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Designing radiotherapy treatments is a complicated and important task that affects patient care, and modern delivery systems enable a physician more flexibility than can be considered. Consequently, treatment design is increasingly automated by techniques of optimization, and many of the advances in the design process are accomplished by a collaboration… (More)

- Julio-Roberto Hasfura-Buenaga, Allen Holder, Jeffrey Stuart
- 2001

The data describing an asymptotic linear program rely on a single parameter , usually referred to as time, and unlike parametric linear programming, asymptotic linear programming is concerned with the steady state behavior as time increases to infinity. The fundamental result of this work shows that the optimal partition for an asymptotic linear program… (More)

A new intrinsic geometry based on a spectral analysis is used to motivate methods for aligning protein folds. The geometry is induced by the fact that a distance matrix can be scaled so that its eigenvalues are positive. We provide a mathematically rigorous development of the intrinsic geometry underlying our spectral approach and use it to motivate two… (More)

- Eivind Almaas, Emily Gruber, Allen Holder, Amy Ko, Michael Macgillivray, Miranda Sawyer
- 2014

Flux balance analysis (FBA) is a standard optimization model that is used to study the metabolisms of cells that are in a steady state of optimal growth. The model optimizes a biologically defined objective while assuming (1) equilibria of a linear system of ordinary differential equations, and (2) deterministic data. However, the steady state assumption is… (More)

Several efficient algorithms to conduct pairwise comparisons among large databases of protein structures have emerged in the recent literature. The central theme is the design of a measure between the Cα atoms of two protein chains, from which dynamic programming is used to compute an alignment. The efficiency and efficacy of these algorithms allows… (More)