--- trunk/chrisDissertation/dissertation.bib 2006/09/21 23:21:37 3016 +++ trunk/chrisDissertation/dissertation.bib 2006/09/27 14:43:49 3029 @@ -2,49 +2,57 @@ %% http://bibdesk.sourceforge.net/ -%% Created for Chris Fennell at 2006-09-21 15:41:30 -0400 +%% Created for Chris Fennell at 2006-09-27 10:13:35 -0400 %% Saved with string encoding Western (ASCII) -@string{acp = {Adv. Chem. Phys.}} +@string{acp = {Adv. Chem. Phys.}} -@string{cp = {Chem. Phys.}} +@string{ccp5 = {CCP5 Quarterly}} -@string{cpl = {Chem. Phys. Lett.}} +@string{cp = {Chem. Phys.}} +@string{cpl = {Chem. Phys. Lett.}} + @string{jacs = {J. Am. Chem. Soc.}} -@string{jcc = {J. Comp. Chem.}} +@string{jcc = {J. Comp. Chem.}} -@string{jcp = {J. Chem. Phys.}} +@string{jcp = {J. Chem. Phys.}} -@string{jml = {J. Mol. Liq.}} +@string{jcop = {J. Comp. Phys.}} -@string{jpc = {J. Phys. Chem.}} +@string{jml = {J. Mol. Liq.}} +@string{jpc = {J. Phys. Chem.}} + @string{jpca = {J. Phys. Chem. A}} @string{jpcb = {J. Phys. Chem. B}} -@string{mp = {Mol. Phys.}} +@string{mp = {Mol. Phys.}} +@string{pams = {Proc. Am. Math Soc.}} + @string{pccp = {Phys. Chem. Chem. Phys.}} @string{pnas = {Proc. Natl. Acad. Sci. USA}} -@string{pra = {Phys. Rev. A}} +@string{pr = {Phys. Rev.}} -@string{prb = {Phys. Rev. B}} +@string{pra = {Phys. Rev. A}} -@string{pre = {Phys. Rev. E}} +@string{prb = {Phys. Rev. B}} -@string{prl = {Phys. Rev. Lett.}} +@string{pre = {Phys. Rev. E}} -@string{rmp = {Rev. Mod. Phys.}} +@string{prl = {Phys. Rev. Lett.}} +@string{rmp = {Rev. Mod. Phys.}} + @book{Tolman38, Address = {New York}, Author = {R.~C. Tolman}, @@ -58,7 +66,7 @@ Author = {D. Beeman}, Date-Added = {2006-09-20 14:44:19 -0400}, Date-Modified = {2006-09-20 14:45:33 -0400}, - Journal = {J. Comp. Phys.}, + Journal = jcop, Pages = {130-139}, Title = {Some Multistep Methods for Use in Molecular Dynamics Calculations}, Volume = {20}, @@ -91,7 +99,7 @@ Date-Added = {2006-09-18 14:20:06 -0400}, Date-Modified = {2006-09-18 14:27:13 -0400}, Doi = {10.1063/1.1931662}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/2005/Abascal_Tip4p-Ice_05.pdf}, Number = {23}, Pages = {234511}, @@ -104,7 +112,7 @@ Date-Added = {2006-09-18 09:40:15 -0400}, Date-Modified = {2006-09-18 09:41:55 -0400}, Doi = {10.1063/1.1862245}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/2005/Vega_MeltTempModels_05.pdf}, Number = {11}, Pages = {114507}, @@ -116,7 +124,7 @@ Author = {S.~C. Harvey and R.~K.-Z. Tan and T.~E. {Cheatham III}}, Date-Added = {2006-09-07 00:53:34 -0400}, Date-Modified = {2006-09-07 00:55:37 -0400}, - Journal = {J. Comp. Chem.}, + Journal = jcc, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Harvey_FlyingIceCube_98.pdf}, Number = {7}, Pages = {726-740}, @@ -128,7 +136,7 @@ Author = {L. Verlet}, Date-Added = {2006-09-06 12:19:09 -0400}, Date-Modified = {2006-09-20 14:22:53 -0400}, - Journal = {Phys. Rev.}, + Journal = pr, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Verlet_EqCorrFunc_67.pdf}, Number = {1}, Pages = {201-214}, @@ -140,7 +148,7 @@ Author = {L. Verlet}, Date-Added = {2006-09-06 12:16:19 -0400}, Date-Modified = {2006-09-20 14:22:43 -0400}, - Journal = {Phys. Rev.}, + Journal = pr, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Verlet_ClassicalFluids_67.pdf}, Number = {1}, Pages = {98-103}, @@ -152,7 +160,7 @@ Author = {C.~J. Thompson}, Date-Added = {2006-09-06 11:59:49 -0400}, Date-Modified = {2006-09-06 12:02:07 -0400}, - Journal = {CCP5 Quarterly}, + Journal = ccp5, Pages = {20-28}, Title = {Use of neighbor lists in molecular dynamics}, Volume = {8}, @@ -162,7 +170,7 @@ Author = {V. Kr\"{a}utler and W.~F. {van Gunsteren} and P.~H. H\"{u}nenberger}, Date-Added = {2006-09-04 00:17:15 -0400}, Date-Modified = {2006-09-04 00:29:36 -0400}, - Journal = {J. Comp. Chem.}, + Journal = jcc, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Krautler_FastSHAKE_01.pdf}, Number = {5}, Pages = {501-508}, @@ -174,7 +182,7 @@ Author = {W.~C. Swope and H.~C. Andersen and P.~H. Berens and K.~R. Wilson}, Date-Added = {2006-09-03 21:47:42 -0400}, Date-Modified = {2006-09-03 21:50:26 -0400}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Swope_VelocityVerlet_82.pdf}, Number = {1}, Pages = {637-649}, @@ -186,7 +194,7 @@ Author = {H.~F. Trotter}, Date-Added = {2006-09-03 18:05:35 -0400}, Date-Modified = {2006-09-03 18:07:32 -0400}, - Journal = {Proc. Am. Math Soc.}, + Journal = pams, Pages = {545-551}, Title = {On the product of Semi-Groups of Operators}, Volume = {10}, @@ -196,7 +204,7 @@ Author = {J. Barojas and D. Levesque and B. Quentrec}, Date-Added = {2006-09-03 14:32:02 -0400}, Date-Modified = {2006-09-03 14:34:00 -0400}, - Journal = {Phys. Rev. A}, + Journal = pra, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/OldPapers/Barojas_EulerSwitch_73.pdf}, Number = {3}, Pages = {1092-1105}, @@ -209,7 +217,7 @@ Date-Added = {2006-08-28 07:48:49 -0400}, Date-Modified = {2006-08-28 07:50:59 -0400}, Doi = {10.1002/jcc.540130515}, - Journal = {J. Comp. Chem.}, + Journal = jcc, Number = {5}, Pages = {651-656}, Title = {Polynomial path for the calculation of liquid state free energies from computer simulations tested on liquid water}, @@ -220,7 +228,7 @@ Author = {L. Pauling}, Date-Added = {2006-08-27 22:01:49 -0400}, Date-Modified = {2006-08-27 22:03:59 -0400}, - Journal = {J. Am. Chem. Soc.}, + Journal = jacs, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/ResidualEntropy/Pauling_ResidEntropy_33.pdf}, Pages = {2680-2684}, Title = {The Structure and Entropy of Ice and of Other Crystals with Some Randomness of Atomic Arrangement}, @@ -232,7 +240,7 @@ Date-Added = {2006-08-27 21:44:08 -0400}, Date-Modified = {2006-08-27 21:47:37 -0400}, Doi = {10.1063/1.1562610}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Research/Water_Models/Nada_6siteH2O_03.pdf}, Number = {16}, Pages = {7401-7413}, @@ -244,7 +252,7 @@ Author = {J.~T. Kindt and C.~A. Schmuttenmaer}, Date-Added = {2006-08-27 13:55:26 -0400}, Date-Modified = {2006-08-27 13:56:35 -0400}, - Journal = {J. Phys. Chem.}, + Journal = jpc, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/ExperimentalWater/Kindt_FarIRDielectricOfPolarLiquids_96.pdf}, Number = {24}, Pages = {10373-10379}, @@ -386,7 +394,7 @@ Author = {J.~D. Bernal and R.~H. Fowler}, Date-Added = {2006-08-24 09:58:00 -0400}, Date-Modified = {2006-08-24 09:59:43 -0400}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/OldPapers/Bernal_TheoryOfWater_33.pdf}, Number = {8}, Pages = {515-548}, @@ -410,7 +418,7 @@ Date-Added = {2006-08-24 09:49:57 -0400}, Date-Modified = {2006-08-24 09:49:57 -0400}, Doi = {10.1063/1.2206581}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/MyPapers/Fennell_PairwiseSummationMethods_06.pdf}, Number = {23}, Pages = {234104(12)}, @@ -424,7 +432,7 @@ Author = {D.~J. Evans and S. Murad}, Date-Added = {2006-08-22 14:23:16 -0400}, Date-Modified = {2006-08-22 14:23:16 -0400}, - Journal = {Mol. Phys.}, + Journal = mp, Pages = {327-331}, Title = {Singularity-free algorithm for molecular dynamics simulation of rigid polyatomics}, Volume = 34, @@ -435,7 +443,7 @@ Date-Added = {2006-08-16 10:42:15 -0400}, Date-Modified = {2006-08-16 10:43:56 -0400}, Doi = {10.1063/1.1605941}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Aguado_MultipoleEwald_03.pdf}, Number = {14}, Pages = {7471-7483}, @@ -473,13 +481,13 @@ @article{Ryckaert77, Author = {J.-P. Ryckaert and G. Ciccotti and H.~J.~C. Berendsen}, Date-Added = {2006-08-06 17:05:44 -0400}, - Date-Modified = {2006-09-05 22:29:01 -0400}, + Date-Modified = {2006-09-27 10:08:56 -0400}, Doi = {10.1016/0021-9991(77)90098-5}, - Journal = {J. Comp. Phys.}, + Journal = jcop, Month = {March}, Number = {3}, Pages = {327-341}, - Title = {Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of {\it n}-alkanes}, + Title = {Numerical integration of the cartesian equations of motion of a system with constraints: \uppercase{m}olecular dynamics of {\it n}-alkanes}, Volume = {23}, Year = {1977}} @@ -487,7 +495,7 @@ Author = {R.~W. Impey and P.~A. Madden and I.~R. McDonald}, Date-Added = {2006-08-03 08:42:21 -0400}, Date-Modified = {2006-08-03 08:44:06 -0400}, - Journal = {Mol. Phys.}, + Journal = mp, Number = {3}, Pages = {513-539}, Title = {Spectroscopic and transport properties of water: \uppercase{M}odel calculations and the interpretation of experimental results}, @@ -498,7 +506,7 @@ Author = {K. Laasonen and M. Sprik and M. Parrinello and R. Car}, Date-Added = {2006-08-02 08:23:46 -0400}, Date-Modified = {2006-08-02 13:09:18 -0400}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Laasonen_AbInitioLiquidWater_93.pdf}, Number = {11}, Pages = {9080-9089}, @@ -511,7 +519,7 @@ Date-Added = {2006-08-02 08:15:11 -0400}, Date-Modified = {2006-08-02 08:16:16 -0400}, Doi = {www.pnas.org/cgi/doi/10.1073/pnas.0602982103}, - Journal = {Proc. Natl. Acad. Sci. USA}, + Journal = pnas, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/2006/Donchev_QuantumWater_06.pdf}, Number = {23}, Pages = {8613-8617}, @@ -534,7 +542,7 @@ Author = {M. Neumann and O. Steinhauser}, Date-Added = {2006-08-01 17:17:52 -0400}, Date-Modified = {2006-08-01 17:18:51 -0400}, - Journal = {Mol. Phys.}, + Journal = mp, Number = {2}, Pages = {437-454}, Title = {The influence of boundary conditions used in machine simulations on the structure of polar systems}, @@ -545,7 +553,7 @@ Author = {M. Neumann}, Date-Added = {2006-08-01 17:16:51 -0400}, Date-Modified = {2006-08-01 17:17:45 -0400}, - Journal = {Mol. Phys.}, + Journal = mp, Number = {4}, Pages = {841-858}, Title = {Dipole moment fluctuation formulas in computer simulations of polar systems}, @@ -580,7 +588,7 @@ Author = {M. Neumann and O. Steinhauser and G.~S. Pawley}, Date-Added = {2006-07-31 10:22:39 -0400}, Date-Modified = {2006-07-31 10:24:17 -0400}, - Journal = {Mol. Phys.}, + Journal = mp, Number = {1}, Pages = {97-113}, Title = {Consistent calculation of the static and frequency-dependent dielectric constant in computer simulations}, @@ -591,7 +599,7 @@ Author = {M. Neumann}, Date-Added = {2006-07-31 10:19:17 -0400}, Date-Modified = {2006-08-02 13:17:58 -0400}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/DielectricConst./Neumann_H2ODielConst_85.pdf}, Number = {12}, Pages = {5663-5672}, @@ -615,7 +623,7 @@ Author = {J.~M. Sorenson and G. Hura and R.~M. Glaeser and T. Head-Gordon}, Date-Added = {2006-07-21 11:41:31 -0400}, Date-Modified = {2006-07-21 11:44:44 -0400}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/ExperimentalWater/THGord_X-RayRadial_2000.pdf}, Number = {20}, Pages = {9149-9161}, @@ -638,7 +646,7 @@ Date-Added = {2006-07-20 15:28:29 -0400}, Date-Modified = {2006-07-20 15:29:45 -0400}, Doi = {10.1021/jp062700h}, - Journal = {J. Phys. Chem. B}, + Journal = jpcb, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/2006/Shi_MixedAtomisticCGIonChannel_06.pdf}, Title = {Mixed Atomistic and Coarse-Grained Molecular Dynamics: Simulation of a Membrane-Bound Ion Channel}, Year = {2006}} @@ -648,7 +656,7 @@ Date-Added = {2006-07-20 15:22:45 -0400}, Date-Modified = {2006-07-20 15:24:22 -0400}, Doi = {10.1063/1.2215614}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/2006/Weis_OrientationalOrderHardSphereDipole_06.pdf}, Number = {3}, Pages = {034504}, @@ -661,7 +669,7 @@ Date-Added = {2006-07-18 10:49:48 -0400}, Date-Modified = {2006-08-19 19:34:36 -0400}, Doi = {10.1063/1.1652434}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Research/Water_Models/Rick_TIP5P-E_04.pdf}, Number = {13}, Pages = {6085-6093}, @@ -674,7 +682,7 @@ Date-Added = {2006-07-18 10:18:42 -0400}, Date-Modified = {2006-07-18 14:21:48 -0400}, Doi = {10.1063/1.1683075}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Research/Water_Models/Horn_TIP4P-Ew_04.pdf}, Number = {20}, Pages = {9665-9678}, @@ -687,7 +695,7 @@ Date-Added = {2006-04-26 09:41:52 -0400}, Date-Modified = {2006-07-18 14:29:43 -0400}, Doi = {10.1016/j.cplett.2004.10.086}, - Journal = {Chem. Phys. Lett.}, + Journal = cpl, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Brodka_PointDipoleSlabEwald_04.pdf}, Pages = {62-67}, Title = {\uppercase{E}wald summation method with electrostatic layer correction for interactions of point dipoles in slab geometry}, @@ -699,7 +707,7 @@ Date-Added = {2006-04-26 09:40:15 -0400}, Date-Modified = {2006-07-18 14:35:47 -0400}, Doi = {10.1063/1.149195}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Joannis_SlabElectrostatics_02.pdf}, Number = {6}, Pages = {2503-2512}, @@ -711,7 +719,7 @@ Author = {M. Kawata and M. Mikami}, Date-Added = {2006-04-26 09:38:01 -0400}, Date-Modified = {2006-07-18 14:31:24 -0400}, - Journal = {Chem. Phys. Lett.}, + Journal = cpl, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Kawata_Rapid2DEwald_01.pdf}, Pages = {157-164}, Title = {Rapid calculation of two-dimensional \uppercase{E}wald summation}, @@ -723,7 +731,7 @@ Date-Added = {2006-04-26 09:36:09 -0400}, Date-Modified = {2006-07-18 14:29:18 -0400}, Doi = {10.1063/1.149195}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Arnold_SlabElectrostatics_02.pdf}, Number = {6}, Pages = {2496-2502}, @@ -745,7 +753,7 @@ Author = {N. Karasawa and W.~A. {Goddard III}}, Date-Added = {2006-03-21 09:11:44 -0500}, Date-Modified = {2006-03-21 09:13:00 -0500}, - Journal = {J. Phys. Chem.}, + Journal = jpc, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Karasawa_LatticSumConvergence_89.pdf}, Pages = {7320-7327}, Title = {Acceleration of Convergence for Lattice Sums}, @@ -768,7 +776,7 @@ Date-Added = {2006-03-19 20:02:25 -0500}, Date-Modified = {2006-09-05 22:30:02 -0400}, Doi = {10.1016/0021-9991(85)90002-6}, - Journal = {J. Comp. Phys.}, + Journal = jcop, Month = {September}, Number = {2}, Pages = {187-207}, @@ -801,7 +809,7 @@ Author = {B.~A. Luty and W.~F. {van~Gunsteren}}, Date-Added = {2006-03-18 20:59:19 -0500}, Date-Modified = {2006-03-18 21:00:33 -0500}, - Journal = {J. Phys. Chem.}, + Journal = jpc, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Luty_PPPMElectrostaticCalculations_96.pdf}, Number = {7}, Pages = {2581-2587}, @@ -825,7 +833,7 @@ Author = {P.~H. H\"{u}nenberger and J.~A. McCammon}, Date-Added = {2006-03-18 20:14:24 -0500}, Date-Modified = {2006-07-18 15:03:36 -0400}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Hunenberger_IonSolutionEwaldArtifacts_99.pdf}, Number = {4}, Pages = {1856-1872}, @@ -837,7 +845,7 @@ Author = {J.~E. Roberts and J. Schnitker}, Date-Added = {2006-03-18 20:12:23 -0500}, Date-Modified = {2006-07-18 15:11:50 -0400}, - Journal = {J. Phys. Chem.}, + Journal = jpc, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Roberts_BoundryConditionsIonWater_95.pdf}, Pages = {1322-1331}, Title = {Boundary Conditions in Sumulations of Aqueous Ionic Solutions: $\mbox{A}$ Systematic Study}, @@ -848,7 +856,7 @@ Author = {J.~E. Roberts and J. Schnitker}, Date-Added = {2006-03-18 20:10:37 -0500}, Date-Modified = {2006-03-18 20:12:19 -0500}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Roberts_IonSolventEwaldProbs_94.pdf}, Number = {6}, Pages = {5024-5031}, @@ -860,7 +868,7 @@ Author = {I.-C. Yeh and M.~L. Berkowitz}, Date-Added = {2006-03-18 19:24:27 -0500}, Date-Modified = {2006-07-18 14:34:09 -0400}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Yeh_SlabCorrectionEwald_99.pdf}, Number = {7}, Pages = {3155-3162}, @@ -892,7 +900,7 @@ Author = {S.~W. {de Leeuw} and J.~W. Perram}, Date-Added = {2006-03-18 19:05:18 -0500}, Date-Modified = {2006-03-18 19:07:48 -0500}, - Journal = {Mol. Phys.}, + Journal = mp, Pages = {1313-1327}, Title = {Electrostatic Lattice Sums for Semi-Infinite Lattices}, Volume = {37}, @@ -913,7 +921,7 @@ Author = {E. Spohr}, Date-Added = {2006-03-18 18:51:02 -0500}, Date-Modified = {2006-03-18 18:52:21 -0500}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Spohr_2DElectrostatics_97.pdf}, Number = {16}, Pages = {6342-6348}, @@ -925,7 +933,7 @@ Author = {D. York and W. Yang}, Date-Added = {2006-03-18 11:52:58 -0500}, Date-Modified = {2006-07-18 14:34:21 -0400}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/York_FFPoissonEwald_94.pdf}, Number = {4}, Pages = {3298-3300}, @@ -937,7 +945,7 @@ Author = {J. Shimada and H. Kaneko and T. Takada}, Date-Added = {2006-03-18 11:10:38 -0500}, Date-Modified = {2006-03-18 11:12:10 -0500}, - Journal = {J. Comp. Chem.}, + Journal = jcc, Pages = {867-78}, Title = {Efficient calculations of Coulombic interactions in biomolecular simulations with periodic boundary conditions}, Volume = {14}, @@ -977,7 +985,7 @@ Author = {J.~W. Perram and H.~G. Petersen and S.~W. {de Leeuw}}, Date-Added = {2006-03-17 13:42:04 -0500}, Date-Modified = {2006-03-17 13:59:01 -0500}, - Journal = {Mol. Phys.}, + Journal = mp, Pages = {875-893}, Title = {An algorithm for the simulation of condensed matter that grows as the 3/2 power of the number of particles}, Volume = {65}, @@ -1009,7 +1017,7 @@ Date-Added = {2006-03-16 09:49:22 -0500}, Date-Modified = {2006-07-18 15:18:48 -0400}, Doi = {10.1021/jp9937757}, - Journal = {J. Phys. Chem. B}, + Journal = jpcb, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/McCammon_ArtificialEwaldPeriodicityMD_00.pdf}, Number = {15}, Pages = {3668-3675}, @@ -1032,7 +1040,7 @@ Author = {H.~G. Petersen}, Date-Added = {2006-03-16 08:43:02 -0500}, Date-Modified = {2006-07-18 14:33:13 -0400}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Petersen_AccuracyofPME_95.pdf}, Month = {September}, Number = {9}, @@ -1045,7 +1053,7 @@ Author = {B.~A. Luty and I.~G. Tironi and W.~F. {van~Gunsteren}}, Date-Added = {2006-03-16 08:39:13 -0500}, Date-Modified = {2006-03-16 08:41:15 -0500}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Luty_LatticeSumElectrostatics_95.pdf}, Number = {8}, Pages = {3014-3021}, @@ -1057,7 +1065,7 @@ Author = {J.~A. Barker and R.~O. Watts}, Date-Added = {2006-03-15 18:58:17 -0500}, Date-Modified = {2006-07-18 14:44:12 -0400}, - Journal = {Mol. Phys.}, + Journal = mp, Pages = {789-792}, Title = {$\mbox{Monte Carlo}$ studies of the dielectric properties of water-like models}, Volume = {26}, @@ -1067,7 +1075,7 @@ Author = {D.~J. Adams and E.~M. Adams and G.~J. Hills}, Date-Added = {2006-03-15 17:46:36 -0500}, Date-Modified = {2006-03-15 17:48:04 -0500}, - Journal = {Mol. Phys.}, + Journal = mp, Number = {2}, Pages = {387-400}, Title = {The computer simulation of polar liquids}, @@ -1078,7 +1086,7 @@ Author = {A. Rahman and F.~H. Stillinger}, Date-Added = {2006-03-15 17:04:53 -0500}, Date-Modified = {2006-03-15 17:07:29 -0500}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Rahman_MDWater_71.pdf}, Month = {October}, Number = {7}, @@ -1091,7 +1099,7 @@ Author = {T.~A. Andrea and W.~C. Swope and H.~C. Andersen}, Date-Added = {2006-03-15 15:16:12 -0500}, Date-Modified = {2006-03-15 15:18:10 -0500}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Andrea_LongRangeForcesInWater_83.pdf}, Number = {9}, Pages = {4576-4584}, @@ -1103,7 +1111,7 @@ Author = {S.~G. Brush and H.~L. Sahlin and E. Teller}, Date-Added = {2006-03-13 16:55:39 -0500}, Date-Modified = {2006-07-18 14:48:59 -0400}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Brush_MCEwaldApplication_66.pdf}, Month = {September}, Number = {6}, @@ -1126,7 +1134,7 @@ Author = {R.~E. Jones and D.~H. Templeton}, Date-Added = {2006-03-13 13:25:58 -0500}, Date-Modified = {2006-07-18 14:24:50 -0400}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Jones_ChargeShapeFunctions_56.pdf}, Number = {5}, Pages = {1062-1063}, @@ -1138,7 +1146,7 @@ Author = {D.~M. Heyes}, Date-Added = {2006-03-13 13:12:45 -0500}, Date-Modified = {2006-03-13 13:14:27 -0500}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Keywords = {Empty Keywords}, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Heyes_CoulombChargeSpreading_81.pdf}, Number = {3}, @@ -1152,7 +1160,7 @@ Date-Added = {2006-03-12 19:26:45 -0500}, Date-Modified = {2006-09-05 22:30:22 -0400}, Doi = {10.1002/jcc.540150702}, - Journal = {J. Comp. Chem.}, + Journal = jcc, Number = {7}, Pages = {667-683}, Title = {New spherical-cutoff methods for long-range forces in macromolecular simulation}, @@ -1175,7 +1183,7 @@ Author = {U. Essmann and L. Perera and M.~L. Berkowitz and T. Darden and H. Lee and L.~G. Pedersen}, Date-Added = {2006-03-05 12:25:25 -0500}, Date-Modified = {2006-07-18 14:30:21 -0400}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Essmann_SmoothPME_95.pdf}, Number = {19}, Pages = {8577-8593}, @@ -1187,7 +1195,7 @@ Author = {S.~M. Kast and K.~F. Schmidt and B. Schilling}, Date-Added = {2006-02-18 16:47:26 -0500}, Date-Modified = {2006-02-18 16:51:25 -0500}, - Journal = {Chem. Phys. Lett.}, + Journal = cpl, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Kast_dampedCoulomb_03.pdf}, Pages = {398-404}, Title = {Integral equation theory for correcting truncation errors in molecular simulations}, @@ -1209,7 +1217,7 @@ Author = {D. Zahn and B. Schilling and S.~M. Kast}, Date-Added = {2006-02-15 09:21:27 -0500}, Date-Modified = {2006-07-18 15:19:05 -0400}, - Journal = {J. Phys. Chem. B}, + Journal = jpcb, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/WolfApplications/Zahn_enhancedWolfH2O_02.pdf}, Number = {41}, Pages = {10725-10732}, @@ -1221,7 +1229,7 @@ Author = {D. Wolf and P. Keblinski and S.~R. Phillpot and J. Eggebrecht}, Date-Added = {2006-02-15 09:09:39 -0500}, Date-Modified = {2006-07-17 12:28:56 -0400}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Wolf_Potential/Wolf_electroCorr_99.pdf}, Number = {17}, Pages = {8255-8282}, @@ -1240,7 +1248,7 @@ @article{Evans77, Author = {D.~J. Evans}, - Journal = {Mol. Phys.}, + Journal = mp, Pages = {317-325}, Title = {On the representation of orientation space}, Volume = 34, @@ -1356,7 +1364,7 @@ @article{Cascales98, Author = {J.~J.~L. Cascales and J.~G.~H. Cifre and J.~G. de~la~Torre}, Date-Modified = {2006-07-18 15:01:21 -0400}, - Journal = {J. Phys. Chem. B}, + Journal = jpcb, Pages = {625-631}, Title = {Anaesthetic mechanism on a model biological membrane: \uppercase{A} molecular dynamics simulation study}, Volume = 102, @@ -1364,7 +1372,7 @@ @article{Bassolino95, Author = {D. Bassolino and H.~E. Alper and T.~R. Stouch}, - Journal = {J. Am. Chem. Soc.}, + Journal = jacs, Pages = {4118-4129}, Title = {MECHANISM OF SOLUTE DIFFUSION THROUGH LIPID BILAYER-MEMBRANES BY MOLECULAR-DYNAMICS SIMULATION}, Volume = 117, @@ -1372,7 +1380,7 @@ @article{Alper95, Author = {H.~E. Alper and T.~R. Stouch}, - Journal = {J. Phys. Chem.}, + Journal = jpc, Pages = {5724-5731}, Title = {ORIENTATION AND DIFFUSION OF A DRUG ANALOG IN BIOMEMBRANES - MOLECULAR-DYNAMICS SIMULATIONS}, Volume = 99, @@ -1380,7 +1388,7 @@ @article{Sok92, Author = {R.~M. Sok and H.~J.~C. Berendsen and W.~F. van~Gunsteren}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Pages = {4699-4704}, Title = {MOLECULAR-DYNAMICS SIMULATION OF THE TRANSPORT OF SMALL MOLECULES ACROSS A POLYMER MEMBRANE}, Volume = 96, @@ -1397,7 +1405,7 @@ @article{Rabani97, Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne}, Date-Modified = {2006-07-18 15:11:37 -0400}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Pages = {6867-6876}, Title = {Calculating the hopping rate for self-diffusion on rough potential energy surfaces: $\mbox{C}$age correlations}, Volume = 107, @@ -1480,7 +1488,7 @@ Date-Modified = {2006-07-18 15:04:56 -0400}, Journal = pre, Pages = {4626-4641}, - Title = {Testing mode-coupling theory for a supercooled binary $\mbox{Lennard-Jones} mixtures: \uppercase{T}he van \uppercase{H}ove corraltion function}, + Title = {Testing mode-coupling theory for a supercooled binary $\mbox{Lennard-Jones}$ mixtures: \uppercase{T}he van \uppercase{H}ove corraltion function}, Volume = 51, Year = 1995} @@ -1570,7 +1578,7 @@ @article{Barenco95, Author = {A. Barenco and C.~H. Bennett and R. Cleve and D.~P. DiVincenzo and N. Margolus and P. Shor and T. Sleator and J.~A. Smolin and H. Weinfurter}, - Journal = {Phys. Rev. A}, + Journal = pra, Pages = {3457-3467}, Title = {elementary gates for quantum computation}, Volume = 52, @@ -1595,7 +1603,7 @@ @article{Calderbank96, Author = {A.~R. Calderbank and P.~W. Shor}, - Journal = {Phys. Rev. A}, + Journal = pra, Pages = {1098-1105}, Title = {Good quantum error-correcting codes exist}, Volume = 54, @@ -1811,7 +1819,7 @@ @article{Brooks83, Author = {B.~R. Brooks and R.~E. Bruccoleri and B.~D. Olafson and D.~J. States and S. Swaminathan and M. Karplus}, Date-Modified = {2006-07-18 15:00:32 -0400}, - Journal = {J. Comp. Chem.}, + Journal = jcc, Pages = {187-217}, Title = {\uppercase{CHARMM: A} Program for Macromolecular Energy, Minimization, and Dynamics Calculations}, Volume = 4, @@ -1936,7 +1944,7 @@ @article{Smith82, Author = {W. Smith}, Date-Modified = {2006-07-18 14:33:49 -0400}, - Journal = {CCP5 Quarterly}, + Journal = ccp5, Pages = {13-25}, Title = {Point multipoles in the \uppercase{E}wald summation}, Volume = 4, @@ -2195,7 +2203,7 @@ @article{Shlesinger84, Author = {M.~F. Shlesinger and E.~W. Montroll}, - Journal = {Proc. Natl. Acad. Sci. USA}, + Journal = pnas, Pages = {1280-1283}, Title = {On the Williams-Watts function of dielectric relaxation}, Volume = 81, @@ -2203,7 +2211,7 @@ @article{Klafter86, Author = {J. Klafter and M.~F. Shlesinger}, - Journal = {Proc. Natl. Acad. Sci. USA}, + Journal = pnas, Pages = {848-851}, Title = {On the relationship among three theories of relaxation in disordered systems}, Volume = 83, @@ -2340,7 +2348,7 @@ @article{Liu96, Author = {Y. Liu and T. Ichiye}, Date-Modified = {2006-08-22 14:39:40 -0400}, - Journal = {Chem. Phys. Lett.}, + Journal = cpl, Pages = {334-340}, Title = {The static dielectric constant of the soft sticky dipole model of liquid water: $\mbox{Monte Carlo}$ simulation}, Volume = 256, @@ -2349,7 +2357,7 @@ @article{Chandra99, Author = {A. Chandra and T. Ichiye}, Date-Modified = {2006-08-22 14:41:50 -0400}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Research/SSDStuff/Chandra_SSDdynamics_99.pdf}, Number = 6, Pages = {2701-2709}, @@ -2437,7 +2445,7 @@ @article{Darden93, Author = {T. Darden and D. York and L. Pedersen}, Date-Modified = {2006-07-18 15:01:45 -0400}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Darden_ParticleMeshEwald_93.pdf}, Number = 12, Pages = {10089-10092}, @@ -2448,7 +2456,7 @@ @article{Goetz98, Author = {R. Goetz and R. Lipowsky}, Date-Modified = {2006-07-18 15:03:05 -0400}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Number = 17, Pages = 7397, Title = {Computer simulations of bilayer membranes: \uppercase{S}elf-assembly and interfacial tension}, @@ -2476,7 +2484,7 @@ @article{Metropolis53, Author = {N. Metropolis and A.~W. Rosenbluth and M.~N. Rosenbluth and A.~H. Teller and E. Teller}, Date-Modified = {2006-03-09 10:44:24 -0500}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Metropolis_MCCalculations_53.pdf}, Pages = {1087-1092}, Title = {Equation of State Calculations by Fast Computing Machines}, @@ -2500,8 +2508,8 @@ Year = 1987} @article{Pearlman95, - Author = {David~A. Pearlman and David~A. Case and James~W. Caldwell and Wilson~S. Ross and Thomas~E. Cheatham~III and Steve DeBolt and David Ferguson and George Seibel and Peter Kollman}, - Date-Modified = {2006-07-18 14:56:08 -0400}, + Author = {David~A. Pearlman and David~A. Case and James~W. Caldwell and Wilson~S. Ross and Thomas~E. {Cheatham~III} and Steve DeBolt and David Ferguson and George Seibel and Peter Kollman}, + Date-Modified = {2006-09-27 10:00:28 -0400}, Journal = {Computer Physics Communications}, Pages = {1-41}, Title = {\uppercase{AMBER}, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics, and free energy calculations to simulate the structural and energetic properties of molecules}, @@ -2545,17 +2553,18 @@ @article{Soper86, Author = {A.~K. Soper and M.~G. Phillips}, + Date-Modified = {2006-09-27 10:08:19 -0400}, Journal = cp, Number = 1, Pages = {47-60}, - Title = {A new determination of the structure of water at 298K}, + Title = {A new determination of the structure of water at 298\uppercase{K}}, Volume = 107, Year = 1986} @article{Plimpton95, Author = {S. Plimpton}, Date-Modified = {2006-02-15 10:30:31 -0500}, - Journal = {J. Comp. Phys.}, + Journal = jcop, Pages = {1-19}, Title = {Fast Parallel Algorithms for Short-Range Molecular Dymanics}, Volume = 117, @@ -2713,7 +2722,7 @@ @article{Nina02, Author = {M. Nina and T. Simonson}, Date-Modified = {2006-07-18 15:08:00 -0400}, - Journal = {J. Phys. Chem. B}, + Journal = jpcb, Pages = {3696-3705}, Title = {Molecular Dynamics of the $\text{tRNA}^{\text{Ala}}$ Acceptor Stem: $\mbox{C}$omparison between Continuum Reaction Field and Particle-Mesh \uppercase{E}wald Electrostatic Treatments}, Volume = 106, @@ -2740,7 +2749,7 @@ @article{Marrink04, Author = {S.~J. Marrink and A.~H. de~Vries and A.~E. Mark}, Date-Modified = {2006-02-15 10:28:28 -0500}, - Journal = {J. Phys. Chem. B}, + Journal = jpcb, Pages = {750-760}, Title = {Coarse Grained Model for Semiquantitative Lipid Simulations}, Volume = 108, @@ -2749,7 +2758,7 @@ @article{Andersen83, Author = {H.~C. Andersen}, Date-Modified = {2006-09-05 22:28:45 -0400}, - Journal = {J. Comp. Phys.}, + Journal = jcop, Pages = {24-34}, Title = {\uppercase{RATTLE: A} Velocity Version of the Shake Algorithm for Molecular Dynamics Calculations}, Volume = 52, @@ -2758,7 +2767,7 @@ @article{Hura00, Author = {G. Hura and J.~M. Sorenson and R.~M. Glaeser and T. Head-Gordon}, Date-Modified = {2006-07-21 11:45:15 -0400}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/ExperimentalWater/THGord_X-RayH2O_2000.pdf}, Pages = {9140-9148}, Title = {A high-quality x-ray scattering experiment on liquid water at ambient conditions}, @@ -2786,7 +2795,7 @@ @article{Egberts88, Author = {E. Egberts and H.~J.~C. Berendsen}, Date-Modified = {2006-02-15 10:16:43 -0500}, - Journal = {J. Chem. Phys.}, + Journal = jcp, Pages = {3718-3732}, Title = {Molecular Dynamics Simulation of a smectic liquid crystal with atomic detail}, Volume = 89, @@ -2795,7 +2804,7 @@ @article{Holz00, Author = {M. Holz and S.~R. Heil and A. Sacco}, Date-Modified = {2006-08-06 14:07:16 -0400}, - Journal = {Phys. Chem. Chem. Phys.}, + Journal = pccp, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/ExperimentalWater/Holz_SelfDiffusionOfWaterFromNMR_00.pdf}, Pages = {4740-4742}, Title = {Temperature-dependent self-diffusion coefficients of water and six selected molecular liquids for calibration in accurate $^1$\uppercase{h nmr pfg} measurements}, @@ -2837,7 +2846,7 @@ @article{Klein01, Author = {J.~C. Shelley andf M.~Y. Shelley and R.~C. Reeder and S. Bandyopadhyay and M.~L. Klein}, Date-Modified = {2006-02-15 10:27:22 -0500}, - Journal = {J. Phys. Chem. B}, + Journal = jpcb, Pages = {4464-4470}, Title = {A Coarse Grain Model for Phospholipid Simulations}, Volume = 105, @@ -2846,7 +2855,7 @@ @article{Marrink03, Author = {S.~J. Marrink and A.~E. Mark}, Date-Modified = {2006-03-16 09:54:52 -0500}, - Journal = {J. Am. Chem. Soc.}, + Journal = jacs, Pages = {15233-15242}, Title = {Molecular Dynamics Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles}, Volume = 125, @@ -2959,7 +2968,7 @@ @article{Ponder87, Author = {J.~W. Ponder and F.~M. Richards}, Date-Modified = {2006-02-15 10:13:45 -0500}, - Journal = {J. Comp. Chem.}, + Journal = jcc, Number = 7, Pages = {1016-1024}, Title = {AN EFFICIENT NEWTON-LIKE METHOD FOR MOLECULAR MECHANICS ENERGY MINIMIZATION OF LARGE MOLECULES}, @@ -2997,7 +3006,7 @@ @article{Meineke05, Author = {M.~A. Meineke and C.~F. {Vardeman II} and T. Lin and C.~J. Fennell and J.~D. Gezelter}, Date-Modified = {2006-07-18 15:22:51 -0400}, - Journal = {J. Comp. Chem.}, + Journal = jcc, Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/MyPapers/Meineke_OOPSE_05.pdf}, Pages = {252-271}, Title = {$\mbox{OOPSE: A}$n Open Source Object-Oriented Parallel Simulation Engine for Molecular Dynamics}, @@ -3168,8 +3177,9 @@ @article{Gallagher03, Author = {K.~R. Gallagher and K.~A. Sharp}, + Date-Modified = {2006-09-27 10:13:16 -0400}, Journal = jacs, - Pages = 9853, + Pages = {9853-9860}, Title = {A New Angle on Heat Capacity Changes in Hydrophobic Solvation}, Volume = 125, Year = 2003}