Two-phase flow analogy as an effective boundary condition for modelling liquids at atomistic resolution

A hybrid Molecular Dynamics/Fluctuating Hydrodynamics framework based on the analogy with two-phase hydrodynamics has been extended to dynamically tracking the feature of interest at all-atom resolution. In the model, the hydrodynamics description is used as an effective boundary condition to close the molecular dynamics solution without resorting to standard periodic boundary conditions. The approach is implemented in a popular Molecular Dynamics package GROMACS and results for two biomolecular systems are reported. A small peptide dialanine and a complete capsid of a virus porcine circovirus 2 in water are considered and shown to reproduce the structural and dynamic properties compared to those obtained in theory, purely atomistic simulations, and experiment.

Practical secure information flow in programming languages

If we classify variables in a program into various security levels, then a secure information flow analysis aims to verify statically that information in a program can flow only in ways consistent with the specified security levels. One well-studied approach is to formulate the rules of the secure information flow analysis as a type system. A major trend of recent research focuses on how to accommodate various sophisticated modern language features. However, this approach often leads to overly complicated and restrictive type systems, making them unfit for practical use. Also, problems essential to practical use, such as type inference and error reporting, have received little attention. This dissertation identified and solved major theoretical and practical hurdles to the application of secure information flow. ^ We adopted a minimalist approach to designing our language to ensure a simple lenient type system. We started out with a small simple imperative language and only added features that we deemed most important for practical use. One language feature we addressed is arrays. Due to the various leaking channels associated with array operations, arrays have received complicated and restrictive typing rules in other secure languages. We presented a novel approach for lenient array operations, which lead to simple and lenient typing of arrays. ^ Type inference is necessary because usually a user is only concerned with the security types for input/output variables of a program and would like to have all types for auxiliary variables inferred automatically. We presented a type inference algorithm B and proved its soundness and completeness. Moreover, algorithm B stays close to the program and the type system and therefore facilitates informative error reporting that is generated in a cascading fashion. Algorithm B and error reporting have been implemented and tested. ^ Lastly, we presented a novel framework for developing applications that ensure user information privacy. In this framework, core computations are defined as code modules that involve input/output data from multiple parties. Incrementally, secure flow policies are refined based on feedback from the type checking/inference. Core computations only interact with code modules from involved parties through well-defined interfaces. All code modules are digitally signed to ensure their authenticity and integrity. ^

Surface mean flow and turbulence structure in tropical cyclone winds

Hurricanes are one of the deadliest and costliest natural hazards affecting the Gulf coast and Atlantic coast areas of the United States. An effective way to minimize hurricane damage is to strengthen structures and buildings. The investigation of surface level hurricane wind behavior and the resultant wind loads on structures is aimed at providing structural engineers with information on hurricane wind characteristics required for the design of safe structures. Information on mean wind profiles, gust factors, turbulence intensity, integral scale, and turbulence spectra and co-spectra is essential for developing realistic models of wind pressure and wind loads on structures. The research performed for this study was motivated by the fact that considerably fewer data and validated models are available for tropical than for extratropical storms. ^ Using the surface wind measurements collected by the Florida Coastal Monitoring Program (FCMP) during hurricane passages over coastal areas, this study presents comparisons of surface roughness length estimates obtained by using several estimation methods, and estimates of the mean wind and turbulence structure of hurricane winds over coastal areas under neutral stratification conditions. In addition, a program has been developed and tested to systematically analyze Wall of Wind (WoW) data, that will make it possible to perform analyses of baseline characteristics of flow obtained in the WoW. This program can be used in future research to compare WoW data with FCMP data, as gust and turbulence generator systems and other flow management devices will be used to create WoW flows that match as closely as possible real hurricane wind conditions. ^ Hurricanes are defined as tropical cyclones for which the maximum 1-minute sustained surface wind speeds exceed 74 mph. FCMP data include data for tropical cyclones with lower sustained speeds. However, for the winds analyzed in this study the speeds were sufficiently high to assure that neutral stratification prevailed. This assures that the characteristics of those winds are similar to those prevailing in hurricanes. For this reason in this study the terms tropical cyclones and hurricanes are used interchangeably. ^

Lattice Boltzmann method for flow and heat transfer in microgeometries

Recent technological developments have made it possible to design various microdevices where fluid flow and heat transfer are involved. For the proper design of such systems, the governing physics needs to be investigated. Due to the difficulty to study complex geometries in micro scales using experimental techniques, computational tools are developed to analyze and simulate flow and heat transfer in microgeometries. However, conventional numerical methods using the Navier-Stokes equations fail to predict some aspects of microflows such as nonlinear pressure distribution, increase mass flow rate, slip flow and temperature jump at the solid boundaries. This necessitates the development of new computational methods which depend on the kinetic theory that are both accurate and computationally efficient. In this study, lattice Boltzmann method (LBM) was used to investigate the flow and heat transfer in micro sized geometries. The LBM depends on the Boltzmann equation which is valid in the whole rarefaction regime that can be observed in micro flows. Results were obtained for isothermal channel flows at Knudsen numbers higher than 0.01 at different pressure ratios. LBM solutions for micro-Couette and micro-Poiseuille flow were found to be in good agreement with the analytical solutions valid in the slip flow regime (0.01 < Kn < 0.1) and direct simulation Monte Carlo solutions that are valid in the transition regime (0.1 < Kn < 10) for pressure distribution and velocity field. The isothermal LBM was further extended to simulate flows including heat transfer. The method was first validated for continuum channel flows with and without constrictions by comparing the thermal LBM results against accurate solutions obtained from analytical equations and finite element method. Finally, the capability of thermal LBM was improved by adding the effect of rarefaction and the method was used to analyze the behavior of gas flow in microchannels. The major finding of this research is that, the newly developed particle-based method described here can be used as an alternative numerical tool in order to study non-continuum effects observed in micro-electro-mechanical-systems (MEMS).

Analytical approximations to predict performance measures of manufacturing systems with job failures and parallel processing

Parallel processing is prevalent in many manufacturing and service systems. Many manufactured products are built and assembled from several components fabricated in parallel lines. An example of this manufacturing system configuration is observed at a manufacturing facility equipped to assemble and test web servers. Characteristics of a typical web server assembly line are: multiple products, job circulation, and paralleling processing. The primary objective of this research was to develop analytical approximations to predict performance measures of manufacturing systems with job failures and parallel processing. The analytical formulations extend previous queueing models used in assembly manufacturing systems in that they can handle serial and different configurations of paralleling processing with multiple product classes, and job circulation due to random part failures. In addition, appropriate correction terms via regression analysis were added to the approximations in order to minimize the gap in the error between the analytical approximation and the simulation models. Markovian and general type manufacturing systems, with multiple product classes, job circulation due to failures, and fork and join systems to model parallel processing were studied. In the Markovian and general case, the approximations without correction terms performed quite well for one and two product problem instances. However, it was observed that the flow time error increased as the number of products and net traffic intensity increased. Therefore, correction terms for single and fork-join stations were developed via regression analysis to deal with more than two products. The numerical comparisons showed that the approximations perform remarkably well when the corrections factors were used in the approximations. In general, the average flow time error was reduced from 38.19% to 5.59% in the Markovian case, and from 26.39% to 7.23% in the general case. All the equations stated in the analytical formulations were implemented as a set of Matlab scripts. By using this set, operations managers of web server assembly lines, manufacturing or other service systems with similar characteristics can estimate different system performance measures, and make judicious decisions - especially setting delivery due dates, capacity planning, and bottleneck mitigation, among others.

Secure information flow via stripping and fast simulation

Type systems for secure information flow aim to prevent a program from leaking information from H (high) to L (low) variables. Traditionally, bisimulation has been the prevalent technique for proving the soundness of such systems. This work introduces a new proof technique based on stripping and fast simulation, and shows that it can be applied in a number of cases where bisimulation fails. We present a progressive development of this technique over a representative sample of languages including a simple imperative language (core theory), a multiprocessing nondeterministic language, a probabilistic language, and a language with cryptographic primitives. In the core theory we illustrate the key concepts of this technique in a basic setting. A fast low simulation in the context of transition systems is a binary relation where simulating states can match the moves of simulated states while maintaining the equivalence of low variables; stripping is a function that removes high commands from programs. We show that we can prove secure information flow by arguing that the stripping relation is a fast low simulation. We then extend the core theory to an abstract distributed language under a nondeterministic scheduler. Next, we extend to a probabilistic language with a random assignment command; we generalize fast simulation to the setting of discrete time Markov Chains, and prove approximate probabilistic noninterference. Finally, we introduce cryptographic primitives into the probabilistic language and prove computational noninterference, provided that the underling encryption scheme is secure.

Carbon nanotube based systems for high energy efficient applications

In the current age of fast-depleting conventional energy sources, top priority is given to exploring non-conventional energy sources, designing highly efficient energy storage systems and converting existing machines/instruments/devices into energy-efficient ones. ‘Energy efficiency’ is one of the important challenges for today’s scientific and research community, worldwide. In line with this demand, the current research was focused on developing two highly energy-efficient devices – field emitters and Li-ion batteries, using beneficial properties of carbon nanotubes (CNT). Interface-engineered, directly grown CNTs were used as cathode in field emitters, while similar structure was applied as anode in Li-ion batteries. Interface engineering was found to offer minimum resistance to electron flow and strong bonding with the substrate. Both field emitters and Li-ion battery anodes were benefitted from these advantages, demonstrating high energy efficiency. Field emitter, developed during this research, could be characterized by low turn-on field, high emission current, very high field enhancement factor and extremely good stability during long-run. Further, application of 3-dimensional design to these field emitters resulted in achieving one of the highest emission current densities reported so far. The 3-D field emitter registered 27 times increase in current density, as compared to their 2-D counterparts. These achievements were further followed by adding new functionalities, transparency and flexibility, to field emitters, keeping in view of current demand for flexible displays. A CNT-graphene hybrid structure showed appreciable emission, along with very good transparency and flexibility. Li-ion battery anodes, prepared using the interface-engineered CNTs, have offered 140% increment in capacity, as compared to conventional graphite anodes. Further, it has shown very good rate capability and an exceptional ‘zero capacity degradation’ during long cycle operation. Enhanced safety and charge transfer mechanism of this novel anode structure could be explained from structural characterization. In an attempt to progress further, CNTs were coated with ultrathin alumina by atomic layer deposition technique. These alumina-coated CNT anodes offered much higher capacity and an exceptional rate capability, with very low capacity degradation in higher current densities. These highly energy efficient CNT based anodes are expected to enhance capacities of future Li-ion batteries.

Development and verification of control and protection strategies in hybrid AC/DC power systems for smart grid applications

Modern power networks incorporate communications and information technology infrastructure into the electrical power system to create a smart grid in terms of control and operation. The smart grid enables real-time communication and control between consumers and utility companies allowing suppliers to optimize energy usage based on price preference and system technical issues. The smart grid design aims to provide overall power system monitoring, create protection and control strategies to maintain system performance, stability and security. This dissertation contributed to the development of a unique and novel smart grid test-bed laboratory with integrated monitoring, protection and control systems. This test-bed was used as a platform to test the smart grid operational ideas developed here. The implementation of this system in the real-time software creates an environment for studying, implementing and verifying novel control and protection schemes developed in this dissertation. Phasor measurement techniques were developed using the available Data Acquisition (DAQ) devices in order to monitor all points in the power system in real time. This provides a practical view of system parameter changes, system abnormal conditions and its stability and security information system. These developments provide valuable measurements for technical power system operators in the energy control centers. Phasor Measurement technology is an excellent solution for improving system planning, operation and energy trading in addition to enabling advanced applications in Wide Area Monitoring, Protection and Control (WAMPAC). Moreover, a virtual protection system was developed and implemented in the smart grid laboratory with integrated functionality for wide area applications. Experiments and procedures were developed in the system in order to detect the system abnormal conditions and apply proper remedies to heal the system. A design for DC microgrid was developed to integrate it to the AC system with appropriate control capability. This system represents realistic hybrid AC/DC microgrids connectivity to the AC side to study the use of such architecture in system operation to help remedy system abnormal conditions. In addition, this dissertation explored the challenges and feasibility of the implementation of real-time system analysis features in order to monitor the system security and stability measures. These indices are measured experimentally during the operation of the developed hybrid AC/DC microgrids. Furthermore, a real-time optimal power flow system was implemented to optimally manage the power sharing between AC generators and DC side resources. A study relating to real-time energy management algorithm in hybrid microgrids was performed to evaluate the effects of using energy storage resources and their use in mitigating heavy load impacts on system stability and operational security.

Does landscape context affect habitat value? The importance of seascape ecology in back-reef systems

Seascape ecology provides a useful framework from which to understand the processes governing spatial variability in ecological patterns. Seascape context, or the composition and pattern of habitat surrounding a focal patch, has the potential to impact resource availability, predator-prey interactions, and connectivity with other habitats. For my dissertation research, I combined a variety of approaches to examine how habitat quality for fishes is influenced by a diverse range of seascape factors in sub-tropical, back-reef ecosystems. In the first part of my dissertation, I examined how seascape context can affect reef fish communities on an experimental array of artificial reefs created in various seascape contexts in Abaco, Bahamas. I found that the amount of seagrass at large spatial scales was an important predictor of community assembly on these reefs. Additionally, seascape context had differing effects on various aspects of habitat quality for the most common reef species, White grunt Haemulon plumierii. The amount of seagrass at large spatial scales had positive effects on fish abundance and secondary production, but not on metrics of condition and growth. The second part of my dissertation focused on how foraging conditions for fish varied across a linear seascape gradient in the Loxahatchee River estuary in Florida, USA. Gray snapper, Lutjanus griseus, traded food quality for quantity along this estuarine gradient, maintaining similar growth rates and condition among sites. Additional work focused on identifying major energy flow pathways to two consumers in oyster-reef food webs in the Loxahatchee. Algal and microphytobenthos resource pools supported most of the production to these consumers, and body size for one of the consumers mediated food web linkages with surrounding mangrove habitats. All of these studies examined a different facet of the importance of seascape context in governing ecological processes occurring in focal habitats and underscore the role of connectivity among habitats in back-reef systems. The results suggest that management approaches consider the surrounding seascape when prioritizing areas for conservation or attempting to understand the impacts of seascape change on focal habitat patches. For this reason, spatially-based management approaches are recommended to most effectively manage back-reef systems.

Information Discovery on Electronic Health Records Using Authority Flow Techniques

Background As the use of electronic health records (EHRs) becomes more widespread, so does the need to search and provide effective information discovery within them. Querying by keyword has emerged as one of the most effective paradigms for searching. Most work in this area is based on traditional Information Retrieval (IR) techniques, where each document is compared individually against the query. We compare the effectiveness of two fundamentally different techniques for keyword search of EHRs. Methods We built two ranking systems. The traditional BM25 system exploits the EHRs' content without regard to association among entities within. The Clinical ObjectRank (CO) system exploits the entities' associations in EHRs using an authority-flow algorithm to discover the most relevant entities. BM25 and CO were deployed on an EHR dataset of the cardiovascular division of Miami Children's Hospital. Using sequences of keywords as queries, sensitivity and specificity were measured by two physicians for a set of 11 queries related to congenital cardiac disease. Results Our pilot evaluation showed that CO outperforms BM25 in terms of sensitivity (65% vs. 38%) by 71% on average, while maintaining the specificity (64% vs. 61%). The evaluation was done by two physicians. Conclusions Authority-flow techniques can greatly improve the detection of relevant information in EHRs and hence deserve further study.

Foundations of quantitative information flow: Channels, cascades, and the information order

Secrecy is fundamental to computer security, but real systems often cannot avoid leaking some secret information. For this reason, the past decade has seen growing interest in quantitative theories of information flow that allow us to quantify the information being leaked. Within these theories, the system is modeled as an information-theoretic channel that specifies the probability of each output, given each input. Given a prior distribution on those inputs, entropy-like measures quantify the amount of information leakage caused by the channel. ^ This thesis presents new results in the theory of min-entropy leakage. First, we study the perspective of secrecy as a resource that is gradually consumed by a system. We explore this intuition through various models of min-entropy consumption. Next, we consider several composition operators that allow smaller systems to be combined into larger systems, and explore the extent to which the leakage of a combined system is constrained by the leakage of its constituents. Most significantly, we prove upper bounds on the leakage of a cascade of two channels, where the output of the first channel is used as input to the second. In addition, we show how to decompose a channel into a cascade of channels. ^ We also establish fundamental new results about the recently-proposed g-leakage family of measures. These results further highlight the significance of channel cascading. We prove that whenever channel A is composition refined by channel B, that is, whenever A is the cascade of B and R for some channel R, the leakage of A never exceeds that of B, regardless of the prior distribution or leakage measure (Shannon leakage, guessing entropy leakage, min-entropy leakage, or g-leakage). Moreover, we show that composition refinement is a partial order if we quotient away channel structure that is redundant with respect to leakage alone. These results are strengthened by the proof that composition refinement is the only way for one channel to never leak more than another with respect to g-leakage. Therefore, composition refinement robustly answers the question of when a channel is always at least as secure as another from a leakage point of view.^

Two-bit pattern analysis for quantitative information flow

Protecting confidential information from improper disclosure is a fundamental security goal. While encryption and access control are important tools for ensuring confidentiality, they cannot prevent an authorized system from leaking confidential information to its publicly observable outputs, whether inadvertently or maliciously. Hence, secure information flow aims to provide end-to-end control of information flow. Unfortunately, the traditionally-adopted policy of noninterference, which forbids all improper leakage, is often too restrictive. Theories of quantitative information flow address this issue by quantifying the amount of confidential information leaked by a system, with the goal of showing that it is intuitively "small" enough to be tolerated. Given such a theory, it is crucial to develop automated techniques for calculating the leakage in a system. ^ This dissertation is concerned with program analysis for calculating the maximum leakage, or capacity, of confidential information in the context of deterministic systems and under three proposed entropy measures of information leakage: Shannon entropy leakage, min-entropy leakage, and g-leakage. In this context, it turns out that calculating the maximum leakage of a program reduces to counting the number of possible outputs that it can produce. ^ The new approach introduced in this dissertation is to determine two-bit patterns, the relationships among pairs of bits in the output; for instance we might determine that two bits must be unequal. By counting the number of solutions to the two-bit patterns, we obtain an upper bound on the number of possible outputs. Hence, the maximum leakage can be bounded. We first describe a straightforward computation of the two-bit patterns using an automated prover. We then show a more efficient implementation that uses an implication graph to represent the two- bit patterns. It efficiently constructs the graph through the use of an automated prover, random executions, STP counterexamples, and deductive closure. The effectiveness of our techniques, both in terms of efficiency and accuracy, is shown through a number of case studies found in recent literature. ^

Variable Speed Limit Strategies to Reduce the Impacts of Traffic Flow Breakdown at Recurrent Freeway Bottlenecks

Variable Speed Limit (VSL) strategies identify and disseminate dynamic speed limits that are determined to be appropriate based on prevailing traffic conditions, road surface conditions, and weather conditions. This dissertation develops and evaluates a shockwave-based VSL system that uses a heuristic switching logic-based controller with specified thresholds of prevailing traffic flow conditions. The system aims to improve operations and mobility at critical bottlenecks. Before traffic breakdown occurrence, the proposed VSL’s goal is to prevent or postpone breakdown by decreasing the inflow and achieving uniform distribution in speed and flow. After breakdown occurrence, the VSL system aims to dampen traffic congestion by reducing the inflow traffic to the congested area and increasing the bottleneck capacity by deactivating the VSL at the head of the congested area. The shockwave-based VSL system pushes the VSL location upstream as the congested area propagates upstream. In addition to testing the system using infrastructure detector-based data, this dissertation investigates the use of Connected Vehicle trajectory data as input to the shockwave-based VSL system performance. Since the field Connected Vehicle data are not available, as part of this research, Vehicle-to-Infrastructure communication is modeled in the microscopic simulation to obtain individual vehicle trajectories. In this system, wavelet transform is used to analyze aggregated individual vehicles’ speed data to determine the locations of congestion. The currently recommended calibration procedures of simulation models are generally based on the capacity, volume and system-performance values and do not specifically examine traffic breakdown characteristics. However, since the proposed VSL strategies are countermeasures to the impacts of breakdown conditions, considering breakdown characteristics in the calibration procedure is important to have a reliable assessment. Several enhancements were proposed in this study to account for the breakdown characteristics at bottleneck locations in the calibration process. In this dissertation, performance of shockwave-based VSL is compared to VSL systems with different fixed VSL message sign locations utilizing the calibrated microscopic model. The results show that shockwave-based VSL outperforms fixed-location VSL systems, and it can considerably decrease the maximum back of queue and duration of breakdown while increasing the average speed during breakdown.

Surface Mean Flow and Turbulence Structure in Tropical Cyclone Winds

Hurricanes are one of the deadliest and costliest natural hazards affecting the Gulf coast and Atlantic coast areas of the United States. An effective way to minimize hurricane damage is to strengthen structures and buildings. The investigation of surface level hurricane wind behavior and the resultant wind loads on structures is aimed at providing structural engineers with information on hurricane wind characteristics required for the design of safe structures. Information on mean wind profiles, gust factors, turbulence intensity, integral scale, and turbulence spectra and co-spectra is essential for developing realistic models of wind pressure and wind loads on structures. The research performed for this study was motivated by the fact that considerably fewer data and validated models are available for tropical than for extratropical storms. Using the surface wind measurements collected by the Florida Coastal Monitoring Program (FCMP) during hurricane passages over coastal areas, this study presents comparisons of surface roughness length estimates obtained by using several estimation methods, and estimates of the mean wind and turbulence structure of hurricane winds over coastal areas under neutral stratification conditions. In addition, a program has been developed and tested to systematically analyze Wall of Wind (WoW) data, that will make it possible to perform analyses of baseline characteristics of flow obtained in the WoW. This program can be used in future research to compare WoW data with FCMP data, as gust and turbulence generator systems and other flow management devices will be used to create WoW flows that match as closely as possible real hurricane wind conditions. Hurricanes are defined as tropical cyclones for which the maximum 1-minute sustained surface wind speeds exceed 74 mph. FCMP data include data for tropical cyclones with lower sustained speeds. However, for the winds analyzed in this study the speeds were sufficiently high to assure that neutral stratification prevailed. This assures that the characteristics of those winds are similar to those prevailing in hurricanes. For this reason in this study the terms tropical cyclones and hurricanes are used interchangeably.

Lattice Boltzmann Method for Flow and Heat Transfer in Microgeometries

Recent technological developments have made it possible to design various microdevices where fluid flow and heat transfer are involved. For the proper design of such systems, the governing physics needs to be investigated. Due to the difficulty to study complex geometries in micro scales using experimental techniques, computational tools are developed to analyze and simulate flow and heat transfer in microgeometries. However, conventional numerical methods using the Navier-Stokes equations fail to predict some aspects of microflows such as nonlinear pressure distribution, increase mass flow rate, slip flow and temperature jump at the solid boundaries. This necessitates the development of new computational methods which depend on the kinetic theory that are both accurate and computationally efficient. In this study, lattice Boltzmann method (LBM) was used to investigate the flow and heat transfer in micro sized geometries. The LBM depends on the Boltzmann equation which is valid in the whole rarefaction regime that can be observed in micro flows. Results were obtained for isothermal channel flows at Knudsen numbers higher than 0.01 at different pressure ratios. LBM solutions for micro-Couette and micro-Poiseuille flow were found to be in good agreement with the analytical solutions valid in the slip flow regime (0.01 < Kn < 0.1) and direct simulation Monte Carlo solutions that are valid in the transition regime (0.1 < Kn < 10) for pressure distribution and velocity field. The isothermal LBM was further extended to simulate flows including heat transfer. The method was first validated for continuum channel flows with and without constrictions by comparing the thermal LBM results against accurate solutions obtained from analytical equations and finite element method. Finally, the capability of thermal LBM was improved by adding the effect of rarefaction and the method was used to analyze the behavior of gas flow in microchannels. The major finding of this research is that, the newly developed particle-based method described here can be used as an alternative numerical tool in order to study non-continuum effects observed in micro-electro-mechanical-systems (MEMS).