Today’s economic conditions force companies and organizations to work more effectively in their processes due to different reasons.  Especially; after the Second World War, owing to the changing business perception and strong competition between companies, new terms such as productivity, flexible systems, efficiency, and lean came into industrial engineering discipline. However, these kinds of terms also brought a new question. How are they reached?  At that point, discrete event simulation has been used as an effective method to give an answer to this question. From this perspective; this project focuses on discrete event simulation and its role in real industrial processes. The main interest of this paper is discrete event simulation, but in this study we also tried to give some detailed information about other types of simulations such as continuous and discrete rate. Basically, we can say that this paper consists of several parts. In the beginning of this paper, the reader can find some theoretical information about simulation itself and the requirements for implementing it on real processes. Secondly, we tried to explain different types of simulations and the reason why we used discrete event simulation instead of continuous or discrete rate in our case study. Furthermore, one of the main areas of this research is to inform the reader about how computer support is used as a simulation tool by today’s companies. To do this, a powerful software, Extendsim8, is described in detail.  The reader is able to find all the information about how to create discrete event models in this software. In case study part, we are able to find the results of the five months work that we did between February and June at GKNDriveline Köping AB in Sweden. In these five months, we had been busy with analyzing an assembly line, collecting data, creating a simulation model, discussion with workers and engineers and doing some tests such as validation & verification. In this part, the reader can find all the information about the production line and the simulation model. In conclusion, reader can find the results of the project at the end with the visualization of future state. As it will be discussed repeatedly in the paper, validation is one of the important steps in a simulation project. Therefore, in order to see the reliability of our simulation model, different calculations and tests were made. Last of all, some of results will be shown by graphs and tables in order to give better insight to reader.

In this thesis, a concept for a modular assembly direct drive permanent magnetgenerator is presented. The maximum forces that act on the different parts of thegenerator during normal operation have been calculated and used in solid mechanicsimulations in SolidWorks. The result is a rough first draft of a generator designwhere the stator has been divided into five modules and the rotor into six modules.This division is done in order to avoid symmetries in the generator that could lead toproblems with self-oscillation.The modulization of the stator brings about certain difficulties, both for the magneticcircuit and for the winding scheme. Different solutions for optimization of themagnetic circuit are analyzed from both a physical and a construction technicalperspective. A winding scheme is produced and the winding process tested in awinding dummy produced according to the conceptual generator design.

The goal of this master´s thesis is to simulate a robotized assembly of a small model of VBG Group couplings. By the software; Process simulate has the simulation model built up and the simulation been done. The simulation model is built up of the coupling parts and resources; conveyor, fixtures, compress machine, grippers, nut and screw sorter. All parts and resources, except the compress machine, the fixture and cage for the shaft, have been designed under the whole project. A study on how assembly simulation works in the software has also been done.

Syftet med detta arbete var att undersöka möjligheterna för montering av ett styrskåp av modell Motoman NX100 NOC1. För detta användes simuleringsprogrammet DELMIA. Roboten som användes nådde inte alla montage om skåpet var stationärt. Därför prövades först ett antal olika förslag för att lösa detta problem genom att transportera skåpet. Det koncept som bedömdes som mest pålitligt användes sedan för att skapa en mer ingående simulering. Detta koncept bygger på en U-formad transportbana med växlingssektioner. Skåpet transporteras först så att montage kan ske på dess framsida. När skåpet har transporterats runt till motsatt sida om roboten, kan montage utföras på skåpets baksida. Konceptet inkluderar montering av skåpets huvudkomponenter. Utrymmeskrav för hantering och infästning av komponenter undersöktes. Montering av kablage är relativt tidskrävande att modellera i DELMIA, så detta var därför inte möjligt att genomföra inom projektets omfattning. Därför har det utelämnats från simuleringen. Roboten som användes var Motoman SDA10, vilken består av två armar. Detta har använts för att undvika verktygsväxling och specialverktyg. Robotens ena arm sköter hantering av komponenter med ett vakuumgripdon. Den andra armen hanterar två olika skruvdragare med hjälp av ett fingergripdon. Den ena skruvdragaren har skruvmatning, medan den andra används för efterdragning. Båda skruvdragare har handtag anpassade för robotens fingergripdon. I konceptet ingår en lösning för att montera komponenter på skåpets dörr, i det fallet att dörren redan har monterats på skåpet. En analys gjordes för att finna vilka svårigheter som finns hos en manuell montering av styrskåpet. Förslag på anpassningar togs fram, där avsikten var att förenkla skåpets montage. Analysmetoden som användes var Product Design for Assembly av Boothroyd G. & Dewhurst P. (1991). Tidsuppskattningarna som togs fram med hjälp av denna metod visade att cykeltiden kan reduceras med 24% genom att implementera anpassningsförslagen. Tidsuppskattningarna är dock endast baserade på montage av skåpets huvudkomponenter. Montering av kablage inkluderas inte i tiderna, då det är utanför omfattningen av detta projekt. Vissa av anpassningarna avser att minska antalet skruvtyper som används vid komponenternas infästning.

<p> Bacterial cell division is an essential process, which is initiated by forming the Z-ring as a cytoskeletal scaffold at the midcell site, followed by the recruitment of a series of divisome proteins. In <i>Escherichia coli</i> (Ec), at least 15 divisome proteins (FtsZ, FtsA, ZipA, FtsK, FtsQ, FtsB, FtsL, FtsI, FtsW, FtsN, FtsE, FtsX, ZapA, AmiC, EnvC) have been implicated in this process. The components of the cell division machinery proteins in <i>Neisseria gonorrhoeae</i> (Ng) differs from <i>E. coli. N. gonorrhoeae</i> possesses FtsA, but lacks FtsB. ZipA and FtsL in <i>N. gonorrhoeae</i> have low identity to ZipA and FtsL from <i>E. coli</i>. Our laboratory has studied the central division protein FtsZ in <i>N. gonorrhoeae</i>. Thus, my research investigated the role of <i>N. gonorrhoeae</i> FtsA in cell division and investigated the interactions between divisome proteins from <i>N. gonorrhoeae</i> to understand divisome assembly.</p> <p>This study determined the association of FtsA_Ng with FtsZ</sub>Ng and other divisome proteins in <i>N. gonorrhoeae</i> and identified the functional domains of FtsA<sun>Ng</sub> involved in these interactions using a bacterial two-hybrid (B2H) assay. FtsA_Ng interacted with FtsZ_Ng, FtsK_Ng, FtsW_Ng, FtsQ_Ng, and FtsN_Ng. Self-interactions of FtsA_Ng and FtsZ_Ng were also detected. FtsI_Ng, FtsE_Ng and FtsX_Ng did not interact with FtsA_Ng. The 2A₁, 2A₂ and 2B domains of FtsA_Ng were sufficient to interact with FtsZ_Ng independently. Domain 2A₁ interacted with FtsK_Ng and FtsN_Ng. Domain 2B of FtsA_Ng interacted with FtsK_Ng, FtsQ_Ng, and FtsN_Ng. Domain 2A₂ of FtsA_Ng interacted with FtsQ_Ng, FtsW_Ng, and FtsN_Ng. These data suggest that FtsA in <i>N. gonorrhoeae</i> plays a key role in interactions with FtsZ and other divisome proteins.</p> <p>The potential interactions between divisome proteins in <i>N. gonorrhoeae</i> were examined using B2H assays. The comparisons between the <i>N. gonorrhoeae</i> divisome protein interaction network and those of <i>E. coli</i> and <i>S. pneumoniae</i> indicates that the divisome protein interactome of <i>N. gonorrhoeae</i> is more similar to that of <i>S. pneumoniae</i> and differs from that of <i>E. coli</i>. The comparisons revealed that compared to the interactions in <i>E. coli</i> and <i>S. pneumoniae</i>, more interactions between divisome proteins upstream of FtsA_Ng (including FtsA_Ng) and downstream of FtsA_Ng were observed in <i>N. gonorrhoeae</i> while fewer interactions between divisome proteins downstream of FtsA_Ng were observed in <i>N. gonorrhoeae</i>. Possible reasons for this include the inability of ZipA_Ng to interact with other divisome proteins and the absence of FtsL and FtsB in <i>N. gonorrhoeae</i>, resulting in the lack of an FtsQ-FtsB-FtsL complex in <i>N. gonorrhoeae</i>. These results indicate a possibly different divisome assembly in <i>N. gonorrhoeae</i> from that proposed models for <i>E. coli</i>.</p> A model for FtsA_Ng structure was predicted based on structural homology modeling with the resolved crystal structure of <i>Thermotoga maritima</i> FtsA. Four domains on the molecule were identified, designated 1A, 1C, 2B and 2A (including 2A₁ and 2A₂). Domains 2A and 2B of FtsA were highly conserved based on multi-sequence alignments of FtsAs from 30 bacteria. FtsA_Ng located to the division site in <i>N. gonorrhoeae</i> cells and the ratio of FtsA to FtsZ ranged from 1:24 to 1: 33 in three <i>N. gonorrhoeae</i> strains, which gave a lower cellular concentration of FtsA compared to other organisms.</p> <p>I also determined that overexpression of FtsA_Ng in <i>E. coli</i> led to cell filamentous in rod-shaped <i>E. coli</i> and cell enlargement and aggregation in mutant, round <i>E. coli</i>. FtsA_Ng failed to complement an <i>ftsA</i>_Ec-deletion <i>E. coli</i> strain although the overexperssion of FtsA_Ng disrupted <i>E. coli</i> cell division. In addition, overexpression of FtsA_Ng only affected cell division in some cells and its localization in <i>E. coli</i> was independent of interaction with <i>E. coli</i> FtsA or FtsZ. These results indicate that FtsA_Ng exhibits a species-specific functionality and <i>E. coli</i> is not a suitable model for studying FtsA_Ng functionality.</p> <p>This is the first study to characterize FtsA from <i>N. gonorrhoeae</i> in cell division. I identified novel functional domains of FtsA_Ng involved in interactions with other divisome proteins. The <i>N. gonorrhoeae</i> divisome protein interaction network determined by B2H assays provides insight into divisome assembly in <i>N. gonorrhoeae</i></p>.

The self-assembly of several pyrene-labelled amphiphilic macromolecules in water was characterized by fluorescence. Information on their self-assembly was obtained by monitoring the level of pyrene aggregation in solution. A measure of the level of association was obtained by determining the fraction of aggregated pyrene of the labelled macromolecules from the global analysis of their monomer and excimer fluorescence decays. Global analysis limits the degrees of freedom of the analysis thus reducing the error on the parameters retrieved from the analysis. Extensive developments in the global analysis of the pyrene monomer and excimer decays enabled the first characterization of the molar absorbance coefficient of the pyrene aggregates formed by aqueous solutions of pyrene-labelled poly(N,N-dimethylacrylamide) (PyPDMA) and poly(ethylene oxide) (PyPEO). The molar absorbance coefficients of the pyrene aggregates determined for PyPDMA and PyPEO were both found to be broader and red-shifted compared to that of unaggregated pyrene. These results agree with observations found in the scientific literature made by using absorption and excitation fluorescence measurements. Attempts to determine the molar absorbance coefficient of pyrene-labelled hydrophobically-modified alkali-swellable emulsion (PyHASE) polymers were unsuccessful. The inability to characterize the pyrene aggregates of PyHASE was attributed to the greater complexity of the PyHASE polymer compared to PyPDMA and PyPEO. For these simpler pyrene-labelled polymers, a protocol has been established which uses the global analysis of the pyrene monomer and excimer decays to determine quantitatively the level of association of pyrene-labelled polymers as well as the molar absorbance coefficient of their aggregates. Changes in the level of aggregation of pyrene-labelled lipids (PLLs) having head groups bearing an alcohol (PSOH) or imido diacetic acid (PSIDA) embedded in 1-palmitoyl-2-oleyl-3-sn-phosphatidylcholines (POPC) or distearylphosphatidylcholine (DSPC) liposomes were probed by fluorescence. Distribution of the PLLs in the fluid POPC membrane was found to be homogeneous while the PLLs phase-separated into amorphous channels created in the DSPC membranes. Multivalent cations Cu2+ and La3+ were found to bind to PSIDA, hindering diffusional encounters between unaggregated PSIDA but leaving the PLL aggregates intact. Using the fluorescence quenching ability of Cu2+, the viscosity of the amorphous channels of the DSPC membrane was determined to be about six times greater than that of the more fluid POPC membrane. Simultaneous rheological and fluorescence measurements were achieved by interfacing a rheometer with time-resolved and steady-state fluorometers using fiber-optic cables. This joint set up enabled the simultaneous rheological and fluorescence measurements of PyHASE solutions having concentrations ranging from 0.5 w/w% to 5 w/w%. The level of association of the PyHASE solutions was tracked using fluorescence at shear rates of 0, 0.1 and 100 s–1. Despite the presence of shear thinning leading to viscosity drops of up to four orders of magnitude, no change in the fluorescence and hence the level of association was observed. The lack of change in level of association implied that the mechanism of shear thinning is due to a switching from inter- to intramolecular association rather than a drop in the level of association. This information will prove useful for future models attempting to predict the rheological behaviour of sheared associative polymers.

Work injury is one of the major obstacles in manufacturing industries especially in production assembly systems all over the world. Work injuries reduce production efficiency and threat human health. Among various types of work injuries, repetitive work injuries are the one that can be easily neglected. This thesis is about the application of computing technology to analysis and synthesis of repetitive work injuries in production assembly systems for the purpose of reduction or elimination of these injuries.<p> A production assembly system consists of the assembly machines, products, tools, humans (workers), and particular environments. Injuries of the worker are basically caused by over stress, strain, and fatigue, which are further related to the workers posture.<p> This research proposed a general methodology for constructing a software system for analysis and simulation of a workers postures in a virtual environment. The implementation of such a computer system was discussed. This research also proposed methods to compute work injury cost. Finally, this research proposed a more systematic method for the synthesis or re-design of worker postures to reduce or eliminate work injuries. The major contribution of this thesis work is to advance computing to work injury analysis and synthesis in production systems. <p> This thesis study concludes that the computer technology is matured enough to highly automate the process of work injury analysis and synthesis. It is possible that a complete design of production systems with consideration of work injuries can be done in a much more efficient manner perhaps reduction of the ramp-up process in the automobile industry from 6 months (typically) to one month in addition to the removal of wasted materials and potential injuries in the ramp-up process.

DNA sequence assembly is one of the fundamental areas of bioinformatics. It involves the correct formation of a genome sequence from its DNA fragments ("reads") by aligning and merging the fragments. There are different sequencing technologies -- some support long DNA reads and the others, shorter DNA reads. There are sequence assembly programs specifically designed for these different types of raw sequencing data.<p> This work explores and experiments with these different types of assembly software in order to compare their performance on the type of data for which they were designed, as well as their performance on data for which they were not designed, and on mixed data. Such results are useful for establishing good procedures and tools for sequence assembly in the current genomic environment where read data of different lengths are available. This work also investigates the effect of the presence or absence of quality information on the results produced by sequence assemblers.<p> Five strategies were used in this research for assembling mixed data sets and the testing was done using a collection of real and artificial data sets for six bacterial organisms. The results show that there is a broad range in the ability of some DNA sequence assemblers to handle data from various sequencing technologies, especially data other than the kind they were designed for. For example, the long-read assemblers PHRAP and MIRA produced good results from assembling 454 data. The results also show the importance of having an effective methodology for assembling mixed data sets. It was found that combining contiguous sequences obtained from short-read assemblers with long DNA reads, and then assembling this combination using long-read assemblers was the most appropriate approach for assembling mixed short and long reads. It was found that the results from assembling the mixed data sets were better than the results obtained from separately assembling individual data from the different sequencing technologies. DNA sequence assemblers which do not depend on the availability of quality information were used to test the effect of the presence of quality values when assembling data. The results show that regardless of the availability of quality information, good results were produced in most of the assemblies.<p> In more general terms, this work shows that the approach or methodology used to assemble DNA sequences from mixed data sources makes a lot of difference in the type of results obtained, and that a good choice of methodology can help reduce the amount of effort spent on a DNA sequence assembly project.

<p>The control of matter and phenomena at the nanoscale is fast becoming one of the most important challenges of the 21st century with wide-ranging applications from energy and health care to computing and material science. Conventional top-down approaches to nanotechnology, having served us well for long, are reaching their inherent limitations. Meanwhile, bottom-up methods such as self-assembly are emerging as viable alternatives for nanoscale fabrication and manipulation.</p><p>A particularly successful bottom up technique is DNA self-assembly where a set of carefully designed DNA strands form a nanoscale object as a consequence of specific, local interactions among the different components, without external direction. The final product of the self-assembly process might be a static nanostructure or a dynamic nanodevice that performs a specific function. Over the past two decades, DNA self-assembly has produced stunning nanoscale objects such as 2D and 3D lattices, polyhedra and addressable arbitrary shaped substrates, and a myriad of nanoscale devices such as molecular tweezers, computational circuits, biosensors and molecular assembly lines. In this dissertation we study multiple problems in the theory, simulations and experiments of DNA self-assembly. </p><p>We extend the Turing-universal mathematical framework of self-assembly known as the Tile Assembly Model by incorporating randomization during the assembly process. This allows us to reduce the tile complexity of linear assemblies. We develop multiple techniques to build linear assemblies of expected length N using far fewer tile types than previously possible.</p><p>We abstract the fundamental properties of DNA and develop a biochemical system, which we call meta-DNA, based entirely on strands of DNA as the only component molecule. We further develop various enzyme-free protocols to manipulate meta-DNA systems and provide strand level details along with abstract notations for these mechanisms. </p><p>We simulate DNA circuits by providing detailed designs for local molecular computations that involve spatially contiguous molecules arranged on addressable substrates via enzyme-free DNA hybridization reaction cascades. We use the Visual DSD simulation software in conjunction with localized reaction rates obtained from biophysical modeling to create chemical reaction networks of localized hybridization circuits that are then model checked using the PRISM model checking software.</p><p>We develop a DNA detection system employing the triggered self-assembly of a novel DNA dendritic nanostructure. Detection begins when a specific, single-stranded target DNA strand triggers a hybridization chain reaction between two distinct DNA hairpins. Each hairpin opens and hybridizes up to two copies of the other, and hence each layer of the growing dendritic nanostructure can in principle accommodate an exponentially increasing number of cognate molecules, generating a nanostructure with high molecular weight. </p><p>We build linear activatable assemblies employing a novel protection/deprotection strategy to strictly enforce the direction of tiling assembly growth to ensure the robustness of the assembly process. Our system consists of two tiles that can form a linear co-polymer. These tiles, which are initially protected such that they do not react with each other, can be activated to form linear co-polymers via the use of a strand displacing enzyme.</p> / Dissertation

Lifes origin is, in many ways, coupled to understanding the evolution of nucleic acids. In contemporary life, proteins and nucleic acids are intricately dependent upon each other for a host of functions including, but not limited to, replication and chemical ligation. Protein enzymes are necessary for the synthesis of DNA and RNA, while nucleic acids are necessary for both the coding and synthesis of proteins. According to the RNA World hypothesis, early life used nucleic acids for both information storage and chemical catalysis before the emergence of protein enzymes. However, it still remains a mystery how nucleic acids were able to assemble and replicate before the advent of protein enzymes. We have utilized the ability of small molecule intercalation to assemble nucleic acids into stable secondary structures. Our motivation in this pursuit comes from the recently proposed Molecular Midwife hypothesis where small molecules may have acted as nanoscale structural scaffolds upon which the nucleic acid bases were able to stack into stable structures and undergo assembly into polymers. We have also found that the kinetics and thermodynamics of small molecule-mediated assembly and secondary structure formation are strongly dependent upon oligonucleotide length. Small molecules bind to nucleic acids by multiple modes of binding and this phenomenon must be properly understood in order to achieve robust and versatile assembly of nucleic acid structures.