4 resultados para spatial and stochastic modelling, bio-chemical kinetics, multi-scale simulation, systems biology

em Duke University


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An overview on processes that are relevant in light-induced fuel generation, such as water photoelectrolysis or carbon dioxide reduction, is given. Considered processes encompass the photophysics of light absorption, excitation energy transfer to catalytically active sites and interfacial reactions at the catalyst/solution phase boundary. The two major routes envisaged for realization of photoelectrocatalytic systems, e.g. bio-inspired single photon catalysis and multiple photon inorganic or hybrid tandem cells, are outlined. For development of efficient tandem cell structures that are based on non-oxidic semiconductors, stabilization strategies are presented. Physical surface passivation is described using the recently introduced nanoemitter concept which is also applicable in photovoltaic (solid state or electrochemical) solar cells and first results with p-Si and p-InP thin films are presented. Solar-to-hydrogen efficiencies reach 12.1% for homoepitaxial InP thin films covered with Rh nanoislands. In the pursuit to develop biologically inspired systems, enzyme adsorption onto electrochemically nanostructured silicon surfaces is presented and tapping mode atomic force microscopy images of heterodimeric enzymes are shown. An outlook towards future envisaged systems is given. © 2010 The Royal Society of Chemistry.

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The spiking activity of nearby cortical neurons is correlated on both short and long time scales. Understanding this shared variability in firing patterns is critical for appreciating the representation of sensory stimuli in ensembles of neurons, the coincident influences of neurons on common targets, and the functional implications of microcircuitry. Our knowledge about neuronal correlations, however, derives largely from experiments that used different recording methods, analysis techniques, and cortical regions. Here we studied the structure of neuronal correlation in area V4 of alert macaques using recording and analysis procedures designed to match those used previously in primary visual cortex (V1), the major input to V4. We found that the spatial and temporal properties of correlations in V4 were remarkably similar to those of V1, with two notable differences: correlated variability in V4 was approximately one-third the magnitude of that in V1 and synchrony in V4 was less temporally precise than in V1. In both areas, spontaneous activity (measured during fixation while viewing a blank screen) was approximately twice as correlated as visual-evoked activity. The results provide a foundation for understanding how the structure of neuronal correlation differs among brain regions and stages in cortical processing and suggest that it is likely governed by features of neuronal circuits that are shared across the visual cortex.

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Recent research into resting-state functional magnetic resonance imaging (fMRI) has shown that the brain is very active during rest. This thesis work utilizes blood oxygenation level dependent (BOLD) signals to investigate the spatial and temporal functional network information found within resting-state data, and aims to investigate the feasibility of extracting functional connectivity networks using different methods as well as the dynamic variability within some of the methods. Furthermore, this work looks into producing valid networks using a sparsely-sampled sub-set of the original data.

In this work we utilize four main methods: independent component analysis (ICA), principal component analysis (PCA), correlation, and a point-processing technique. Each method comes with unique assumptions, as well as strengths and limitations into exploring how the resting state components interact in space and time.

Correlation is perhaps the simplest technique. Using this technique, resting-state patterns can be identified based on how similar the time profile is to a seed region’s time profile. However, this method requires a seed region and can only identify one resting state network at a time. This simple correlation technique is able to reproduce the resting state network using subject data from one subject’s scan session as well as with 16 subjects.

Independent component analysis, the second technique, has established software programs that can be used to implement this technique. ICA can extract multiple components from a data set in a single analysis. The disadvantage is that the resting state networks it produces are all independent of each other, making the assumption that the spatial pattern of functional connectivity is the same across all the time points. ICA is successfully able to reproduce resting state connectivity patterns for both one subject and a 16 subject concatenated data set.

Using principal component analysis, the dimensionality of the data is compressed to find the directions in which the variance of the data is most significant. This method utilizes the same basic matrix math as ICA with a few important differences that will be outlined later in this text. Using this method, sometimes different functional connectivity patterns are identifiable but with a large amount of noise and variability.

To begin to investigate the dynamics of the functional connectivity, the correlation technique is used to compare the first and second halves of a scan session. Minor differences are discernable between the correlation results of the scan session halves. Further, a sliding window technique is implemented to study the correlation coefficients through different sizes of correlation windows throughout time. From this technique it is apparent that the correlation level with the seed region is not static throughout the scan length.

The last method introduced, a point processing method, is one of the more novel techniques because it does not require analysis of the continuous time points. Here, network information is extracted based on brief occurrences of high or low amplitude signals within a seed region. Because point processing utilizes less time points from the data, the statistical power of the results is lower. There are also larger variations in DMN patterns between subjects. In addition to boosted computational efficiency, the benefit of using a point-process method is that the patterns produced for different seed regions do not have to be independent of one another.

This work compares four unique methods of identifying functional connectivity patterns. ICA is a technique that is currently used by many scientists studying functional connectivity patterns. The PCA technique is not optimal for the level of noise and the distribution of the data sets. The correlation technique is simple and obtains good results, however a seed region is needed and the method assumes that the DMN regions is correlated throughout the entire scan. Looking at the more dynamic aspects of correlation changing patterns of correlation were evident. The last point-processing method produces a promising results of identifying functional connectivity networks using only low and high amplitude BOLD signals.