Facilitating insight into a simulation model using visualization and dynamic model previews

This paper shows how model simplification, by replacing iterative steps with unitary predictive equations, can enable dynamic interaction with a complex simulation process. Model previews extend the techniques of dynamic querying and query previews into the context of ad hoc simulation model exploration. A case study is presented within the domain of counter-current chromatography. The relatively novel method of insight evaluation was applied, given the exploratory nature of the task. The evaluation data show that the trade-off in accuracy is far outweighed by benefits of dynamic interaction. The number of insights gained using the enhanced interactive version of the computer model was more than six times higher than the number of insights gained using the basic version of the model. There was also a trend for dynamic interaction to facilitate insights of greater domain importance

Advanced modelling and visualisation of liquid-liquid separations of complex sample components, with variable phase distribution and mode of operation

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.This research is about liquid-liquid chromatography modelling. While the main focus was on liquid-liquid chromatography, where the stationary and mobile phases are both liquid, theory of different types of chromatography, including the currently most used techniques, were considered as well. The main goal of this research was to develop a versatile liquid-liquid separation model, able to model all potential operating scenarios and modes of operation. A second goal was to create effective and usable interfaces to such a model, implying primarily information visualisation, and secondarily educative visualisation. The first model developed was a model based on Counter-Current Distribution. Next a new more elemental model was developed, the probabilistic model, which better models continuous liquid-liquid chromatography techniques. Finally, a more traditional model was developed using transport theory. These models were used and compared to experimental data taken from literature. The models were demonstrated to model all main liquid-liquid chromatography techniques, incorporated the different modes of operation, and were able to accurately model many sample components and complex sample injections. A model interface was developed, permitting functional and effective model configuration, exploration and analysis using visualisation and interactivity. Different versions of the interface were then evaluated using questionnaires, group interviews and Insight Evaluation. The visualisation and interactivity enhancements have proven to contribute understanding and insight of the underlying chromatography process. This also proved the value of the Insight Evaluation method, providing valuable qualitative evaluation results desired for this model interface evaluation. A prototype of a new graphical user interface developed, and showed great potential for combining model parameter input and exploring the liquid-liquid chromatography processes. Additionally, a new visualisation method was developed that can accurately visualise different modes of operation. This was used to create animations, which were also evaluated. The results of this evaluation show the new visualisation helps understanding of the liquid-liquid chromatography process amongst CCC novices. The model software will be a valuable tool for industry for predicting, evaluating and validating experimental separations and production processes. While effective models already existed, the use of interactive visualisation permits users to explore the relationship between parameters and performances in a simpler yet more powerful way. It will also be a valuable tool for academia for teaching & training, both staff and students, on how to use the technology. Prior to this work no such tool existed or existing tools were limited in their accessibility and educational value.This study was supported by Brunel University and the Royal Academy of Engineering

Toroidal coil chromatography: The effect of scale-up and "g" field on stage efficiency

This work was supported by the UK BBSRC (Follow-on Grant No. BB/FOF/206) following on from the BBSRC protein purification study (DEMPRO-Grant No. BB/C506364/1). This article is available from the specified link - Copyright @ 2010 Springer BVSelected test results have been taken from various publications and resolution and stage efficiency measured using an established model. All experiments used the same sample and, where possible, the same sample loading. The results show that stage mixing efficiencies have increased from 1.1% in 1998 to greater than 25% in the latest scaled-up version of a Toroidal coil chromatography (TCC) instrument working at 240g.This article has been made available through the Brunel Open Access Publishing Fun

In planta localisation patterns of MADS domain proteins during floral development in Arabidopsis thaliana

Background: MADS domain transcription factors play important roles in various developmental processes in flowering plants. Members of this family play a prominent role in the transition to flowering and the specification of floral organ identity. Several studies reported mRNA expression patterns of the genes encoding these MADS domain proteins, however, these studies do not provide the necessary information on the temporal and spatial localisation of the proteins. We have made GREEN FLUORESCENT PROTEIN (GFP) translational fusions with the four MADS domain proteins SEPALLATA3, AGAMOUS, FRUITFULL and APETALA1 from the model plant Arabidopsis thaliana and analysed the protein localisation patterns in living plant tissues by confocal laser scanning microscopy (CLSM). Results: We unravelled the protein localisation patterns of the four MADS domain proteins at a cellular and subcellular level in inflorescence and floral meristems, during development of the early flower bud stages, and during further differentiation of the floral organs. The protein localisation patterns revealed a few deviations from known mRNA expression patterns, suggesting a non-cell autonomous action of these factors or alternative control mechanisms. In addition, we observed a change in the subcellular localisation of SEPALLATA3 from a predominantly nuclear localisation to a more cytoplasmic localisation, occurring specifically during petal and stamen development. Furthermore, we show that the down-regulation of the homeodomain transcription factor WUSCHEL in ovular tissues is preceded by the occurrence of both AGAMOUS and SEPALLATA3 proteins, supporting the hypothesis that both proteins together suppress WUSCHEL expression in the ovule. Conclusion: This approach provides a highly detailed in situ map of MADS domain protein presence during early and later stages of floral development. The subcellular localisation of the transcription factors in the cytoplasm, as observed at certain stages during development, points to mechanisms other than transcriptional control. Together this information is essential to understand the role of these proteins in the regulatory processes that drive floral development and leads to new hypotheses

Waiting and Residence Times of Brownian Interface Fluctuations

We report on the residence times of capillary waves above a given height $h$ and on the typical waiting time in between such fluctuations. The measurements were made on phase separated colloid-polymer systems by laser scanning confocal microscopy. Due to the Brownian character of the process, the stochastics vary with the chosen measurement interval $\Delta t$. In experiments, the discrete scanning times are a practical cutoff and we are able to measure the waiting time as a function of this cutoff. The measurement interval dependence of the observed waiting and residence times turns out to be solely determined by the time dependent height-height correlation function $g(t)$. We find excellent agreement with the theory presented here along with the experiments.Comment: 5 figure

MADS-complexes regulate transcriptome dynamics during pollen maturation

Pollen transcript profiling of mutants defective in MADS-domain MIKC* protein complexes suggests they control a transcriptional network directing cellular differentiation during pollen maturation