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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},
102  year = {1987},
103  author = {M.~P. Allen and D.~J. Tildesley},
104  address = {New York},
105 }
106
91   @ARTICLE{Allison1991,
92    author = {S. A. Allison},
93    title = {A Brownian Dynamics Algorithm for Arbitrary Rigid Bodies - Application
# Line 247 | Line 231 | Encoding: GBK
231    uri = {<Go to ISI>://000221146400009},
232   }
233  
250 @ARTICLE{Barojas1973,
251  author = {J. Barojas and D. Levesque},
252  title = {Simulation of Diatomic Homonuclear Liquids},
253  journal = {Phys. Rev. A},
254  year = {1973},
255  volume = {7},
256  pages = {1092-1105},
257 }
258
234   @ARTICLE{Barth1998,
235    author = {E. Barth and T. Schlick},
236    title = {Overcoming stability limitations in biomolecular dynamics. I. Combining
# Line 430 | Line 405 | Encoding: GBK
405  
406   @ARTICLE{Berkov2005,
407    author = {D. V. Berkov and N. L. Gorn},
408 +  title = {Stochastic dynamic simulations of fast remagnetization processes:
409 +        recent advances and applications},
410 +  journal = {Journal of Magnetism and Magnetic Materials},
411 +  year = {2005},
412 +  volume = {290},
413 +  pages = {442-448},
414 +  month = {Apr},
415 +  abstract = {Numerical simulations of fast remagnetization processes using stochastic
416 +        dynamics are widely used to study various magnetic systems. In this
417 +        paper, we first address several crucial methodological problems
418 +        of such simulations: (i) the influence of finite-element discretization
419 +        on simulated dynamics, (ii) choice between Ito and Stratonovich
420 +        stochastic calculi by the solution of micromagnetic stochastic equations
421 +        of motion and (iii) non-trivial correlation properties of the random
422 +        (thermal) field. Next, we discuss several examples to demonstrate
423 +        the great potential of the Langevin dynamics for studying fast remagnetization
424 +        processes in technically relevant applications: we present numerical
425 +        analysis of equilibrium magnon spectra in patterned structures,
426 +        study thermal noise effects on the magnetization dynamics of nanoelements
427 +        in pulsed fields and show some results for a remagnetization dynamics
428 +        induced by a spin-polarized current. (c) 2004 Elsevier B.V. All
429 +        rights reserved.},
430 +  annote = {Part 1 Sp. Iss. SI 922KU Times Cited:2 Cited References Count:25},
431 +  issn = {0304-8853},
432 +  uri = {<Go to ISI>://000228837600109},
433 + }
434 +
435 + @ARTICLE{Berkov2005a,
436 +  author = {D. V. Berkov and N. L. Gorn},
437    title = {Magnetization precession due to a spin-polarized current in a thin
438          nanoelement: Numerical simulation study},
439    journal = {Physical Review B},
# Line 460 | Line 464 | Encoding: GBK
464    uri = {<Go to ISI>://000232228500058},
465   }
466  
463 @ARTICLE{Berkov2005a,
464  author = {D. V. Berkov and N. L. Gorn},
465  title = {Stochastic dynamic simulations of fast remagnetization processes:
466        recent advances and applications},
467  journal = {Journal of Magnetism and Magnetic Materials},
468  year = {2005},
469  volume = {290},
470  pages = {442-448},
471  month = {Apr},
472  abstract = {Numerical simulations of fast remagnetization processes using stochastic
473        dynamics are widely used to study various magnetic systems. In this
474        paper, we first address several crucial methodological problems
475        of such simulations: (i) the influence of finite-element discretization
476        on simulated dynamics, (ii) choice between Ito and Stratonovich
477        stochastic calculi by the solution of micromagnetic stochastic equations
478        of motion and (iii) non-trivial correlation properties of the random
479        (thermal) field. Next, we discuss several examples to demonstrate
480        the great potential of the Langevin dynamics for studying fast remagnetization
481        processes in technically relevant applications: we present numerical
482        analysis of equilibrium magnon spectra in patterned structures,
483        study thermal noise effects on the magnetization dynamics of nanoelements
484        in pulsed fields and show some results for a remagnetization dynamics
485        induced by a spin-polarized current. (c) 2004 Elsevier B.V. All
486        rights reserved.},
487  annote = {Part 1 Sp. Iss. SI 922KU Times Cited:2 Cited References Count:25},
488  issn = {0304-8853},
489  uri = {<Go to ISI>://000228837600109},
490 }
491
467   @ARTICLE{Berkov2002,
468    author = {D. V. Berkov and N. L. Gorn and P. Gornert},
469    title = {Magnetization dynamics in nanoparticle systems: Numerical simulation
# Line 970 | Line 945 | Encoding: GBK
945    annote = {Ya587 Times Cited:35 Cited References Count:32},
946    issn = {0021-9606},
947    uri = {<Go to ISI>://A1997YA58700024},
973 }
974
975 @BOOK{Gamma1994,
976  title = {Design Patterns: Elements of Reusable Object-Oriented Software},
977  publisher = {Perason Education},
978  year = {1994},
979  author = {E. Gamma, R. Helm, R. Johnson and J. Vlissides},
980  address = {London},
981  chapter = {7},
948   }
949  
950   @ARTICLE{Edwards2005,
# Line 1109 | Line 1075 | Encoding: GBK
1075    annote = {633AD Times Cited:2 Cited References Count:43},
1076    issn = {0006-3495},
1077    uri = {<Go to ISI>://000180256300012},
1112 }
1113
1114 @BOOK{Frenkel1996,
1115  title = {Understanding Molecular Simulation : From Algorithms to Applications},
1116  publisher = {Academic Press},
1117  year = {1996},
1118  author = {D. Frenkel and B. Smit},
1119  address = {New York},
1078   }
1079  
1080   @ARTICLE{Gay1981,
# Line 1163 | Line 1121 | Encoding: GBK
1121    annote = {257MM Times Cited:2 Cited References Count:82},
1122    issn = {1022-1344},
1123    uri = {<Go to ISI>://000083785700002},
1166 }
1167
1168 @BOOK{Goldstein2001,
1169  title = {Classical Mechanics},
1170  publisher = {Addison Wesley},
1171  year = {2001},
1172  author = {H. Goldstein and C. Poole and J. Safko},
1173  address = {San Francisco},
1174  edition = {3rd},
1124   }
1125  
1126   @ARTICLE{Gray2003,
# Line 1408 | Line 1357 | Encoding: GBK
1357    annote = {Ju251 Times Cited:55 Cited References Count:44},
1358    issn = {0006-3495},
1359    uri = {<Go to ISI>://A1992JU25100002},
1411 }
1412
1413 @BOOK{Hockney1981,
1414  title = {Computer Simulation Using Particles},
1415  publisher = {McGraw-Hill},
1416  year = {1981},
1417  author = {R.W. Hockney and J.W. Eastwood},
1418  address = {New York},
1360   }
1361  
1362   @ARTICLE{Hoover1985,
# Line 1454 | Line 1395 | Encoding: GBK
1395    annote = {870FJ Times Cited:0 Cited References Count:63},
1396    issn = {0021-9606},
1397    uri = {<Go to ISI>://000225042700059},
1398 + }
1399 +
1400 + @ARTICLE{Humphrey1996,
1401 +  author = {W. Humphrey and A. Dalke and K. Schulten},
1402 +  title = {VMD: Visual molecular dynamics},
1403 +  journal = {Journal of Molecular Graphics},
1404 +  year = {1996},
1405 +  volume = {14},
1406 +  pages = {33-\&},
1407 +  number = {1},
1408 +  month = {Feb},
1409 +  abstract = {VMD is a molecular graphics program designed for the display and analysis
1410 +        of molecular assemblies, in particular biopolymers such as proteins
1411 +        and nucleic acids. VMD can simultaneously display any number of
1412 +        structures using a wide variety of rendering styles and coloring
1413 +        methods. Molecules are displayed as one or more ''representations,''
1414 +        in which each representation embodies a particular rendering method
1415 +        and coloring scheme for a selected subset of atoms. The atoms displayed
1416 +        in each representation are chosen using an extensive atom selection
1417 +        syntax, which includes Boolean operators and regular expressions.
1418 +        VMD provides a complete graphical user interface for program control,
1419 +        as well as a text interface using the Tcl embeddable parser to allow
1420 +        for complex scripts with variable substitution, control loops, and
1421 +        function calls. Full session logging is supported, which produces
1422 +        a VMD command script for later playback. High-resolution raster
1423 +        images of displayed molecules may be produced by generating input
1424 +        scripts for use by a number of photorealistic image-rendering applications.
1425 +        VMD has also been expressly designed with the ability to animate
1426 +        molecular dynamics (MD) simulation trajectories, imported either
1427 +        from files or from a direct connection to a running MD simulation.
1428 +        VMD is the visualization component of MDScope, a set of tools for
1429 +        interactive problem solving in structural biology, which also includes
1430 +        the parallel MD program NAMD, and the MDCOMM software used to connect
1431 +        the visualization and simulation programs. VMD is written in C++,
1432 +        using an object-oriented design; the program, including source code
1433 +        and extensive documentation, is freely available via anonymous ftp
1434 +        and through the World Wide Web.},
1435 +  annote = {Uh515 Times Cited:1418 Cited References Count:19},
1436 +  issn = {0263-7855},
1437 +  uri = {<Go to ISI>://A1996UH51500005},
1438   }
1439  
1440   @ARTICLE{Izaguirre2001,
# Line 1497 | Line 1478 | Encoding: GBK
1478    uri = {<Go to ISI>://000166676100020},
1479   }
1480  
1500 @ARTICLE{Torre1977,
1501  author = {Jose Garcia De La Torre, V.A. Bloomfield},
1502  title = {Hydrodynamic properties of macromolecular complexes. I. Translation},
1503  journal = {Biopolymers},
1504  year = {1977},
1505  volume = {16},
1506  pages = {1747-1763},
1507 }
1508
1481   @ARTICLE{Kane2000,
1482    author = {C. Kane and J. E. Marsden and M. Ortiz and M. West},
1483    title = {Variational integrators and the Newmark algorithm for conservative
# Line 1659 | Line 1631 | Encoding: GBK
1631    annote = {Part 1 646CM Times Cited:15 Cited References Count:38},
1632    issn = {1063-651X},
1633    uri = {<Go to ISI>://000181017300042},
1662 }
1663
1664 @BOOK{Leach2001,
1665  title = {Molecular Modeling: Principles and Applications},
1666  publisher = {Pearson Educated Limited},
1667  year = {2001},
1668  author = {A. Leach},
1669  address = {Harlow, England},
1670  edition = {2nd},
1634   }
1635  
1636   @ARTICLE{Leimkuhler1999,
# Line 1698 | Line 1661 | Encoding: GBK
1661    uri = {<Go to ISI>://000080466800007},
1662   }
1663  
1701 @BOOK{Leimkuhler2004,
1702  title = {Simulating Hamiltonian Dynamics},
1703  publisher = {Cambridge University Press},
1704  year = {2004},
1705  author = {B. Leimkuhler and S. Reich},
1706  address = {Cambridge},
1707 }
1708
1664   @ARTICLE{Levelut1981,
1665    author = {A. M. Levelut and R. J. Tarento and F. Hardouin and M. F. Achard
1666          and G. Sigaud},
# Line 1796 | Line 1751 | Encoding: GBK
1751    uri = {<Go to ISI>://A1994QF46400002},
1752   }
1753  
1799 @BOOK{Marion1990,
1800  title = {Classical Dynamics of Particles and Systems},
1801  publisher = {Academic Press},
1802  year = {1990},
1803  author = {J.~B. Marion},
1804  address = {New York},
1805  edition = {2rd},
1806 }
1807
1754   @ARTICLE{Marrink1994,
1755    author = {S. J. Marrink and H. J. C. Berendsen},
1756    title = {Simulation of Water Transport through a Lipid-Membrane},
# Line 1878 | Line 1824 | Encoding: GBK
1824    uri = {<Go to ISI>://000077902200006},
1825   }
1826  
1827 < @ARTICLE{McLachlan1993,
1828 <  author = {R.~I McLachlan},
1829 <  title = {Explicit Lie-Poisson integration and the Euler equations},
1830 <  journal = {prl},
1831 <  year = {1993},
1832 <  volume = {71},
1833 <  pages = {3043-3046},
1827 > @ARTICLE{Matthey2004,
1828 >  author = {T. Matthey and T. Cickovski and S. Hampton and A. Ko and Q. Ma and
1829 >        M. Nyerges and T. Raeder and T. Slabach and J. A. Izaguirre},
1830 >  title = {ProtoMol, an object-oriented framework for prototyping novel algorithms
1831 >        for molecular dynamics},
1832 >  journal = {Acm Transactions on Mathematical Software},
1833 >  year = {2004},
1834 >  volume = {30},
1835 >  pages = {237-265},
1836 >  number = {3},
1837 >  month = {Sep},
1838 >  abstract = {PROTOMOL is a high-performance framework in C++ for rapid prototyping
1839 >        of novel algorithms for molecular dynamics and related applications.
1840 >        Its flexibility is achieved primarily through the use of inheritance
1841 >        and design patterns (object-oriented programming): Performance is
1842 >        obtained by using templates that enable generation of efficient
1843 >        code for sections critical to performance (generic programming).
1844 >        The framework encapsulates important optimizations that can be used
1845 >        by developers, such as parallelism in the force computation. Its
1846 >        design is based on domain analysis of numerical integrators for
1847 >        molecular dynamics (MD) and of fast solvers for the force computation,
1848 >        particularly due to electrostatic interactions. Several new and
1849 >        efficient algorithms are implemented in PROTOMOL. Finally, it is
1850 >        shown that PROTOMOL'S sequential performance is excellent when compared
1851 >        to a leading MD program, and that it scales well for moderate number
1852 >        of processors. Binaries and source codes for Windows, Linux, Solaris,
1853 >        IRIX, HP-UX, and AIX platforms are available under open source license
1854 >        at http://protomol.sourceforge.net.},
1855 >  annote = {860EP Times Cited:2 Cited References Count:52},
1856 >  issn = {0098-3500},
1857 >  uri = {<Go to ISI>://000224325600001},
1858   }
1859  
1860   @ARTICLE{McLachlan1998,
# Line 1956 | Line 1926 | Encoding: GBK
1926    annote = {911NS Times Cited:0 Cited References Count:14},
1927    issn = {1615-3375},
1928    uri = {<Go to ISI>://000228011900003},
1929 + }
1930 +
1931 + @ARTICLE{Meineke2005,
1932 +  author = {M. A. Meineke and C. F. Vardeman and T. Lin and C. J. Fennell and
1933 +        J. D. Gezelter},
1934 +  title = {OOPSE: An object-oriented parallel simulation engine for molecular
1935 +        dynamics},
1936 +  journal = {Journal of Computational Chemistry},
1937 +  year = {2005},
1938 +  volume = {26},
1939 +  pages = {252-271},
1940 +  number = {3},
1941 +  month = {Feb},
1942 +  abstract = {OOPSE is a new molecular dynamics simulation program that is capable
1943 +        of efficiently integrating equations of motion for atom types with
1944 +        orientational degrees of freedom (e.g. #sticky# atoms and point
1945 +        dipoles). Transition metals can also be simulated using the embedded
1946 +        atom method (EAM) potential included in the code. Parallel simulations
1947 +        are carried out using the force-based decomposition method. Simulations
1948 +        are specified using a very simple C-based meta-data language. A
1949 +        number of advanced integrators are included, and the basic integrator
1950 +        for orientational dynamics provides substantial improvements over
1951 +        older quaternion-based schemes. (C) 2004 Wiley Periodicals, Inc.},
1952 +  annote = {891CF Times Cited:1 Cited References Count:56},
1953 +  issn = {0192-8651},
1954 +  uri = {<Go to ISI>://000226558200006},
1955   }
1956  
1957   @ARTICLE{Melchionna1993,
# Line 2018 | Line 2014 | Encoding: GBK
2014    uri = {<Go to ISI>://000174410500001},
2015   }
2016  
2021 @ARTICLE{Metropolis1949,
2022  author = {N. Metropolis and S. Ulam},
2023  title = {The $\mbox{Monte Carlo}$ Method},
2024  journal = {J. Am. Stat. Ass.},
2025  year = {1949},
2026  volume = {44},
2027  pages = {335-341},
2028 }
2029
2017   @ARTICLE{Mielke2004,
2018    author = {S. P. Mielke and W. H. Fink and V. V. Krishnan and N. Gronbech-Jensen
2019          and C. J. Benham},
# Line 2168 | Line 2155 | Encoding: GBK
2155    annote = {491UW Times Cited:48 Cited References Count:25},
2156    issn = {0021-9606},
2157    uri = {<Go to ISI>://000172129300049},
2171 }
2172
2173 @BOOK{Olver1986,
2174  title = {Applications of Lie groups to differential equatitons},
2175  publisher = {Springer},
2176  year = {1986},
2177  author = {P.J. Olver},
2178  address = {New York},
2158   }
2159  
2160   @ARTICLE{Omelyan1998,
# Line 2325 | Line 2304 | Encoding: GBK
2304    uri = {<Go to ISI>://000077460000052},
2305   }
2306  
2307 + @ARTICLE{Parr1995,
2308 +  author = {T. J. Parr and R. W. Quong},
2309 +  title = {Antlr - a Predicated-Ll(K) Parser Generator},
2310 +  journal = {Software-Practice \& Experience},
2311 +  year = {1995},
2312 +  volume = {25},
2313 +  pages = {789-810},
2314 +  number = {7},
2315 +  month = {Jul},
2316 +  abstract = {Despite the parsing power of LR/LALR algorithms, e.g. YACC, programmers
2317 +        often choose to write recursive-descent parsers by hand to obtain
2318 +        increased flexibility, better error handling, and ease of debugging.
2319 +        We introduce ANTLR, a public-domain parser generator that combines
2320 +        the flexibility of hand-coded parsing with the convenience of a
2321 +        parser generator, which is a component of PCCTS. ANTLR has many
2322 +        features that make it easier to use than other language tools. Most
2323 +        important, ANTLR provides predicates which let the programmer systematically
2324 +        direct the parse via arbitrary expressions using semantic and syntactic
2325 +        context; in practice, the use of predicates eliminates the need
2326 +        to hand-tweak the ANTLR output, even for difficult parsing problems.
2327 +        ANTLR also integrates the description of lexical and syntactic analysis,
2328 +        accepts LL(k) grammars for k > 1 with extended BNF notation, and
2329 +        can automatically generate abstract syntax trees. ANTLR is widely
2330 +        used, with over 1000 registered industrial and academic users in
2331 +        37 countries. It has been ported to many popular systems such as
2332 +        the PC, Macintosh, and a variety of UNIX platforms; a commercial
2333 +        C++ front-end has been developed as a result of one of our industrial
2334 +        collaborations.},
2335 +  annote = {Rk104 Times Cited:19 Cited References Count:10},
2336 +  issn = {0038-0644},
2337 +  uri = {<Go to ISI>://A1995RK10400004},
2338 + }
2339 +
2340   @ARTICLE{Pastor1988,
2341    author = {R. W. Pastor and B. R. Brooks and A. Szabo},
2342    title = {An Analysis of the Accuracy of Langevin and Molecular-Dynamics Algorithms},
# Line 2367 | Line 2379 | Encoding: GBK
2379    uri = {<Go to ISI>://A1985AKB9300008},
2380   }
2381  
2370 @ARTICLE{Rotne1969,
2371  author = {F. Perrin},
2372  title = {Variational treatment of hydrodynamic interaction in polymers},
2373  journal = {J. Chem. Phys.},
2374  year = {1969},
2375  volume = {50},
2376  pages = {4831¨C4837},
2377 }
2378
2379 @ARTICLE{Perrin1936,
2380  author = {F. Perrin},
2381  title = {Mouvement brownien d'un ellipsoid(II). Rotation libre et depolarisation
2382        des fluorescences. Translation et diffusion de moleculese ellipsoidales},
2383  journal = {J. Phys. Radium},
2384  year = {1936},
2385  volume = {7},
2386  pages = {1-11},
2387 }
2388
2389 @ARTICLE{Perrin1934,
2390  author = {F. Perrin},
2391  title = {Mouvement brownien d'un ellipsoid(I). Dispersion dielectrique pour
2392        des molecules ellipsoidales},
2393  journal = {J. Phys. Radium},
2394  year = {1934},
2395  volume = {5},
2396  pages = {497-511},
2397 }
2398
2382   @ARTICLE{Petrache1998,
2383    author = {H. I. Petrache and S. Tristram-Nagle and J. F. Nagle},
2384    title = {Fluid phase structure of EPC and DMPC bilayers},
# Line 2425 | Line 2408 | Encoding: GBK
2408    annote = {130AT Times Cited:98 Cited References Count:39},
2409    issn = {0009-3084},
2410    uri = {<Go to ISI>://000076497600007},
2428 }
2429
2430 @ARTICLE{Powles1973,
2431  author = {J.~G. Powles},
2432  title = {A general ellipsoid can not always serve as a modle for the rotational
2433        diffusion properties of arbitrary shaped rigid molecules},
2434  journal = {Advan. Phys.},
2435  year = {1973},
2436  volume = {22},
2437  pages = {1-56},
2411   }
2412  
2413   @ARTICLE{Recio2004,
# Line 2752 | Line 2725 | Encoding: GBK
2725    annote = {Uq975 Times Cited:32 Cited References Count:33},
2726    issn = {0009-2614},
2727    uri = {<Go to ISI>://A1996UQ97500017},
2728 + }
2729 +
2730 + @ARTICLE{Schaps1999,
2731 +  author = {G. L. Schaps},
2732 +  title = {Compiler construction with ANTLR and Java - Tools for building tools},
2733 +  journal = {Dr Dobbs Journal},
2734 +  year = {1999},
2735 +  volume = {24},
2736 +  pages = {84-+},
2737 +  number = {3},
2738 +  month = {Mar},
2739 +  annote = {163EC Times Cited:0 Cited References Count:0},
2740 +  issn = {1044-789X},
2741 +  uri = {<Go to ISI>://000078389200023},
2742   }
2743  
2744   @ARTICLE{Shen2002,
# Line 2922 | Line 2909 | Encoding: GBK
2909    uri = {<Go to ISI>://000230332400077},
2910   }
2911  
2925 @BOOK{Tolman1979,
2926  title = {The Principles of Statistical Mechanics},
2927  publisher = {Dover Publications, Inc.},
2928  year = {1979},
2929  author = {R.~C. Tolman},
2930  address = {New York},
2931  chapter = {2},
2932  pages = {19-22},
2933 }
2934
2912   @ARTICLE{Tu1995,
2913    author = {K. Tu and D. J. Tobias and M. L. Klein},
2914    title = {Constant pressure and temperature molecular dynamics simulation of
# Line 2991 | Line 2968 | Encoding: GBK
2968    annote = {Je891 Times Cited:680 Cited References Count:19},
2969    issn = {0021-9606},
2970    uri = {<Go to ISI>://A1992JE89100044},
2994 }
2995
2996 @BOOK{Varadarajan1974,
2997  title = {Lie groups, Lie algebras, and their representations},
2998  publisher = {Prentice-Hall},
2999  year = {1974},
3000  author = {V.S. Varadarajan},
3001  address = {New York},
2971   }
2972  
3004 @ARTICLE{Wegener1979,
3005  author = {W.~A. Wegener, V.~J. Koester and R.~M. Dowben},
3006  title = {A general ellipsoid can not always serve as a modle for the rotational
3007        diffusion properties of arbitrary shaped rigid molecules},
3008  journal = {Proc. Natl. Acad. Sci.},
3009  year = {1979},
3010  volume = {76},
3011  pages = {6356-6360},
3012  number = {12},
3013 }
3014
3015 @ARTICLE{Wilson2006,
3016  author = {G.~V. Wilson },
3017  title = {Where's the Real Bottleneck in Scientific Computing?},
3018  journal = {American Scientist},
3019  year = {2006},
3020  volume = {94},
3021 }
3022
2973   @ARTICLE{Withers2003,
2974    author = {I. M. Withers},
2975    title = {Effects of longitudinal quadrupoles on the phase behavior of a Gay-Berne

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