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+  annote = {973OH Times Cited:1 Cited References Count:33},
+  issn = {0021-9606},
+  uri = {<Go to ISI>://000232532000064},
-+
+}
-+
-+
+@BOOK{Alexander1987,
-+
+  title = {A Pattern Language: Towns, Buildings, Construction},
-+
+  publisher = {Oxford University Press},
-+
+  year = {1987},
-+
+  author = {C. Alexander},
-+
+  address = {New York},
+@BOOK{Allen1987,
+  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 = {Ya587 Times Cited:35 Cited References Count:32},
+  issn = {0021-9606},
+  uri = {<Go to ISI>://A1997YA58700024},
-+
+}
-+
-+
+@BOOK{Gamma1994,
-+
+  title = {Design Patterns: Elements of Reusable Object-Oriented Software},
-+
+  publisher = {Perason Education},
-+
+  year = {1994},
-+
+  author = {E. Gamma, R. Helm, R. Johnson and J. Vlissides},
-+
+  address = {London},
-+
+  chapter = {7},
+@ARTICLE{Edwards2005,
+  uri = {<Go to ISI>://A1978FP21600004},
-+
+@ARTICLE{Evans1977,
-+
+  author = {D. J. Evans},
-+
+  title = {Representation of Orientation Space},
-+
+  journal = {Molecular Physics},
-+
+  year = {1977},
-+
+  volume = {34},
-+
+  pages = {317-325},
-+
+  number = {2},
-+
+  annote = {Ds757 Times Cited:271 Cited References Count:18},
-+
+  issn = {0026-8976},
-+
+  uri = {<Go to ISI>://A1977DS75700002},
-+
+}
-+
+@ARTICLE{Fennell2004,
+  author = {C. J. Fennell and J. D. Gezelter},
+  title = {On the structural and transport properties of the soft sticky dipole
+  uri = {<Go to ISI>://000180256300012},
-+
+@BOOK{Frenkel1996,
-+
+  title = {Understanding Molecular Simulation : From Algorithms to Applications},
-+
+  publisher = {Academic Press},
-+
+  year = {1996},
-+
+  author = {D. Frenkel and B. Smit},
-+
+  address = {New York},
-+
+}
-+
+@ARTICLE{Gay1981,
+  author = {J. G. Gay and B. J. Berne},
+  title = {Modification of the Overlap Potential to Mimic a Linear Site-Site
+  annote = {257MM Times Cited:2 Cited References Count:82},
+  issn = {1022-1344},
+  uri = {<Go to ISI>://000083785700002},
-+
+}
-+
-+
+@ARTICLE{Goetz1998,
-+
+  author = {R. Goetz and R. Lipowsky},
-+
+  title = {Computer simulations of bilayer membranes: Self-assembly and interfacial
-+
+    tension},
-+
+  journal = {Journal of Chemical Physics},
-+
+  year = {1998},
-+
+  volume = {108},
-+
+  pages = {7397},
-+
+  number = {17},
+@BOOK{Goldstein2001,
+  address = {New York},
-+
+@ARTICLE{Hoover1985,
-+
+  author = {W. G. Hoover},
-+
+  title = {Canonical Dynamics - Equilibrium Phase-Space Distributions},
-+
+  journal = {Physical Review A},
-+
+  year = {1985},
-+
+  volume = {31},
-+
+  pages = {1695-1697},
-+
+  number = {3},
-+
+  annote = {Acr30 Times Cited:1809 Cited References Count:11},
-+
+  issn = {1050-2947},
-+
+  uri = {<Go to ISI>://A1985ACR3000056},
-+
+}
-+
+@ARTICLE{Huh2004,
+  author = {Y. Huh and N. M. Cann},
+  title = {Discrimination in isotropic, nematic, and smectic phases of chiral
+  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,
+  author = {J. A. Izaguirre and D. P. Catarello and J. M. Wozniak and R. D. Skeel},
+  title = {Langevin stabilization of molecular dynamics},
+  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
+  author = {J.~B. Marion},
+  address = {New York},
+  edition = {2rd},
-+
+}
-+
-+
+@ARTICLE{Marrink1994,
-+
+  author = {S. J. Marrink and H. J. C. Berendsen},
-+
+  title = {Simulation of Water Transport through a Lipid-Membrane},
-+
+  journal = {Journal of Physical Chemistry},
-+
+  year = {1994},
-+
+  volume = {98},
-+
+  pages = {4155-4168},
-+
+  number = {15},
-+
+  month = {Apr 14},
-+
+  abstract = {To obtain insight in the process of water permeation through a lipid
-+
+    membrane, we performed molecular dynamics simulations on a phospholipid
-+
+    (DPPC)/water system with atomic detail. Since the actual process
-+
+    of permeation is too slow to be studied directly, we deduced the
-+
+    permeation rate indirectly via computation of the free energy and
-+
+    diffusion rate profiles of a water molecule across the bilayer.
-+
+    We conclude that the permeation of water through a lipid membrane
-+
+    cannot be described adequately by a simple homogeneous solubility-diffusion
-+
+    model. Both the excess free energy and the diffusion rate strongly
-+
+    depend on the position in the membrane, as a result from the inhomogeneous
-+
+    nature of the membrane. The calculated excess free energy profile
-+
+    has a shallow slope and a maximum height of 26 kJ/mol. The diffusion
-+
+    rate is highest in the middle of the membrane where the lipid density
-+
+    is low. In the interfacial region almost all water molecules are
-+
+    bound by the lipid headgroups, and the diffusion turns out to be
-+
+order of magnitude smaller. The total transport process is essentially
-+
+    determined by the free energy barrier. The rate-limiting step is
-+
+    the permeation through the dense part of the lipid tails, where
-+
+    the resistance is highest. We found a permeation rate of 7(+/-3)
-+
+    x 10(-2) cm/s at 350 K, comparable to experimental values for DPPC
-+
+    membranes, if corrected for the temperature of the simulation. Taking
-+
+    the inhomogeneity of the membrane into account, we define a new
-+
+    ''four-region'' model which seems to be more realistic than the
-+
+    ''two-phase'' solubility-diffusion model.},
-+
+  annote = {Ng219 Times Cited:187 Cited References Count:25},
-+
+  issn = {0022-3654},
-+
+  uri = {<Go to ISI>://A1994NG21900040},
-+
+}
-+
-+
+@ARTICLE{Marrink2004,
-+
+  author = {S.~J. Marrink and A.~H. de~Vries and A.~E. Mark},
-+
+  title = {Coarse Grained Model for Semiquantitative Lipid Simulations},
-+
+  journal = {J. Phys. Chem. B},
-+
+  year = {2004},
-+
+  volume = {108},
-+
+  pages = {750-760},
+@ARTICLE{Marsden1998,
+  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,
+  author = {R.~I McLachlan},
+  title = {Explicit Lie-Poisson integration and the Euler equations},
+  pages = {3043-3046},
-<
+@ARTICLE{McLachlan1998a,
->
+@ARTICLE{McLachlan1998,
+  author = {R. I. McLachlan and G. R. W. Quispel},
+  title = {Generating functions for dynamical systems with symmetries, integrals,
+    and differential invariants},
+  uri = {<Go to ISI>://000071558900021},
-<
+@ARTICLE{McLachlan1998,
->
+@ARTICLE{McLachlan1998a,
+  author = {R. I. McLachlan and G. R. W. Quispel and G. S. Turner},
+  title = {Numerical integrators that preserve symmetries and reversing symmetries},
+  journal = {Siam Journal on Numerical Analysis},
+  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},
-+
+  journal = {Molecular Physics},
-+
+  year = {1993},
-+
+  volume = {78},
-+
+  pages = {533-544},
-+
+  number = {3},
-+
+  month = {Feb 20},
-+
+  abstract = {In this paper we write down equations of motion (following the approach
-+
+    pioneered by Hoover) for an exact isothermal-isobaric molecular
-+
+    dynamics simulation, and we extend them to multiple thermostating
-+
+    rates, to a shape-varying cell and to molecular systems, coherently
-+
+    with the previous 'extended system method'. An integration scheme
-+
+    is proposed together with a numerical illustration of the method.},
-+
+  annote = {Kq355 Times Cited:172 Cited References Count:17},
-+
+  issn = {0026-8976},
-+
+  uri = {<Go to ISI>://A1993KQ35500002},
-+
+}
-+
+@ARTICLE{Memmer2002,
+  author = {R. Memmer},
+  title = {Liquid crystal phases of achiral banana-shaped molecules: a computer
+  annote = {146XW Times Cited:66 Cited References Count:45},
+  issn = {0163-1829},
+  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,
+  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,
+  author = {H. I. Petrache and S. Tristram-Nagle and J. F. Nagle},
+  title = {Fluid phase structure of EPC and DMPC bilayers},
+  annote = {990XA Times Cited:3 Cited References Count:72},
+  issn = {0959-9428},
+  uri = {<Go to ISI>://000233775500001},
-+
+}
-+
-+
+@ARTICLE{Roux1991,
-+
+  author = {B. Roux and M. Karplus},
-+
+  title = {Ion-Transport in a Gramicidin-Like Channel - Dynamics and Mobility},
-+
+  journal = {Journal of Physical Chemistry},
-+
+  year = {1991},
-+
+  volume = {95},
-+
+  pages = {4856-4868},
-+
+  number = {12},
-+
+  month = {Jun 13},
-+
+  abstract = {The mobility of water, Na+. and K+ has been calculated inside a periodic
-+
+    poly-(L,D)-alanine beta-helix, a model for the interior of the gramicidin
-+
+    channel. Because of the different dynamical regimes for the three
-+
+    species (high barrier for Na+, low barrier for K+, almost free diffusion
-+
+    for water), different methods are used to calculate the mobilities.
-+
+    By use of activated dynamics and a potential of mean force determined
-+
+    previously (Roux, B.; Karplus, M. Biophys. J. 1991, 59, 961), the
-+
+    barrier crossing rate of Na+ ion is determined. The motion of Na+
-+
+    at the transition state is controlled by local interactions and
-+
+    collisions with the neighboring carbonyls and the two nearest water
-+
+    molecules. There are significant deviations from transition-state
-+
+    theory; the transmission coefficient is equal to 0.11. The water
-+
+    and K+ motions are found to be well described by a diffusive model;
-+
+    the motion of K+ appears to be controlled by the diffusion of water.
-+
+    The time-dependent friction functions of Na+ and K+ ions in the
-+
+    periodic beta-helix are calculated and analyzed by using a generalized
-+
+    Langevin equation approach. Both Na+ and K+ suffer many rapid collisions,
-+
+    and their dynamics is overdamped and noninertial. Thus, the selectivity
-+
+    sequence of ions in the beta-helix is not influenced strongly by
-+
+    their masses.},
-+
+  annote = {Fr756 Times Cited:97 Cited References Count:65},
-+
+  issn = {0022-3654},
-+
+  uri = {<Go to ISI>://A1991FR75600049},
+@ARTICLE{Roy2005,
+  uri = {<Go to ISI>://000080181500004},
-+
+@ARTICLE{Sasaki2004,
-+
+  author = {Y. Sasaki and R. Shukla and B. D. Smith},
-+
+  title = {Facilitated phosphatidylserine flip-flop across vesicle and cell
-+
+    membranes using urea-derived synthetic translocases},
-+
+  journal = {Organic \& Biomolecular Chemistry},
-+
+  year = {2004},
-+
+  volume = {2},
-+
+  pages = {214-219},
-+
+  number = {2},
-+
+  abstract = {Tris(2-aminoethyl) amine derivatives with appended urea and sulfonamide
-+
+    groups are shown to facilitate the translocation of fluorescent
-+
+    phospholipid probes and endogenous phosphatidylserine across vesicle
-+
+    and erythrocyte cell membranes. The synthetic translocases appear
-+
+    to operate by binding to the phospholipid head groups and forming
-+
+    lipophilic supramolecular complexes which diffuse through the non-polar
-+
+    interior of the bilayer membrane.},
-+
+  annote = {760PX Times Cited:8 Cited References Count:25},
-+
+  issn = {1477-0520},
-+
+  uri = {<Go to ISI>://000187843800012},
-+
+}
-+
+@ARTICLE{Satoh1996,
+  author = {K. Satoh and S. Mita and S. Kondo},
+  title = {Monte Carlo simulations using the dipolar Gay-Berne model: Effect
+  annote = {Uq975 Times Cited:32 Cited References Count:33},
+  issn = {0009-2614},
+  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},
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+  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,
+  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
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+    Interface Standard},
-+
+  journal = {Journal of Computational Chemistry},
-+
+  year = {1995},
-+
+  volume = {16},
-+
+  pages = {1420-1427},
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+  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,
+  author = {W.~A. Wegener, V.~J. Koester and R.~M. Dowben},
+  title = {A general ellipsoid can not always serve as a modle for the rotational
+  number = {12},
-+
+@ARTICLE{Wilson2006,
-+
+  author = {G.~V. Wilson },
-+
+  title = {Where's the Real Bottleneck in Scientific Computing?},
-+
+  journal = {American Scientist},
-+
+  year = {2006},
-+
+  volume = {94},
-+
+}
-+
+@ARTICLE{Withers2003,
+  author = {I. M. Withers},
+  title = {Effects of longitudinal quadrupoles on the phase behavior of a Gay-Berne
+  uri = {<Go to ISI>://A1990EJ79800009},
-<
+@Book{Frenkel1996,
-<
+  author =   {D. Frenkel and B. Smit},
-<
+  title =    {Understanding Molecular Simulation : From Algorithms
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+                  to Applications},
-<
+  publisher =    {Academic Press},
-<
+  year =     1996,
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+  address =  {New York}
->
+@Article{Blum1972,
->
+  author =   {L. Blum and A.~J. Torruella},
->
+  title =    {Computer simulations of bilayer membranes: Self-assembly and interfacial tension},
->
+  journal =  {Journal of Chemical Physics},
->
+  year =     1972,
->
+  volume =   56,
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+  number =   1,
->
+  pages =    {303-309}
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-+
+@Article{Stone1978,
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+  author =   {A.~J. Stone},
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+  title =    {The description of bimolecular potentials, forces and torques: the S and V function expansions},
-+
+  journal =  {Molecular Physics},
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+  year =     1978,
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+  volume =   36,
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+  number =   1,
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+  pages =    {241-256}
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+}
-+
-+
+@Article{Berardi2003,
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+  author =   {R. Berardi, M. Cecchini and C. Zannoni},
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+  title =    {A Monte Carlo study of the chiral columnar organizations of dissymmetric discotic mesogens},
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+  journal =  {Journal of Chemical Physics},
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+  year =     2003,
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+  volume =   119,
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+  number =   18,
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+  pages =    {9933-9946}
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+}
-+
-+
+@Article{Beard2000,
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+  author =   {D. A. Beard and T. Schlick},
-+
+  title =    {Inertial Stochastic Dynamics. I. Long-time-step Methods for Langevin Dynamics},
-+
+  journal =  {Journal of Chemical Physics},
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+  year =     2000,
-+
+  volume =   112,
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+  number =   17,
-+
+  pages =    {7313-7322}
-+
+}
-+
-+
+@BOOK{Hirsch1997,
-+
+  title = {Differential Topology},
-+
+  publisher = {Springer},
-+
+  year = {1997},
-+
+  author = {M.W. Hirsch},
-+
+  address = {New York}
-+
+}
-+
-+
+@BOOK{Jost2002,
-+
+  title = {Riemannian Geometry and Geometric Analysis},
-+
+  publisher = {Springer-Verlag},
-+
+  year = {2002},
-+
+  author = {J. Jost},
-+
+  address = {Berlin}
-+
+}
-+
-+
+@BOOK{McDuff1998,
-+
+  title = {Introduction to Symplectic Topology },
-+
+  publisher = {Oxford Mathematical Monographs},
-+
+  year = {1998},
-+
+  author = {D. McDuff and D. Salamon},
-+
+  address = {Oxford}
-+
+}
-+
-+
+@Article{Matubayasi1999,
-+
+  author =   {N. Matubayasi and M. Nakahara},
-+
+  title =    {Reversible molecular dynamics for rigid bodies and hybrid Monte Carlo},
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+  journal =  {Journal of Chemical Physics},
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+  year =     1999,
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+  volume =   110,
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+  number =   7,
-+
+  pages =    {3291-3301}
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+}
-+
-+
+@Article{Miller2002,
-+
+  author =   {T.F. Miller III, M. Eleftheriou},
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+  title =    {Symplectic quaternion scheme for biophysical molecular dynamics},
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+  journal =  {Journal of Chemical Physics},
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+  year =     1999,
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+  volume =   116,
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+  number =   20,
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+  pages =    {8649-8659}
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+}
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+@Article{McMillan1971,
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+  author =   {W.L. McMillan},
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+  title =    {Simple Molecular Model for the Smectic A Phase of Liquid Crystals},
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+  journal =  {Journal of Chemical Physics},
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+  year =     1971,
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+  volume =   4,
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+  number =   3,
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+  pages =    {1238�C1246 }
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+}
-+
-+
+@Article{Gilmore1974,
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+  author =   {R. Gilmore},
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+  title =    {Baker-Campbell-Hausdorff Formulas},
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+  journal =  {Journal of Mathematical Physics},
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+  year =     1974,
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+  volume =   15,
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+  number =   12,
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+  pages =    {2090-2092}
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+}
-+
-+
+@Article{Strang1968,
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+  author =   {G. Strang},
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+  title =    {On the construction and comparision of difference schemes},
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+  journal =  {SIAM Journal on Numerical Analysis},
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+  year =     1968,
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+  volume =   5,
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+  number =   3,
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+  pages =    {506-517}
-+
+}

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Comparing trunk/tengDissertation/dissertation.bib (file contents): Revision 2801 by tim, Tue Jun 6 14:56:36 2006 UTC vs. Revision 2941 by tim, Mon Jul 17 20:01:05 2006 UTC

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Comparing trunk/tengDissertation/dissertation.bib (file contents):
Revision 2801 by tim, Tue Jun 6 14:56:36 2006 UTC vs.
Revision 2941 by tim, Mon Jul 17 20:01:05 2006 UTC