag maximum and minimum are suppressed. As in the atmosphere friction is often small but non-zero outside the boundary layer, modelling of the drag amplification mechanism addressed here should be quite sensitive to the type of turbulence closure employed in numerical models, or to computational dissipation in nominally inviscid simulations.

Femtosecond pulse shaping using differential evolutionary algorithm and wavelet operators

Evolutionary meta-algorithms for pulse shaping of broadband femtosecond duration laser pulses are proposed. The genetic algorithm searching the evolutionary landscape for desired pulse shapes consists of a population of waveforms (genes), each made from two concatenated vectors, specifying phases and magnitudes, respectively, over a range of frequencies. Frequency domain operators such as mutation, two-point crossover average crossover, polynomial phase mutation, creep and three-point smoothing as well as a time-domain crossover are combined to produce fitter offsprings at each iteration step. The algorithm applies roulette wheel selection; elitists and linear fitness scaling to the gene population. A differential evolution (DE) operator that provides a source of directed mutation and new wavelet operators are proposed. Using properly tuned parameters for DE, the meta-algorithm is used to solve a waveform matching problem. Tuning allows either a greedy directed search near the best known solution or a robust search across the entire parameter space.

Terahertz pulse imaging of stratified architectural materials for cultural heritage studies

Terahertz pulse imaging (TPI) is a novel noncontact, nondestructive technique for the examination of cultural heritage artifacts. It has the advantage of broadband spectral range, time-of-flight depth resolution, and penetration through optically opaque materials. Fiber-coupled, portable, time-domain terahertz systems have enabled this technique to move out of the laboratory and into the field. Much like the rings of a tree, stratified architectural materials give the chronology of their environmental and aesthetic history. This work concentrates on laboratory models of stratified mosaics and fresco paintings, specimens extracted from a neolithic excavation site in Catalhoyuk, Turkey, and specimens measured at the medieval Eglise de Saint Jean-Baptiste in Vif, France. Preparatory spectroscopic studies of various composite materials, including lime, gypsum and clay plasters are presented to enhance the interpretation of results and with the intent to aid future computer simulations of the TPI of stratified architectural material. The breadth of the sample range is a demonstration of the cultural demand and public interest in the life history of buildings. The results are an illustration of the potential role of TPI in providing both a chronological history of buildings and in the visualization of obscured wall paintings and mosaics.

Femto-chemometrics: the signal processing of fast pulse transients

Traditional chemometrics techniques are augmented with algorithms tailored specifically for the de-noising and analysis of femtosecond duration pulse datasets. The new algorithms provide additional insights on sample responses to broadband excitation and multi-moded propagation phenomena.

A dynamic causal model of the coupling between pulse stimulation and neural activity

We present a dynamic causal model that can explain context-dependent changes in neural responses, in the rat barrel cortex, to an electrical whisker stimulation at different frequencies. Neural responses were measured in terms of local field potentials. These were converted into current source density (CSD) data, and the time series of the CSD sink was extracted to provide a time series response train. The model structure consists of three layers (approximating the responses from the brain stem to the thalamus and then the barrel cortex), and the latter two layers contain nonlinearly coupled modules of linear second-order dynamic systems. The interaction of these modules forms a nonlinear regulatory system that determines the temporal structure of the neural response amplitude for the thalamic and cortical layers. The model is based on the measured population dynamics of neurons rather than the dynamics of a single neuron and was evaluated against CSD data from experiments with varying stimulation frequency (1–40 Hz), random pulse trains, and awake and anesthetized animals. The model parameters obtained by optimization for different physiological conditions (anesthetized or awake) were significantly different. Following Friston, Mechelli, Turner, and Price (2000), this work is part of a formal mathematical system currently being developed (Zheng et al., 2005) that links stimulation to the blood oxygen level dependent (BOLD) functional magnetic resonance imaging (fMRI) signal through neural activity and hemodynamic variables. The importance of the model described here is that it can be used to invert the hemodynamic measurements of changes in blood flow to estimate the underlying neural activity.

Terahertz pulse investigation of paleolithic wall etchings

Results are presented of an examination of flow rock-covered Paleoloithic cave art using time-domain terahertz reflectometry.