Engineering the transition from non-living to living matter

Re-creating and understanding the origin of life represents one of the major challenges facing the scientific community. We will never know exactly how life started on planet Earth, however, we can reconstruct the most likely chemical pathways that could have contributed to the formation of the first living systems. Traditionally, prebiotic chemistry has investigated the formation of modern life’s precursors and their self-organisation under very specific conditions thought to be ‘plausible’. So far, this approach has failed to produce a living system from the bottom-up. In the work presented herein, two different approaches are employed to explore the transition from inanimate to living matter. The development of microfluidic technology during the last decades has changed the way traditional chemical and biological experiments are performed. Microfluidics allows the handling of low volumes of reagents with very precise control. The use of micro-droplets generated within microfluidic devices is of particular interest to the field of Origins of Life and Artificial Life. Whilst many efforts have been made aiming to construct cell-like compartments from modern biological constituents, these are usually very difficult to handle. However, microdroplets can be easily generated and manipulated at kHz rates, making it suitable for high-throughput experimentation and analysis of compartmentalised chemical reactions. Therefore, we decided to develop a microfluidic device capable of manipulating microdroplets in such a way that they could be efficiently mixed, split and sorted within iterative cycles. Since no microfluidic technology had been developed before in the Cronin Group, the first chapter of this thesis describes the soft lithographic methods and techniques developed to fabricate microfluidic devices. Also, special attention is placed on the generation of water-in-oil microdroplets, and the subsequent modules required for the manipulation of the droplets such as: droplet fusers, splitters, sorters and single/multi-layer micromechanical valves. Whilst the first part of this thesis describes the development of a microfluidic platform to assist chemical evolution, finding a compatible set of chemical building blocks capable of reacting to form complex molecules with endowed replicating or catalytic activity was challenging. Abstract 10 Hence, the second part of this thesis focuses on potential chemistry that will ultimately possess the properties mentioned above. A special focus is placed on the formation of peptide bonds from unactivated amino acids, despite being one of the greatest challenges in prebiotic chemistry. As opposed to classic prebiotic experiments, in which a specific set of conditions is studied to fit a particular hypothesis, we took a different approach: we explored the effects of several parameters at once on a model polymerisation reaction, without constraints on hypotheses on the nature of optimum conditions or plausibility. This was facilitated by development of a new high-throughput automated platform, allowing the exploration of a much larger number of parameters. This led us to discover that peptide bond formation is less challenging than previously imagined. Having established the right set of conditions under which peptide bond formation was enhanced, we then explored the co-oligomerisation between different amino acids, aiming for the formation of heteropeptides with different structure or function. Finally, we studied the effect of various environmental conditions (rate of evaporation, presence of salts or minerals) in the final product distribution of our oligomeric products.

Study the methods of connecting jacket to the seabed and choosing the best method for Persian Gulf according to soil characteristics

Offshore structures with numerous applications in different environments throughout the world and used at different depths. Due to the expansion of marine industries, including offshore oil industry in Iran , particularly in the Persian Gulf region, in order to more accurately model these structures and to prevent incidents such as the Overturning of the platform serious damage to the South Pars Phase ١٣ was platforms, the use New Technic is essential technologies. One of the methods that are used in the construction of offshore wind turbines, using a pre-pile. In this method, a template is constructed with the dimensions specified in the workshop. After making templates using special vessels for placement in the desired location on the sea bed is carried, then the template is placed on the sea bed, Then, using a hammer for Pile Driving Operation Started Vibration hammer and fit the template of 3 or 4 piles of crushed within this template on the seabed . The next step piling, templates have been removed from the site And Jacket placed on piles. The system was installed on the deck on piles and Consequently Deck Load pile inserted on .It should be noted that the design of these types of platforms, base diameter of the pile diameter independent of the choice as one of the major advantages of this system is. This thesis examines a Template Fixed Platform in the oil Soroush Using the Pre-Piling and the Common Piling systems in the Persian Gulf were studied and the effect of different design compared to the Pre-Piling Platforms Persian Gulf were evaluated. The results suggest that Pre-Piling system compared with conventional systems piling in the Persian Gulf, as a more appropriate model structure and behavior Top Model economic efficiency is selected. It should be noted that all calculations and analyzes were performed using Software Abaqus.

ENGINEERING HIERARCHICAL MESO-/MICROPOROUS LAMELLAR ZEOLITES WITH VARIABLE TEXTURAL AND CATALYTIC PROPERTIES

Meso-/microporous zeolites combine the charactersitics of well-defined micropores of zeolite with efficient mass transfer consequences of mesopores to increase the efficiency of the catalysts in reactions involving bulky molecules. Different methods such as demetallation and templating have been explored for the synthesis of meso-/microporous zeolites. However, they all have limitations in production of meso-/microporous zeolites with tunable textural and catalytic properties using few synthesis steps. To address this challenge, a simple one-step dual template synthesis approach has been developed in this work to engineer lamellar meso-/microporous zeolites structures with tunable textural and catalytic properties. First, one-step dual template synthesis of meso-/microporous mordenite framework inverted (MFI) zeolite structures was investigated. Tetrapropyl ammonium hydroxide (TPAOH) and diquaternary ammonium surfactant ([C22H45-N+(CH3)2-C6H12-N+(CH3)2-C6H13]Br2, C22-6-6) were used as templates to produce micropores and mesopores, respectively. The variation in concentration ratios of dual templates and hydrothermal synthesis conditions resulted in production of multi-lamellar MFI and the hybrid lamellar-bulk MFI (HLBM) zeolite structures. The relationship between the morphology, porosity, acidity, and catalytic properties of these catalysts was systematically studied. Then, the validity of the proposed synthesis approach for production of other types of zeolites composites was examined by creating a meso-/microporous bulk polymorph A (BEA)-lamellar MFI (BBLM) composite. The resulted composite samples showed higher catalytic stability compared to their single component zeolites. The studies demonstrated the high potential of the one-step dual template synthesis procedure for engineering the textural and catalytic properties of the synthesized zeolites.

Methods for Modeling and Analyzing Concurrent Software

Concurrent software executes multiple threads or processes to achieve high performance. However, concurrency results in a huge number of different system behaviors that are difficult to test and verify. The aim of this dissertation is to develop new methods and tools for modeling and analyzing concurrent software systems at design and code levels. This dissertation consists of several related results. First, a formal model of Mondex, an electronic purse system, is built using Petri nets from user requirements, which is formally verified using model checking. Second, Petri nets models are automatically mined from the event traces generated from scientific workflows. Third, partial order models are automatically extracted from some instrumented concurrent program execution, and potential atomicity violation bugs are automatically verified based on the partial order models using model checking. Our formal specification and verification of Mondex have contributed to the world wide effort in developing a verified software repository. Our method to mine Petri net models automatically from provenance offers a new approach to build scientific workflows. Our dynamic prediction tool, named McPatom, can predict several known bugs in real world systems including one that evades several other existing tools. McPatom is efficient and scalable as it takes advantage of the nature of atomicity violations and considers only a pair of threads and accesses to a single shared variable at one time. However, predictive tools need to consider the tradeoffs between precision and coverage. Based on McPatom, this dissertation presents two methods for improving the coverage and precision of atomicity violation predictions: 1) a post-prediction analysis method to increase coverage while ensuring precision; 2) a follow-up replaying method to further increase coverage. Both methods are implemented in a completely automatic tool.

Using Research Methods in Human Computer Interaction to Design Technology for Resilience

Research in human computer interaction (HCI) covers both technological and human behavioural concerns. As a consequence, the contributions made in HCI research tend to be aware to either engineering or the social sciences. In HCI the purpose of practical research contributions is to reveal unknown insights about human behaviour and its relationship to technology. Practical research methods normally used in HCI include formal experiments, field experiments, field studies, interviews, focus groups, surveys, usability tests, case studies, diary studies, ethnography, contextual inquiry, experience sampling, and automated data collection. In this paper, we report on our experience using the evaluation methods focus groups, surveys and interviews and how we adopted these methods to develop artefacts: either interface’s design or information and technological systems. Four projects are examples of the different methods application to gather information about user’s wants, habits, practices, concerns and preferences. The goal was to build an understanding of the attitudes and satisfaction of the people who might interact with a technological artefact or information system. Conversely, we intended to design for information systems and technological applications, to promote resilience in organisations (a set of routines that allow to recover from obstacles) and user’s experiences. Organisations can here also be viewed within a system approach, which means that the system perturbations even failures could be characterized and improved. The term resilience has been applied to everything from the real estate, to the economy, sports, events, business, psychology, and more. In this study, we highlight that resilience is also made up of a number of different skills and abilities (self-awareness, creating meaning from other experiences, self-efficacy, optimism, and building strong relationships) that are a few foundational ingredients, which people should use along with the process of enhancing an organisation’s resilience. Resilience enhances knowledge of resources available to people confronting existing problems.

New Rigorous Decomposition Methods for Mixed-integer Linear and Nonlinear Programming

Process systems design, operation and synthesis problems under uncertainty can readily be formulated as two-stage stochastic mixed-integer linear and nonlinear (nonconvex) programming (MILP and MINLP) problems. These problems, with a scenario based formulation, lead to large-scale MILPs/MINLPs that are well structured. The first part of the thesis proposes a new finitely convergent cross decomposition method (CD), where Benders decomposition (BD) and Dantzig-Wolfe decomposition (DWD) are combined in a unified framework to improve the solution of scenario based two-stage stochastic MILPs. This method alternates between DWD iterations and BD iterations, where DWD restricted master problems and BD primal problems yield a sequence of upper bounds, and BD relaxed master problems yield a sequence of lower bounds. A variant of CD, which includes multiple columns per iteration of DW restricted master problem and multiple cuts per iteration of BD relaxed master problem, called multicolumn-multicut CD is then developed to improve solution time. Finally, an extended cross decomposition method (ECD) for solving two-stage stochastic programs with risk constraints is proposed. In this approach, a CD approach at the first level and DWD at a second level is used to solve the original problem to optimality. ECD has a computational advantage over a bilevel decomposition strategy or solving the monolith problem using an MILP solver. The second part of the thesis develops a joint decomposition approach combining Lagrangian decomposition (LD) and generalized Benders decomposition (GBD), to efficiently solve stochastic mixed-integer nonlinear nonconvex programming problems to global optimality, without the need for explicit branch and bound search. In this approach, LD subproblems and GBD subproblems are systematically solved in a single framework. The relaxed master problem obtained from the reformulation of the original problem, is solved only when necessary. A convexification of the relaxed master problem and a domain reduction procedure are integrated into the decomposition framework to improve solution efficiency. Using case studies taken from renewable resource and fossil-fuel based application in process systems engineering, it can be seen that these novel decomposition approaches have significant benefit over classical decomposition methods and state-of-the-art MILP/MINLP global optimization solvers.

Engineering interfacial silicon dioxide for improved metal-insulator-semiconductor silicon photoanode water splitting performance

Silicon photoanodes protected by atomic layer deposited (ALD) TiO2 show promise as components of water splitting devices that may enable the large-scale production of solar fuels and chemicals. Minimizing the resistance of the oxide corrosion protection layer is essential for fabricating efficient devices with good fill factor. Recent literature reports have shown that the interfacial SiO2 layer, interposed between the protective ALD-TiO2 and the Si anode, acts as a tunnel oxide that limits hole conduction from the photoabsorbing substrate to the surface oxygen evolution catalyst. Herein, we report a significant reduction of bilayer resistance, achieved by forming stable, ultrathin (<1.3 nm) SiO2 layers, allowing fabrication of water splitting photoanodes with hole conductances near the maximum achievable with the given catalyst and Si substrate. Three methods for controlling the SiO2 interlayer thickness on the Si(100) surface for ALD-TiO2 protected anodes were employed: (1) TiO2 deposition directly on an HF-etched Si(100) surface, (2) TiO2 deposition after SiO2 atomic layer deposition on an HF-etched Si(100) surface, and (3) oxygen scavenging, post-TiO2 deposition to decompose the SiO2 layer using a Ti overlayer. Each of these methods provides a progressively superior means of reliably thinning the interfacial SiO2 layer, enabling the fabrication of efficient and stable water oxidation silicon anodes.

Evaluating Methods of Calculating the Fixed Fee on Professional Service Contracts

The South Carolina Department of Transportation routinely retains Professional Consulting Engineering firms to provide engineering design and related professional services for the preparation of construction plans or design-build Request for Proposal bid packages for a wide variety of Federal-aid Highway Program roadway and bridge construction projects throughout South Carolina.The purpose of this project is to examine the current process of determining a "Fair and Reasonable" fixed fee for professional service contracts and to evaluate possible alternative methods including practices in other states that may improve the process, particularly in light of the considerable variation in audited overhead rates among consulting firms. In reviewing such alternative methods particular attention will be given to evaluating the potential impact of the method as an incentive to consulting firms to effectively manage their overhead costs.

Ravines in Angola. Causes and restraint methods

The Earth we know today was not always so. Over millions of years have undergone significant ch an g e s brought about by numerous geological phenomena aimed at your balance, some internal order, creating new geological formations and other external order smoothing formations previously created. From t h e tectonic standpoint, Angola is located in a relatively stable area which gives it a certain p ri v i l e g e w h e n compared with some Asian countries or even Americans where quite often occur earthquakes and volcanic eruptions. However, the same cannot be said in relation to the occurrence of an external geodynamics phenomena, such as the ravines, which in recent years has taken shape in many provinces, especially due to anthropogenic activity, giving rise to geological hazards, increasing the risk of damage in buildings and others infrastructures, losses direct or indirect in economic activities and loss of human lives. We understand that the reducing of these risks starts, in particular, by their identification, for later take preventive measures. This work is the result of some research work carried out by the authors through erosion courses of s o i l and stabilization of soils subject to erosion phenomena, carried out by Engineering Laboratory of Angola (LEA). For the realization of this work, we resorted to cartographic data query, literature, listening to s o m e o f the provincial representatives and local residents, as well as the observation in lo co o f s o m e af f e ct ed areas. The results allow us to infer that the main provinces affected by ravine phenomenon are located in Central and Northern highlands, as well as in the eastern region, and more recently in Cuando-Cub an go province. Not ruling out, however, other regions, such as in Luanda and Cabinda [1]. Relatively the causes, we can say that the ravines in Angola are primarily due to the combination of three natural factors: climate, topography and type of soil [2]. When we add the anthropogenic activit y , namely the execution of construction works, the drainage system obstructio n, exploration of m i n e ral s, agriculture and fires, it is verified an increasing of the phenomenon, often requiring immedi at e act i o n . These interventions can be done through structural or engineering measures and by the stabilization measures on the degraded soil cover [3]. We present an example of stabilization measures throu g h t h e deployment of a local vegetation called Pennisetum purpureum. It is expected that the results may contribute to a better understanding of the causes of the ravine phenomenon in Angola and that the adopted stabilization method can be adapted in other affected provinces in order to prevent and making the contention of the ravines.

Cross-correlations between weather variables in Australia

The information on climate variations is essential for the research of many subjects, such as the performance of buildings and agricultural production. However, recorded meteorological data are often incomplete. There may be a limited number of locations recorded, while the number of recorded climatic variables and the time intervals can also be inadequate. Therefore, the hourly data of key weather parameters as required by many building simulation programmes are typically not readily available. To overcome this gap in measured information, several empirical methods and weather data generators have been developed. They generally employ statistical analysis techniques to model the variations of individual climatic variables, while the possible interactions between different weather parameters are largely ignored. Based on a statistical analysis of 10 years historical hourly climatic data over all capital cities in Australia, this paper reports on the finding of strong correlations between several specific weather variables. It is found that there are strong linear correlations between the hourly variations of global solar irradiation (GSI) and dry bulb temperature (DBT), and between the hourly variations of DBT and relative humidity (RH). With an increase in GSI, DBT would generally increase, while the RH tends to decrease. However, no such a clear correlation can be found between the DBT and atmospheric pressure (P), and between the DBT and wind speed. These findings will be useful for the research and practice in building performance simulation.