Matching Items (6)
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- All Subjects: Operations Research
- Creators: Yan, Hao
Description
Solution conformations and dynamics of proteins and protein-DNA complexes are often difficult to predict from their crystal structures. The crystal structure only shows a snapshot of the different conformations these biological molecules can have in solution. Multiple different conformations can exist in solution and potentially have more importance in the biological activity. DNA sliding clamps are a family of proteins with known crystal structures. These clamps encircle the DNA and enable other proteins to interact more efficiently with the DNA. Eukaryotic PCNA and prokaryotic β clamp are two of these clamps, some of the most stable homo-oligomers known. However, their solution stability and conformational equilibrium have not been investigated in depth before. Presented here are the studies involving two sliding clamps: yeast PCNA and bacterial β clamp. These studies show that the β clamp has a very different solution stability than PCNA. These conclusions were reached through various different fluorescence-based experiments, including fluorescence correlation spectroscopy (FCS), Förster resonance energy transfer (FRET), single molecule fluorescence, and various time resolved fluorescence techniques. Interpretations of these, and all other, fluorescence-based experiments are often affected by the properties of the fluorophores employed. Often the fluorescence properties of these fluorophores are influenced by their microenvironments. Fluorophores are known to sometimes interact with biological molecules, and this can have pronounced effects on the rotational mobility and photophysical properties of the dye. Misunderstanding the effect of these photophysical and rotational properties can lead to a misinterpretation of the obtained data. In this thesis, photophysical behaviors of various organic dyes were studied in the presence of deoxymononucleotides to examine more closely how interactions between fluorophores and DNA bases can affect fluorescent properties. Furthermore, the properties of cyanine dyes when bound to DNA and the effect of restricted rotation on FRET are presented in this thesis. This thesis involves studying fluorophore photophysics in various microenvironments and then expanding into the solution stability and dynamics of the DNA sliding clamps.
ContributorsRanjit, Suman (Author) / Levitus, Marcia (Thesis advisor) / Lindsay, Stuart (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2013
Description
For multiple reasons, the consumption of fresh fruits and vegetables in the United States has progressively increased. This has resulted in increased domestic production and importation of these products. The associated logistics is complex due to the perishability of these products, and most current logistics systems rely on marketing and supply chains practices that result in high levels of food waste and limited offer diversity. For instance, given the lack of critical mass, small growers are conspicuously absent from mainstream distribution channels. One way to obtain these critical masses is using associative schemes such as co-ops. However, the success level of traditional associate schemes has been mixed at best. This dissertation develops decision support tools to facilitate the formation of coalitions of small growers in complementary production regions to act as a single-like supplier. Thus, this dissertation demonstrates the benefits and efficiency that could be achieved by these coalitions, presents a methodology to efficiently distribute the value of a new identified market opportunity among the growers participating in the coalition, and develops a negotiation framework between a buyer(s) and the agent representing the coalition that results in a prototype contract.There are four main areas of research contributions in this dissertation. The first is the development of optimization tools to allocate a market opportunity to potential production regions while considering consumer preferences for special denomination labels such as “local”, “organic”, etc. The second contribution is in the development of a stochastic optimization and revenue-distribution framework for the formation of coalitions of growers to maximize the captured value of a market opportunity. The framework considers the growers’ individual preferences and production characteristics (yields, resources, etc.) to develop supply contracts that entice their participation in the coalition. The third area is the development of a negotiation mechanism to design contracts between buyers and groups of growers considering the profit expectations and the variability of the future demand. The final contribution is the integration of these models and tools into a framework capable of transforming new market opportunities into implementable production plans and contractual agreement between the different supply chain participants.
ContributorsUlloa, Rodrigo (Author) / Villalobos, Jesus (Thesis advisor) / Fowler, John (Committee member) / Mac Cawley, Alejandro (Committee member) / Yan, Hao (Committee member) / Phelan, Patrick (Committee member) / Arizona State University (Publisher)
Created2022
Description
Assembly lines are low-cost production systems that manufacture similar finished units in large quantities. Manufacturers utilize mixed-model assembly lines to produce customized items that are not identical but share some general features in response to consumer needs. To maintain efficiency, the aim is to find the best feasible option to balance the lines efficiently; allocating each task to a workstation to satisfy all restrictions and fulfill all operational requirements in such a way that the line has the highest performance and maximum throughput. The work to be done at each workstation and line depends on the precise product configuration and is not constant across all models. This research seeks to enhance the subject of assembly line balancing by establishing a model for creating the most efficient assembly system. Several realistic characteristics are included into efficient optimization techniques and mathematical models to provide a more comprehensive model for building assembly systems. This involves analyzing the learning growth by task, employing parallel line designs, and configuring mixed models structure under particular constraints and criteria. This dissertation covers a gap in the literature by utilizing some exact and approximation modeling approaches. These methods are based on mathematical programming techniques, including integer and mixed integer models and heuristics. In this dissertation, heuristic approximations are employed to address problem-solving challenges caused by the problem's combinatorial complexity. This study proposes a model that considers learning curve effects and dynamic demand. This is exemplified in instances of a new assembly line, new employees, introducing new products or simply implementing engineering change orders. To achieve a cost-based optimal solution, an integer mathematical formulation is proposed to minimize the production line's total cost under the impact of learning and demand fulfillment. The research further creates approaches to obtain a comprehensive model in the case of single and mixed models for parallel lines systems. Optimization models and heuristics are developed under various aspects, such as cycle times by line and tooling considerations. Numerous extensions are explored effectively to analyze the cost impact under certain constraints and implications. The implementation results demonstrate that the proposed models and heuristics provide valuable insights.
ContributorsAlhomaidi, Esam (Author) / Askin, Ronald G (Thesis advisor) / Yan, Hao (Committee member) / Iquebal, Ashif (Committee member) / Sefair, Jorge (Committee member) / Arizona State University (Publisher)
Created2023
Description
This dissertation addresses access management problems that occur in both emergency and outpatient clinics with the objective of allocating the available resources to improve performance measures by considering the trade-offs. Two main settings are considered for estimating patient willingness-to-wait (WtW) behavior for outpatient appointments with statistical analyses of data: allocation of the limited booking horizon to patients of different priorities by using time windows in an outpatient setting considering patient behavior, and allocation of hospital beds to admitted Emergency Department (ED) patients. For each chapter, a different approach based on the problem context is developed and the performance is analyzed by implementing analytical and simulation models. Real hospital data is used in the analyses to provide evidence that the methodologies introduced are beneficial in addressing real life problems, and real improvements can be achievable by using the policies that are suggested.
This dissertation starts with studying an outpatient clinic context to develop an effective resource allocation mechanism that can improve patient access to clinic appointments. I first start with identifying patient behavior in terms of willingness-to-wait to an outpatient appointment. Two statistical models are developed to estimate patient WtW distribution by using data on booked appointments and appointment requests. Several analyses are conducted on simulated data to observe effectiveness and accuracy of the estimations.
Then, this dissertation introduces a time windows based policy that utilizes patient behavior to improve access by using appointment delay as a lever. The policy improves patient access by allocating the available capacity to the patients from different priorities by dividing the booking horizon into time intervals that can be used by each priority group which strategically delay lower priority patients.
Finally, the patient routing between ED and inpatient units to improve the patient access to hospital beds is studied. The strategy that captures the trade-off between patient safety and quality of care is characterized as a threshold type. Through the simulation experiments developed by real data collected from a hospital, the achievable improvement of implementing such a strategy that considers the safety-quality of care trade-off is illustrated.
This dissertation starts with studying an outpatient clinic context to develop an effective resource allocation mechanism that can improve patient access to clinic appointments. I first start with identifying patient behavior in terms of willingness-to-wait to an outpatient appointment. Two statistical models are developed to estimate patient WtW distribution by using data on booked appointments and appointment requests. Several analyses are conducted on simulated data to observe effectiveness and accuracy of the estimations.
Then, this dissertation introduces a time windows based policy that utilizes patient behavior to improve access by using appointment delay as a lever. The policy improves patient access by allocating the available capacity to the patients from different priorities by dividing the booking horizon into time intervals that can be used by each priority group which strategically delay lower priority patients.
Finally, the patient routing between ED and inpatient units to improve the patient access to hospital beds is studied. The strategy that captures the trade-off between patient safety and quality of care is characterized as a threshold type. Through the simulation experiments developed by real data collected from a hospital, the achievable improvement of implementing such a strategy that considers the safety-quality of care trade-off is illustrated.
ContributorsKilinc, Derya (Author) / Gel, Esma (Thesis advisor) / Pasupathy, Kalyan (Committee member) / Sefair, Jorge (Committee member) / Sir, Mustafa (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2019
Description
Modern manufacturing systems are part of a complex supply chain where customer preferences are constantly evolving. The rapidly evolving market demands manufacturing organizations to be increasingly agile and flexible. Medium term capacity planning for manufacturing systems employ queueing network models based on stationary demand assumptions. However, these stationary demand assumptions are not very practical for rapidly evolving supply chains. Nonstationary demand processes provide a reasonable framework to capture the time-varying nature of modern markets. The analysis of queues and queueing networks with time-varying parameters is mathematically intractable. In this dissertation, heuristics which draw upon existing steady state queueing results are proposed to provide computationally efficient approximations for dynamic multi-product manufacturing systems modeled as time-varying queueing networks with multiple customer classes (product types). This dissertation addresses the problem of performance evaluation of such manufacturing systems.
This dissertation considers the two key aspects of dynamic multi-product manufacturing systems - namely, performance evaluation and optimal server resource allocation. First, the performance evaluation of systems with infinite queueing room and a first-come first-serve service paradigm is considered. Second, systems with finite queueing room and priorities between product types are considered. Finally, the optimal server allocation problem is addressed in the context of dynamic multi-product manufacturing systems. The performance estimates developed in the earlier part of the dissertation are leveraged in a simulated annealing algorithm framework to obtain server resource allocations.
This dissertation considers the two key aspects of dynamic multi-product manufacturing systems - namely, performance evaluation and optimal server resource allocation. First, the performance evaluation of systems with infinite queueing room and a first-come first-serve service paradigm is considered. Second, systems with finite queueing room and priorities between product types are considered. Finally, the optimal server allocation problem is addressed in the context of dynamic multi-product manufacturing systems. The performance estimates developed in the earlier part of the dissertation are leveraged in a simulated annealing algorithm framework to obtain server resource allocations.
ContributorsJampani Hanumantha, Girish (Author) / Askin, Ronald (Thesis advisor) / Ju, Feng (Committee member) / Yan, Hao (Committee member) / Mirchandani, Pitu (Committee member) / Arizona State University (Publisher)
Created2020
Description
Deoxyribonucleic acid (DNA), a biopolymer well known for its role in preserving genetic information in biology, is now drawing great deal of interest from material scientists. Ease of synthesis, predictable molecular recognition via Watson-Crick base pairing, vast numbers of available chemical modifications, and intrinsic nanoscale size makes DNA a suitable material for the construction of a plethora of nanostructures that can be used as scaffold to organize functional molecules with nanometer precision. This dissertation focuses on DNA-directed organization of metallic nanoparticles into well-defined, discrete structures and using them to study photonic interaction between fluorophore and metal particle. Presented here are a series of studies toward this goal. First, a novel and robust strategy of DNA functionalized silver nanoparticles (AgNPs) was developed and DNA functionalized AgNPs were employed for the organization of discrete well-defined dimeric and trimeric structures using a DNA triangular origami scaffold. Assembly of 1:1 silver nanoparticle and gold nanoparticle heterodimer has also been demonstrated using the same approach. Next, the triangular origami structures were used to co-assemble gold nanoparticles (AuNPs) and fluorophores to study the distance dependent and nanogap dependencies of the photonic interactions between them. These interactions were found to be consistent with the full electrodynamic simulations. Further, a gold nanorod (AuNR), an anisotropic nanoparticle was assembled into well-defined dimeric structures with predefined inter-rod angles. These dimeric structures exhibited unique optical properties compared to single AuNR that was consistent with the theoretical calculations. Fabrication of otherwise difficult to achieve 1:1 AuNP- AuNR hetero dimer, where the AuNP can be selectively placed at the end-on or side-on positions of anisotropic AuNR has also been shown. Finally, a click chemistry based approach was developed to organize sugar modified DNA on a particular arm of a DNA origami triangle and used them for site-selective immobilization of small AgNPs.
ContributorsPal, Suchetan (Author) / Liu, Yan (Thesis advisor) / Yan, Hao (Thesis advisor) / Lindsay, Stuart (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2012