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Biological Networks: Modeling And Structural Analysis, Emad Y. Ramadan
Biological Networks: Modeling And Structural Analysis, Emad Y. Ramadan
Computer Science Theses & Dissertations
Biological networks are receiving increased attention due to their importance in understanding life at the cellular level. There exist many different kinds of biological networks, and different models have been proposed for them. In this dissertation we focus on suitable network models for representing experimental data on protein interaction networks and protein complex networks (protein complexes are groups of proteins that associate to accomplish some function in the cell), and to design algorithms for exploring such networks. Our goal is to enable biologists to identify the general principles that govern the organization of protein-protein interaction networks and protein complex networks. …
Improved Constrained Global Optimization For Estimating Molecular Structure From Atomic Distances, Terri Marie Grant
Improved Constrained Global Optimization For Estimating Molecular Structure From Atomic Distances, Terri Marie Grant
Mathematics & Statistics Theses & Dissertations
Determination of molecular structure is commonly posed as a nonlinear optimization problem. The objective functions rely on a vast amount of structural data. As a result, the objective functions are most often nonconvex, nonsmooth, and possess many local minima. Furthermore, introduction of additional structural data into the objective function creates barriers in finding the global minimum, causes additional computational issues associated with evaluating the function, and makes physical constraint enforcement intractable. To combat the computational problems associated with standard nonlinear optimization formulations, Williams et al. (2001) proposed an atom-based optimization, referred to as GNOMAD, which complements a simple interatomic distance …