The bulk of this thesis considers how biological rhythms (oscillators) can be made to synchronize their rhythms by virtue of coupling to an external signal. Such externally controlled synchronization, known as entrainment, is explored using a synthetic biology approach in E.~coli, where I have used rationally designed gene circuits as an experimental model. Two novel modes of entrainment are explored: entrainment by competition between components for degradation, and entrainment by a noisy (aperiodic) stimulus. Both of these modes of entrainment can be shown to strongly synchronize ensembles of synthetic gene oscillators, and thus, these modes of entrainment may be important to understand the appearance of synchrony in natural systems. In addition to the study of entrainment, this thesis contains a general background of relevant material, contributions to the biophysics of multisite proteases, and updated protocols for experimental procedures in microfluidics and microscopy. / Ph. D.

Sequential learning refers to the ability to learn the temporal and ordinal patterns of one’s environment. The current study examines the effects of synchronous and asynchronous temporal patterns on sequential learning. Twenty healthy adults participants (11 females, 18–34 years old) performed two versions of a visual sequential learning paradigm while event-related potentials (ERPs) were recorded. Reaction times to the targets following two predictor types were also recorded. Reaction time data revealed that learning occurred in both temporal conditions, although overall the synchronous condition was responded to faster. On the other hand, the mean ERP amplitudes between 300 and 700ms post-predictor onset revealed an interaction between timing condition and predictability in the posterior regions of interest. Specifically, the ERP results indicated that learning of the statistical contingencies between items was more pronounced for the synchronous temporal condition compared to the asynchronous condition.

Approved for public release, distribution is unlimited / The objective of this thesis is to obtain a better understanding of cloud-top entrainment through an in-depth analysis of entrainment-zone structure. In situ aircraft measurements taken during the Atlantic Stratocumulus Transition Experiment (ASTEX) were used for this purpose. Using data collected from multiple cloud-top penetrations, the presence of an interfacial layer in-between the top of the cloud mixed-layer and the base of the free atmosphere is identified and consequently defined as the entrainment zone. The depth of the entrainment zone is on the order of tens of meters, where turbulence and sometimes cloud droplets are detectable. Inhomogeneous mixing was found to occur within the entrainment zone. Parcels of inversion-layer air and boundary-layer air are identified within the entrainment zone. Analyses suggest that turbulence intensity and cloud amount in the entrainment zone vary depending on the distribution of entrainment mixing fraction. Furthermore, continuous mixing in the entrainment zone appears to dissipate the upper-cloud layer. However, continuous dissipation of the upper-cloud layer has not been observed. Further study is needed to determine the interaction between cloud-top entrainment and the full integration of boundary-layer dynamics. / Captain, United States Air Force

The adhesion and resuspension of nanoparticles is important in applications ranging from semiconductor manufacturing to pollution management. The objective of this work is to understand the effect of particle size on re-entrainment of nanometer scale particles. One of the major contributions is to reduce the randomness introduced in past measurements on resuspension by controlling humidity, temperature, material and the distribution of shape and particle sizes. In the process of studying particle size, the effect of surface roughness was also found. Measurements of the detachment fraction of carbon particles as a function of flow rate show three distinct regimes that we attribute to the dominance of drag, energy accumulation by particles, and collision and agglomeration respectively. Experiments with silica nanoparticles on silica microspheres show the detachment fraction to increase non-linearly with particle diameter and to decrease with the substrate diameter. We attribute the former to the dominance of the drag moment over the adhesive moment. We attribute the influence of the substrates to the surface roughness being comparable to the size of the nanoparticles. This work provides new empirical insight into the interaction of nanoparticles with surfaces and fluid flows.

Spatial and temporal characteristics of dust storm activity in Saudi Arabia has been established using coarse-particle (PM10) dust concentrations recorded by the KACST monitoring network during the 2000-2003 period, backward trajectory analysis and satellite imagery. Thirty three major dust episodes impacted Riyadh city during the 2000-2003 period. The majority of these intense dust episodes are experienced during the March-August period with interannual and monthly variability in both intensity and frequency. Using TOMS images in conjunction with the backward trajectories corresponding to these 33 major episodes, the dust source regions have been identified. The most vulnerable dust source areas within these identified source regions have also been determined by compiling satellite images of dusty days from the true color SeaWiFs and high resolution MODIS archives over a six-year period (2000-2005). In total 45 dust-source areas have been identified in 9 local source regions and 4 external ones. Furthermore, 38 episodes of high fine-particle (PM2.5) and PM10 dust concentrations were observed at Riyadh city and 16 and 6 episodes of elevated PM10 dust concentrations were observed at Dammam and Jeddah cities, respectively, during March-September 2006, corresponding to the dust season in Saudi Arabia. During these episodes, Riyadh city was significantly impacted by dust from the southern Iraqi source areas and the eastern source areas located to the north and to the northeast of the city, respectively. Moreover, Dammam city was also significantly impacted by dust from the southern Iraqi source areas whereas Jeddah city was evenly impacted by dust from northeastern-northwestern sources to the city, with somewhat higher PM10 concentrations from African dust source areas, located to the northwest of the city. Analysis of meteorological maps of surface pressure as well as upper air data associated with high airborne dust concentrations in Saudi Arabia was successfully performed. This analysis revealed seven common types of dust storms, triggered by a clear seasonal distribution of meteorological conditions: (1) frontal, (2) Haboob, (3) jets convergence, (4) jet streak, (5) Shamal, (6) cyclonic, and (7) gap. The majority of dust episodes that impacted Riyadh city during the study period were triggered by Haboob (~ 42 %) and Shamal (~ 37 %). Additional analyses, including elemental, ionic and biological analyses as well as model analyses were used to further characterize the airborne dust in Saudi Arabia.

The circadian clock is an endogenous timer that allows an organism to anticipate and properly prepare for the daily changes in the environment. This preparation occurs in the form of daily rhythms in metabolism, physiology, and behavior. These approximately 24-hour rhythms are reset upon environmental time cues such as the daily light/dark and temperature cycles. The unicellular green alga Chlamydomonas reinhardtii is a useful model organism for circadian clock research. It shows several well-characterized circadian rhythms of behavior, and the monitoring of its rhythm of phototaxis, or swimming towards light, has been automated. The receptors involved in entraining the clock to the daily light/dark cycle have not yet been identified in this organism. Previous research has shown that blue, green, and red light are effective in resetting the clock in C. reinhardtii. This study focused on identifying the blue light sensor for resetting. One possibility was reception through photosynthesis. This was tested by looking for a defect in the ability to reset the clock upon blue light in cultures treated with the photosynthesis inhibitor DCMU. It was found that photosynthesis does not mediate this process. Instead, a photoreceptor must be involved, and plant-like cryptochrome was the most probable candidate, as it is known to perform this function in higher plants. To determine if plant-like cryptochrome serves this function, available transformants of C. reinhardtii with an RNA interference construct designed to knockdown plant-like cryptochrome expression were used. In this study, the transformants were screened for a reduction in cryptochrome amount using western blot analysis. The two strains with consistently the largest knockdown were tested for defects in resetting the circadian clock upon blue light pulses. Neither strain was found to be less sensitive than the parent strain to blue light induced entrainment. On the contrary, one strain was significantly more sensitive than the parent strain, which suggests a possible inhibitory role for plant-like cryptochrome in the photoentrainment of the clock to blue light in this organism.

Our limited knowledge of convection and its poor representation in climate models is one of the factors that most hamper our ability to understand and predict the climate system. In this thesis, the dynamics of shallow cumulus convection are probed using Large-eddy simulations (LES) and simple models. / Earth and Planetary Sciences

In this work high-resolution numerical simulation (Large-Eddie Simulation, LES) has been used to study the characteristic factors causing and influencing the development of moist convective clouds. Through this work a 1D cloud-model was derived from first principles to represent the vertical profile of individual convective clouds. A microphysics framework was implemented to ensure identical behaviour in LES and cloud-model integration where the microphysical processes represented are numerically integrated using a novel adaptive step microphysics integration which uses the physical speed at which a process takes place to adjust the integration step size (in space and time). This work also introduces a simple representation of cloud-droplet formation which allows for super-saturation to exist in-cloud and through this provide more physical representation of the in-cloud state. Together with high-resolution simulation of isolated individual and interacting multiple clouds in environmental conditions leading to shallow convection, the 1D cloud-model was used to infer that the principal influence on moist convective clouds is the entrainment of air from a cloud’s immediate environment which is significantly different from the environmental mean state. This suggests that convection parameterisations must represent the influence of moist convective downdrafts to properly predict the vertical structure of convective clouds so as to correctly predict the cloud-top height and vertical transport. Finally it was found that cloud-base radius is not in itself adequate as a means of classification for defining cloud-types as clouds with the same cloud-base radius showed large variation (≈ 600m) in cloud-top height. Based on simulations of individual convective clouds it was found that 3D simulations are necessary to capture the full dynamic behaviour of convective clouds (2D axisymmetric simulations have too little entrainment) and that agreement with the 1D cloud-model could only be found when entrainment was diagnosed from simulation instead of being parameterised by the traditional Morton-Turner model and only for 2D axisymmetric simulations, suggesting that the 1D cloud-model will require further extension or the diagnosis of entrainment improved.

Phonological awareness is an important component of early literacy and many children struggle to master its key elements, such as the ability to hear syllables and rhymes within the speech stream. The hypothesis explored within this study is that since music and language have parallel auditory perceptual mechanisms then training in rhythmic activities, such as music, could lead to increased understanding of the rhythmic nature required to decode early language and literacy skills. Previous research investigating the relationship between the constructs of music perception and phonological awareness has been promising, but generally inconclusive. Within the study I examine whether there is a link between the temporal processing required to process rhythmic entrainment in both phonological awareness skills and music. The data are interpreted with respect to a theoretical framework linking music and language based on temporal sampling. The ‘temporal sampling theory’ (Goswami, 2011) suggests that the decoding of both language and music is linked to the perception of accent and beat, and that the ability to hear the onset of these accents is critical within a stream of auditory events. To this end rhythmic entrainment tasks were presented in a range of musical activities including drumming along to music and singing nursery songs and rhymes. The musical and rhythmic activities were given in several different forms, to see which would be most effective in showing the children’s ability to synchronise to a beat. These were all presented at four pulse rates (400 ms, 500 ms, 666 ms, 1000 ms). Data were collected over a period of 2 years commencing in November 2009. In Study1 93 4 and 5-year-old children were tested and in Study 2 data were collected from a further 99. In addition to psychometric tests for IQ, Word Recall, teachers from the schools provided information from the children’s Foundation Stage profiles. Phonological awareness skills (syllable and rhyme) were also measured, as was reading development. Overall, children showed greater temporal accuracy (rhythmic entrainment) in keeping time with a musical piece than in keeping time with a metronome. Entrainment accuracy was greatest at the 500 ms rate, the only rate for which entrainment was as accurate with music and metronome. Individual differences in rhythmic entrainment whilst drumming were not linked to I.Q. Children were more temporally accurate when singing than in the rhythmic entrainment tasks and temporal accuracy at pulse rates of 500 ms (2 Hz) and 666 ms (1.5 Hz) showed some significant links to rhyme awareness and to reading. Temporal accuracy in singing a rhyming word on time was also greatest at 500 ms, although simply singing along to music did not show a preferred rate. Unexpectedly, temporal accuracy in singing was linked to I.Q., and was not linked independently to syllable and rhyme awareness. However, temporal accuracy in singing at the 500 ms rate was linked to reading. In Sample 2 of the PhD I report on the results of a seven-week three group matched intervention study of 99 children. The intervention was designed to investigate whether a short intervention of either music or ‘rhythmic speech’ based around the preferred rate of 500ms would lead to improved phonological awareness skills. Group 1 was given a programme of music games and songs, and group 2 was given a matched programme of games and ‘rhythmic speech’, without musical accompaniment or singing, to promote syllable and rhyme awareness. A third group, who received no additional training acted as a control. The results show that an intervention based on rhythmic structure in either a rhythmic speech form or in musical form can be successful in improving children’s phonological awareness skills. The rhythmic speech programme proved to be a more successful vehicle than the music intervention in improving the phonological skills of this group of 90 children. Both interventions were successful in improving both rhyme and syllable awareness, but the greatest improvements came in the syllable tests. There was further evidence that an intervention in either rhythmic speech or music would impact on the children’s future reading skills. Both interventions produced significantly higher correlations with a Word Reading test than the control group. There was no evidence to suggest that a musical intervention based on tapping along to a beat was of more benefit than one based on rhythmic speech. Overall the evidence gathered from the data in this study does suggest that there are direct links between rhythmic awareness, as measured by tapping to an isochronous beat, and the children’s capacity to decode phonological information. The favoured rate at which the brain processes information in both domains, thus linking them together, is at a pulse rate with an Inter Onset Interval set to 500ms. This study’s results could be used to support the development of rhythmic based interventions, in both a rhythmic speech and musical form in support of early literacy skills in 4 and 5 –year –old children.

Virtually nothing is known about how internal circadian clocks interact with daily environmental cycles in nature. Previous work has shown that temperature and light are both able to successfully entrain (synchronize) circadian rhythms in eclosion (adult emergence) and locomotor activity in Sarcophaga crassipalpis when applied independently. However, much less work has been done to evaluate the relative strength of these Zeitgebers (time cues) when applied simultaneously. In nature, light and temperature cycles generally maintain a fixed relationship with one another, with peak soil and air temperature occurring about three hours after peak brightness each day. By manipulating the relationship between these Zeitgebers this project aims to evaluate the effects of conflicting environmental information on eclosion and locomotor activity rhythms in S. crassipalpis. We measured locomotor and eclosion activity under three temperature/light cycle regimes: 1) in-phase temperature and light cycles, with light and thermophase (warm-period) onset occurring simultaneously, 2) thermophase-delayed, beginning six hours after the onset of photoperiod (light-period), or 3) out-of-phase, with the beginning of photophase corresponding to the end of thermophase. In all experiments, eclosion times are very close to thermophase onset, while locomotor activity does not always hold the same phase position. In fact, in the out-of-phase experiment, locomotor activity is almost entirely synchronized with photophase while eclosion appears to anticipate thermophase onset. These findings suggest that eclosion and locomotor activity rhythms are controlled by different circadian oscillators. This fits with the ecological context of these vital life events. Timing of eclosion is critically important to wing development and the survival of the adult. This process is initiated after being underground, with minimal to no light input, for two weeks – therefore, the most reliable Zeitgeber would be daily soil temperature cycling. As these flies are diurnal, one could reasonably expect light to be the primary Zeitgeber for adult activity, as it is more consistent than temperature cycling. Overall, this implies that an organism’s life history and natural environment must be considered when investigating the circadian clock.