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Comparing trunk/tengDissertation/dissertation.bib (file contents):
Revision 2837 by tim, Wed Jun 7 01:49:15 2006 UTC vs.
Revision 2838 by tim, Fri Jun 9 02:29:06 2006 UTC

+  uri = {<Go to ISI>://000225042700059},
-+
+@ARTICLE{Humphrey1996,
-+
+  author = {W. Humphrey and A. Dalke and K. Schulten},
-+
+  title = {VMD: Visual molecular dynamics},
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+  journal = {Journal of Molecular Graphics},
-+
+  year = {1996},
-+
+  volume = {14},
-+
+  pages = {33-\&},
-+
+  number = {1},
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+  month = {Feb},
-+
+  abstract = {VMD is a molecular graphics program designed for the display and analysis
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+        of molecular assemblies, in particular biopolymers such as proteins
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+        and nucleic acids. VMD can simultaneously display any number of
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+        structures using a wide variety of rendering styles and coloring
-+
+        methods. Molecules are displayed as one or more ''representations,''
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+        in which each representation embodies a particular rendering method
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+        and coloring scheme for a selected subset of atoms. The atoms displayed
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+        in each representation are chosen using an extensive atom selection
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+        syntax, which includes Boolean operators and regular expressions.
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+        VMD provides a complete graphical user interface for program control,
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+        as well as a text interface using the Tcl embeddable parser to allow
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+        for complex scripts with variable substitution, control loops, and
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+        function calls. Full session logging is supported, which produces
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+        a VMD command script for later playback. High-resolution raster
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+        images of displayed molecules may be produced by generating input
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+        scripts for use by a number of photorealistic image-rendering applications.
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+        VMD has also been expressly designed with the ability to animate
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+        molecular dynamics (MD) simulation trajectories, imported either
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+        from files or from a direct connection to a running MD simulation.
-+
+        VMD is the visualization component of MDScope, a set of tools for
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+        interactive problem solving in structural biology, which also includes
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+        the parallel MD program NAMD, and the MDCOMM software used to connect
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+        the visualization and simulation programs. VMD is written in C++,
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+        using an object-oriented design; the program, including source code
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+        and extensive documentation, is freely available via anonymous ftp
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+        and through the World Wide Web.},
-+
+  annote = {Uh515 Times Cited:1418 Cited References Count:19},
-+
+  issn = {0263-7855},
-+
+  uri = {<Go to ISI>://A1996UH51500005},
-+
+}
-+
+@ARTICLE{Izaguirre2001,
+  author = {J. A. Izaguirre and D. P. Catarello and J. M. Wozniak and R. D. Skeel},
+  title = {Langevin stabilization of molecular dynamics},
+  annote = {154RH Times Cited:88 Cited References Count:36},
+  issn = {0010-3616},
+  uri = {<Go to ISI>://000077902200006},
-+
+}
-+
-+
+@ARTICLE{Matthey2004,
-+
+  author = {T. Matthey and T. Cickovski and S. Hampton and A. Ko and Q. Ma and
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+        M. Nyerges and T. Raeder and T. Slabach and J. A. Izaguirre},
-+
+  title = {ProtoMol, an object-oriented framework for prototyping novel algorithms
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+        for molecular dynamics},
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+  journal = {Acm Transactions on Mathematical Software},
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+  year = {2004},
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+  volume = {30},
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+  pages = {237-265},
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+  number = {3},
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+  month = {Sep},
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+  abstract = {PROTOMOL is a high-performance framework in C++ for rapid prototyping
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+        of novel algorithms for molecular dynamics and related applications.
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+        Its flexibility is achieved primarily through the use of inheritance
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+        and design patterns (object-oriented programming): Performance is
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+        obtained by using templates that enable generation of efficient
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+        code for sections critical to performance (generic programming).
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+        The framework encapsulates important optimizations that can be used
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+        by developers, such as parallelism in the force computation. Its
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+        design is based on domain analysis of numerical integrators for
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+        molecular dynamics (MD) and of fast solvers for the force computation,
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+        particularly due to electrostatic interactions. Several new and
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+        efficient algorithms are implemented in PROTOMOL. Finally, it is
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+        shown that PROTOMOL'S sequential performance is excellent when compared
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+        to a leading MD program, and that it scales well for moderate number
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+        of processors. Binaries and source codes for Windows, Linux, Solaris,
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+        IRIX, HP-UX, and AIX platforms are available under open source license
-+
+        at http://protomol.sourceforge.net.},
-+
+  annote = {860EP Times Cited:2 Cited References Count:52},
-+
+  issn = {0098-3500},
-+
+  uri = {<Go to ISI>://000224325600001},
+@ARTICLE{McLachlan1993,
+  annote = {911NS Times Cited:0 Cited References Count:14},
+  issn = {1615-3375},
+  uri = {<Go to ISI>://000228011900003},
-+
+}
-+
-+
+@ARTICLE{Meineke2005,
-+
+  author = {M. A. Meineke and C. F. Vardeman and T. Lin and C. J. Fennell and
-+
+        J. D. Gezelter},
-+
+  title = {OOPSE: An object-oriented parallel simulation engine for molecular
-+
+        dynamics},
-+
+  journal = {Journal of Computational Chemistry},
-+
+  year = {2005},
-+
+  volume = {26},
-+
+  pages = {252-271},
-+
+  number = {3},
-+
+  month = {Feb},
-+
+  abstract = {OOPSE is a new molecular dynamics simulation program that is capable
-+
+        of efficiently integrating equations of motion for atom types with
-+
+        orientational degrees of freedom (e.g. #sticky# atoms and point
-+
+        dipoles). Transition metals can also be simulated using the embedded
-+
+        atom method (EAM) potential included in the code. Parallel simulations
-+
+        are carried out using the force-based decomposition method. Simulations
-+
+        are specified using a very simple C-based meta-data language. A
-+
+        number of advanced integrators are included, and the basic integrator
-+
+        for orientational dynamics provides substantial improvements over
-+
+        older quaternion-based schemes. (C) 2004 Wiley Periodicals, Inc.},
-+
+  annote = {891CF Times Cited:1 Cited References Count:56},
-+
+  issn = {0192-8651},
-+
+  uri = {<Go to ISI>://000226558200006},
+@ARTICLE{Melchionna1993,
+  uri = {<Go to ISI>://000077460000052},
-+
+@ARTICLE{Parr1995,
-+
+  author = {T. J. Parr and R. W. Quong},
-+
+  title = {Antlr - a Predicated-Ll(K) Parser Generator},
-+
+  journal = {Software-Practice \& Experience},
-+
+  year = {1995},
-+
+  volume = {25},
-+
+  pages = {789-810},
-+
+  number = {7},
-+
+  month = {Jul},
-+
+  abstract = {Despite the parsing power of LR/LALR algorithms, e.g. YACC, programmers
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+        often choose to write recursive-descent parsers by hand to obtain
-+
+        increased flexibility, better error handling, and ease of debugging.
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+        We introduce ANTLR, a public-domain parser generator that combines
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+        the flexibility of hand-coded parsing with the convenience of a
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+        parser generator, which is a component of PCCTS. ANTLR has many
-+
+        features that make it easier to use than other language tools. Most
-+
+        important, ANTLR provides predicates which let the programmer systematically
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+        direct the parse via arbitrary expressions using semantic and syntactic
-+
+        context; in practice, the use of predicates eliminates the need
-+
+        to hand-tweak the ANTLR output, even for difficult parsing problems.
-+
+        ANTLR also integrates the description of lexical and syntactic analysis,
-+
+        accepts LL(k) grammars for k > 1 with extended BNF notation, and
-+
+        can automatically generate abstract syntax trees. ANTLR is widely
-+
+        used, with over 1000 registered industrial and academic users in
-+
+countries. It has been ported to many popular systems such as
-+
+        the PC, Macintosh, and a variety of UNIX platforms; a commercial
-+
+        C++ front-end has been developed as a result of one of our industrial
-+
+        collaborations.},
-+
+  annote = {Rk104 Times Cited:19 Cited References Count:10},
-+
+  issn = {0038-0644},
-+
+  uri = {<Go to ISI>://A1995RK10400004},
-+
+}
-+
+@ARTICLE{Pastor1988,
+  author = {R. W. Pastor and B. R. Brooks and A. Szabo},
+  title = {An Analysis of the Accuracy of Langevin and Molecular-Dynamics Algorithms},
+  uri = {<Go to ISI>://A1996UQ97500017},
-+
+@ARTICLE{Schaps1999,
-+
+  author = {G. L. Schaps},
-+
+  title = {Compiler construction with ANTLR and Java - Tools for building tools},
-+
+  journal = {Dr Dobbs Journal},
-+
+  year = {1999},
-+
+  volume = {24},
-+
+  pages = {84-+},
-+
+  number = {3},
-+
+  month = {Mar},
-+
+  annote = {163EC Times Cited:0 Cited References Count:0},
-+
+  issn = {1044-789X},
-+
+  uri = {<Go to ISI>://000078389200023},
-+
+}
-+
+@ARTICLE{Shen2002,
+  author = {M. Y. Shen and K. F. Freed},
+  title = {Long time dynamics of met-enkephalin: Comparison of explicit and

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Comparing trunk/tengDissertation/dissertation.bib (file contents): Revision 2837 by tim, Wed Jun 7 01:49:15 2006 UTC vs. Revision 2838 by tim, Fri Jun 9 02:29:06 2006 UTC

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Comparing trunk/tengDissertation/dissertation.bib (file contents):
Revision 2837 by tim, Wed Jun 7 01:49:15 2006 UTC vs.
Revision 2838 by tim, Fri Jun 9 02:29:06 2006 UTC