Structure Determination Computational Structural Biology

Williams, and J. R. Heath. Electronically configurable moleculear-based logic gates. Science, 285:391–394, 1999. A. Colllins, A. Zomorodian, G. Carlsson, and L. Guibas. A barcode shape descriptor for curve point cloud data, 2004. To be published in Proc. Symp. Point-Based Graph. T. H. Cormen, C. E. Leiserson, and R. L. Rivest. Introduction to Algorithms. The MIT Press, Cambridge, MA, 1994. T. E. Creighton. Proteins. Structures and Molecular Principles. Freeman, New York, 1984. B. Curless and M. Levoy. A volumetric method for building complex models from range images. In SIGGRAPH 96 Conference Proceedings, pages 303–312, 1996. M. Davis. The Undecidable. Raven Press Books, LTD., Hewlett, NY, 1965. M. de Berg and M. van Kreveld. Trekking in the alps without freezing and getting tired. In Proc. 1st Europ. Sympos. Alg, pages 121–132, 1993. M. de Berg, M. van Kreveld, M. Overmars, and O. Schwarzkopf. Computational Geometry: Algorithms and Applications . Springer-Verlag, New York, 1997. W. de Leeuw and R. van Liere. Collapsing flow topology using area metrics. In Proc. 10th Ann. IEEE Conf. Visualization , pages 349–354, 1999. B. Delaunay. Sur la sphère vide. Izv. Akad. Nauk SSSR, Otdelenie Matematicheskii i Estestvennyka Nauk , 7:793–800, 1934. C. J. A. Delfinado and H. Edelsbrunner. An incremental algorithm for Betti numbers of simplicial complexes on the 3-sphere. Comput. Aided Geom. Design, 12:771–784, 1995. T. K. Dey, H. Edelsbrunner, G. Guha, and D. V. Nekhayev. Topology preserving edge contraction. Publ. Inst. Math. Beograd N.S., 66:23–45, 1999. D. Dummit and R. Foote. Abstract Algebra. John Wiley Sons, Inc., New York, 1999. M. D. Dyksterhouse. An alpha-shape view of our universe. Master’s thesis, University of Illinois at Urbana-Champaign, Urbana, IL, 1992. H. Edelsbrunner. The union of balls and its dual shape. Discrete Comput. Geom., 13: 415–440, 1995. H. Edelsbrunner, J. Harer, and A. Zomorodian. Hierarchical Morse-Smale complexes for piecewise linear 2-manifolds. Discrete Comput. Geom., 30:87–107, 2003. H. Edelsbrunner, D. G. Kirkpatrick, and R. Seidel. On the shape of a set of points in the plane. IEEE Trans. Inform. Theory, IT–29:551–559, 1983. H. Edelsbrunner, D. Letscher, and A. Zomorodian. Topological persistence and simplification. Discrete Comput. Geom., 28:511–533, 2002. H. Edelsbrunner and E. P. Mücke. Simulation of simplicity: A technique to cope with degenerate cases in geometric algorithms. ACM Trans. Graphics, 9:66–104, 1990. H. Edelsbrunner and E. P. Mücke. Three-dimensional alpha shapes. ACM Trans. Graphics , 13:43–72, 1994. H. Edelsbrunner and A. Zomorodian. Computing linking numbers in a filtration. Homology, Homotopy and Applications , 52:19–37, 2003. D. Eisenbud. Commutative Algebra with a View Toward Algebraic Theory. Springer, New York, 1995. J. El-Sana and A. Varshney. Topology simplification for polygonal virtual environments. IEEE Trans. Visualization Comput. Graphics , 4:133–144, 1998. E. Flapan. When Topology Meets Chemistry : A Topological Look at Molecular Chirality . Cambridge University Press, New York, 2000. J. D. Foley, A. van Dam, S. K. Feiner, J. F. Hughes, and R. L. Phillips. Computer Graphics: Principles and Practice . Addison Wesley, Reading, MA, second edition, 1996. A. T. Fomenko and S. V. Matveev. Algorithmic and Computer Methods for