Allen Holder

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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)
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)
In this paper we introduce a p-median problem based clustering heuristic for selecting efficient beam angles for intensity modulated radiation therapy. The essence of the method described here is the clustering of beam angles according to probability that an angle will be observed in the final solution and similarities among different angles and the(More)
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)