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Computational Modeling Studies of Fundamental Aerosol-Cloud Interactions
Get PDFBasic questions regarding the interaction between changes in human activity and the atmosphere remain unanswered. Among these, the link between aerosol particles and cloud formation and development, especially in an altered climate, is a large point of uncertainty in recent climate projections. This should come as no surprise given the uncertainty in model parameters required to predict droplet activation, even in the most detailed models used for climate predictions. Here, a detailed spectral mixed-phase microphysics scheme and a state-of-the-art continuous two-dimensional (2-D) aerosol-droplet microphysics scheme have been developed and coupled to the Weather Research and Forecasting (WRF) model to more closely analyze the effects of aerosol perturbations on single clouds or cloud systems with the hope of ultimately improving numerical parameterizations used by microphysics schemes in general circulation models (GCMs).
The continuous 2-D aerosol-droplet model is developed to explicitly treat the entire spectrum of aerosol, haze droplets, cloud droplets, and drizzle drops while allowing the solute mass spectrum to evolve within the droplets. In other words, the aerosol mass is conserved and regeneration of aerosol particles upon droplet evaporation is physically accurate without any a priori assumptions. The model is tested by performing simulations of marine stratocumulus and the results are compared with those from the aforementioned bin and bulk models. It is shown that microphysical processing of aerosols alone results in a large shift in the aerosol spectrum toward larger particles (via collision-coalescence of droplets). This could have potentially large effects on the activation of regenerated particles. Future studies with the model will address the need for better parameterizations of the aerosol regeneration process.
The spectral mixed-phase microphysics scheme is used in conjunction with a two-moment bulk microphysics model to study the effect of aerosol perturbations on deep convective clouds. The bin model shows that with an increase in aerosol number concentration comes an invigoration and a decrease in precipitation. On the other hand, the bulk model suggests that the storm ought to weaken and precipitation will increase in a more polluted environment. The invigoration predicted by the bin model is a result of the suppression of the collision-coalescence process that permits more droplets to be lofted above the freezing level, hence increasing the bulk freezing rate aloft. The additional freezing and subsequent deposition acts to increase the latent heating and thus increase buoyancy. However, the cloud particles in the polluted cases are now smaller and more numerous and consequently have a shorter evaporation/sublimation timescale and a longer sedimentation time-scale. The ultimate result is for precipitation to decrease in conjunction with a moistening of the mid- to upper-troposphere. The difference in the sign of the aerosol effect between the two models is thought to be related to the saturation adjustment scheme used in the bulk model and is addressed by including an explicit treatment of condensation and activation within the bulk model, similar to the algorithm utilized in the bin model. The results of the inter-model comparison demonstrate the significance of the saturation adjustment assumption on the sign and magnitude of the aerosol effect on deep convective clouds.</p
The Regulatory Origin of Oral and Aboral Mesoderm in Sea Urchin Embryos
Get PDFGene regulatory networks (GRN) underlie the control processes that are executed during embryonic development. Their constituents are transcription factors that regulate downstream targets, including other transcription factors. The regulatory architecture of a GRN reveals how discrete developmental tasks, such as cell specification, are implemented.
We here expand the GRN underlying development of sea urchin non-skeletogenic mesoderm (NSM). NSM cells are the offspring of the inner ring of the veg2 cells that lie adjacent to the skeletogenic mesoderm (SM) and receive the Delta signal presented by these cells. Perturbation of Delta reveals that all NSM-specific genes are activated by Delta, but also indicate that Delta has few direct targets. A large number of genes are activated only after delta expression in the SM disappears, thus indicating that these genes are indirect targets and downstream of early NSM transcription factors. We show that the second phase of delta expresion (in the NSM) activates the foxY gene; loss of NSM Delta does not interfere with early NSM specification but instead abolishes development of late mesoderm derivates.
NSM is partitioned into an oral and an aboral segment as a consequence of Nodal signaling. However, Nodal activates the homeobox gene not, which represses early NSM genes on the oral side, causing them to become restricted to the aboral side. This allows oral NSM genes to be activated. Oral NSM genes can be expressed throughout the entire NSM if aboral NSM specification is perturbed. This shows that the driver of NSM genes is present throughout the NSM, making SM Delta a likely candidate. We examine the regulatory state of oral and aboral NSM segments and show that a GRN subcircuit on the aboral side locks down its expression. The sets of regulatory genes on both sides of the NSM are entirely distinct and mutually exclusive.</p
Thermal Ignition
Get PDFAccidental ignition of flammable gases is a critical safety concern in many industrial applications. Particularly in the aviation industry, the main areas of concern on an aircraft are the fuel tank and adjoining regions, where spilled fuel has a high likelihood of creating a flammable mixture. To this end, a fundamental understanding of the ignition phenomenon is necessary in order to develop more accurate test methods and standards as a means of designing safer air vehicles. The focus of this work is thermal ignition, particularly auto-ignition with emphasis on the effect of heating rate, hot surface ignition and flame propagation, and puffing flames.
Combustion of hydrocarbon fuels is traditionally separated into slow reaction, cool flame, and ignition regimes based on pressure and temperature. Standard tests, such as the ASTM E659, are used to determine the lowest temperature required to ignite a specific fuel mixed with air at atmospheric pressure. It is expected that the initial pressure and the rate at which the mixture is heated also influences the limiting temperature and the type of combustion. This study investigates the effect of heating rate, between 4 and 15 K/min, and initial pressure, in the range of 25 to 100 kPa, on ignition of n-hexane air mixtures. Mixtures with equivalence ratio ranging from 0.6 to = 1.2 were investigated. The problem is also modeled computationally using an extension of Semenov's classical auto-ignition theory with a detailed chemical mechanism. Experiments and simulations both show that in the same reactor either a slow reaction or an ignition event can take place depending on the heating rate. Analysis of the detailed chemistry demonstrates that a mixture which approaches the ignition region slowly undergoes a significant modification of its composition. This change in composition induces a progressive shift of the explosion limit until the mixture is no longer flammable. A mixture that approaches the ignition region sufficiently rapidly undergoes only a moderate amount of thermal decomposition and explodes quite violently. This behavior can also be captured and analyzed using a one-step reaction model, where the heat release is in competition with the depletion of reactants.
Hot surface ignition is examined using a glow plug or heated nickel element in a series of premixed n-hexane air mixtures. High-speed schlieren photography, a thermocouple, and a fast response pressure transducer are used to record flame characteristics such as ignition temperature, flame speed, pressure rises, and combustion mode. The ignition event is captured by considering the dominant balance of diffusion and chemical reaction that occurs near a hot surface. Experiments and models show a dependence of ignition temperature on mixture composition, initial pressure, and hot surface size. The mixtures exhibit the known lower flammability limit where the maximum temperature of the hot surface was insufficient at igniting the mixture. Away from the lower flammability limit, the ignition temperature drops to an almost constant value over a wide range of equivalence ratios (0.7 to 2.8) with large variations as the upper flammability limit is approached. Variations in the initial pressure and equivalence ratio also give rise to different modes of combustion: single flame, re-ignition, and puffing flames. These results are successfully compared to computational results obtained using a flamelet model and a detailed chemical mechanism for n-heptane. These different regimes can be delineated by considering the competition between inertia, i.e., flame propagation, and buoyancy, which can be expressed in the Richardson number.
In experiments of hot surface ignition and subsequent flame propagation a 10 Hz puffing flame instability is visible in mixtures that are stagnant and premixed prior to the ignition sequence. By varying the size of the hot surface, power input, and combustion vessel volume, we determined that the instability is a function of the interaction of the flame with the fluid flow induced by the combustion products rather than the initial plume established by the hot surface. The phenomenon is accurately reproduced in numerical simulations and a detailed flow field analysis revealed a competition between the inflow velocity at the base of the flame and the flame propagation speed. The increasing inflow velocity, which exceeds the flame propagation speed, is ultimately responsible for creating a puff. The puff is then accelerated upward, allowing for the creation of the subsequent instabilities. The frequency of the puffing is proportional to the gravitational acceleration and inversely proportional to the flame speed. We propose a relation describing the dependence of the frequency on gravitational acceleration, hot surface diameter, and flame speed. This relation shows good agreement for lean and rich n-hexane-air as well as lean hydrogen-air flames.</p
Asymptotic Properties of Orthogonal and Extremal Polynomials
Get PDFThis thesis is devoted to asymptotic properties of extremal polynomials in a variety of settings. Special attention is given to the orthonormal and monic orthogonal polynomials. Given a positive real number q and a measure with compact and infinite support in the complex plane, one can define - for every natural number n - a monic polynomial of degree n having minimal Lq-norm with respect to the given measure among all monic polynomials of the same degree. Dividing this polynomial by its norm produces a normalized extremal polynomial. We will study the asymptotic behavior of these extremal polynomials when the given measure is of a certain very general form. Our results concerning extremal polynomial asymptotics will include Szego asymptotics, ratio asymptotics, and relative asymptotics. We will also study the associated Christoffel functions and the weak asymptotic behavior of sequences of measures derived from the normalized extremal polynomials
Optimization of the GluC1/IVM Neuronal Silencing Tool via Protein Engineering
Get PDFA variety of genetically encoded tools have been developed for deciphering the neural circuitry of the brain. Such tools allow physical manipulation of neuronal excitability in a reversible, cell-specific manner, enabling researchers to establish how electrical activity and connectivity facilitate the information processing that mediates perception and drives behavior. An expanding toolkit of engineered neuroreceptors, particularly those actuated by orthogonal pharmacological ligands, provide noninvasive manipulation of regional or disperse neuronal populations with adequate spatiotemporal precision and great potential for multiplexing. We previously engineered an invertebrate glutamate-gated chloride channel (GluCl αβ) that enabled pharmacologically induced silencing of electrical activity in targeted CNS neurons in vivo by the anthelmintic drug compound ivermectin (IVM; Lerchner et al., 2007). With this receptor, GluCl opt α-CFP + opt β-YFP Y182F, the concentration of IVM necessary to elicit a consistent silencing phenotype was higher than expected, raising concern about its potential side effects. Considerable variability in the extent of spike suppression was also apparent and was attributed to variable co-expression levels of α and β subunits. Thus, a rational protein engineering strategy was employed to optimize the GluCl/IVM tool. To increase agonist sensitivity, a gain-of-function gating mutation involving the highly conserved leucine 9’ residue of the α pore-lining M2 transmembrane domain was introduced. Various mutations at this position facilitate channel opening in the absence and presence of ligand. Analysis of side chain properties revealed that helix-destabilizing energy correlated with increases in agonist sensitivity. One mutation, L9’F, enhances β subunit incorporation to substantially increase IVM sensitivity without permitting unliganded channel opening. Removal of an arginine-based ER retention motif (RSR_AAA) from the intracellular loop of β promoted plasma membrane expression of heteromeric GluCl αβ by preventing ER-associated degradation of the β subunit. An additional monomeric XFP mutation complements these effects. The newly engineered GluCl opt α-mXFP L9’F + opt β-mXFP Y182F RSR_AAA receptor significantly increases conductance and reduces variability in evoked spike generation in vitro using a lower concentration of IVM. This receptor, dubbed ‘GluClv2.0’, is an improved tool for IVM-induced silencing
Geodynamics of Earth’s Deep Mantle
Get PDFSeismic tomography and waveform modeling reveal several prominent structures in the Earth's lower mantle: (1) the D" discontinuity, defined by a seismic velocity increase of 1-3% about 250 km above the core-mantle boundary (CMB), (2) Ultralow-velocity zones (ULVZs), which are thin, isolated patches with anomalously low seismic wavespeed at the CMB, and (3) two large, low-shear velocity provinces (LLSVPs) beneath Africa and the Pacific Ocean. The geodynamics of these structures are investigated using numerical convection models that include new discoveries in mineral physics and recent insight from seismology. In addition, I assess the influence of an iron spin transition in a major lower mantle mineral (ferropericlase) on the style and vigor of mantle convection.
A phase change model for the D" discontinuity produces significant thermal and phase heterogeneity over small distances due to the interaction of slabs, plumes, and a phase transition. Perturbations to seismic arrivals are linked to the evolutionary stage of slabs and plumes and can be used to determine phase boundary properties, volumetric wavespeed anomaly beneath the discontinuity, and possibly the lengthscale of slab folding near the CMB.
I simulate convection within D" to deduce the stability and morphology of a chemically distinct iron-enriched ULVZ. The chemical density anomaly largely dictates ULVZ shape, and the prescribed initial thickness (proxy for volume) of the chemically distinct layer controls its size. I synthesize the dynamic results with a Voigt-Reuss-Hill mixing model to provide insight into the inherent seismic trade-off between ULVZ thickness and wavespeed reduction.
The dynamics of the LLSVPs are investigated using global 3-D models of thermochemical structures that incorporate paleogeographic constraints from 250 Ma to present day. The structures deform and migrate along the CMB, either by coupling to plate motions or in response to slab stresses. Slabs from Paleo-Tethys and Tethys Ocean subduction push the African structure further to the southwest than inferred from tomography. Dense and viscous slabs can severely compromise the stability of thermochemical structures with a high bulk modulus at the CMB.
Finally, I explore the consequences of the intrinsic density change caused by the Fe2+ spin transition in ferropericlase on the style and vigor of mantle convection. The transition generates a net driving density difference for both upwellings and downwellings that dominantly enhances the positive thermal buoyancy of plumes in 2-D cylindrical geometry. Although the additional buoyancy does not fundamentally alter large-scale dynamics, the Nusselt number increases by 5-10%, and vertical velocities increase by 10--40% in the lower mantle. Advective heat transport is more effective and temperatures in the CMB region are reduced by up to 12%.</p
Cavity Ringdown Spectroscopy, Kinetics, and Quantum Chemistry of Atmospherically Relevant Reactions
Get PDFThis thesis describes laboratory experiments and electronic structure calculations on three chemical systems relevant to tropospheric ozone chemistry: peroxynitrous acid (HOONO), hydroxymethylperoxy radical formed from HO2 + HCHO (R1), and products of alkoxy isomerization (R2). R1 and R2 were studied experimentally using a gas flow cell that combined UV photolysis with cavity ringdown spectroscopy (CRDS). All chemical systems were studied using electronic structure calculations and kinetics modeling.
HOONO is one of the products of the reaction OH + NO2, and acts as a temporary reservoir for HOx and NOx in the atmosphere. Torsional excitation of HOONO will break its internal hydrogen bond, leading to sequence band formation in the OH stretch spectrum. Chapter 3 describes a calculated 3-dimensional potential energy surface to examine torsional mode coupling and sequence band formation. We apply these results to previous CRDS kinetics studies of HOONO.
The reaction of HO2 with carbonyls is believed to be a major sink of HOx and carbonyl compounds at reduced temperatures. R1 is the simplest of these reactions. Despite numerous previous studies, considerable uncertainty exists on the activation energy and rate constant of R1. Chapters 4-6 describe CRDS and electronic structure studies on the isomerization product, hydroxymethylperoxy. CRDS was used to make the first measurements of the OH stretch and A-X electronic spectra, and the kinetics of hydroxymethylperoxy chemistry. Electronic structure calculations were used to simulate the spectroscopic bands and examine the conformers of hydroxymethylperoxy and 2-hydroxyisopropylperoxy.
Atmospheric alkoxy radicals can isomerize or react with O2, and each pathway has a different impact on ozone chemistry. Chapters 7-10 describe cavity ringdown spectroscopy, kinetics, and electronic structure calculations on the n-butoxy and 2-pentoxy isomerization products, specifically δ-HOC4H8•, δ-HOC4H8OO•, δ-HO-1-C5H10•, and δ-HO-1-C5H10OO•. CRDS was used to make the first measurements of the A-X electronic spectrum of δ-HOC4H8OO• and clean OH stretch spectra of all four radicals. Relative kinetics data previously obtained using CRDS were reanalyzed to include the effects of additional alkoxy reactions. Electronic structure calculations were performed to explain the observations that the OH stretch absorption cross section differs between HOR• and HOROO•.</p
Design of Molecules and Materials for Applications in Clean Energy, Catalysis and Molecular Machines Through Quantum Mechanics, Molecular Dynamics and Monte Carlo Simulations
Get PDFWe use a multiparadigm, multiscale strategy based on quantum mechanics (QM), first-principles QM-based molecular mechanics (MD) and grand canonical Monte Carlo (GCMC) to rationally design new molecules and materials for clean energy (H2 and CH4 storage), catalysis (O2 evolution, metal organic complexes) and molecular architectures (rotaxanes, hydrogels). This thesis is organized in seven chapters and shows that it is crucial to understand the scale of the system to be studied, the insight obtained can be used to rationally design new molecules and materials for desirable applications; as well as to guide and complement experimental studies. Chapter 1 discusses the specific details of the proposed methodology, including the theoretical underpinning of each modeling paradigm, potential limitations, and how we use these for in silico characterization and design optimization. Chapter 2 covers the structure prediction and characterization of metal-organic complex arrays (MOCA) through QM and force-field-based molecular mechanics. The methodology is inspired by the approach used for enzymatic systems, considering that experimentally determining their three-dimensional structure remains an open challenge. Chapter 3 describes the use of transition state theory for the calculation of reaction rates in polymer hydrogel network formation. This enables the determination of optimum concentrations for polymerization reactions and preparation of coarse-grained force elds. Chapter 4 describes the work performed on Stoddard's rotaxane dumbbells, where we explained origin for the template-directed synthesis through QM-derived free energies. We also give a consistent explanation for the role of the counter anion. Chapter 5 presents the simulation results for a tetranuclear cluster model for O2 evolution, based on CaMn304 and Mn4O4 clusters. We demonstrate how to calculate their oxidation potentials and propose new molecular designs that resemble the oxygen evolution complex (OEC) both structurally and electronically. Chapter 6 presents our findings for CH4 storage. Using a second-order Moller-Plesset perturbation theory force field and GCMC we propose a framework for optimal delivery. Chapter 7 presents our designed materials for hydrogen storage and the validation of our methodology against experimental results. We based our predictions in QM and GCMC calculations through the development of our own first-principles vdW force eld. Our results demonstrate novel frameworks capable of achieving the DOE energy density target for 2015. Finally, we show the generalization of adsorption phenomena for any porous material based on topological constraints
Hybrid Human-Machine Vision Systems: Image Annotation using Crowds, Experts and Machines
Get PDFThe amount of digital image and video data keeps increasing at an ever-faster rate. While "big data" holds the promise of leading science to new discoveries, raw image data in itself is not of much use. In order to statistically analyze the data, it must be quantified and annotated. We argue that entirely automated methods are not accurate enough to annotate data in the short term. Crowdsourcing is an alternative that provides higher accuracy, but is too expensive to scale to millions of images. Instead, the solution is hybrid human-machine vision systems, where the work of both humans and machines is balanced to be as cost-effective and accurate as possible. With this goal in mind, we begin by categorizing different types of image annotations, and describe how nonexpert annotators can be trained to carry out challenging image annotation tasks. Having identified which types of annotations are appropriate for most tasks, including binary, confidence, pair-wise and continuous annotations, we present models for crowdsourcing annotations from hundreds of expert and nonexpert annotators (humans). By trading off the bias and expertise of multiple annotators, we show that it is possible to achieve high-quality annotations with very few labels. We show that the number of labels can be further reduced by actively choosing the best annotators to carry out most of the work. Finally, we study the problem of estimating the performance of automated classifiers (machines) used to annotate large datasets where few ground truth labels are available. Using a semisupervised model for classifier confidence scores, we show that it is possible to accurately estimate classifier performance with very few labels
Applications of Coding in Network Communications
Get PDFThis thesis uses the tool of network coding to investigate fast peer-to-peer file distribution, anonymous communication, robust network construction under uncertainty, and prioritized transmission.
In a peer-to-peer file distribution system, we use a linear optimization approach to show that the network coding framework significantly simplifies analysis even in scenarios where the optimal solution does not require coding. We also study the effect of requiring reciprocity and the impact of dynamically changing network scenarios.
Second, we investigate anonymous routing in peer-to-peer networks. The goal is to design and analyze a peer-to-peer system that hides the identities of source and sink pairs against adversarial nodes. We first propose a protocol for subgraph construction signaling. The protocol uses path diversity rather than cryptographic keys. We prove information theoretic security of the proposed protocol. We investigate a variety of deterministic and randomized subgraph designs. We also give a reverse path construction mechanism, with which a sink can reply to the source without knowing the source identity. We next investigate anonymous data transmission using network coding. Again, path diversity (with network coding) is used to hide the identities of source and sink pairs. We investigate the effect of subgraph shape on anonymity and congestion arising from traffic shaping constraints, demonstrating the tradeoff between the two through simulations.
Third, we study the problem of network construction under uncertainty about link-loss rates. We prove that both maximizing throughput and minimizing cost are coNP-hard problems. We find polynomial time-solvable solutions that outperform other deterministic approaches.
Lastly, we investigate strategies for communication under a system that prioritizes data based on the worth of data and the probability of successful transmission. Only the highest priority data is transmitted when communication is very limited.</p