Path: utzoo!attcan!uunet!tut.cis.ohio-state.edu!purdue!gatech!rutgers!aramis.rutgers.edu!athos.rutgers.edu!nanotech From: thearlin@vdsvax.crd.ge.com (Thearling Kurt H) Newsgroups: sci.nanotech Subject: Molecular Biology and Computation Bibliography Message-ID: Date: 18 Aug 89 00:50:04 GMT Sender: nanotech@athos.rutgers.edu Lines: 162 Approved: nanotech@aramis.rutgers.edu Here's a list of references for a combination of the fields of Biology and Computation. It includes refrecences on Molecular Computation, Computer-Aided Protein Design, Modeling Biomolecules, and others. Since my background is in computer science rather than biology, the biology does not usually get too technically detailed. kurt ----------------------------------------------------------------------- Kurt Thearling 1101 W. Springfield Avenue University of Illinois Urbana, Il 61801 Coordinated Science Lab kurt@bach.csg.uiuc.edu ----------------------------------------------------------------------- ----------------------------------------------------------------------- Biology and Computation (and vice-versa): A List of References ----------------------------------------------------------------------- R.M. Baer and H.M. Martinez "Automata and Biology" Annual Review of Biophysics and Bioengineering, Vol. 3, 1974, pp. 255-291 V. Brendel and H.G. Busse "Genome Structure Described by Formal Languages" Nucleic Acids Research, Vol. 12, Number 5, 1984, pp. 2561-2567 C. Burks and J.D. Farmer "Towards Modeling DNA Sequences as Automata" Physica 10D (1984), pp. 157-167 F.L. Carter "Prospects for Computation at the Molecular Size Level" Proceedings of the Spring 1984 COMPCON, pp. 110-114 F.L. Carter "The Molecular Device Computer: Point of Departure for Large Scale Cellular Automata" Physica 10D (1984), pp. 175-194 G.J. Chaitin "To a Mathematical Definition of 'Life'" ACM SIGACT News, Jan. 1970, pp. 12-18 G.J. Chaitin "Toward a Mathematical Definition of 'Life'" in _The_Maximum_Entropy_Formalism_, ed. by R.D. Levine and M. Tribus, MIT Press, 1979, pp. 477-498 M. Conrad "On Design Principles for a Molecular Computer" Communications of the ACM, May 1985, pp. 464-480 M. Conrad "Molecular Computer Design: A Synthetic Approach to Brain Theory" in _Real_Brains_Artificial_Minds_, ed. by J.L. Casti and A. Karlqvist, North-Holland, 1988(?) M. Conrad "The Lure of Molecular Computing" IEEE Spectrum, Oct. 1986, pp. 55-60 W.F. DeGrado, Z.R. Wasserman, and J.D. Lear "Protein Design, a Minimalist Approach" Science, 3 Feb. 1989, pp. 622-243 C. DeLisi "Computers in Molecular Biology: Current Applications and Emerging Trends" Science, 1 April 1988, pp. 47-240 W. Ebeling, R. Feistel, and H. Herzel "Dynamics and Complexity of Biomolecules" Physica Scripta, Vol. 35, 1987, pp. 761-768 M. Eigen "Macromolecular Evolution" in _Emerging_Syntheses_in_Science_, ed. by D. Pines, Addison-Wesley, 1977, pp. 21-41 J.D. Farmer, S.A. Kaufman, N.H. Packard, and A.S. Perleson "Adaptive Dynamic Networks as Models for the Immune System and Autocatalytic Sets" Annals of the New York Academy of Sciences, Vol. 504, pp. 118-131 J.D. Farmer, S.A. Kaufman, and N.H. Packard "Autocatalytic Replication of Polymers" Physica 22D (1986), pp. 50-67 M.W. Feldman "Evolutionary Theory of Genotypes and Phenotypes: Towards a Mathematical Synthesis" in _Emerging_Syntheses_in_Science_, ed. by D. Pines, Addison-Wesley, 1977, pp. 43-52 H. Frauenfelder "Biomolecules" in _Emerging_Syntheses_in_Science_, ed. by D. Pines, Addison-Wesley, 1977, pp. 155-165 F. Frohlich "The Linguistic Structure of the Chromosome Genetic Code and Language" in _Synergetics:_A_Workshop_, ed. by H. Haken, Springer-Verlag, 1977, pp. 267-274 E.F. Mallove "Sequencing the Human Genome: Computers take a Leading Role" Computers in Scince, Premiere Issue 1987, pp. 41-51 J.A. McCammon "Computer-Aided Molecular Design" Science, 23 Oct. 1987, pp. 486-491 J.R. Milch "Computers Based on Molecular Implementations of Cellular Automata" in _Molecular_Electronic_Devices_ (Proceedings of the 3rd International Symposium on Molecular Electronic Devices), ed. by F.L. Carter, R. Siatkowski, and H. Wohltjen, North-Holland, 1986, pp. 303-317 M. Radman and R. Wagner "The High Fidelity of DNA Duplication" Scientific American, Aug. 1988, pp. 40-46 A.C. Scott "Solitons in Biological Molecules" in _Emerging_Syntheses_in_Science_, ed. by D. Pines, Addison-Wesley, 1977, pp. 133-151 D.B. Searls "Representing Genetic Information with Formal Grammars" Proceedings of AAAI-88, 1988, pp. 386-391 J.B. Tucker "Designing Molecules by Computer" High Technology, Jan. 1984, pp. 52-59 J.B. Tucker "Biochips: Can Molecules Compute" High Technology, Feb. 1984, pp. 36-47 J.B. Tucker "Gene Machines: The Second Wave" High Technology, Mar. 1984, pp. 50-59 J.B. Tucker "Proteins to Order" High Technology, Dec. 1985, pp. 26-44 K.M. Ulmer "Protein Engineering" Science, 11 Feb. 1983, pp. 666-671 L.V. Yakushevich "Nonlinear DNA Dynamics: A New Model" Physics Letters A, 17 April 1989, pp. 413-417 ----------------------------------------------------------------------- End of Reference List -----------------------------------------------------------------------