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A novel and robust automated docking method that predicts the bound conformations of flexible ligands to macromolecular targets has been developed and tested, in combination with a new scoring function that estimates the free energy change upon binding. Interestingly, this method applies a Lamarckian model of genetics, in which environmental adaptations of(More)
Automatic measurement of blood vessel tortuosity is a useful capability for automatic ophthalmological diagnostic tools. We describe a suite of automated tortuosity measures for blood vessel segments extracted from RGB retinal images. The tortuosity measures were evaluated in two classification tasks: (1) classifying the tortuosity of blood vessel segments(More)
Evolutionary algorithms have been successfully applied to a variety of molecular structure prediction problems. In this paper we reconsider the design of genetic algorithms that have been applied to a simple protein structure prediction problem. Our analysis considers the impact of several algorithmic factors for this problem: the conformational(More)
Following the events of September 11, 2001, in the United States, world public awareness for possible terrorist attacks on water supply systems has increased dramatically. Among the different threats for a water distribution system, the most difficult to address is a deliberate chemical or biological contaminant injection, due to both the uncertainty of the(More)
We present a model for optimizing the placement of sensors in municipal water networks to detect maliciously-injected contaminants. An optimal sensor configuration minimizes the expected fraction of the population at risk. We formulate this problem as an integer program, which can be solved with generally available IP solvers. We find optimal sensor(More)
We describe Pyomo, an open source software package for modeling and solving mathematical programs in Python. Pyomo can be used to define abstract and concrete problems, create problem instances, and solve these instances with standard open-source and commercial solvers. Pyomo provides a capability that is commonly associated with algebraic modeling(More)
This paper examines the effects of relaxed synchronization on both the numerical and parallel efficiency of parallel genetic algorithms (GAs). We describe a coarse-grain geographically structured parallel genetic algorithm. Our experiments provide preliminary evidence that asynchronous versions of these algorithms have a lower run time than synchronous GAs.(More)