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# Line 88 | Line 88 | Encoding: GBK
88    uri = {<Go to ISI>://000232532000064},
89   }
90  
91 + @BOOK{Alexander1987,
92 +  title = {A Pattern Language: Towns, Buildings, Construction},
93 +  publisher = {Oxford University Press},
94 +  year = {1987},
95 +  author = {C. Alexander},
96 +  address = {New York},
97 + }
98 +
99   @BOOK{Allen1987,
100    title = {Computer Simulations of Liquids},
101    publisher = {Oxford University Press},
# Line 518 | Line 526 | Encoding: GBK
526    year = {1980},
527    volume = {19},
528    pages = {751-766},
529 + }
530 +
531 + @ARTICLE{Brenner1967,
532 +  author = {H. Brenner },
533 +  title = {Coupling between the Translational and Rotational Brownian Motions
534 +        of Rigid Particles of Arbitrary shape},
535 +  journal = {J. Collid. Int. Sci.},
536 +  year = {1967},
537 +  volume = {23},
538 +  pages = {407-436},
539 + }
540 +
541 + @ARTICLE{Brooks1983,
542 +  author = {B. R. Brooks and R. E. Bruccoleri and B. D. Olafson and D. J. States
543 +        and S. Swaminathan and M. Karplus},
544 +  title = {Charmm - a Program for Macromolecular Energy, Minimization, and Dynamics
545 +        Calculations},
546 +  journal = {Journal of Computational Chemistry},
547 +  year = {1983},
548 +  volume = {4},
549 +  pages = {187-217},
550 +  number = {2},
551 +  annote = {Qp423 Times Cited:6414 Cited References Count:96},
552 +  issn = {0192-8651},
553 +  uri = {<Go to ISI>://A1983QP42300010},
554   }
555  
556   @ARTICLE{Brunger1984,
# Line 962 | Line 995 | Encoding: GBK
995    annote = {Ya587 Times Cited:35 Cited References Count:32},
996    issn = {0021-9606},
997    uri = {<Go to ISI>://A1997YA58700024},
998 + }
999 +
1000 + @BOOK{Gamma1994,
1001 +  title = {Design Patterns: Elements of Reusable Object-Oriented Software},
1002 +  publisher = {Perason Education},
1003 +  year = {1994},
1004 +  author = {E. Gamma, R. Helm, R. Johnson and J. Vlissides},
1005 +  address = {London},
1006 +  chapter = {7},
1007   }
1008  
1009   @ARTICLE{Edwards2005,
# Line 1015 | Line 1057 | Encoding: GBK
1057    annote = {Fp216 Times Cited:785 Cited References Count:42},
1058    issn = {0021-9606},
1059    uri = {<Go to ISI>://A1978FP21600004},
1060 + }
1061 +
1062 + @ARTICLE{Evans1977,
1063 +  author = {D. J. Evans},
1064 +  title = {Representation of Orientation Space},
1065 +  journal = {Molecular Physics},
1066 +  year = {1977},
1067 +  volume = {34},
1068 +  pages = {317-325},
1069 +  number = {2},
1070 +  annote = {Ds757 Times Cited:271 Cited References Count:18},
1071 +  issn = {0026-8976},
1072 +  uri = {<Go to ISI>://A1977DS75700002},
1073   }
1074  
1075   @ARTICLE{Fennell2004,
# Line 1081 | Line 1136 | Encoding: GBK
1136    uri = {<Go to ISI>://000180256300012},
1137   }
1138  
1139 + @BOOK{Frenkel1996,
1140 +  title = {Understanding Molecular Simulation : From Algorithms to Applications},
1141 +  publisher = {Academic Press},
1142 +  year = {1996},
1143 +  author = {D. Frenkel and B. Smit},
1144 +  address = {New York},
1145 + }
1146 +
1147   @ARTICLE{Gay1981,
1148    author = {J. G. Gay and B. J. Berne},
1149    title = {Modification of the Overlap Potential to Mimic a Linear Site-Site
# Line 1378 | Line 1441 | Encoding: GBK
1441    year = {1981},
1442    author = {R.W. Hockney and J.W. Eastwood},
1443    address = {New York},
1444 + }
1445 +
1446 + @ARTICLE{Hoover1985,
1447 +  author = {W. G. Hoover},
1448 +  title = {Canonical Dynamics - Equilibrium Phase-Space Distributions},
1449 +  journal = {Physical Review A},
1450 +  year = {1985},
1451 +  volume = {31},
1452 +  pages = {1695-1697},
1453 +  number = {3},
1454 +  annote = {Acr30 Times Cited:1809 Cited References Count:11},
1455 +  issn = {1050-2947},
1456 +  uri = {<Go to ISI>://A1985ACR3000056},
1457   }
1458  
1459   @ARTICLE{Huh2004,
# Line 1405 | Line 1481 | Encoding: GBK
1481    uri = {<Go to ISI>://000225042700059},
1482   }
1483  
1484 + @ARTICLE{Humphrey1996,
1485 +  author = {W. Humphrey and A. Dalke and K. Schulten},
1486 +  title = {VMD: Visual molecular dynamics},
1487 +  journal = {Journal of Molecular Graphics},
1488 +  year = {1996},
1489 +  volume = {14},
1490 +  pages = {33-\&},
1491 +  number = {1},
1492 +  month = {Feb},
1493 +  abstract = {VMD is a molecular graphics program designed for the display and analysis
1494 +        of molecular assemblies, in particular biopolymers such as proteins
1495 +        and nucleic acids. VMD can simultaneously display any number of
1496 +        structures using a wide variety of rendering styles and coloring
1497 +        methods. Molecules are displayed as one or more ''representations,''
1498 +        in which each representation embodies a particular rendering method
1499 +        and coloring scheme for a selected subset of atoms. The atoms displayed
1500 +        in each representation are chosen using an extensive atom selection
1501 +        syntax, which includes Boolean operators and regular expressions.
1502 +        VMD provides a complete graphical user interface for program control,
1503 +        as well as a text interface using the Tcl embeddable parser to allow
1504 +        for complex scripts with variable substitution, control loops, and
1505 +        function calls. Full session logging is supported, which produces
1506 +        a VMD command script for later playback. High-resolution raster
1507 +        images of displayed molecules may be produced by generating input
1508 +        scripts for use by a number of photorealistic image-rendering applications.
1509 +        VMD has also been expressly designed with the ability to animate
1510 +        molecular dynamics (MD) simulation trajectories, imported either
1511 +        from files or from a direct connection to a running MD simulation.
1512 +        VMD is the visualization component of MDScope, a set of tools for
1513 +        interactive problem solving in structural biology, which also includes
1514 +        the parallel MD program NAMD, and the MDCOMM software used to connect
1515 +        the visualization and simulation programs. VMD is written in C++,
1516 +        using an object-oriented design; the program, including source code
1517 +        and extensive documentation, is freely available via anonymous ftp
1518 +        and through the World Wide Web.},
1519 +  annote = {Uh515 Times Cited:1418 Cited References Count:19},
1520 +  issn = {0263-7855},
1521 +  uri = {<Go to ISI>://A1996UH51500005},
1522 + }
1523 +
1524   @ARTICLE{Izaguirre2001,
1525    author = {J. A. Izaguirre and D. P. Catarello and J. M. Wozniak and R. D. Skeel},
1526    title = {Langevin stabilization of molecular dynamics},
# Line 1446 | Line 1562 | Encoding: GBK
1562    uri = {<Go to ISI>://000166676100020},
1563   }
1564  
1449 – @ARTICLE{Gray2003,
1450 –  author = {J.~J Gray,S. Moughon, C. Wang },
1451 –  title = {Protein-protein docking with simultaneous optimization of rigid-body
1452 –        displacement and side-chain conformations},
1453 –  journal = {jmb},
1454 –  year = {2003},
1455 –  volume = {331},
1456 –  pages = {281-299},
1457 – }
1458 –
1565   @ARTICLE{Torre1977,
1566    author = {Jose Garcia De La Torre, V.A. Bloomfield},
1567    title = {Hydrodynamic properties of macromolecular complexes. I. Translation},
# Line 1463 | Line 1569 | Encoding: GBK
1569    year = {1977},
1570    volume = {16},
1571    pages = {1747-1763},
1572 + }
1573 +
1574 + @ARTICLE{Kale1999,
1575 +  author = {L. Kale and R. Skeel and M. Bhandarkar and R. Brunner and A. Gursoy
1576 +        and N. Krawetz and J. Phillips and A. Shinozaki and K. Varadarajan
1577 +        and K. Schulten},
1578 +  title = {NAMD2: Greater scalability for parallel molecular dynamics},
1579 +  journal = {Journal of Computational Physics},
1580 +  year = {1999},
1581 +  volume = {151},
1582 +  pages = {283-312},
1583 +  number = {1},
1584 +  month = {May 1},
1585 +  abstract = {Molecular dynamics programs simulate the behavior of biomolecular
1586 +        systems, leading to understanding of their functions. However, the
1587 +        computational complexity of such simulations is enormous. Parallel
1588 +        machines provide the potential to meet this computational challenge.
1589 +        To harness this potential, it is necessary to develop a scalable
1590 +        program. It is also necessary that the program be easily modified
1591 +        by application-domain programmers. The NAMD2 program presented in
1592 +        this paper seeks to provide these desirable features. It uses spatial
1593 +        decomposition combined with force decomposition to enhance scalability.
1594 +        It uses intelligent periodic load balancing, so as to maximally
1595 +        utilize the available compute power. It is modularly organized,
1596 +        and implemented using Charm++, a parallel C++ dialect, so as to
1597 +        enhance its modifiability. It uses a combination of numerical techniques
1598 +        and algorithms to ensure that energy drifts are minimized, ensuring
1599 +        accuracy in long running calculations. NAMD2 uses a portable run-time
1600 +        framework called Converse that also supports interoperability among
1601 +        multiple parallel paradigms. As a result, different components of
1602 +        applications can be written in the most appropriate parallel paradigms.
1603 +        NAMD2 runs on most parallel machines including workstation clusters
1604 +        and has yielded speedups in excess of 180 on 220 processors. This
1605 +        paper also describes the performance obtained on some benchmark
1606 +        applications. (C) 1999 Academic Press.},
1607 +  annote = {194FM Times Cited:373 Cited References Count:51},
1608 +  issn = {0021-9991},
1609 +  uri = {<Go to ISI>://000080181500013},
1610   }
1611  
1612   @ARTICLE{Kane2000,
# Line 1764 | Line 1908 | Encoding: GBK
1908    edition = {2rd},
1909   }
1910  
1911 + @ARTICLE{Marrink1994,
1912 +  author = {S. J. Marrink and H. J. C. Berendsen},
1913 +  title = {Simulation of Water Transport through a Lipid-Membrane},
1914 +  journal = {Journal of Physical Chemistry},
1915 +  year = {1994},
1916 +  volume = {98},
1917 +  pages = {4155-4168},
1918 +  number = {15},
1919 +  month = {Apr 14},
1920 +  abstract = {To obtain insight in the process of water permeation through a lipid
1921 +        membrane, we performed molecular dynamics simulations on a phospholipid
1922 +        (DPPC)/water system with atomic detail. Since the actual process
1923 +        of permeation is too slow to be studied directly, we deduced the
1924 +        permeation rate indirectly via computation of the free energy and
1925 +        diffusion rate profiles of a water molecule across the bilayer.
1926 +        We conclude that the permeation of water through a lipid membrane
1927 +        cannot be described adequately by a simple homogeneous solubility-diffusion
1928 +        model. Both the excess free energy and the diffusion rate strongly
1929 +        depend on the position in the membrane, as a result from the inhomogeneous
1930 +        nature of the membrane. The calculated excess free energy profile
1931 +        has a shallow slope and a maximum height of 26 kJ/mol. The diffusion
1932 +        rate is highest in the middle of the membrane where the lipid density
1933 +        is low. In the interfacial region almost all water molecules are
1934 +        bound by the lipid headgroups, and the diffusion turns out to be
1935 +        1 order of magnitude smaller. The total transport process is essentially
1936 +        determined by the free energy barrier. The rate-limiting step is
1937 +        the permeation through the dense part of the lipid tails, where
1938 +        the resistance is highest. We found a permeation rate of 7(+/-3)
1939 +        x 10(-2) cm/s at 350 K, comparable to experimental values for DPPC
1940 +        membranes, if corrected for the temperature of the simulation. Taking
1941 +        the inhomogeneity of the membrane into account, we define a new
1942 +        ''four-region'' model which seems to be more realistic than the
1943 +        ''two-phase'' solubility-diffusion model.},
1944 +  annote = {Ng219 Times Cited:187 Cited References Count:25},
1945 +  issn = {0022-3654},
1946 +  uri = {<Go to ISI>://A1994NG21900040},
1947 + }
1948 +
1949   @ARTICLE{Marsden1998,
1950    author = {J. E. Marsden and G. W. Patrick and S. Shkoller},
1951    title = {Multisymplectic geometry, variational integrators, and nonlinear
# Line 1797 | Line 1979 | Encoding: GBK
1979    annote = {154RH Times Cited:88 Cited References Count:36},
1980    issn = {0010-3616},
1981    uri = {<Go to ISI>://000077902200006},
1982 + }
1983 +
1984 + @ARTICLE{Matthey2004,
1985 +  author = {T. Matthey and T. Cickovski and S. Hampton and A. Ko and Q. Ma and
1986 +        M. Nyerges and T. Raeder and T. Slabach and J. A. Izaguirre},
1987 +  title = {ProtoMol, an object-oriented framework for prototyping novel algorithms
1988 +        for molecular dynamics},
1989 +  journal = {Acm Transactions on Mathematical Software},
1990 +  year = {2004},
1991 +  volume = {30},
1992 +  pages = {237-265},
1993 +  number = {3},
1994 +  month = {Sep},
1995 +  abstract = {PROTOMOL is a high-performance framework in C++ for rapid prototyping
1996 +        of novel algorithms for molecular dynamics and related applications.
1997 +        Its flexibility is achieved primarily through the use of inheritance
1998 +        and design patterns (object-oriented programming): Performance is
1999 +        obtained by using templates that enable generation of efficient
2000 +        code for sections critical to performance (generic programming).
2001 +        The framework encapsulates important optimizations that can be used
2002 +        by developers, such as parallelism in the force computation. Its
2003 +        design is based on domain analysis of numerical integrators for
2004 +        molecular dynamics (MD) and of fast solvers for the force computation,
2005 +        particularly due to electrostatic interactions. Several new and
2006 +        efficient algorithms are implemented in PROTOMOL. Finally, it is
2007 +        shown that PROTOMOL'S sequential performance is excellent when compared
2008 +        to a leading MD program, and that it scales well for moderate number
2009 +        of processors. Binaries and source codes for Windows, Linux, Solaris,
2010 +        IRIX, HP-UX, and AIX platforms are available under open source license
2011 +        at http://protomol.sourceforge.net.},
2012 +  annote = {860EP Times Cited:2 Cited References Count:52},
2013 +  issn = {0098-3500},
2014 +  uri = {<Go to ISI>://000224325600001},
2015   }
2016  
2017   @ARTICLE{McLachlan1993,
# Line 1808 | Line 2023 | Encoding: GBK
2023    pages = {3043-3046},
2024   }
2025  
2026 < @ARTICLE{McLachlan1998a,
2026 > @ARTICLE{McLachlan1998,
2027    author = {R. I. McLachlan and G. R. W. Quispel},
2028    title = {Generating functions for dynamical systems with symmetries, integrals,
2029          and differential invariants},
# Line 1829 | Line 2044 | Encoding: GBK
2044    uri = {<Go to ISI>://000071558900021},
2045   }
2046  
2047 < @ARTICLE{McLachlan1998,
2047 > @ARTICLE{McLachlan1998a,
2048    author = {R. I. McLachlan and G. R. W. Quispel and G. S. Turner},
2049    title = {Numerical integrators that preserve symmetries and reversing symmetries},
2050    journal = {Siam Journal on Numerical Analysis},
# Line 1877 | Line 2092 | Encoding: GBK
2092    annote = {911NS Times Cited:0 Cited References Count:14},
2093    issn = {1615-3375},
2094    uri = {<Go to ISI>://000228011900003},
2095 + }
2096 +
2097 + @ARTICLE{Meineke2005,
2098 +  author = {M. A. Meineke and C. F. Vardeman and T. Lin and C. J. Fennell and
2099 +        J. D. Gezelter},
2100 +  title = {OOPSE: An object-oriented parallel simulation engine for molecular
2101 +        dynamics},
2102 +  journal = {Journal of Computational Chemistry},
2103 +  year = {2005},
2104 +  volume = {26},
2105 +  pages = {252-271},
2106 +  number = {3},
2107 +  month = {Feb},
2108 +  abstract = {OOPSE is a new molecular dynamics simulation program that is capable
2109 +        of efficiently integrating equations of motion for atom types with
2110 +        orientational degrees of freedom (e.g. #sticky# atoms and point
2111 +        dipoles). Transition metals can also be simulated using the embedded
2112 +        atom method (EAM) potential included in the code. Parallel simulations
2113 +        are carried out using the force-based decomposition method. Simulations
2114 +        are specified using a very simple C-based meta-data language. A
2115 +        number of advanced integrators are included, and the basic integrator
2116 +        for orientational dynamics provides substantial improvements over
2117 +        older quaternion-based schemes. (C) 2004 Wiley Periodicals, Inc.},
2118 +  annote = {891CF Times Cited:1 Cited References Count:56},
2119 +  issn = {0192-8651},
2120 +  uri = {<Go to ISI>://000226558200006},
2121 + }
2122 +
2123 + @ARTICLE{Melchionna1993,
2124 +  author = {S. Melchionna and G. Ciccotti and B. L. Holian},
2125 +  title = {Hoover Npt Dynamics for Systems Varying in Shape and Size},
2126 +  journal = {Molecular Physics},
2127 +  year = {1993},
2128 +  volume = {78},
2129 +  pages = {533-544},
2130 +  number = {3},
2131 +  month = {Feb 20},
2132 +  abstract = {In this paper we write down equations of motion (following the approach
2133 +        pioneered by Hoover) for an exact isothermal-isobaric molecular
2134 +        dynamics simulation, and we extend them to multiple thermostating
2135 +        rates, to a shape-varying cell and to molecular systems, coherently
2136 +        with the previous 'extended system method'. An integration scheme
2137 +        is proposed together with a numerical illustration of the method.},
2138 +  annote = {Kq355 Times Cited:172 Cited References Count:17},
2139 +  issn = {0026-8976},
2140 +  uri = {<Go to ISI>://A1993KQ35500002},
2141   }
2142  
2143   @ARTICLE{Memmer2002,
# Line 2226 | Line 2487 | Encoding: GBK
2487    uri = {<Go to ISI>://000077460000052},
2488   }
2489  
2490 + @ARTICLE{Parr1995,
2491 +  author = {T. J. Parr and R. W. Quong},
2492 +  title = {Antlr - a Predicated-Ll(K) Parser Generator},
2493 +  journal = {Software-Practice \& Experience},
2494 +  year = {1995},
2495 +  volume = {25},
2496 +  pages = {789-810},
2497 +  number = {7},
2498 +  month = {Jul},
2499 +  abstract = {Despite the parsing power of LR/LALR algorithms, e.g. YACC, programmers
2500 +        often choose to write recursive-descent parsers by hand to obtain
2501 +        increased flexibility, better error handling, and ease of debugging.
2502 +        We introduce ANTLR, a public-domain parser generator that combines
2503 +        the flexibility of hand-coded parsing with the convenience of a
2504 +        parser generator, which is a component of PCCTS. ANTLR has many
2505 +        features that make it easier to use than other language tools. Most
2506 +        important, ANTLR provides predicates which let the programmer systematically
2507 +        direct the parse via arbitrary expressions using semantic and syntactic
2508 +        context; in practice, the use of predicates eliminates the need
2509 +        to hand-tweak the ANTLR output, even for difficult parsing problems.
2510 +        ANTLR also integrates the description of lexical and syntactic analysis,
2511 +        accepts LL(k) grammars for k > 1 with extended BNF notation, and
2512 +        can automatically generate abstract syntax trees. ANTLR is widely
2513 +        used, with over 1000 registered industrial and academic users in
2514 +        37 countries. It has been ported to many popular systems such as
2515 +        the PC, Macintosh, and a variety of UNIX platforms; a commercial
2516 +        C++ front-end has been developed as a result of one of our industrial
2517 +        collaborations.},
2518 +  annote = {Rk104 Times Cited:19 Cited References Count:10},
2519 +  issn = {0038-0644},
2520 +  uri = {<Go to ISI>://A1995RK10400004},
2521 + }
2522 +
2523   @ARTICLE{Pastor1988,
2524    author = {R. W. Pastor and B. R. Brooks and A. Szabo},
2525    title = {An Analysis of the Accuracy of Langevin and Molecular-Dynamics Algorithms},
# Line 2295 | Line 2589 | Encoding: GBK
2589    year = {1934},
2590    volume = {5},
2591    pages = {497-511},
2592 + }
2593 +
2594 + @ARTICLE{Petrache2000,
2595 +  author = {H.~I. Petrache and S.~W. Dodd and M.~F. Brown},
2596 +  title = {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines
2597 +        Determined by $^2\text{H}$ {\sc nmr} Spectroscopy},
2598 +  journal = {Biophysical Journal},
2599 +  year = {2000},
2600 +  volume = {79},
2601 +  pages = {3172-3192},
2602   }
2603  
2604   @ARTICLE{Petrache1998,
# Line 2458 | Line 2762 | Encoding: GBK
2762    uri = {<Go to ISI>://000233775500001},
2763   }
2764  
2765 + @ARTICLE{Roux1991,
2766 +  author = {B. Roux and M. Karplus},
2767 +  title = {Ion-Transport in a Gramicidin-Like Channel - Dynamics and Mobility},
2768 +  journal = {Journal of Physical Chemistry},
2769 +  year = {1991},
2770 +  volume = {95},
2771 +  pages = {4856-4868},
2772 +  number = {12},
2773 +  month = {Jun 13},
2774 +  abstract = {The mobility of water, Na+. and K+ has been calculated inside a periodic
2775 +        poly-(L,D)-alanine beta-helix, a model for the interior of the gramicidin
2776 +        channel. Because of the different dynamical regimes for the three
2777 +        species (high barrier for Na+, low barrier for K+, almost free diffusion
2778 +        for water), different methods are used to calculate the mobilities.
2779 +        By use of activated dynamics and a potential of mean force determined
2780 +        previously (Roux, B.; Karplus, M. Biophys. J. 1991, 59, 961), the
2781 +        barrier crossing rate of Na+ ion is determined. The motion of Na+
2782 +        at the transition state is controlled by local interactions and
2783 +        collisions with the neighboring carbonyls and the two nearest water
2784 +        molecules. There are significant deviations from transition-state
2785 +        theory; the transmission coefficient is equal to 0.11. The water
2786 +        and K+ motions are found to be well described by a diffusive model;
2787 +        the motion of K+ appears to be controlled by the diffusion of water.
2788 +        The time-dependent friction functions of Na+ and K+ ions in the
2789 +        periodic beta-helix are calculated and analyzed by using a generalized
2790 +        Langevin equation approach. Both Na+ and K+ suffer many rapid collisions,
2791 +        and their dynamics is overdamped and noninertial. Thus, the selectivity
2792 +        sequence of ions in the beta-helix is not influenced strongly by
2793 +        their masses.},
2794 +  annote = {Fr756 Times Cited:97 Cited References Count:65},
2795 +  issn = {0022-3654},
2796 +  uri = {<Go to ISI>://A1991FR75600049},
2797 + }
2798 +
2799   @ARTICLE{Roy2005,
2800    author = {A. Roy and N. V. Madhusudana},
2801    title = {A frustrated packing model for the B-6-B-1-SmAP(A) sequence of phases
# Line 2578 | Line 2916 | Encoding: GBK
2916    uri = {<Go to ISI>://000080181500004},
2917   }
2918  
2919 + @ARTICLE{Sasaki2004,
2920 +  author = {Y. Sasaki and R. Shukla and B. D. Smith},
2921 +  title = {Facilitated phosphatidylserine flip-flop across vesicle and cell
2922 +        membranes using urea-derived synthetic translocases},
2923 +  journal = {Organic \& Biomolecular Chemistry},
2924 +  year = {2004},
2925 +  volume = {2},
2926 +  pages = {214-219},
2927 +  number = {2},
2928 +  abstract = {Tris(2-aminoethyl) amine derivatives with appended urea and sulfonamide
2929 +        groups are shown to facilitate the translocation of fluorescent
2930 +        phospholipid probes and endogenous phosphatidylserine across vesicle
2931 +        and erythrocyte cell membranes. The synthetic translocases appear
2932 +        to operate by binding to the phospholipid head groups and forming
2933 +        lipophilic supramolecular complexes which diffuse through the non-polar
2934 +        interior of the bilayer membrane.},
2935 +  annote = {760PX Times Cited:8 Cited References Count:25},
2936 +  issn = {1477-0520},
2937 +  uri = {<Go to ISI>://000187843800012},
2938 + }
2939 +
2940   @ARTICLE{Satoh1996,
2941    author = {K. Satoh and S. Mita and S. Kondo},
2942    title = {Monte Carlo simulations using the dipolar Gay-Berne model: Effect
# Line 2598 | Line 2957 | Encoding: GBK
2957    annote = {Uq975 Times Cited:32 Cited References Count:33},
2958    issn = {0009-2614},
2959    uri = {<Go to ISI>://A1996UQ97500017},
2960 + }
2961 +
2962 + @ARTICLE{Schaps1999,
2963 +  author = {G. L. Schaps},
2964 +  title = {Compiler construction with ANTLR and Java - Tools for building tools},
2965 +  journal = {Dr Dobbs Journal},
2966 +  year = {1999},
2967 +  volume = {24},
2968 +  pages = {84-+},
2969 +  number = {3},
2970 +  month = {Mar},
2971 +  annote = {163EC Times Cited:0 Cited References Count:0},
2972 +  issn = {1044-789X},
2973 +  uri = {<Go to ISI>://000078389200023},
2974   }
2975  
2976   @ARTICLE{Shen2002,
# Line 2847 | Line 3220 | Encoding: GBK
3220    address = {New York},
3221   }
3222  
3223 + @ARTICLE{Vincent1995,
3224 +  author = {J. J. Vincent and K. M. Merz},
3225 +  title = {A Highly Portable Parallel Implementation of Amber4 Using the Message-Passing
3226 +        Interface Standard},
3227 +  journal = {Journal of Computational Chemistry},
3228 +  year = {1995},
3229 +  volume = {16},
3230 +  pages = {1420-1427},
3231 +  number = {11},
3232 +  month = {Nov},
3233 +  abstract = {We have implemented a portable parallel version of the macromolecular
3234 +        modeling package AMBER4. The message passing paradigm was used.
3235 +        All message passing constructs are compliant with the Message Passing
3236 +        Interface (MPI) standard. The molecular dynamics/minimization module
3237 +        MINMD and the free-energy perturbation module Gibbs have been implemented
3238 +        in parallel on a number of machines, including a Gray T3D, an IBM
3239 +        SP1/SP2, and a collection of networked workstations. In addition,
3240 +        the code has been tested with an MPI implementation from Argonne
3241 +        National Laboratories/Mississippi State University which runs on
3242 +        many parallel machines. The goal of this work is to decrease the
3243 +        amount of time required to perform molecular dynamics simulations.
3244 +        Performance results for a Lipid bilayer molecular dynamics simulation
3245 +        on a Gray T3D, an IBM SP1/SPZ and a Gray C90 are compared. (C) 1995
3246 +        by John Wiley & Sons, Inc.},
3247 +  annote = {Ta403 Times Cited:16 Cited References Count:23},
3248 +  issn = {0192-8651},
3249 +  uri = {<Go to ISI>://A1995TA40300009},
3250 + }
3251 +
3252   @ARTICLE{Wegener1979,
3253    author = {W.~A. Wegener, V.~J. Koester and R.~M. Dowben},
3254    title = {A general ellipsoid can not always serve as a modle for the rotational
# Line 2858 | Line 3260 | Encoding: GBK
3260    number = {12},
3261   }
3262  
3263 + @ARTICLE{Wilson2006,
3264 +  author = {G.~V. Wilson },
3265 +  title = {Where's the Real Bottleneck in Scientific Computing?},
3266 +  journal = {American Scientist},
3267 +  year = {2006},
3268 +  volume = {94},
3269 + }
3270 +
3271   @ARTICLE{Withers2003,
3272    author = {I. M. Withers},
3273    title = {Effects of longitudinal quadrupoles on the phase behavior of a Gay-Berne

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