
Chemistry: G25.2601
Biology: G23.2601
Mathematics: G63.2856.003
Computer Science: G22.3033.11
Sackler: G16.2607
Time: Thursdays, 12:452:45pm
Location: 1003 Main Building
General Reference List

M.P. Allen and D.J. Tildesley.
Computer Simulation of Liquids.
Oxford University Press, New York, 1987.
[Good advanced reference book for molecular simulations]
 A.D. Bates and A. Maxwell.
DNA Topology.
In Focus series, Oxford Univeristy Press, New York, 1993.
[Beautiful paperback on the highter organizational forms of DNA]
 C. Branden and J. Tooze.
Introduction to Protein Structure.
second edition, Garland Publishing Inc., New York, 1999.
[An uptodate and nicely illustrated protein structure textbook
dealing with basic structural principles as well as the relationship
among structure, function, and enginnering. The latter part includes
chapters on transcription regulation, signal transduction, immune
regulation,
membrane and fibrous prteins, and virus structures.]
 P. Bratley, B. L. Fox, and L. E. Schrage.
A Guide to Simulation.
SpringerVerlag, New York, 1987.
[Good introduction to Monte Carlo simulations]
 C. L. Brooks, III, M. Karplus, and B.M. Pettitt.
A Theoretical Perspective of Dynamics, Structure, and Thermodynamics.
Wiley Interscience, New York, 1988.
[Nice collection on protein simulations]
 U. Burkert and N.L. Allinger.
Molecular Mechanics.
American Chemical Society, Washington D.C., 1980.
[Basic introductory monograph on molecular mechanics]
 C.R. Cantor and P.R. Schimmel.
Biophysical Chemistry.
Vol.1,2,3. W.H. Freeman and Company, San Fransisco, 1980.
[Basic introductory monograph on molecular mechanics]
 N. R. Cohen, Editor.
Guidebook on Molecular Modeling in Drug Design.
Academic Press, San Diego, 1996.
[Modern reference for molecular modeling as applied to drug design problems, containing contributed chapters by industrial and academic scientists, on problem formulation (database analysis, docking), modeling tools, and medicinal chemistry applications]

Computational Molecular Dynamics: Challenges, Methods,
Ideas  Proceedings of the 2nd International Symposium
on Algorithms for Macromolecular Modelling, Berlin, May 2124, 1997,
P. Deuflhard, J. Hermans, B. Leimkuhler, A. E. Mark, S. Reich,. R. D.
Skeel, Eds.,
Lecture Notes in Computational Science and Engineering, Vol. 4
(Series Editors M. Griebel, D. E. Keyes, R. M. Nieminen,
D. Roose, and T. Schlick), SpringerVerlag, Berlin and New York, 1999.
[Collection of articles from the presentations invited to the
May 1997 Berlin
conference on macromolecularsimulation algorithms. The books contains
sections
on the following topics: conformational dynamics, thermodynamic modeling,
enhanced timestepping algorithms, quantumclassical simulations, and
parallel
force field evaluation]
 T.E. Creighton, Editor.
Protein Folding.
W.H. Freeman & Company, New York, 1992.
[Nice collection with general topics regarding prteins covered]
 D. Eisenberg and D. Crothers.
Physcial Chemistry with Applications to the Life Science.
Benjamin Cummings, Menlo Park, California, 1979.
[Wonderful physical chemistry textbook, with useful biomolecular information]
 A. Fersht.
Structure and Mechanism in Protein Science: A Guide to Enzyme
Catalysis and Protein Folding.
W. H. Freeman and Company, New York, 1999.
[A comprehensive perspective of both enzyme catalysis and protein folding
by a pioneer researcher, an updated version of the author's
1995 text on Enzyme Structure and Mechanism; the text reviews protein structure,
emphasizing general principles, as well as reviewing
recent advances and insights from theoretical approaches]
 D. Frenkel and B. Smit.
Understanding Molecular Simulations. From Algorithms to Applications.
Academic Press, San Diego, California, 1996.
[Excellent introduction to computer simulation of molecular systems, containing a
nice mix of mathematical details and more informal, decriptive text. The
focus is on onte Carlo and molecular dynamics methodologies, through comparison
and contrast analysis, including simple algorithmes and
numerical illustrations. Some improtant recent methodological advances are
also included]
 L.M. Gierasch and J. King, Editors.
Protein Folding, Deciphering the Second Half of the Genetic Code.
AAAS, Washington D.C., 1990.
[Interesting and beautifully illustrated colletion of articles; best bet: Jane
Richardson's origami analogues of protein folding motifs!]
 H. Gould and J. Tobochnik.
An Introduction to Computer Simulation Metheods: Appkications to Physical Systems.
Part 1 and 2
AddisonWesley, Reading, MA, 1988.
[A good introduction to computer simulations, with a focus on
classical mechanics in Part 1 and statistical
physics in Part 2. The material is made highly accessible to
undergraduates by the inclusion of many simple numerical examples,
useful illustrations, and programming segments.]
 A.Y. Grosberg and A.R. Khokhlov.
Giant Molecules. Here, There, and Everywhere...
Academic Press, San Diego, California, 1997.
[A lively introduction to polymer physics, with nice illustrations
and enticing color plates, aptly fitting a beautiful subject. In the format
of a coffeetable book, the authors cover important subjects like the
wide range of polymeric subjects, ideal chain models and their properties, Brownian
motion, biological polymers, and polymer dynamics. An accompnaying CDROM
animates polymer motion, incluidng reptation and coil collapse.]
 J.M. Haile.
Molecular Dynamics Simulations: Elementary Methods.
Wiley, New York, 1992.
[Elementary text on molecular dynamics]
 M. Kalos and P. A. Whitlock.
Monte Carlo Methods.
John Wiley
& Sons, New York, 1986.
[Good introduction to Monte Carlo techniques ]
 A. R. Leach.
Molecular Modelling. Principles and Applications.
Addison Wesley Longman, Essex, England, 1996.
[Broad introduction to many aspects of
molecular modeling and computational chemistry techniques,
covering basic concepts, quantum and molecular mechanics models,
techniques for energy minimization, molecular dynamics, Monte Carlo sampling,
free energy simulations, and drug design applications]
 K.B. Lipkowitz and D.B. Boyd, Editors.
Reviews in Computational Chemistry.
VCH Publishers, New York, 1990 
[Nice series of book, with volumes appearing annually
with comprehensive reviews and tutorials
on many aspects of computational chemistry]
 J.A. McCammon and S.C. Harvey.
Dynamics of Proteins and Nucleic
Acids.
Cambridge University Press, Cambridge, 1987.
[First book on biomolecular dynamics simulations]
 D.A. McQuarrie.
Statistical Mechanics.
Harper Collins
Publishers, New York, 1976.
[Good reference text]
 National Research Council report.
Mathematical Challenges from Theoretical / Computational Chemistry,
National Academy Press, Washington D.C., 1995.
[Panel report on the opportunities for collaboration,
past achievments, and future possibilities between mathematical
and chemical scientists]
URL: http://www.nap.edu/readingroom/books/mctcc/.
 D.C. Rapaport.
The Art of Molecular Dynamics Simulation.
Cambridge University Press, Cambridge, England., 1995.
[Elementary ext on molecular dynamics focusing on software details]
 W. Saenger.
Principles of Nucleic Acid Structure.
Springer Advanced Texts in Chemistry, SpringerVerlag, New York, 1984.
[Wonderful guide to the richness of DNA structure, with
an amazing breadth of topics]
 R.R. Sinden.
DNA Structure and Function.
cademic Press, San Diego, California, 1994.
[Nice uptodate textbook on DNA structure]
 G.E. Schulz and R.H. Schirmer.
Principles of Protein Structure.
Springer Advanced Texts in Chemistry, SpringerVerlag, New York, 1990.
[Nice advanced text on the rapidlychanging field of protein
folding]
 L. Stryer.
Biochemistry.
W.H. Freeman, New York, latest edition (fourth in 1995).
[Wonderful biochemistry textbook, up to date]
 W. Van Gunsteren and P. Weiner, Editors (1989)
and
W. Van Gunsteren, P. Weiner, and A.T. Wilkinson, Editors (1993, 1996):
Computer Simulation of
Biomolecular Systems: Theoretical and Experimentational Applications.
Vol. 1,2,3. ESCOM, Leiden, The Netherlands, 1989, 1993, 1996.
[Good series on biomolecular simulations, covering
both algorithms and applications]
