[ViewVC] Diff of: group/trunk/tengDissertation/dissertation.bib

Comparing trunk/tengDissertation/dissertation.bib (file contents):
Revision 2807 by tim, Wed Jun 7 01:49:15 2006 UTC vs.
Revision 2841 by tim, Fri Jun 9 03:19:29 2006 UTC

+  pages = {751-766},
-+
+@ARTICLE{Brenner1967,
-+
+  author = {H. Brenner },
-+
+  title = {Coupling between the Translational and Rotational Brownian Motions
-+
+        of Rigid Particles of Arbitrary shape},
-+
+  journal = {J. Collid. Int. Sci.},
-+
+  year = {1967},
-+
+  volume = {23},
-+
+  pages = {407-436},
-+
+}
-+
-+
+@ARTICLE{Brooks1983,
-+
+  author = {B. R. Brooks and R. E. Bruccoleri and B. D. Olafson and D. J. States
-+
+        and S. Swaminathan and M. Karplus},
-+
+  title = {Charmm - a Program for Macromolecular Energy, Minimization, and Dynamics
-+
+        Calculations},
-+
+  journal = {Journal of Computational Chemistry},
-+
+  year = {1983},
-+
+  volume = {4},
-+
+  pages = {187-217},
-+
+  number = {2},
-+
+  annote = {Qp423 Times Cited:6414 Cited References Count:96},
-+
+  issn = {0192-8651},
-+
+  uri = {<Go to ISI>://A1983QP42300010},
-+
+}
-+
+@ARTICLE{Brunger1984,
+  author = {A. Brunger and C. L. Brooks and M. Karplus},
+  title = {Stochastic Boundary-Conditions for Molecular-Dynamics Simulations
+  annote = {870FJ Times Cited:0 Cited References Count:63},
+  issn = {0021-9606},
+  uri = {<Go to ISI>://000225042700059},
-+
+}
-+
-+
+@ARTICLE{Humphrey1996,
-+
+  author = {W. Humphrey and A. Dalke and K. Schulten},
-+
+  title = {VMD: Visual molecular dynamics},
-+
+  journal = {Journal of Molecular Graphics},
-+
+  year = {1996},
-+
+  volume = {14},
-+
+  pages = {33-\&},
-+
+  number = {1},
-+
+  month = {Feb},
-+
+  abstract = {VMD is a molecular graphics program designed for the display and analysis
-+
+        of molecular assemblies, in particular biopolymers such as proteins
-+
+        and nucleic acids. VMD can simultaneously display any number of
-+
+        structures using a wide variety of rendering styles and coloring
-+
+        methods. Molecules are displayed as one or more ''representations,''
-+
+        in which each representation embodies a particular rendering method
-+
+        and coloring scheme for a selected subset of atoms. The atoms displayed
-+
+        in each representation are chosen using an extensive atom selection
-+
+        syntax, which includes Boolean operators and regular expressions.
-+
+        VMD provides a complete graphical user interface for program control,
-+
+        as well as a text interface using the Tcl embeddable parser to allow
-+
+        for complex scripts with variable substitution, control loops, and
-+
+        function calls. Full session logging is supported, which produces
-+
+        a VMD command script for later playback. High-resolution raster
-+
+        images of displayed molecules may be produced by generating input
-+
+        scripts for use by a number of photorealistic image-rendering applications.
-+
+        VMD has also been expressly designed with the ability to animate
-+
+        molecular dynamics (MD) simulation trajectories, imported either
-+
+        from files or from a direct connection to a running MD simulation.
-+
+        VMD is the visualization component of MDScope, a set of tools for
-+
+        interactive problem solving in structural biology, which also includes
-+
+        the parallel MD program NAMD, and the MDCOMM software used to connect
-+
+        the visualization and simulation programs. VMD is written in C++,
-+
+        using an object-oriented design; the program, including source code
-+
+        and extensive documentation, is freely available via anonymous ftp
-+
+        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,
+  pages = {1747-1763},
-+
+@ARTICLE{Kale1999,
-+
+  author = {L. Kale and R. Skeel and M. Bhandarkar and R. Brunner and A. Gursoy
-+
+        and N. Krawetz and J. Phillips and A. Shinozaki and K. Varadarajan
-+
+        and K. Schulten},
-+
+  title = {NAMD2: Greater scalability for parallel molecular dynamics},
-+
+  journal = {Journal of Computational Physics},
-+
+  year = {1999},
-+
+  volume = {151},
-+
+  pages = {283-312},
-+
+  number = {1},
-+
+  month = {May 1},
-+
+  abstract = {Molecular dynamics programs simulate the behavior of biomolecular
-+
+        systems, leading to understanding of their functions. However, the
-+
+        computational complexity of such simulations is enormous. Parallel
-+
+        machines provide the potential to meet this computational challenge.
-+
+        To harness this potential, it is necessary to develop a scalable
-+
+        program. It is also necessary that the program be easily modified
-+
+        by application-domain programmers. The NAMD2 program presented in
-+
+        this paper seeks to provide these desirable features. It uses spatial
-+
+        decomposition combined with force decomposition to enhance scalability.
-+
+        It uses intelligent periodic load balancing, so as to maximally
-+
+        utilize the available compute power. It is modularly organized,
-+
+        and implemented using Charm++, a parallel C++ dialect, so as to
-+
+        enhance its modifiability. It uses a combination of numerical techniques
-+
+        and algorithms to ensure that energy drifts are minimized, ensuring
-+
+        accuracy in long running calculations. NAMD2 uses a portable run-time
-+
+        framework called Converse that also supports interoperability among
-+
+        multiple parallel paradigms. As a result, different components of
-+
+        applications can be written in the most appropriate parallel paradigms.
-+
+        NAMD2 runs on most parallel machines including workstation clusters
-+
+        and has yielded speedups in excess of 180 on 220 processors. This
-+
+        paper also describes the performance obtained on some benchmark
-+
+        applications. (C) 1999 Academic Press.},
-+
+  annote = {194FM Times Cited:373 Cited References Count:51},
-+
+  issn = {0021-9991},
-+
+  uri = {<Go to ISI>://000080181500013},
-+
+}
-+
+@ARTICLE{Kane2000,
+  author = {C. Kane and J. E. Marsden and M. Ortiz and M. West},
+  title = {Variational integrators and the Newmark algorithm for conservative
+  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
-+
+        M. Nyerges and T. Raeder and T. Slabach and J. A. Izaguirre},
-+
+  title = {ProtoMol, an object-oriented framework for prototyping novel algorithms
-+
+        for molecular dynamics},
-+
+  journal = {Acm Transactions on Mathematical Software},
-+
+  year = {2004},
-+
+  volume = {30},
-+
+  pages = {237-265},
-+
+  number = {3},
-+
+  month = {Sep},
-+
+  abstract = {PROTOMOL is a high-performance framework in C++ for rapid prototyping
-+
+        of novel algorithms for molecular dynamics and related applications.
-+
+        Its flexibility is achieved primarily through the use of inheritance
-+
+        and design patterns (object-oriented programming): Performance is
-+
+        obtained by using templates that enable generation of efficient
-+
+        code for sections critical to performance (generic programming).
-+
+        The framework encapsulates important optimizations that can be used
-+
+        by developers, such as parallelism in the force computation. Its
-+
+        design is based on domain analysis of numerical integrators for
-+
+        molecular dynamics (MD) and of fast solvers for the force computation,
-+
+        particularly due to electrostatic interactions. Several new and
-+
+        efficient algorithms are implemented in PROTOMOL. Finally, it is
-+
+        shown that PROTOMOL'S sequential performance is excellent when compared
-+
+        to a leading MD program, and that it scales well for moderate number
-+
+        of processors. Binaries and source codes for Windows, Linux, Solaris,
-+
+        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,
+  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,
+  author = {S. Melchionna and G. Ciccotti and B. L. Holian},
+  title = {Hoover Npt Dynamics for Systems Varying in Shape and Size},
+  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
-+
+        often choose to write recursive-descent parsers by hand to obtain
-+
+        increased flexibility, better error handling, and ease of debugging.
-+
+        We introduce ANTLR, a public-domain parser generator that combines
-+
+        the flexibility of hand-coded parsing with the convenience of a
-+
+        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
-+
+        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},
+  year = {1934},
+  volume = {5},
+  pages = {497-511},
-+
+}
-+
-+
+@ARTICLE{Petrache2000,
-+
+  author = {H.~I. Petrache and S.~W. Dodd and M.~F. Brown},
-+
+  title = {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines
-+
+        Determined by $^2\text{H}$ {\sc nmr} Spectroscopy},
-+
+  journal = {Biophysical Journal},
-+
+  year = {2000},
-+
+  volume = {79},
-+
+  pages = {3172-3192},
+@ARTICLE{Petrache1998,
+  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
+  year = {1974},
+  author = {V.S. Varadarajan},
+  address = {New York},
-+
+}
-+
-+
+@ARTICLE{Vincent1995,
-+
+  author = {J. J. Vincent and K. M. Merz},
-+
+  title = {A Highly Portable Parallel Implementation of Amber4 Using the Message-Passing
-+
+        Interface Standard},
-+
+  journal = {Journal of Computational Chemistry},
-+
+  year = {1995},
-+
+  volume = {16},
-+
+  pages = {1420-1427},
-+
+  number = {11},
-+
+  month = {Nov},
-+
+  abstract = {We have implemented a portable parallel version of the macromolecular
-+
+        modeling package AMBER4. The message passing paradigm was used.
-+
+        All message passing constructs are compliant with the Message Passing
-+
+        Interface (MPI) standard. The molecular dynamics/minimization module
-+
+        MINMD and the free-energy perturbation module Gibbs have been implemented
-+
+        in parallel on a number of machines, including a Gray T3D, an IBM
-+
+        SP1/SP2, and a collection of networked workstations. In addition,
-+
+        the code has been tested with an MPI implementation from Argonne
-+
+        National Laboratories/Mississippi State University which runs on
-+
+        many parallel machines. The goal of this work is to decrease the
-+
+        amount of time required to perform molecular dynamics simulations.
-+
+        Performance results for a Lipid bilayer molecular dynamics simulation
-+
+        on a Gray T3D, an IBM SP1/SPZ and a Gray C90 are compared. (C) 1995
-+
+        by John Wiley & Sons, Inc.},
-+
+  annote = {Ta403 Times Cited:16 Cited References Count:23},
-+
+  issn = {0192-8651},
-+
+  uri = {<Go to ISI>://A1995TA40300009},
+@ARTICLE{Wegener1979,

Diff Legend

-–
+Removed lines
-+
+Added lines
-<
+Changed lines
->
+Changed lines

Comparing trunk/tengDissertation/dissertation.bib (file contents): Revision 2807 by tim, Wed Jun 7 01:49:15 2006 UTC vs. Revision 2841 by tim, Fri Jun 9 03:19:29 2006 UTC

Diff Legend

Comparing trunk/tengDissertation/dissertation.bib (file contents):
Revision 2807 by tim, Wed Jun 7 01:49:15 2006 UTC vs.
Revision 2841 by tim, Fri Jun 9 03:19:29 2006 UTC