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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 +
107   @ARTICLE{Allison1991,
108    author = {S. A. Allison},
109    title = {A Brownian Dynamics Algorithm for Arbitrary Rigid Bodies - Application
# Line 229 | Line 245 | Encoding: GBK
245    annote = {816YY Times Cited:8 Cited References Count:35},
246    issn = {0021-9606},
247    uri = {<Go to ISI>://000221146400009},
248 + }
249 +
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  
259   @ARTICLE{Barth1998,
# Line 405 | Line 430 | Encoding: GBK
430  
431   @ARTICLE{Berkov2005,
432    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},
433    title = {Magnetization precession due to a spin-polarized current in a thin
434          nanoelement: Numerical simulation study},
435    journal = {Physical Review B},
# Line 464 | Line 460 | Encoding: GBK
460    uri = {<Go to ISI>://000232228500058},
461   }
462  
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 +
492   @ARTICLE{Berkov2002,
493    author = {D. V. Berkov and N. L. Gorn and P. Gornert},
494    title = {Magnetization dynamics in nanoparticle systems: Numerical simulation
# Line 501 | 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 945 | 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 1077 | 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 1121 | Line 1188 | Encoding: GBK
1188    annote = {257MM Times Cited:2 Cited References Count:82},
1189    issn = {1022-1344},
1190    uri = {<Go to ISI>://000083785700002},
1191 + }
1192 +
1193 + @BOOK{Goldstein2001,
1194 +  title = {Classical Mechanics},
1195 +  publisher = {Addison Wesley},
1196 +  year = {2001},
1197 +  author = {H. Goldstein and C. Poole and J. Safko},
1198 +  address = {San Francisco},
1199 +  edition = {3rd},
1200   }
1201  
1202   @ARTICLE{Gray2003,
# Line 1359 | Line 1435 | Encoding: GBK
1435    uri = {<Go to ISI>://A1992JU25100002},
1436   }
1437  
1438 + @BOOK{Hockney1981,
1439 +  title = {Computer Simulation Using Particles},
1440 +  publisher = {McGraw-Hill},
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},
# Line 1476 | Line 1560 | Encoding: GBK
1560    annote = {397CQ Times Cited:14 Cited References Count:36},
1561    issn = {0021-9606},
1562    uri = {<Go to ISI>://000166676100020},
1563 + }
1564 +
1565 + @ARTICLE{Torre1977,
1566 +  author = {Jose Garcia De La Torre, V.A. Bloomfield},
1567 +  title = {Hydrodynamic properties of macromolecular complexes. I. Translation},
1568 +  journal = {Biopolymers},
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 1633 | Line 1764 | Encoding: GBK
1764    uri = {<Go to ISI>://000181017300042},
1765   }
1766  
1767 + @BOOK{Leach2001,
1768 +  title = {Molecular Modeling: Principles and Applications},
1769 +  publisher = {Pearson Educated Limited},
1770 +  year = {2001},
1771 +  author = {A. Leach},
1772 +  address = {Harlow, England},
1773 +  edition = {2nd},
1774 + }
1775 +
1776   @ARTICLE{Leimkuhler1999,
1777    author = {B. Leimkuhler},
1778    title = {Reversible adaptive regularization: perturbed Kepler motion and classical
# Line 1659 | Line 1799 | Encoding: GBK
1799    annote = {199EE Times Cited:11 Cited References Count:48},
1800    issn = {1364-503X},
1801    uri = {<Go to ISI>://000080466800007},
1802 + }
1803 +
1804 + @BOOK{Leimkuhler2004,
1805 +  title = {Simulating Hamiltonian Dynamics},
1806 +  publisher = {Cambridge University Press},
1807 +  year = {2004},
1808 +  author = {B. Leimkuhler and S. Reich},
1809 +  address = {Cambridge},
1810   }
1811  
1812   @ARTICLE{Levelut1981,
# Line 1751 | Line 1899 | Encoding: GBK
1899    uri = {<Go to ISI>://A1994QF46400002},
1900   }
1901  
1902 + @BOOK{Marion1990,
1903 +  title = {Classical Dynamics of Particles and Systems},
1904 +  publisher = {Academic Press},
1905 +  year = {1990},
1906 +  author = {J.~B. Marion},
1907 +  address = {New York},
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},
# Line 1855 | Line 2012 | Encoding: GBK
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,
2018 +  author = {R.~I McLachlan},
2019 +  title = {Explicit Lie-Poisson integration and the Euler equations},
2020 +  journal = {prl},
2021 +  year = {1993},
2022 +  volume = {71},
2023 +  pages = {3043-3046},
2024   }
2025  
2026   @ARTICLE{McLachlan1998,
# Line 2012 | Line 2178 | Encoding: GBK
2178    annote = {531HT Times Cited:12 Cited References Count:37},
2179    issn = {0267-8292},
2180    uri = {<Go to ISI>://000174410500001},
2181 + }
2182 +
2183 + @ARTICLE{Metropolis1949,
2184 +  author = {N. Metropolis and S. Ulam},
2185 +  title = {The $\mbox{Monte Carlo}$ Method},
2186 +  journal = {J. Am. Stat. Ass.},
2187 +  year = {1949},
2188 +  volume = {44},
2189 +  pages = {335-341},
2190   }
2191  
2192   @ARTICLE{Mielke2004,
# Line 2157 | Line 2332 | Encoding: GBK
2332    uri = {<Go to ISI>://000172129300049},
2333   }
2334  
2335 + @BOOK{Olver1986,
2336 +  title = {Applications of Lie groups to differential equatitons},
2337 +  publisher = {Springer},
2338 +  year = {1986},
2339 +  author = {P.J. Olver},
2340 +  address = {New York},
2341 + }
2342 +
2343   @ARTICLE{Omelyan1998,
2344    author = {I. P. Omelyan},
2345    title = {On the numerical integration of motion for rigid polyatomics: The
# Line 2379 | Line 2562 | Encoding: GBK
2562    uri = {<Go to ISI>://A1985AKB9300008},
2563   }
2564  
2565 + @ARTICLE{Rotne1969,
2566 +  author = {F. Perrin},
2567 +  title = {Variational treatment of hydrodynamic interaction in polymers},
2568 +  journal = {J. Chem. Phys.},
2569 +  year = {1969},
2570 +  volume = {50},
2571 +  pages = {4831¨C4837},
2572 + }
2573 +
2574 + @ARTICLE{Perrin1936,
2575 +  author = {F. Perrin},
2576 +  title = {Mouvement brownien d'un ellipsoid(II). Rotation libre et depolarisation
2577 +        des fluorescences. Translation et diffusion de moleculese ellipsoidales},
2578 +  journal = {J. Phys. Radium},
2579 +  year = {1936},
2580 +  volume = {7},
2581 +  pages = {1-11},
2582 + }
2583 +
2584 + @ARTICLE{Perrin1934,
2585 +  author = {F. Perrin},
2586 +  title = {Mouvement brownien d'un ellipsoid(I). Dispersion dielectrique pour
2587 +        des molecules ellipsoidales},
2588 +  journal = {J. Phys. Radium},
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,
2605    author = {H. I. Petrache and S. Tristram-Nagle and J. F. Nagle},
2606    title = {Fluid phase structure of EPC and DMPC bilayers},
# Line 2408 | Line 2630 | Encoding: GBK
2630    annote = {130AT Times Cited:98 Cited References Count:39},
2631    issn = {0009-3084},
2632    uri = {<Go to ISI>://000076497600007},
2633 + }
2634 +
2635 + @ARTICLE{Powles1973,
2636 +  author = {J.~G. Powles},
2637 +  title = {A general ellipsoid can not always serve as a modle for the rotational
2638 +        diffusion properties of arbitrary shaped rigid molecules},
2639 +  journal = {Advan. Phys.},
2640 +  year = {1973},
2641 +  volume = {22},
2642 +  pages = {1-56},
2643   }
2644  
2645   @ARTICLE{Recio2004,
# Line 2909 | Line 3141 | Encoding: GBK
3141    uri = {<Go to ISI>://000230332400077},
3142   }
3143  
3144 + @BOOK{Tolman1979,
3145 +  title = {The Principles of Statistical Mechanics},
3146 +  publisher = {Dover Publications, Inc.},
3147 +  year = {1979},
3148 +  author = {R.~C. Tolman},
3149 +  address = {New York},
3150 +  chapter = {2},
3151 +  pages = {19-22},
3152 + }
3153 +
3154   @ARTICLE{Tu1995,
3155    author = {K. Tu and D. J. Tobias and M. L. Klein},
3156    title = {Constant pressure and temperature molecular dynamics simulation of
# Line 2968 | Line 3210 | Encoding: GBK
3210    annote = {Je891 Times Cited:680 Cited References Count:19},
3211    issn = {0021-9606},
3212    uri = {<Go to ISI>://A1992JE89100044},
3213 + }
3214 +
3215 + @BOOK{Varadarajan1974,
3216 +  title = {Lie groups, Lie algebras, and their representations},
3217 +  publisher = {Prentice-Hall},
3218 +  year = {1974},
3219 +  author = {V.S. Varadarajan},
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
3255 +        diffusion properties of arbitrary shaped rigid molecules},
3256 +  journal = {Proc. Natl. Acad. Sci.},
3257 +  year = {1979},
3258 +  volume = {76},
3259 +  pages = {6356-6360},
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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