Dimensionality hyper-reduction and machine learning for dynamical systems with varying parameters

Thesis (Ph.D.)--University of Washington, 2016-08

The Plastic Coupled Map Lattice: a Novel Image‐processing Paradigm

Coupled map lattices (CML) can describe many relaxation and optimization algorithms currently used in image processing. We recently introduced the ‘‘plastic‐CML’’ as a paradigm to extract (segment) objects in an image. Here, the image is applied by a set of forces to a metal sheet which is allowed to undergo plastic deformation parallel to the applied forces. In this paper we present an analysis of our ‘‘plastic‐CML’’ in one and two dimensions, deriving the nature and stability of its stationary solutions. We also detail how to use the CML in image processing, how to set the system parameters and present examples of it at work. We conclude that the plastic‐CML is able to segment images with large amounts of noise and large dynamic range of pixel values, and is suitable for a very large scale integration(VLSI) implementation.

A large study on the effect of code obfuscation on the quality of java code

Context: Obfuscation is a common technique used to protect software against mali- cious reverse engineering. Obfuscators manipulate the source code to make it harder to analyze and more difficult to understand for the attacker. Although different ob- fuscation algorithms and implementations are available, they have never been directly compared in a large scale study. Aim: This paper aims at evaluating and quantifying the effect of several different obfuscation implementations (both open source and commercial), to help developers and project manager to decide which one could be adopted. Method: In this study we applied 44 obfuscations to 18 subject applications covering a total of 4 millions lines of code. The effectiveness of these source code obfuscations has been measured using 10 code metrics, considering modularity, size and complexity of code. Results: Results show that some of the considered obfuscations are effective in mak- ing code metrics change substantially from original to obfuscated code, although this change (called potency of the obfuscation) is different on different metrics. In the pa- per we recommend which obfuscations to select, given the security requirements of the software to be protected.

In silico metabolic modelling of Saccharomyces cerevisiae for the overproduction of succinate using OptKnock and OptGene

Succinate is a naturally occurring metabolite in organism’s cell and is industrially important chemical with various applications in food and pharmaceutical industry. It is also widely used to produce bio-degradable plastics, surfactants, detergents etc. In last decades, emphasis has been given to bio-based chemical production using industrial biotechnology route rather than fossil-based production considering sustainability and environment friendly economy. In this thesis I am presenting a computational model for silico metabolic engineering of Saccharomyces cerevisiae for large scale production of succinate. For metabolic modelling, I have used OptKnock and OptGene optimization algorithms to identify the reactions to delete from the genome-scale metabolic model of S. cerevisiae to overproduce succinate by coupling with organism’s growth. Both OptKnock and OptGene proposed numerous straightforward and non-intuitive deletion strategies when number of constraints including growth constraint to the model were applied. The most interesting strategy identified by both algorithms was deletion combination of pyruvate decarboxylase and Ubiquinol:ferricytochrome c reductase(respiratory enzyme) reactions thereby also suggesting anaerobic fermentation of the organism in glucose medium. Such strategy was never reported earlier for growth-coupled succinate production in S.cerevisiae.

Millennial-scale fluctuations of the European Ice Sheet at the end of the last glacial, and their potential impact on global climate

Reconstructing Northern Hemisphere ice-sheet oscillations and meltwater routing to the ocean is important to better understand the mechanisms behind abrupt climate changes. To date, research efforts have mainly focused on the North American (Laurentide) ice-sheets (LIS), leaving the potential role of the European Ice Sheet (EIS), and of the Scandinavian ice-sheet (SIS) in particular, largely unexplored. Using neodymium isotopes in detrital sediments deposited off the Channel River, we provide a continuous and well-dated record for the evolution of the EIS southern margin through the end of the last glacial period and during the deglaciation. Our results reveal that the evolution of EIS margins was accompanied with substantial ice recession (especially of the SIS) and simultaneous release of meltwater to the North Atlantic. These events occurred both in the course of the EIS to its LGM position (i.e., during Heinrich Stadial –HS– 3 and HS2; ∼31–29 ka and ∼26–23 ka, respectively) and during the deglaciation (i.e., at ∼22 ka, ∼20–19 ka and from 18.2 ± 0.2 to 16.7 ± 0.2 ka that corresponds to the first part of HS1). The deglaciation was discontinuous in character, and similar in timing to that of the southern LIS margin, with moderate ice-sheet retreat (from 22.5 ± 0.2 ka in the Baltic lowlands) as soon as the northern summer insolation increase (from ∼23 ka) and an acceleration of the margin retreat thereafter (from ∼20 ka). Importantly, our results show that EIS retreat events and release of meltwater to the North Atlantic during the deglaciation coincide with AMOC destabilisation and interhemispheric climate changes. They thus suggest that the EIS, together with the LIS, could have played a critical role in the climatic reorganization that accompanied the last deglaciation. Finally, our data suggest that meltwater discharges to the North Atlantic produced by large-scale recession of continental parts of Northern Hemisphere ice sheets during HS, could have been a possible source for the oceanic perturbations (i.e., AMOC shutdown) responsible for the marine-based ice stream purge cycle, or so-called HE's, that punctuate the last glacial period.

Scheduling of track inspection and maintenance activities in railroad networks

The U.S. railroad companies spend billions of dollars every year on railroad track maintenance in order to ensure safety and operational efficiency of their railroad networks. Besides maintenance costs, other costs such as train accident costs, train and shipment delay costs and rolling stock maintenance costs are also closely related to track maintenance activities. Optimizing the track maintenance process on the extensive railroad networks is a very complex problem with major cost implications. Currently, the decision making process for track maintenance planning is largely manual and primarily relies on the knowledge and judgment of experts. There is considerable potential to improve the process by using operations research techniques to develop solutions to the optimization problems on track maintenance. In this dissertation study, we propose a range of mathematical models and solution algorithms for three network-level scheduling problems on track maintenance: track inspection scheduling problem (TISP), production team scheduling problem (PTSP) and job-to-project clustering problem (JTPCP). TISP involves a set of inspection teams which travel over the railroad network to identify track defects. It is a large-scale routing and scheduling problem where thousands of tasks are to be scheduled subject to many difficult side constraints such as periodicity constraints and discrete working time constraints. A vehicle routing problem formulation was proposed for TISP, and a customized heuristic algorithm was developed to solve the model. The algorithm iteratively applies a constructive heuristic and a local search algorithm in an incremental scheduling horizon framework. The proposed model and algorithm have been adopted by a Class I railroad in its decision making process. Real-world case studies show the proposed approach outperforms the manual approach in short-term scheduling and can be used to conduct long-term what-if analyses to yield managerial insights. PTSP schedules capital track maintenance projects, which are the largest track maintenance activities and account for the majority of railroad capital spending. A time-space network model was proposed to formulate PTSP. More than ten types of side constraints were considered in the model, including very complex constraints such as mutual exclusion constraints and consecution constraints. A multiple neighborhood search algorithm, including a decomposition and restriction search and a block-interchange search, was developed to solve the model. Various performance enhancement techniques, such as data reduction, augmented cost function and subproblem prioritization, were developed to improve the algorithm. The proposed approach has been adopted by a Class I railroad for two years. Our numerical results show the model solutions are able to satisfy all hard constraints and most soft constraints. Compared with the existing manual procedure, the proposed approach is able to bring significant cost savings and operational efficiency improvement. JTPCP is an intermediate problem between TISP and PTSP. It focuses on clustering thousands of capital track maintenance jobs (based on the defects identified in track inspection) into projects so that the projects can be scheduled in PTSP. A vehicle routing problem based model and a multiple-step heuristic algorithm were developed to solve this problem. Various side constraints such as mutual exclusion constraints and rounding constraints were considered. The proposed approach has been applied in practice and has shown good performance in both solution quality and efficiency.

Monitoramento por microcontrolador do cultivo de spirulina em fotobiorreator raceway

A oportunidade de produção de biomassa microalgal tem despertado interesse pelos diversos destinos que a mesma pode ter, seja na produção de bioenergia, como fonte de alimento ou servindo como produto da biofixação de dióxido de carbono. Em geral, a produção em larga escala de cianobactérias e microalgas é feita com acompanhamento através de análises físicoquímicas offline. Neste contexto, o objetivo deste trabalho foi monitorar a concentração celular em fotobiorreator raceway para produção de biomassa microalgal usando técnicas de aquisição digital de dados e controle de processos, pela aquisição de dados inline de iluminância, concentração de biomassa, temperatura e pH. Para tal fim foi necessário construir sensor baseado em software capaz de determinar a concentração de biomassa microalgal a partir de medidas ópticas de intensidade de radiação monocromática espalhada e desenvolver modelo matemático para a produção da biomassa microalgal no microcontrolador, utilizando algoritmo de computação natural no ajuste do modelo. Foi projetado, construído e testado durante cultivos de Spirulina sp. LEB 18, em escala piloto outdoor, um sistema autônomo de registro de informações advindas do cultivo. Foi testado um sensor de concentração de biomassa baseado na medição da radiação passante. Em uma segunda etapa foi concebido, construído e testado um sensor óptico de concentração de biomassa de Spirulina sp. LEB 18 baseado na medição da intensidade da radiação que sofre espalhamento pela suspensão da cianobactéria, em experimento no laboratório, sob condições controladas de luminosidade, temperatura e fluxo de suspensão de biomassa. A partir das medidas de espalhamento da radiação luminosa, foi construído um sistema de inferência neurofuzzy, que serve como um sensor por software da concentração de biomassa em cultivo. Por fim, a partir das concentrações de biomassa de cultivo, ao longo do tempo, foi prospectado o uso da plataforma Arduino na modelagem empírica da cinética de crescimento, usando a Equação de Verhulst. As medidas realizadas no sensor óptico baseado na medida da intensidade da radiação monocromática passante através da suspensão, usado em condições outdoor, apresentaram baixa correlação entre a concentração de biomassa e a radiação, mesmo para concentrações abaixo de 0,6 g/L. Quando da investigação do espalhamento óptico pela suspensão do cultivo, para os ângulos de 45º e 90º a radiação monocromática em 530 nm apresentou um comportamento linear crescente com a concentração, apresentando coeficiente de determinação, nos dois casos, 0,95. Foi possível construir um sensor de concentração de biomassa baseado em software, usando as informações combinadas de intensidade de radiação espalhada nos ângulos de 45º e 135º com coeficiente de determinação de 0,99. É factível realizar simultaneamente a determinação inline de variáveis do processo de cultivo de Spirulina e a modelagem cinética empírica do crescimento do micro-organismo através da equação de Verhulst, em microcontrolador Arduino.

Purificação de C-ficocianina e sua incorporação em nanofibras

C-ficocianina (C-FC) é uma ficobiliproteína, de cor natural azul, com diversas aplicações na indústria alimentícia, farmacêutica e biomédica, dependendo do seu grau específico de pureza, que pode variar de 0,7 a 4,0, com respectivo aumento de seu valor comercial. Essa pureza é alcançada através de diversas técnicas de purificação, que podem ser aplicadas em diferentes sequências. Um destes processos de purificação de proteínas baseia-se na cromatografia de troca iônica, que utiliza trocadores que adsorvem as proteínas como resultado de interações iônicas entre a superfície da proteína e o trocador. Resinas e colunas de leito expandido podem ser utilizadas para aumentar a produtividade dessa técnica. É fundamental conhecer o perfil do processo de adsorção, para melhor aplicá-lo como ferramenta para o design e otimização de parâmetros operacionais. Outra tecnologia para o tratamento de biomoléculas é a ultrafiltração. Esta técnica é aplicável em larga escala, apresenta baixa complexidade de aplicação e pode ser realizada em condições brandas, minimizando o dano para o produto. Para aumentar a estabilidade da C-FC, e facilitar a sua aplicação, podem ser avaliadas técnicas recentes, não exploradas para este fim, como as nanofibras obtidas através do processo de electrospinning. Estas fibras possuem uma área superficial específica extremamente elevada devido a seu pequeno diâmetro. O objetivo deste trabalho foi avaliar parâmetros de adsorção e diferentes técnicas para purificação de C-ficocianina de Spirulina platensis e obter nanofibras poliméricas incorporadas de C-ficocianina. O trabalho foi dividido em quatro artigos. No primeiro artigo, foram avaliados os parâmetros e as isotermas de adsorção de C-ficocianina em resina de troca iônica para leito expandido Streamline® DEAE. Verificou-se que o maior coeficiente de partição foi obtido em pH 7,5, nas temperaturas de 15 e 25 °C. As isotermas de adsorção da Cficocianina foram bem representadas pelos modelos de Langmuir, de Freundlich e de Langmuir-Freundlich, sendo os valores estimados para Qm e Kd obtidos pela isoterma de Langmuir foram, respectivamente, 33,92 mg.mL-1 e 0,123 mg.mL-1, respectivamente. No segundo artigo foi avaliada a purificação de C-FC até grau alimentar, utilizando ultrafiltração (UF). Com a membrana de 50 kDa, identificou-se que somente a temperatura e a aplicação de diferentes ciclos de diafiltração (DF) causaram influência significativa sobre a purificação e recuperação da C-ficocianina. Foram então aplicados o aumento gradativo da quantidade de ciclos, e a diafiltração previamente à ultrafiltração (DF/UF), onde obteve-se um extrato de Cficocianina com pureza de 0,95. No terceiro artigo foram propostos processos de purificação, envolvendo a utilização das diferentes técnicas para obtenção de C-FC com diferentes purezas. Determinou-se que a partir de cromatografia de troca iônica em leito fixo seguido de DF/UF, obtém-se C-FC para uso em cosméticos e a partir de precipitação com sulfato de amônio, e DF/UF obtém-se C-FC para uso em biomarcadores. Com uma sequência de precipitação com sulfato de amônio, DF/UF e cromatografia de troca iônica em leito fixo chega-se a C-FC de grau analítico. No último artigo, C-FC foi incorporada a nanofibras de óxido de polietileno (PEO) através de processo de electrospinning. Foram determinadas a condutividade da solução de C-FC/PEO, a estrutura e comportamento termogravimétrico das nanofibras formadas. Soluções de polímeros com concentração de 6 e 8% proporcionaram a formação de nanofibras com diâmetro médio inferior a 800 nm, homogêneas, sem a presença de gotas. A análise termogravimétrica identificou aumento na resistência térmica da C-FC incorporada nas fibras.

Application of the latency insertion method (LIM) to the analysis of large circuit interconnect networks

The focus of this research is to explore the applications of the finite difference formulation based on the latency insertion method (LIM) to the analysis of circuit interconnects. Special attention is devoted to addressing the issues that arise in very large networks such as on-chip signal and power distribution networks. We demonstrate that the LIM has the power and flexibility to handle various types of analysis required at different stages of circuit design. The LIM is particularly suitable for simulations of very large scale linear networks and can significantly outperform conventional circuit solvers (such as SPICE).

Rôle des protéoglycanes à héparane sulfate dans le transfert de gène des cellules CHO et HEK293

La possibilité de programmer une cellule dans le but de produire une protéine d’intérêt est apparue au début des années 1970 avec l’essor du génie génétique. Environ dix années plus tard, l’insuline issue de la plateforme de production microbienne Escherichia coli, fut la première protéine recombinante (r-protéine) humaine commercialisée. Les défis associés à la production de r-protéines plus complexes et glycosylées ont amené l’industrie biopharmaceutique à développer des systèmes d’expression en cellules de mammifères. Ces derniers permettent d’obtenir des protéines humaines correctement repliées et de ce fait, biologiquement actives. Afin de transférer le gène d’intérêt dans les cellules de mammifères, le polyéthylènimine (PEI) est certainement un des vecteurs synthétiques le plus utilisé en raison de son efficacité, mais aussi sa simplicité d’élaboration, son faible coût et sa stabilité en solution qui facilite son utilisation. Il est donc largement employé dans le contexte de la production de r-protéines à grande échelle et fait l’objet d’intenses recherches dans le domaine de la thérapie génique non virale. Le PEI est capable de condenser efficacement l’ADN plasmidique (vecteur d’expression contenant le gène d’intérêt) pour former des complexes de petites tailles appelés polyplexes. Ces derniers doivent contourner plusieurs étapes limitantes afin de délivrer le gène d’intérêt au noyau de la cellule hôte. Dans les conditions optimales du transfert de gène par le PEI, les polyplexes arborent une charge positive nette interagissant de manière électrostatique avec les protéoglycanes à héparane sulfate (HSPG) qui décorent la surface cellulaire. On observe deux familles d’HSPG exprimés en abondance à la surface des cellules de mammifères : les syndécanes (4 membres, SDC1-4) et les glypicanes (6 membres, GPC1-6). Si l’implication des HSPG dans l’attachement cellulaire des polyplexes est aujourd’hui largement acceptée, leur rôle individuel vis-à-vis de cet attachement et des étapes subséquentes du transfert de gène reste à confirmer. Après avoir optimisées les conditions de transfection des cellules de mammifères CHO et HEK293 dans le but de produire des r-protéines secrétées, nous avons entrepris des cinétiques de capture, d’internalisation des polyplexes et aussi d’expression du transgène afin de mieux comprendre le processus de transfert de gène. Nous avons pu observer des différences au niveau de ces paramètres de transfection dépendamment du système d’expression et des caractéristiques structurelles du PEI utilisé. Ces résultats présentés sous forme d’articles scientifiques constituent une base solide de l’enchaînement dans le temps des évènements essentiels à une transfection efficace des cellules CHO et HEK293 par le PEI. Chaque type cellulaire possède un profil d’expression des HSPG qui lui est propre, ces derniers étant plus ou moins permissifs au transfert de gène. En effet, une étude menée dans notre laboratoire montre que les SDC1 et SDC2 ont des rôles opposés vis-à-vis du transfert de gène. Alors que tous deux sont capables de lier les polyplexes, l’expression de SDC1 permet leur internalisation contrairement à l’expression de SDC2 qui l’inhibe. De plus, lorsque le SDC1 est exprimé à la surface des cellules HEK293, l’efficacité de transfection est augmentée de douze pourcents. En utilisant la capacité de SDC1 à induire l’internalisation des polyplexes, nous avons étudié le trafic intracellulaire des complexes SDC1 / polyplexes dans les cellules HEK293. De plus, nos observations suggèrent une nouvelle voie par laquelle les polyplexes pourraient atteindre efficacement le noyau cellulaire. Dans le contexte du transfert de gène, les HSPG sont essentiellement étudiés dans leur globalité. S’il est vrai que le rôle des syndécanes dans ce contexte est le sujet de quelques études, celui des glypicanes est inexploré. Grâce à une série de traitements chimiques et enzymatiques visant une approche « perte de fonction », l’importance de la sulfatation comme modification post-traductionnelle, l’effet des chaînes d’héparanes sulfates mais aussi des glypicanes sur l’attachement, l’internalisation des polyplexes, et l’expression du transgène ont été étudiés dans les cellules CHO et HEK293. L’ensemble de nos observations indique clairement que le rôle des HSPG dans le transfert de gène devrait être investigué individuellement plutôt que collectivement. En effet, le rôle spécifique de chaque membre des HSPG sur la capture des polyplexes et leur permissivité à l’expression génique demeure encore inconnu. En exprimant de manière transitoire chaque membre des syndécanes et glypicanes à la surface des cellules CHO, nous avons déterminé leur effet inhibiteur ou activateur sur la capture des polyplexes sans pouvoir conclure quant à l’effet de cette surexpression sur l’efficacité de transfection. Par contre, lorsqu’ils sont présents dans le milieu de culture, le domaine extracellulaire des HSPG réduit l’efficacité de transfection des cellules CHO sans induire la dissociation des polyplexes. Curieusement, lorsque chaque HSPG est exprimé de manière stable dans les cellules CHO, seulement une légère modulation de l’expression du transgène a pu être observée. Ces travaux ont contribué à la compréhension des mécanismes d'action du vecteur polycationique polyéthylènimine et à préciser le rôle des protéoglycanes à héparane sulfate dans le transfert de gène des cellules CHO et HEK293.

Synthèse de sulfilimines et de sulfoximines catalysée par les métaux de transition

Les sulfilimines et les sulfoximines sont des motifs structuraux dont l’intérêt synthétique est grandissant, notamment du fait de leurs applications en chimie médicinale et en agrochimie. Les travaux rapportés dans cet ouvrage décrivent le développement de nouvelles méthodes de synthèse efficaces pour la production de ces unités atypiques. Ces méthodes sont basées sur la réactivité d’une source d’azote électrophile, vis-à-vis de thioéthers et de sulfoxydes. L’utilisation d’un complexe métallique introduit en quantité catalytique a permis de favoriser le processus réactionnel. En tirant bénéfice de l’expertise de notre groupe de recherche sur le développement de réactions d’amination stéréosélectives de liaisons C-H et d’aziridination de styrènes, nous avons d’abord étudié la réactivité des N-mésyloxycarbamates comme source d’azote électrophile. Après avoir optimisé sa synthèse sur grande échelle, ce réactif chiral a été utilisé dans des réactions d’amination de thioéthers et de sulfoxydes, catalysées par un dimère de rhodium (II) chiral. Un processus diastéréosélectif efficace a été mis au point, permettant de produire des sulfilimines et des sulfoximines chirales avec d’excellents rendements et sélectivités. Au cours de l’optimisation de cette méthode de synthèse, nous avons pu constater l’effet déterminant de certains additifs sur la réactivité et la sélectivité de la réaction. Une étude mécanistique a été entreprise afin de comprendre leur mode d’action. Il a été observé qu’une base de Lewis telle que le 4-diméthylaminopyridine (DMAP) pouvait se coordiner au dimère de rhodium(II) et modifier ses propriétés structurales et redox. Les résultats que nous avons obtenus suggèrent que l’espèce catalytique active est un dimère de rhodium de valence mixte Rh(II)/Rh(III). Nous avons également découvert que l’incorporation de sels de bispyridinium avait une influence cruciale sur la diastéréosélectivité de la réaction. D’autres expériences sur la nature du groupe partant du réactif N-sulfonyloxycarbamate nous ont permis de postuler qu’une espèce nitrénoïde de rhodium était l’intermédiaire clé du processus d’amination. De plus, l’exploitation des techniques de chimie en débit continu nous a permis de développer une méthode d’amination de thioéthers et de sulfoxydes très performante, en utilisant les azotures comme source d’azote électrophile. Basée sur la décompositon photochimique d’azotures en présence d’un complexe de fer (III) simple et commercialement disponible, nous avons été en mesure de produire des sulfilimines et des sulfoximines avec d’excellents rendements. Le temps de résidence du procédé d’amination a pu être sensiblement réduit par la conception d’un nouveau type de réacteur photochimique capillaire. Ces améliorations techniques ont permis de rendre la synthèse plus productive, ce qui constitue un élément important d’un point de vue industriel.

Geological realism in hydrogeological and geophysical inverse modeling: A review

Scientific curiosity, exploration of georesources and environmental concerns are pushing the geoscientific research community toward subsurface investigations of ever-increasing complexity. This review explores various approaches to formulate and solve inverse problems in ways that effectively integrate geological concepts with geophysical and hydrogeological data. Modern geostatistical simulation algorithms can produce multiple subsurface realizations that are in agreement with conceptual geological models and statistical rock physics can be used to map these realizations into physical properties that are sensed by the geophysical or hydrogeological data. The inverse problem consists of finding one or an ensemble of such subsurface realizations that are in agreement with the data. The most general inversion frameworks are presently often computationally intractable when applied to large-scale problems and it is necessary to better understand the implications of simplifying (1) the conceptual geological model (e.g., using model compression); (2) the physical forward problem (e.g., using proxy models); and (3) the algorithm used to solve the inverse problem (e.g., Markov chain Monte Carlo or local optimization methods) to reach practical and robust solutions given today's computer resources and knowledge. We also highlight the need to not only use geophysical and hydrogeological data for parameter estimation purposes, but also to use them to falsify or corroborate alternative geological scenarios.

RACISM IN DIGITAL ERA: DEVELOPMENT AND INITIAL VALIDATION OF THE PERCEIVED ONLINE RACISM SCALE (PORS V1.0)

Racism continues to thrive on the Internet. Yet, little is known about racism in online settings and the potential consequences. The purpose of this study was to develop the Perceived Online Racism Scale (PORS), the first measure to assess people’s perceived online racism experiences as they interact with others and consume information on the Internet. Items were developed through a multi-stage process based on literature review, focus-groups, and qualitative data collection. Based on a racially diverse large-scale sample (N = 1023), exploratory and confirmatory factor analyses provided support for a 30-item bifactor model with the following three factors: (a) 14-item PORS-IP (personal experiences of racism in online interactions), (b) 5-item PORS-V (observations of other racial/ethnic minorities being offended), and (c) 11-item PORS-I (consumption of online contents and information denigrating racial/ethnic minorities and highlighting racial injustice in society). Initial construct validity examinations suggest that PORS is significantly linked to psychological distress.

Improved production of chlorogenic acid from cell suspension cultures of Lonicera macranthoids

Purpose: To evaluate the potential of Lonicera macranthoids Hand. -Mazz. Yulei1 suspension culture system for enhanced production of the main secondary metabolite, chlorogenic acid. Methods: The callus of L. macranthoides Hand.-Mazz. “Yulei1” was suspension cultured in B5 liquid medium supplemented with different plant growth regulators. Biomass accumulation was calculated by weight method and chlorogenic acid production was measured using high performance liquid chromatography (HPLC). HPLC was carried out on C18 analytical column at 35 °C and the detection wavelength was set at 324 nm. Results: The results showed that maximum accumulation of biomass and chlorogenic acid were achieved 15 days after culture growth. The optimized conditions for biomass accumulation and chlorogenic acid production were 50 g/L of inoculum on fresh weight basis, B5 medium supplemented with plant growth regulators, 30 - 40 g/L sucrose and initial medium pH of 5.5. Maximum accumulation of chlorogenic acid and biomass were observed when the culture medium was supplemented with 2.0 mg/L6-BA. Optimal accumulation of chlorogenic acid was observed using combination of hormones 2.0 mg/L 6-Benzyladenine (BA) + 0.5 mg/L2, 4-Dichlorophenoxyacetic acid (2,4-D), while optimal accumulation of biomass was observed with 2.0 mg/L 6-BA + 2.0 mg/L2, 4-D. In addition, phenylalanine also contributed to the synthesis of chlorogenic acid at a concentration > 50 mg/L. Conclusion: Cell suspension cultures of L. macranthoides Hand.-Mazz. “Yulei1” have successfully been established. The findings provide a potential basis for large scale production of chlorogenic acid using cell suspension cultures of L. macranthoides.

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.