ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/tengDissertation/dissertation.bib
(Generate patch)

Comparing trunk/tengDissertation/dissertation.bib (file contents):
Revision 2789 by tim, Mon Jun 5 21:00:46 2006 UTC vs.
Revision 2839 by tim, Fri Jun 9 02:41:58 2006 UTC

# Line 88 | Line 88 | Encoding: GBK
88    uri = {<Go to ISI>://000232532000064},
89   }
90  
91 – @BOOK{Allen1987,
92 –  title = {Computer Simulations of Liquids},
93 –  publisher = {Oxford University Press},
94 –  year = {1987},
95 –  author = {M.~P. Allen and D.~J. Tildesley},
96 –  address = {New York},
97 – }
98 –
91   @ARTICLE{Allison1991,
92    author = {S. A. Allison},
93    title = {A Brownian Dynamics Algorithm for Arbitrary Rigid Bodies - Application
# Line 239 | Line 231 | Encoding: GBK
231    uri = {<Go to ISI>://000221146400009},
232   }
233  
242 – @ARTICLE{Barojas1973,
243 –  author = {J. Barojas and D. Levesque},
244 –  title = {Simulation of Diatomic Homonuclear Liquids},
245 –  journal = {Phys. Rev. A},
246 –  year = {1973},
247 –  volume = {7},
248 –  pages = {1092-1105},
249 – }
250 –
234   @ARTICLE{Barth1998,
235    author = {E. Barth and T. Schlick},
236    title = {Overcoming stability limitations in biomolecular dynamics. I. Combining
# Line 422 | 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 452 | Line 464 | Encoding: GBK
464    uri = {<Go to ISI>://000232228500058},
465   }
466  
455 – @ARTICLE{Berkov2005a,
456 –  author = {D. V. Berkov and N. L. Gorn},
457 –  title = {Stochastic dynamic simulations of fast remagnetization processes:
458 –        recent advances and applications},
459 –  journal = {Journal of Magnetism and Magnetic Materials},
460 –  year = {2005},
461 –  volume = {290},
462 –  pages = {442-448},
463 –  month = {Apr},
464 –  abstract = {Numerical simulations of fast remagnetization processes using stochastic
465 –        dynamics are widely used to study various magnetic systems. In this
466 –        paper, we first address several crucial methodological problems
467 –        of such simulations: (i) the influence of finite-element discretization
468 –        on simulated dynamics, (ii) choice between Ito and Stratonovich
469 –        stochastic calculi by the solution of micromagnetic stochastic equations
470 –        of motion and (iii) non-trivial correlation properties of the random
471 –        (thermal) field. Next, we discuss several examples to demonstrate
472 –        the great potential of the Langevin dynamics for studying fast remagnetization
473 –        processes in technically relevant applications: we present numerical
474 –        analysis of equilibrium magnon spectra in patterned structures,
475 –        study thermal noise effects on the magnetization dynamics of nanoelements
476 –        in pulsed fields and show some results for a remagnetization dynamics
477 –        induced by a spin-polarized current. (c) 2004 Elsevier B.V. All
478 –        rights reserved.},
479 –  annote = {Part 1 Sp. Iss. SI 922KU Times Cited:2 Cited References Count:25},
480 –  issn = {0304-8853},
481 –  uri = {<Go to ISI>://000228837600109},
482 – }
483 –
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 1017 | Line 1000 | Encoding: GBK
1000    uri = {<Go to ISI>://A1978FP21600004},
1001   }
1002  
1003 + @ARTICLE{Evans1977,
1004 +  author = {D. J. Evans},
1005 +  title = {Representation of Orientation Space},
1006 +  journal = {Molecular Physics},
1007 +  year = {1977},
1008 +  volume = {34},
1009 +  pages = {317-325},
1010 +  number = {2},
1011 +  annote = {Ds757 Times Cited:271 Cited References Count:18},
1012 +  issn = {0026-8976},
1013 +  uri = {<Go to ISI>://A1977DS75700002},
1014 + }
1015 +
1016   @ARTICLE{Fennell2004,
1017    author = {C. J. Fennell and J. D. Gezelter},
1018    title = {On the structural and transport properties of the soft sticky dipole
# Line 1127 | Line 1123 | Encoding: GBK
1123    uri = {<Go to ISI>://000083785700002},
1124   }
1125  
1130 – @BOOK{Goldstein2001,
1131 –  title = {Classical Mechanics},
1132 –  publisher = {Addison Wesley},
1133 –  year = {2001},
1134 –  author = {H. Goldstein and C. Poole and J. Safko},
1135 –  address = {San Francisco},
1136 –  edition = {3rd},
1137 – }
1138 –
1126   @ARTICLE{Gray2003,
1127    author = {J. J. Gray and S. Moughon and C. Wang and O. Schueler-Furman and
1128          B. Kuhlman and C. A. Rohl and D. Baker},
# Line 1372 | Line 1359 | Encoding: GBK
1359    uri = {<Go to ISI>://A1992JU25100002},
1360   }
1361  
1362 < @BOOK{Hockney1981,
1363 <  title = {Computer Simulation Using Particles},
1364 <  publisher = {McGraw-Hill},
1365 <  year = {1981},
1366 <  author = {R.W. Hockney and J.W. Eastwood},
1367 <  address = {New York},
1362 > @ARTICLE{Hoover1985,
1363 >  author = {W. G. Hoover},
1364 >  title = {Canonical Dynamics - Equilibrium Phase-Space Distributions},
1365 >  journal = {Physical Review A},
1366 >  year = {1985},
1367 >  volume = {31},
1368 >  pages = {1695-1697},
1369 >  number = {3},
1370 >  annote = {Acr30 Times Cited:1809 Cited References Count:11},
1371 >  issn = {1050-2947},
1372 >  uri = {<Go to ISI>://A1985ACR3000056},
1373   }
1374  
1375   @ARTICLE{Huh2004,
# Line 1403 | 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 1446 | Line 1478 | Encoding: GBK
1478    uri = {<Go to ISI>://000166676100020},
1479   }
1480  
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 –
1459 – @ARTICLE{Torre1977,
1460 –  author = {Jose Garcia De La Torre, V.A. Bloomfield},
1461 –  title = {Hydrodynamic properties of macromolecular complexes. I. Translation},
1462 –  journal = {Biopolymers},
1463 –  year = {1977},
1464 –  volume = {16},
1465 –  pages = {1747-1763},
1466 – }
1467 –
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 1620 | Line 1633 | Encoding: GBK
1633    uri = {<Go to ISI>://000181017300042},
1634   }
1635  
1623 – @BOOK{Leach2001,
1624 –  title = {Molecular Modeling: Principles and Applications},
1625 –  publisher = {Pearson Educated Limited},
1626 –  year = {2001},
1627 –  author = {A. Leach},
1628 –  address = {Harlow, England},
1629 –  edition = {2nd},
1630 – }
1631 –
1636   @ARTICLE{Leimkuhler1999,
1637    author = {B. Leimkuhler},
1638    title = {Reversible adaptive regularization: perturbed Kepler motion and classical
# Line 1657 | Line 1661 | Encoding: GBK
1661    uri = {<Go to ISI>://000080466800007},
1662   }
1663  
1660 – @BOOK{Leimkuhler2004,
1661 –  title = {Simulating Hamiltonian Dynamics},
1662 –  publisher = {Cambridge University Press},
1663 –  year = {2004},
1664 –  author = {B. Leimkuhler and S. Reich},
1665 –  address = {Cambridge},
1666 – }
1667 –
1664   @ARTICLE{Levelut1981,
1665    author = {A. M. Levelut and R. J. Tarento and F. Hardouin and M. F. Achard
1666          and G. Sigaud},
# Line 1755 | Line 1751 | Encoding: GBK
1751    uri = {<Go to ISI>://A1994QF46400002},
1752   }
1753  
1754 < @BOOK{Marion1990,
1755 <  title = {Classical Dynamics of Particles and Systems},
1756 <  publisher = {Academic Press},
1757 <  year = {1990},
1758 <  author = {J.~B. Marion},
1759 <  address = {New York},
1760 <  edition = {2rd},
1754 > @ARTICLE{Marrink1994,
1755 >  author = {S. J. Marrink and H. J. C. Berendsen},
1756 >  title = {Simulation of Water Transport through a Lipid-Membrane},
1757 >  journal = {Journal of Physical Chemistry},
1758 >  year = {1994},
1759 >  volume = {98},
1760 >  pages = {4155-4168},
1761 >  number = {15},
1762 >  month = {Apr 14},
1763 >  abstract = {To obtain insight in the process of water permeation through a lipid
1764 >        membrane, we performed molecular dynamics simulations on a phospholipid
1765 >        (DPPC)/water system with atomic detail. Since the actual process
1766 >        of permeation is too slow to be studied directly, we deduced the
1767 >        permeation rate indirectly via computation of the free energy and
1768 >        diffusion rate profiles of a water molecule across the bilayer.
1769 >        We conclude that the permeation of water through a lipid membrane
1770 >        cannot be described adequately by a simple homogeneous solubility-diffusion
1771 >        model. Both the excess free energy and the diffusion rate strongly
1772 >        depend on the position in the membrane, as a result from the inhomogeneous
1773 >        nature of the membrane. The calculated excess free energy profile
1774 >        has a shallow slope and a maximum height of 26 kJ/mol. The diffusion
1775 >        rate is highest in the middle of the membrane where the lipid density
1776 >        is low. In the interfacial region almost all water molecules are
1777 >        bound by the lipid headgroups, and the diffusion turns out to be
1778 >        1 order of magnitude smaller. The total transport process is essentially
1779 >        determined by the free energy barrier. The rate-limiting step is
1780 >        the permeation through the dense part of the lipid tails, where
1781 >        the resistance is highest. We found a permeation rate of 7(+/-3)
1782 >        x 10(-2) cm/s at 350 K, comparable to experimental values for DPPC
1783 >        membranes, if corrected for the temperature of the simulation. Taking
1784 >        the inhomogeneity of the membrane into account, we define a new
1785 >        ''four-region'' model which seems to be more realistic than the
1786 >        ''two-phase'' solubility-diffusion model.},
1787 >  annote = {Ng219 Times Cited:187 Cited References Count:25},
1788 >  issn = {0022-3654},
1789 >  uri = {<Go to ISI>://A1994NG21900040},
1790   }
1791  
1792   @ARTICLE{Marsden1998,
# Line 1799 | 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{McLachlan1998a,
1860 > @ARTICLE{McLachlan1998,
1861    author = {R. I. McLachlan and G. R. W. Quispel},
1862    title = {Generating functions for dynamical systems with symmetries, integrals,
1863          and differential invariants},
# Line 1829 | Line 1878 | Encoding: GBK
1878    uri = {<Go to ISI>://000071558900021},
1879   }
1880  
1881 < @ARTICLE{McLachlan1998,
1881 > @ARTICLE{McLachlan1998a,
1882    author = {R. I. McLachlan and G. R. W. Quispel and G. S. Turner},
1883    title = {Numerical integrators that preserve symmetries and reversing symmetries},
1884    journal = {Siam Journal on Numerical Analysis},
# Line 1877 | 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,
1958 +  author = {S. Melchionna and G. Ciccotti and B. L. Holian},
1959 +  title = {Hoover Npt Dynamics for Systems Varying in Shape and Size},
1960 +  journal = {Molecular Physics},
1961 +  year = {1993},
1962 +  volume = {78},
1963 +  pages = {533-544},
1964 +  number = {3},
1965 +  month = {Feb 20},
1966 +  abstract = {In this paper we write down equations of motion (following the approach
1967 +        pioneered by Hoover) for an exact isothermal-isobaric molecular
1968 +        dynamics simulation, and we extend them to multiple thermostating
1969 +        rates, to a shape-varying cell and to molecular systems, coherently
1970 +        with the previous 'extended system method'. An integration scheme
1971 +        is proposed together with a numerical illustration of the method.},
1972 +  annote = {Kq355 Times Cited:172 Cited References Count:17},
1973 +  issn = {0026-8976},
1974 +  uri = {<Go to ISI>://A1993KQ35500002},
1975   }
1976  
1977   @ARTICLE{Memmer2002,
# Line 1919 | Line 2014 | Encoding: GBK
2014    uri = {<Go to ISI>://000174410500001},
2015   }
2016  
1922 – @ARTICLE{Metropolis1949,
1923 –  author = {N. Metropolis and S. Ulam},
1924 –  title = {The $\mbox{Monte Carlo}$ Method},
1925 –  journal = {J. Am. Stat. Ass.},
1926 –  year = {1949},
1927 –  volume = {44},
1928 –  pages = {335-341},
1929 – }
1930 –
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 2071 | Line 2157 | Encoding: GBK
2157    uri = {<Go to ISI>://000172129300049},
2158   }
2159  
2074 – @BOOK{Olver1986,
2075 –  title = {Applications of Lie groups to differential equatitons},
2076 –  publisher = {Springer},
2077 –  year = {1986},
2078 –  author = {P.J. Olver},
2079 –  address = {New York},
2080 – }
2081 –
2160   @ARTICLE{Omelyan1998,
2161    author = {I. P. Omelyan},
2162    title = {On the numerical integration of motion for rigid polyatomics: The
# Line 2224 | Line 2302 | Encoding: GBK
2302    annote = {146XW Times Cited:66 Cited References Count:45},
2303    issn = {0163-1829},
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,
# Line 2268 | Line 2379 | Encoding: GBK
2379    uri = {<Go to ISI>://A1985AKB9300008},
2380   }
2381  
2271 – @ARTICLE{Rotne1969,
2272 –  author = {F. Perrin},
2273 –  title = {Variational treatment of hydrodynamic interaction in polymers},
2274 –  journal = {J. Chem. Phys.},
2275 –  year = {1969},
2276 –  volume = {50},
2277 –  pages = {4831¨C4837},
2278 – }
2279 –
2280 – @ARTICLE{Perrin1936,
2281 –  author = {F. Perrin},
2282 –  title = {Mouvement brownien d'un ellipsoid(II). Rotation libre et depolarisation
2283 –        des fluorescences. Translation et diffusion de moleculese ellipsoidales},
2284 –  journal = {J. Phys. Radium},
2285 –  year = {1936},
2286 –  volume = {7},
2287 –  pages = {1-11},
2288 – }
2289 –
2290 – @ARTICLE{Perrin1934,
2291 –  author = {F. Perrin},
2292 –  title = {Mouvement brownien d'un ellipsoid(I). Dispersion dielectrique pour
2293 –        des molecules ellipsoidales},
2294 –  journal = {J. Phys. Radium},
2295 –  year = {1934},
2296 –  volume = {5},
2297 –  pages = {497-511},
2298 – }
2299 –
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 2328 | Line 2410 | Encoding: GBK
2410    uri = {<Go to ISI>://000076497600007},
2411   }
2412  
2331 – @ARTICLE{Powles1973,
2332 –  author = {J.~G. Powles},
2333 –  title = {A general ellipsoid can not always serve as a modle for the rotational
2334 –        diffusion properties of arbitrary shaped rigid molecules},
2335 –  journal = {Advan. Phys.},
2336 –  year = {1973},
2337 –  volume = {22},
2338 –  pages = {1-56},
2339 – }
2340 –
2413   @ARTICLE{Recio2004,
2414    author = {J. Fernandez-Recio and M. Totrov and R. Abagyan},
2415    title = {Identification of protein-protein interaction sites from docking
# Line 2458 | Line 2530 | Encoding: GBK
2530    uri = {<Go to ISI>://000233775500001},
2531   }
2532  
2533 + @ARTICLE{Roux1991,
2534 +  author = {B. Roux and M. Karplus},
2535 +  title = {Ion-Transport in a Gramicidin-Like Channel - Dynamics and Mobility},
2536 +  journal = {Journal of Physical Chemistry},
2537 +  year = {1991},
2538 +  volume = {95},
2539 +  pages = {4856-4868},
2540 +  number = {12},
2541 +  month = {Jun 13},
2542 +  abstract = {The mobility of water, Na+. and K+ has been calculated inside a periodic
2543 +        poly-(L,D)-alanine beta-helix, a model for the interior of the gramicidin
2544 +        channel. Because of the different dynamical regimes for the three
2545 +        species (high barrier for Na+, low barrier for K+, almost free diffusion
2546 +        for water), different methods are used to calculate the mobilities.
2547 +        By use of activated dynamics and a potential of mean force determined
2548 +        previously (Roux, B.; Karplus, M. Biophys. J. 1991, 59, 961), the
2549 +        barrier crossing rate of Na+ ion is determined. The motion of Na+
2550 +        at the transition state is controlled by local interactions and
2551 +        collisions with the neighboring carbonyls and the two nearest water
2552 +        molecules. There are significant deviations from transition-state
2553 +        theory; the transmission coefficient is equal to 0.11. The water
2554 +        and K+ motions are found to be well described by a diffusive model;
2555 +        the motion of K+ appears to be controlled by the diffusion of water.
2556 +        The time-dependent friction functions of Na+ and K+ ions in the
2557 +        periodic beta-helix are calculated and analyzed by using a generalized
2558 +        Langevin equation approach. Both Na+ and K+ suffer many rapid collisions,
2559 +        and their dynamics is overdamped and noninertial. Thus, the selectivity
2560 +        sequence of ions in the beta-helix is not influenced strongly by
2561 +        their masses.},
2562 +  annote = {Fr756 Times Cited:97 Cited References Count:65},
2563 +  issn = {0022-3654},
2564 +  uri = {<Go to ISI>://A1991FR75600049},
2565 + }
2566 +
2567   @ARTICLE{Roy2005,
2568    author = {A. Roy and N. V. Madhusudana},
2569    title = {A frustrated packing model for the B-6-B-1-SmAP(A) sequence of phases
# Line 2576 | Line 2682 | Encoding: GBK
2682    annote = {194FM Times Cited:14 Cited References Count:32},
2683    issn = {0021-9991},
2684    uri = {<Go to ISI>://000080181500004},
2685 + }
2686 +
2687 + @ARTICLE{Sasaki2004,
2688 +  author = {Y. Sasaki and R. Shukla and B. D. Smith},
2689 +  title = {Facilitated phosphatidylserine flip-flop across vesicle and cell
2690 +        membranes using urea-derived synthetic translocases},
2691 +  journal = {Organic \& Biomolecular Chemistry},
2692 +  year = {2004},
2693 +  volume = {2},
2694 +  pages = {214-219},
2695 +  number = {2},
2696 +  abstract = {Tris(2-aminoethyl) amine derivatives with appended urea and sulfonamide
2697 +        groups are shown to facilitate the translocation of fluorescent
2698 +        phospholipid probes and endogenous phosphatidylserine across vesicle
2699 +        and erythrocyte cell membranes. The synthetic translocases appear
2700 +        to operate by binding to the phospholipid head groups and forming
2701 +        lipophilic supramolecular complexes which diffuse through the non-polar
2702 +        interior of the bilayer membrane.},
2703 +  annote = {760PX Times Cited:8 Cited References Count:25},
2704 +  issn = {1477-0520},
2705 +  uri = {<Go to ISI>://000187843800012},
2706   }
2707  
2708   @ARTICLE{Satoh1996,
# Line 2598 | 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 2768 | Line 2909 | Encoding: GBK
2909    uri = {<Go to ISI>://000230332400077},
2910   }
2911  
2771 – @BOOK{Tolman1979,
2772 –  title = {The Principles of Statistical Mechanics},
2773 –  publisher = {Dover Publications, Inc.},
2774 –  year = {1979},
2775 –  author = {R.~C. Tolman},
2776 –  address = {New York},
2777 –  chapter = {2},
2778 –  pages = {19-22},
2779 – }
2780 –
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 2837 | Line 2968 | Encoding: GBK
2968    annote = {Je891 Times Cited:680 Cited References Count:19},
2969    issn = {0021-9606},
2970    uri = {<Go to ISI>://A1992JE89100044},
2840 – }
2841 –
2842 – @BOOK{Varadarajan1974,
2843 –  title = {Lie groups, Lie algebras, and their representations},
2844 –  publisher = {Prentice-Hall},
2845 –  year = {1974},
2846 –  author = {V.S. Varadarajan},
2847 –  address = {New York},
2971   }
2972  
2850 – @ARTICLE{Wegener1979,
2851 –  author = {W.~A. Wegener, V.~J. Koester and R.~M. Dowben},
2852 –  title = {A general ellipsoid can not always serve as a modle for the rotational
2853 –        diffusion properties of arbitrary shaped rigid molecules},
2854 –  journal = {Proc. Natl. Acad. Sci.},
2855 –  year = {1979},
2856 –  volume = {76},
2857 –  pages = {6356-6360},
2858 –  number = {12},
2859 – }
2860 –
2973   @ARTICLE{Withers2003,
2974    author = {I. M. Withers},
2975    title = {Effects of longitudinal quadrupoles on the phase behavior of a Gay-Berne

Diff Legend

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