Coupled CFD Shape Optimization for aerodynamic profiles

The present document deals with the optimization of shape of aerodynamic profiles -- The objective is to reduce the drag coefficient on a given profile without penalising the lift coefficient -- A set of control points defining the geometry are passed and parameterized as a B-Spline curve -- These points are modified automatically by means of CFD analysis -- A given shape is defined by an user and a valid volumetric CFD domain is constructed from this planar data and a set of user-defined parameters -- The construction process involves the usage of 2D and 3D meshing algorithms that were coupled into own- code -- The volume of air surrounding the airfoil and mesh quality are also parametrically defined -- Some standard NACA profiles were used by obtaining first its control points in order to test the algorithm -- Navier-Stokes equations were solved for turbulent, steady-state ow of compressible uids using the k-epsilon model and SIMPLE algorithm -- In order to obtain data for the optimization process an utility to extract drag and lift data from the CFD simulation was added -- After a simulation is run drag and lift data are passed to the optimization process -- A gradient-based method using the steepest descent was implemented in order to define the magnitude and direction of the displacement of each control point -- The control points and other parameters defined as the design variables are iteratively modified in order to achieve an optimum -- Preliminary results on conceptual examples show a decrease in drag and a change in geometry that obeys to aerodynamic behavior principles

Clustering through post inhibitory rebound in synaptically coupled neurons

Post inhibitory rebound is a nonlinear phenomenon present in a variety of nerve cells. Following a period of hyper-polarization this effect allows a neuron to fire a spike or packet of spikes before returning to rest. It is an important mechanism underlying central pattern generation for heartbeat, swimming and other motor patterns in many neuronal systems. In this paper we consider how networks of neurons, which do not intrinsically oscillate, may make use of inhibitory synaptic connections to generate large scale coherent rhythms in the form of cluster states. We distinguish between two cases i) where the rebound mechanism is due to anode break excitation and ii) where rebound is due to a slow T-type calcium current. In the former case we use a geometric analysis of a McKean type model to obtain expressions for the number of clusters in terms of the speed and strength of synaptic coupling. Results are found to be in good qualitative agreement with numerical simulations of the more detailed Hodgkin-Huxley model. In the second case we consider a particular firing rate model of a neuron with a slow calcium current that admits to an exact analysis. Once again existence regions for cluster states are explicitly calculated. Both mechanisms are shown to prefer globally synchronous states for slow synapses as long as the strength of coupling is sufficiently large. With a decrease in the duration of synaptic inhibition both systems are found to break into clusters. A major difference between the two mechanisms for cluster generation is that anode break excitation can support clusters with several groups, whilst slow T-type calcium currents predominantly give rise to clusters of just two (anti-synchronous) populations.

Directed percolation in a two dimensional stochastic fire-diffuse-fire model

In this paper we establish, from extensive numerical experiments, that the two dimensional stochastic fire-diffuse-fire model belongs to the directed percolation universality class. This model is an idealized model of intracellular calcium release that retains the both the discrete nature of calcium stores and the stochastic nature of release. It is formed from an array of noisy threshold elements that are coupled only by a diffusing signal. The model supports spontaneous release events that can merge to form spreading circular and spiral waves of activity. The critical level of noise required for the system to exhibit a non-equilibrium phase-transition between propagating and non-propagating waves is obtained by an examination of the \textit{local slope} $\delta(t)$ of the survival probability, $\Pi(t) \propto \exp(- \delta(t))$, for a wave to propagate for a time $t$.

Toward assessing the effects of aerosols on deep convection: a numerical study using the WRF-Chemistry model

As the formative agents of cloud droplets, aerosols play an undeniably important role in the development of clouds and precipitation. Few meteorological models have been developed or adapted to simulate aerosols and their contribution to cloud and precipitation processes. The Weather Research and Forecasting model (WRF) has recently been coupled with an atmospheric chemistry suite and is jointly referred to as WRF-Chem, allowing atmospheric chemistry and meteorology to influence each other’s evolution within a mesoscale modeling framework. Provided that the model physics are robust, this framework allows the feedbacks between aerosol chemistry, cloud physics, and dynamics to be investigated. This study focuses on the effects of aerosols on meteorology, specifically, the interaction of aerosol chemical species with microphysical processes represented within the framework of the WRF-Chem. Aerosols are represented by eight size bins using the Model for Simulating Aerosol Interactions and Chemistry (MOSAIC) sectional parameterization, which is linked to the Purdue Lin bulk microphysics scheme. The aim of this study is to examine the sensitivity of deep convective precipitation modeled by the 2D WRF-Chem to varying aerosol number concentration and aerosol type. A systematic study has been performed regarding the effects of aerosols on parameters such as total precipitation, updraft/downdraft speed, distribution of hydrometeor species, and organizational features, within idealized maritime and continental thermodynamic environments. Initial results were obtained using WRFv3.0.1, and a second series of tests were run using WRFv3.2 after several changes to the activation, autoconversion, and Lin et al. microphysics schemes added by the WRF community, as well as the implementation of prescribed vertical levels by the author. The results of WRFv3.2 runs contrasted starkly with WRFv3.0.1 runs. The WRFv3.0.1 runs produced a propagating system resembling a developing squall line, whereas the WRFv3.2 runs did not. The response of total precipitation, updraft/downdraft speeds, and system organization to increasing aerosol concentrations were opposite between runs with different versions of WRF. Results of the WRFv3.2 runs, however, were in better agreement in timing and magnitude of vertical velocity and hydrometeor content with a WRFv3.0.1 run using single-moment Lin et al. microphysics, than WRFv3.0.1 runs with chemistry. One result consistent throughout all simulations was an inhibition in warm-rain processes due to enhanced aerosol concentrations, which resulted in a delay of precipitation onset that ranged from 2-3 minutes in WRFv3.2 runs, and up to 15 minutes in WRFv.3.0.1 runs. This result was not observed in a previous study by Ntelekos et al. (2009) using the WRF-Chem, perhaps due to their use of coarser horizontal and vertical resolution within their experiment. The changes to microphysical processes such as activation and autoconversion from WRFv3.0.1 to WRFv3.2, along with changes in the packing of vertical levels, had more impact than the varying aerosol concentrations even though the range of aerosol tested was greater than that observed in field studies. In order to take full advantage of the input of aerosols now offered by the chemistry module in WRF, the author recommends that a fully double-moment microphysics scheme be linked, rather than the limited double-moment Lin et al. scheme that currently exists. With this modification, the WRF-Chem will be a powerful tool for studying aerosol-cloud interactions and allow comparison of results with other studies using more modern and complex microphysical parameterizations.

Existence and wandering of bumps in a spiking neural network model

We study spatially localized states of a spiking neuronal network populated by a pulse coupled phase oscillator known as the lighthouse model. We show that in the limit of slow synaptic interactions in the continuum limit the dynamics reduce to those of the standard Amari model. For non-slow synaptic connections we are able to go beyond the standard firing rate analysis of localized solutions allowing us to explicitly construct a family of co-existing one-bump solutions, and then track bump width and firing pattern as a function of system parameters. We also present an analysis of the model on a discrete lattice. We show that multiple width bump states can co-exist and uncover a mechanism for bump wandering linked to the speed of synaptic processing. Moreover, beyond a wandering transition point we show that the bump undergoes an effective random walk with a diffusion coefficient that scales exponentially with the rate of synaptic processing and linearly with the lattice spacing.

Exotic dynamics in a firing rate model of neural tissue with threshold accommodation

Many of the equations describing the dynamics of neural systems are written in terms of firing rate functions, which themselves are often taken to be threshold functions of synaptic activity. Dating back to work by Hill in 1936 it has been recognized that more realistic models of neural tissue can be obtained with the introduction of state-dependent dynamic thresholds. In this paper we treat a specific phenomenological model of threshold accommodation that mimics many of the properties originally described by Hill. Importantly we explore the consequences of this dynamic threshold at the tissue level, by modifying a standard neural field model of Wilson-Cowan type. As in the case without threshold accommodation classical Mexican-Hat connectivity is shown to allow for the existence of spatially localized states (bumps) in both one and two dimensions. Importantly an analysis of bump stability in one dimension, using recent Evans function techniques, shows that bumps may undergo instabilities leading to the emergence of both breathers and traveling waves. Moreover, a similar analysis for traveling pulses leads to the conditions necessary to observe a stable traveling breather. In the regime where a bump solution does not exist direct numerical simulations show the possibility of self-replicating bumps via a form of bump splitting. Simulations in two space dimensions show analogous localized and traveling solutions to those seen in one dimension. Indeed dynamical behavior in this neural model appears reminiscent of that seen in other dissipative systems that support localized structures, and in particular those of coupled cubic complex Ginzburg-Landau equations. Further numerical explorations illustrate that the traveling pulses in this model exhibit particle like properties, similar to those of dispersive solitons observed in some three component reaction-diffusion systems. A preliminary account of this work first appeared in S Coombes and M R Owen, Bumps, breathers, and waves in a neural network with spike frequency adaptation, Physical Review Letters 94 (2005), 148102(1-4).

Oceanic control of multidecadal variability in an idealized coupled GCM

Idealized ocean models are known to develop intrinsic multidecadal oscillations of the meridional overturning circulation (MOC). Here we explore the role of ocean–atmosphere interactions on this low-frequency variability. We use a coupled ocean–atmosphere model set up in a flat-bottom aquaplanet geometry with two meridional boundaries. The model is run at three different horizontal resolutions (4°, 2° and 1°) in both the ocean and atmosphere. At all resolutions, the MOC exhibits spontaneous variability on multidecadal timescales in the range 30–40 years, associated with the propagation of large-scale baroclinic Rossby waves across the Atlantic-like basin. The unstable region of growth of these waves through the long wave limit of baroclinic instability shifts from the eastern boundary at coarse resolution to the western boundary at higher resolution. Increasing the horizontal resolution enhances both intrinsic atmospheric variability and ocean–atmosphere interactions. In particular, the simulated atmospheric annular mode becomes significantly correlated to the MOC variability at 1° resolution. An ocean-only simulation conducted for this specific case underscores the disruptive but not essential influence of air–sea interactions on the low-frequency variability. This study demonstrates that an atmospheric annular mode leading MOC changes by about 2 years (as found at 1° resolution) does not imply that the low-frequency variability originates from air–sea interactions.

Optimization of microwave-assisted extration of phenolic compounds from tomao by full factorial design coupled with response surface methodology

Tomato (Lycopersicon esculentum Mill.), apart from being a functional food rich in carotenoids, vitamins and minerals, is also an important source of phenolic compounds [1 ,2]. As antioxidants, these functional molecules play an important role in the prevention of human pathologies and have many applications in nutraceutical, pharmaceutical and cosmeceutical industries. Therefore, the recovery of added-value phenolic compounds from natural sources, such as tomato surplus or industrial by-products, is highly desirable. Herein, the microwave-assisted extraction of the main phenolic acids and flavonoids from tomato was optimized. A S-Ieve! full factorial Box-Behnken design was implemented and response surface methodology used for analysis. The extraction time (0-20 min), temperature (60-180 "C), ethanol percentage (0-100%), solidlliquid ratio (5-45 g/L) and microwave power (0-400 W) were studied as independent variables. The phenolic profile of the studied tomato variety was initially characterized by HPLC-DAD-ESIIMS [2]. Then, the effect of the different extraction conditions, as defined by the used experimental design, on the target compounds was monitored by HPLC-DAD, using their UV spectra and retention time for identification and a series of calibrations based on external standards for quantification. The proposed model was successfully implemented and statistically validated. The microwave power had no effect on the extraction process. Comparing with the optimal extraction conditions for flavonoids, which demanded a short processing time (2 min), a low temperature (60 "C) and solidlliquid ratio (5 g/L), and pure ethanol, phenolic acids required a longer processing time ( 4.38 min), a higher temperature (145.6 •c) and solidlliquid ratio (45 g/L), and water as extraction solvent. Additionally, the studied tomato variety was highlighted as a source of added-value phenolic acids and flavonoids.

Mode locking in a spatially extended neuron model: active soma and compartmental tree

Understanding the mode-locked response of excitable systems to periodic forcing has important applications in neuroscience. For example it is known that spatially extended place cells in the hippocampus are driven by the theta rhythm to generate a code conveying information about spatial location. Thus it is important to explore the role of neuronal dendrites in generating the response to periodic current injection. In this paper we pursue this using a compartmental model, with linear dynamics for each compartment, coupled to an active soma model that generates action potentials. By working with the piece-wise linear McKean model for the soma we show how the response of the whole neuron model (soma and dendrites) can be written in closed form. We exploit this to construct a stroboscopic map describing the response of the spatially extended model to periodic forcing. A linear stability analysis of this map, together with a careful treatment of the non-differentiability of the soma model, allows us to construct the Arnol'd tongue structure for 1:q states (one action potential for q cycles of forcing). Importantly we show how the presence of quasi-active membrane in the dendrites can influence the shape of tongues. Direct numerical simulations confirm our theory and further indicate that resonant dendritic membrane can enlarge the windows in parameter space for chaotic behavior. These simulations also show that the spatially extended neuron model responds differently to global as opposed to point forcing. In the former case spatio-temporal patterns of activity within an Arnol'd tongue are standing waves, whilst in the latter they are traveling waves.

THE INFLUENCE OF MOTIVATION ON EMOTION REGULATION AND MOTOR PERFORMANCE: EXAMINATION OF A NEURO-AFFECTIVE MODEL

Mental stress is known to disrupt the execution of motor performance and can lead to decrements in the quality of performance, however, individuals have shown significant differences regarding how fast and well they can perform a skilled task according to how well they can manage stress and emotion. The purpose of this study was to advance our understanding of how the brain modulates emotional reactivity under different motivational states to achieve differential performance in a target shooting task that requires precision visuomotor coordination. In order to study the interactions in emotion regulatory brain areas (i.e. the ventral striatum, amygdala, prefrontal cortex) and the autonomic nervous system, reward and punishment interventions were employed and the resulting behavioral and physiological responses contrasted to observe the changes in shooting performance (i.e. shooting accuracy and stability of aim) and neuro-cognitive processes (i.e. cognitive load and reserve) during the shooting task. Thirty-five participants, aged 18 to 38 years, from the Reserve Officers’ Training Corp (ROTC) at the University of Maryland were recruited to take 30 shots at a bullseye target in three different experimental conditions. In the reward condition, $1 was added to their total balance for every 10-point shot. In the punishment condition, $1 was deducted from their total balance if they did not hit the 10-point area. In the neutral condition, no money was added or deducted from their total balance. When in the reward condition, which was reportedly most enjoyable and least stressful of the conditions, heart rate variability was found to be positively related to shooting scores, inversely related to variability in shooting performance and positively related to alpha power (i.e. less activation) in the left temporal region. In the punishment (and most stressful) condition, an increase in sympathetic response (i.e. increased LF/HF ratio) was positively related to jerking movements as well as variability of placement (on the target) in the shots taken. This, coupled with error monitoring activity in the anterior cingulate cortex, suggests evaluation of self-efficacy might be driving arousal regulation, thus affecting shooting performance. Better performers showed variable, increasing high-alpha power in the temporal region during the aiming period towards taking the shot which could indicate an adaptive strategy of engagement. They also showed lower coherence during hit shots than missed shots which was coupled with reduced jerking movements and better precision and accuracy. Frontal asymmetry measures revealed possible influence of the prefrontal lobe in driving this effect in reward and neutral conditions. The possible interactions, reasons behind these findings and implications are discussed.

Quantifying the Resilience of an Urban Traffic-Electric Power Coupled System

Transportation system resilience has been the subject of several recent studies. To assess the resilience of a transportation network, however, it is essential to model its interactions with and reliance on other lifelines. In this work, a bi-level, mixed-integer, stochastic program is presented for quantifying the resilience of a coupled traffic-power network under a host of potential natural or anthropogenic hazard-impact scenarios. A two-layer network representation is employed that includes details of both systems. Interdependencies between the urban traffic and electric power distribution systems are captured through linking variables and logical constraints. The modeling approach was applied on a case study developed on a portion of the signalized traffic-power distribution system in southern Minneapolis. The results of the case study show the importance of explicitly considering interdependencies between critical infrastructures in transportation resilience estimation. The results also provide insights on lifeline performance from an alternative power perspective.

DEVELOPMENT OF A 2-DIMENSIONAL FINITE VOLUME MODEL TO ASSESS HYDRODYNAMIC AND MICROBIAL CONTROLS ON DNAPL DISSOLUTION AND DETOXIFICATION

Tetrachloroethene (PCE) and trichloroethene (TCE) form dense non-aqueous phase liquids (DNAPLs), which are persistent groundwater contaminants. DNAPL dissolution can be "bioenhanced" via dissolved contaminant biodegradation at the DNAPL-water interface. This research hypothesized that: (1) competitive interactions between different dehalorespiring strains can significantly impact the bioenhancement effect, and extent of PCE dechlorination; and (2) hydrodynamics will affect the outcome of competition and the potential for bioenhancement and detoxification. A two-dimensional coupled flowtransport model was developed, with a DNAPL pool source and multiple microbial species. In the scenario presented, Dehalococcoides mccartyi 195 competes with Desulfuromonas michiganensis for the electron acceptors PCE and TCE. Simulations under biostimulation and low velocity (vx) conditions suggest that the bioenhancement with Dsm. michiganensis alone was modestly increased by Dhc. mccartyi 195. However, the presence of Dhc. mccartyi 195 enhanced the extent of PCE transformation. Hydrodynamic conditions impacted the results by changing the dominant population under low and high vx conditions.

Transcription-Coupled DNA Supercoiling in Escherichia Coli: Mechanisms and Biological Functions

Transcription by RNA polymerase can induce the formation of hypernegatively supercoiled DNA both in vivo and in vitro. This phenomenon has been explained by a “twin-supercoiled-domain” model of transcription where a positively supercoiled domain is generated ahead of the RNA polymerase and a negatively supercoiled domain behind it. In E. coli cells, transcription-induced topological change of chromosomal DNA is expected to actively remodel chromosomal structure and greatly influence DNA transactions such as transcription, DNA replication, and recombination. In this study, an IPTG-inducible, two-plasmid system was established to study transcription-coupled DNA supercoiling (TCDS) in E. coli topA strains. By performing topology assays, biological studies, and RT-PCR experiments, TCDS in E. coli topA strains was found to be dependent on promoter strength. Expression of a membrane-insertion protein was not needed for strong promoters, although co-transcriptional synthesis of a polypeptide may be required. More importantly, it was demonstrated that the expression of a membrane-insertion tet gene was not sufficient for the production of hypernegatively supercoiled DNA. These phenomenon can be explained by the “twin-supercoiled-domain” model of transcription where the friction force applied to E. coli RNA polymerase plays a critical role in the generation of hypernegatively supercoiled DNA. Additionally, in order to explore whether TCDS is able to greatly influence a coupled DNA transaction, such as activating a divergently-coupled promoter, an in vivo system was set up to study TCDS and its effects on the supercoiling-sensitive leu-500 promoter. The leu-500 mutation is a single A-to-G point mutation in the -10 region of the promoter controlling the leu operon, and the AT to GC mutation is expected to increase the energy barrier for the formation of a functional transcription open complex. Using luciferase assays and RT-PCR experiments, it was demonstrated that transient TCDS, “confined” within promoter regions, is responsible for activation of the coupled transcription initiation of the leu-500 promoter. Taken together, these results demonstrate that transcription is a major chromosomal remodeling force in E. coli cells.

Women-led Community Development Organizations (CDOs) in Miami-Dade County: A Model of Community Development Efforts Impacting the Economic Security of Women

Recent studies on the economic status of women in Miami-Dade County (MDC) reveal an alarming rate of economic insecurity and significant obstacles for women to achieve economic security. Consistent barriers to women’s economic security affect not only the health and wellbeing of women and their families, but also economic prospects for the community. A key study reveals in Miami-Dade County, “Thirty-nine percent of single female-headed families with at least one child are living at or below the federal poverty level” and “over half of working women do not earn adequate income to cover their basic necessities” (Brion 2009, 1). Moreover, conventional measures of poverty do not adequately capture women’s struggles to support themselves and their families, nor do they document the numbers of women seeking basic self-sufficiency. Even though there is lack of accurate data on women in the county, which is a critical problem, there is also a dearth of social science research on existing efforts to enhance women’s economic security in Miami-Dade County. My research contributes to closing the information gap by examining the characteristics and strategies of women-led community development organizations (CDOs) in MDC, working to address women’s economic insecurity. The research is informed by a framework developed by Marilyn Gittell, who pioneered an approach to study women-led CDOs in the United States. On the basis of research in nine U.S. cities, she concluded that women-led groups increased community participation and “by creating community networks and civic action, they represent a model for community development efforts” (Gittell, et al. 2000, 123). My study documents the strategies and networks of women-led CDOs in MDC that prioritize women’s economic security. Their strategies are especially important during these times of economic recession and government reductions in funding towards social services. The focus of the research is women-led CDOs that work to improve social services access, economic opportunity, civic participation and capacity, and women’s rights. Although many women-led CDOs prioritize building social infrastructures that promote change, inequalities in economic and political status for women without economic security remain a challenge (Young 2004). My research supports previous studies by Gittell, et al., finding that women-led CDOs in Miami-Dade County have key characteristics of a model of community development efforts that use networking and collaboration to strengthen their broad, integrated approach. The resulting community partnerships, coupled with participation by constituents in the development process, build a foundation to influence policy decisions for social change. In addition, my findings show that women-led CDOs in Miami-Dade County have a major focus on alleviating poverty and economic insecurity, particularly that of women. Finally, it was found that a majority of the five organizations network transnationally, using lessons learned to inform their work of expanding the agency of their constituents and placing the economic empowerment of women as central in the process of family and community development.

Development of a Coupling Model for Fluid-Structure Interaction using the Mesh-free Finite Element Method and the Lattice Boltzmann Method

In the presented thesis work, the meshfree method with distance fields was coupled with the lattice Boltzmann method to obtain solutions of fluid-structure interaction problems. The thesis work involved development and implementation of numerical algorithms, data structure, and software. Numerical and computational properties of the coupling algorithm combining the meshfree method with distance fields and the lattice Boltzmann method were investigated. Convergence and accuracy of the methodology was validated by analytical solutions. The research was focused on fluid-structure interaction solutions in complex, mesh-resistant domains as both the lattice Boltzmann method and the meshfree method with distance fields are particularly adept in these situations. Furthermore, the fluid solution provided by the lattice Boltzmann method is massively scalable, allowing extensive use of cutting edge parallel computing resources to accelerate this phase of the solution process. The meshfree method with distance fields allows for exact satisfaction of boundary conditions making it possible to exactly capture the effects of the fluid field on the solid structure.