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Revision 2639 by chrisfen, Mon Mar 20 02:00:26 2006 UTC

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43   @STRING{prl = "Phys. Rev. Lett."}
44  
45   @STRING{rmp = "Rev. Mod. Phys."}
46 +
47 +
48 + @article{Roux99,
49 +        Author = {B. Roux and T. Simonson},
50 +        Date-Added = {2006-03-19 20:10:18 -0500},
51 +        Date-Modified = {2006-03-19 20:12:10 -0500},
52 +        Journal = {Biophys. Chem.},
53 +        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Roux_ImplicitSolventModels_99.pdf},
54 +        Pages = {1-20},
55 +        Title = {Implicit solvent models},
56 +        Volume = {78},
57 +        Year = {1999}}
58 +
59 + @article{Rokhlin85,
60 +        Author = {V. Rokhlin},
61 +        Date-Added = {2006-03-19 20:02:25 -0500},
62 +        Date-Modified = {2006-03-19 20:04:19 -0500},
63 +        Doi = {10.1016/0021-9991(85)90002-6},
64 +        Journal = {J. Comput. Phys.},
65 +        Month = {September},
66 +        Number = {2},
67 +        Pages = {187-207},
68 +        Title = {Rapid solution of integral equations of classical potential theory},
69 +        Volume = {60},
70 +        Year = {1985}}
71 +
72 + @article{Grossfield00,
73 +        Author = {A. Grossfield and J. Sachs and T.~B. Woolf},
74 +        Date-Added = {2006-03-19 19:52:19 -0500},
75 +        Date-Modified = {2006-03-19 19:54:14 -0500},
76 +        Journal = {Proteins},
77 +        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Membrane/Grossfield_dipoleLatticeMembrane_00.pdf},
78 +        Pages = {211-223},
79 +        Title = {Dipole Lattice Membrane Model for Protein Calculations},
80 +        Volume = {41},
81 +        Year = {2000}}
82 +
83 + @article{Born20,
84 +        Author = {M. Born},
85 +        Date-Added = {2006-03-19 18:05:01 -0500},
86 +        Date-Modified = {2006-03-19 18:07:42 -0500},
87 +        Journal = {Z. Physik},
88 +        Pages = {45-48},
89 +        Title = {Volumen und hydratationswame der ionen},
90 +        Volume = {1},
91 +        Year = {1920}}
92 +
93 + @article{Luty96,
94 +        Author = {B.~A. Luty and W.~F. {van~Gunsteren}},
95 +        Date-Added = {2006-03-18 20:59:19 -0500},
96 +        Date-Modified = {2006-03-18 21:00:33 -0500},
97 +        Journal = {J. Phys. Chem.},
98 +        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Luty_PPPMElectrostaticCalculations_96.pdf},
99 +        Number = {7},
100 +        Pages = {2581-2587},
101 +        Title = {Calculating Electrostatic Interactions Using the Particle-Particle Particle-Mesh Method with Nonperiodic Long-Range Interactions},
102 +        Volume = {100},
103 +        Year = {1996}}
104 +
105 + @article{Rhee89,
106 +        Author = {Y.-J. Rhee and J.~W. Halley and J. Hautman and A. Rahman},
107 +        Date-Added = {2006-03-18 20:48:07 -0500},
108 +        Date-Modified = {2006-03-18 20:51:09 -0500},
109 +        Journal = {Phys. Rev. B},
110 +        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Rhee_finiteDimensionEwald_88.pdf},
111 +        Number = {1},
112 +        Pages = {36-42},
113 +        Title = {Ewald methods in molecular dynamics for systems of finite extent in one of three dimensions},
114 +        Volume = {40},
115 +        Year = {1989}}
116 +
117 + @article{Hunenberger99a,
118 +        Author = {P.~H. H\"{u}nenberger and J.~A. McCammon},
119 +        Date-Added = {2006-03-18 20:14:24 -0500},
120 +        Date-Modified = {2006-03-18 20:16:01 -0500},
121 +        Journal = {J. Chem. Phys.},
122 +        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Hunenberger_IonSolutionEwaldArtifacts_99.pdf},
123 +        Number = {4},
124 +        Pages = {1856-1872},
125 +        Title = {Ewald artifacts in computer simulations of ionic solvation and ion -- ion interaction: A continuum electrostatics study},
126 +        Volume = {110},
127 +        Year = {1999}}
128 +
129 + @article{Roberts95,
130 +        Author = {J.~E. Roberts and J. Schnitker},
131 +        Date-Added = {2006-03-18 20:12:23 -0500},
132 +        Date-Modified = {2006-03-18 20:13:36 -0500},
133 +        Journal = {J. Phys. Chem.},
134 +        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Roberts_BoundryConditionsIonWater_95.pdf},
135 +        Pages = {1322-1331},
136 +        Title = {Boundary Conditions in Sumulations of Aqueous Ionic Solutions: A Systematic Study},
137 +        Volume = {99},
138 +        Year = {1995}}
139 +
140 + @article{Roberts94,
141 +        Author = {J.~E. Roberts and J. Schnitker},
142 +        Date-Added = {2006-03-18 20:10:37 -0500},
143 +        Date-Modified = {2006-03-18 20:12:19 -0500},
144 +        Journal = {J. Chem. Phys.},
145 +        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Roberts_IonSolventEwaldProbs_94.pdf},
146 +        Number = {6},
147 +        Pages = {5024-5031},
148 +        Title = {How the unit cell surface charge distriubution affects the energetics of ion-solvent interactions in simulations},
149 +        Volume = {101},
150 +        Year = {1994}}
151 +
152 + @article{Yeh99,
153 +        Author = {I.-C. Yeh and M.~L. Berkowitz},
154 +        Date-Added = {2006-03-18 19:24:27 -0500},
155 +        Date-Modified = {2006-03-18 19:26:08 -0500},
156 +        Journal = {J. Chem. Phys.},
157 +        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Yeh_SlabCorrectionEwald_99.pdf},
158 +        Number = {7},
159 +        Pages = {3155-3162},
160 +        Title = {Ewald summation for systems with slab geometry},
161 +        Volume = {111},
162 +        Year = {1999}}
163 +
164 + @article{Parry76,
165 +        Author = {D.~E. Parry},
166 +        Date-Added = {2006-03-18 19:11:01 -0500},
167 +        Date-Modified = {2006-03-18 19:14:01 -0500},
168 +        Journal = {Surf. Sci.},
169 +        Pages = {195},
170 +        Title = {Errata: The electrostatic potential in the surface region of an ionic crystal},
171 +        Volume = {54},
172 +        Year = {1976}}
173 +
174 + @article{Parry75,
175 +        Author = {D.~E. Parry},
176 +        Date-Added = {2006-03-18 19:08:40 -0500},
177 +        Date-Modified = {2006-03-18 19:16:14 -0500},
178 +        Journal = {Surf. Sci.},
179 +        Pages = {433-440},
180 +        Title = {The electrostatic potential in the surface region of an ionic crystal},
181 +        Volume = {49},
182 +        Year = {1975}}
183 +
184 + @article{deLeeuw79,
185 +        Author = {S.~W. {de Leeuw} and J.~W. Perram},
186 +        Date-Added = {2006-03-18 19:05:18 -0500},
187 +        Date-Modified = {2006-03-18 19:07:48 -0500},
188 +        Journal = {Mol. Phys.},
189 +        Pages = {1313-1327},
190 +        Title = {Electrostatic Lattice Sums for Semi-Infinite Lattices},
191 +        Volume = {37},
192 +        Year = {1979}}
193 +
194 + @article{Heyes77,
195 +        Author = {D.~M. Heyes and M. Barber and J.~H.~R. Clarke},
196 +        Date-Added = {2006-03-18 19:02:16 -0500},
197 +        Date-Modified = {2006-03-18 19:04:48 -0500},
198 +        Journal = {J. Chem. Soc., Faraday Trans. II},
199 +        Number = {7},
200 +        Pages = {1485-1496},
201 +        Title = {Molecular dynamics computer simulation of surface properties of crystalline potassium chloride},
202 +        Volume = {73},
203 +        Year = {1977}}
204 +
205 + @article{Spohr97,
206 +        Author = {E. Spohr},
207 +        Date-Added = {2006-03-18 18:51:02 -0500},
208 +        Date-Modified = {2006-03-18 18:52:21 -0500},
209 +        Journal = {J. Chem. Phys.},
210 +        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Spohr_2DElectrostatics_97.pdf},
211 +        Number = {16},
212 +        Pages = {6342-6348},
213 +        Title = {Effect of electrostatic boundary conditions and system size on the interfacial properties of water and aqueous solutions},
214 +        Volume = {107},
215 +        Year = {1997}}
216 +
217 + @article{York94,
218 +        Author = {D. York and W. Yang},
219 +        Date-Added = {2006-03-18 11:52:58 -0500},
220 +        Date-Modified = {2006-03-18 11:54:19 -0500},
221 +        Journal = {J. Chem. Phys.},
222 +        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/York_FFPoissonEwald_94.pdf},
223 +        Number = {4},
224 +        Pages = {3298-3300},
225 +        Title = {The fast Fourier Poisson method for calculating Ewald sums},
226 +        Volume = {101},
227 +        Year = {1994}}
228 +
229 + @article{Shimada93,
230 +        Author = {J. Shimada and H. Kaneko and T. Takada},
231 +        Date-Added = {2006-03-18 11:10:38 -0500},
232 +        Date-Modified = {2006-03-18 11:12:10 -0500},
233 +        Journal = {J. Comp. Chem.},
234 +        Pages = {867-78},
235 +        Title = {Efficient calculations of Coulombic interactions in biomolecular simulations with periodic boundary conditions},
236 +        Volume = {14},
237 +        Year = {1993}}
238 +
239 + @article{Luty94,
240 +        Author = {B.~A. Luty and M.~E. Davis and I.~G. Tironi and W.~F. {van~Gunsteren}},
241 +        Date-Added = {2006-03-18 10:37:17 -0500},
242 +        Date-Modified = {2006-03-18 11:09:55 -0500},
243 +        Journal = {Mol. Simul.},
244 +        Pages = {11-20},
245 +        Title = {A comparison of particle-particle particle-mesh and Ewald methods for calculating electrostatic interactions in periodic systems},
246 +        Volume = {14},
247 +        Year = {1994}}
248 +
249 + @book{Hockney81,
250 +        Address = {New York},
251 +        Author = {R.~W. Hockney and J.~W. Eastwood},
252 +        Date-Added = {2006-03-18 10:33:19 -0500},
253 +        Date-Modified = {2006-03-18 10:35:04 -0500},
254 +        Publisher = {McGraw-Hill},
255 +        Title = {Computer Simulation Using Particles},
256 +        Year = {1981}}
257  
258 + @article{Sagui99,
259 +        Author = {C. Sagui and T.~A. Darden},
260 +        Date-Added = {2006-03-17 18:27:01 -0500},
261 +        Date-Modified = {2006-03-17 18:29:36 -0500},
262 +        Journal = {Annu. Rev. Biophys. Biomol. Struct.},
263 +        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Wolf_Potential/toCite/Darden_electrostaticInBiomolecules_99.pdf},
264 +        Pages = {155-179},
265 +        Title = {Molecular Dynamics Simulations of Biomolecules: Long-Range Electrostatic Effects},
266 +        Volume = {28},
267 +        Year = {1999}}
268  
269 + @article{Perram88,
270 +        Author = {J.~W. Perram and H.~G. Petersen and S.~W. {de Leeuw}},
271 +        Date-Added = {2006-03-17 13:42:04 -0500},
272 +        Date-Modified = {2006-03-17 13:59:01 -0500},
273 +        Journal = {Mol. Phys.},
274 +        Pages = {875-893},
275 +        Title = {An algorithm for the simulation of condensed matter that grows as the 3/2 power of the number of particles},
276 +        Volume = {65},
277 +        Year = {1988}}
278 +
279 + @article{Woodcock71,
280 +        Author = {L.~V. Woodcock and K. Singer},
281 +        Date-Added = {2006-03-17 11:14:17 -0500},
282 +        Date-Modified = {2006-03-17 11:16:52 -0500},
283 +        Journal = {Trans. Faraday Soc.},
284 +        Pages = {12-30},
285 +        Title = {Thermodynamic and Structural Properties of Liquid Ionic Salts Obtained by Monte Carlo Computation},
286 +        Volume = {67},
287 +        Year = {1971}}
288 +
289 + @article{Smith81,
290 +        Author = {E.~R. Smith},
291 +        Date-Added = {2006-03-16 13:47:17 -0500},
292 +        Date-Modified = {2006-03-16 13:48:34 -0500},
293 +        Journal = {Proc. R. Soc. London Ser. A},
294 +        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Smith_ElectrostaticEnergyInIonicCrystals_81.pdf},
295 +        Pages = {475-505},
296 +        Title = {Electrostatic Energy in Ionic Crystals},
297 +        Volume = {375},
298 +        Year = {1981}}
299 +
300 + @article{Weber00,
301 +        Author = {W. Weber and P.~H. H\"{u}nenberger and J.~A. McCammon},
302 +        Date-Added = {2006-03-16 09:49:22 -0500},
303 +        Date-Modified = {2006-03-16 09:51:17 -0500},
304 +        Doi = {10.1021/jp9937757},
305 +        Journal = {J. Phys. Chem. B},
306 +        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/McCammon_ArtificialEwaldPeriodicityMD_00.pdf},
307 +        Number = {15},
308 +        Pages = {3668-3675},
309 +        Title = {Molecular Dynamics Simulations of a Polyalanine Octapeptide under Ewald Boundary Conditions: Influence of Artificial Periodicity on Peptide Conformation},
310 +        Volume = {104},
311 +        Year = {2000}}
312 +
313 + @article{Hunenberger99b,
314 +        Author = {P.~H. H\"{u}nenberger and J.~A. McCammon},
315 +        Date-Added = {2006-03-16 09:45:10 -0500},
316 +        Date-Modified = {2006-03-18 20:16:16 -0500},
317 +        Journal = {Biophys. Chem.},
318 +        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/McCammon_ArtificialEwaldPeriodicity_99.pdf},
319 +        Pages = {69-88},
320 +        Title = {Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study},
321 +        Volume = {78},
322 +        Year = {1999}}
323 +
324 + @article{Petersen95,
325 +        Author = {H.~G. Petersen},
326 +        Date-Added = {2006-03-16 08:43:02 -0500},
327 +        Date-Modified = {2006-03-16 08:44:32 -0500},
328 +        Journal = {J. Chem. Phys.},
329 +        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Petersen_AccuracyofPME_95.pdf},
330 +        Month = {September},
331 +        Number = {9},
332 +        Pages = {3668-3679},
333 +        Title = {Accuracy and efficiency of the particle mesh Ewald method},
334 +        Volume = {103},
335 +        Year = {1995}}
336 +
337 + @article{Luty95,
338 +        Author = {B.~A. Luty and I.~G. Tironi and W.~F. {van~Gunsteren}},
339 +        Date-Added = {2006-03-16 08:39:13 -0500},
340 +        Date-Modified = {2006-03-16 08:41:15 -0500},
341 +        Journal = {J. Chem. Phys.},
342 +        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Luty_LatticeSumElectrostatics_95.pdf},
343 +        Number = {8},
344 +        Pages = {3014-3021},
345 +        Title = {Lattice-sum methods for calculating electrostatic interactions in molecular simulations},
346 +        Volume = {103},
347 +        Year = {1995}}
348 +
349 + @article{Barker73,
350 +        Author = {J.~A. Barker and R.~O. Watts },
351 +        Date-Added = {2006-03-15 18:58:17 -0500},
352 +        Date-Modified = {2006-03-18 11:36:56 -0500},
353 +        Journal = {Mol. Phys.},
354 +        Pages = {789-792},
355 +        Title = {Monte Carlo studies of the dielectric properties of water-like models},
356 +        Volume = {26},
357 +        Year = {1973}}
358 +
359 + @article{Adams79,
360 +        Author = {D.~J. Adams and E.~M. Adams and G.~J. Hills},
361 +        Date-Added = {2006-03-15 17:46:36 -0500},
362 +        Date-Modified = {2006-03-15 17:48:04 -0500},
363 +        Journal = {Mol. Phys.},
364 +        Number = {2},
365 +        Pages = {387-400},
366 +        Title = {The computer simulation of polar liquids},
367 +        Volume = {38},
368 +        Year = {1979}}
369 +
370 + @article{Rahman71,
371 +        Author = {A. Rahman and F.~H. Stillinger},
372 +        Date-Added = {2006-03-15 17:04:53 -0500},
373 +        Date-Modified = {2006-03-15 17:07:29 -0500},
374 +        Journal = {J. Chem. Phys.},
375 +        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Rahman_MDWater_71.pdf},
376 +        Month = {October},
377 +        Number = {7},
378 +        Pages = {3336-3359},
379 +        Title = {Molecular Dynamics Study of Liquid Water},
380 +        Volume = {55},
381 +        Year = {1971}}
382 +
383 + @article{Andrea83,
384 +        Author = {T.~A. Andrea and W.~C. Swope and H.~C. Andersen},
385 +        Date-Added = {2006-03-15 15:16:12 -0500},
386 +        Date-Modified = {2006-03-15 15:18:10 -0500},
387 +        Journal = {J. Chem. Phys.},
388 +        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/WaterSimulation/Andrea_LongRangeForcesInWater_83.pdf},
389 +        Number = {9},
390 +        Pages = {4576-4584},
391 +        Title = {The role of long ranged forces in determining the structure and properties of liquid water},
392 +        Volume = {79},
393 +        Year = {1983}}
394 +
395 + @article{Brush66,
396 +        Author = {S.~G. Brush and H.~L. Sahlin and E. Teller},
397 +        Date-Added = {2006-03-13 16:55:39 -0500},
398 +        Date-Modified = {2006-03-13 17:01:15 -0500},
399 +        Journal = {J. Chem. Phys.},
400 +        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Brush_MCEwaldApplication_66.pdf},
401 +        Month = {September},
402 +        Number = {6},
403 +        Pages = {2102-2118},
404 +        Title = {Monte Carlo Study of a One-Component Plasma. I},
405 +        Volume = {45},
406 +        Year = {1966}}
407 +
408 + @article{Ewald21,
409 +        Author = {P.~P. Ewald},
410 +        Date-Added = {2006-03-13 13:32:04 -0500},
411 +        Date-Modified = {2006-03-16 22:39:27 -0500},
412 +        Journal = {Ann. Physik},
413 +        Pages = {253-287},
414 +        Title = {Die Berechnung optischer und elektrostatischer Gitterpotential},
415 +        Volume = {64},
416 +        Year = {1921}}
417 +
418 + @article{Jones56,
419 +        Author = {R.~E. Jones and D.~H. Templeton},
420 +        Date-Added = {2006-03-13 13:25:58 -0500},
421 +        Date-Modified = {2006-03-13 13:27:15 -0500},
422 +        Journal = {J. Chem. Phys.},
423 +        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Jones_ChargeShapeFunctions_56.pdf},
424 +        Number = {5},
425 +        Pages = {1062-1063},
426 +        Title = {Optimum Atomic Shape for Bertaut Series},
427 +        Volume = {25},
428 +        Year = {1956}}
429 +
430 + @article{Heyes81,
431 +        Author = {D.~M. Heyes},
432 +        Date-Added = {2006-03-13 13:12:45 -0500},
433 +        Date-Modified = {2006-03-13 13:14:27 -0500},
434 +        Journal = {J. Chem. Phys.},
435 +        Keywords = {Empty Keywords},
436 +        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Heyes_CoulombChargeSpreading_81.pdf},
437 +        Number = {3},
438 +        Pages = {1924-1929},
439 +        Title = {Electrostatic potentials and fields in infinite point charge lattices},
440 +        Volume = {74},
441 +        Year = {1981}}
442 +
443 + @article{Steinbach94,
444 +        Author = {P.~J. Steinbach and B.~R. Brooks},
445 +        Date-Added = {2006-03-12 19:26:45 -0500},
446 +        Date-Modified = {2006-03-12 19:29:43 -0500},
447 +        Doi = {10.1002/jcc.540150702},
448 +        Journal = {J. Comput. Chem.},
449 +        Number = {7},
450 +        Pages = {667-683},
451 +        Title = {New spherical-cutoff methods for long-range forces in macromolecular simulation},
452 +        Volume = {15},
453 +        Year = {1994}}
454 +
455   @article{deLeeuw80,
456          Author = {S.~W. {de Leeuw} and J.~W. Perram and E.~R. Smith},
457          Date-Added = {2006-03-07 10:26:31 -0500},
# Line 65 | Line 472
472          Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Wolf_Potential/toCite/Essmann_SmoothPME_95.pdf},
473          Number = {19},
474          Pages = {8577-8593},
475 <        Title = {A smooth particle mesh Ewald method },
475 >        Title = {A smooth particle mesh Ewald method},
476          Volume = {103},
477          Year = {1995}}
478  
# Line 1444 | Line 1851
1851  
1852   @article{Darden93,
1853          Author = {T. Darden and D. York and L. Pedersen},
1854 <        Date-Modified = {2006-02-15 10:09:52 -0500},
1854 >        Date-Modified = {2006-03-16 08:37:25 -0500},
1855          Journal = {Journal of Chemical Physics},
1856 +        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Darden_ParticleMeshEwald_93.pdf},
1857          Number = 12,
1858          Pages = {10089-10092},
1859          Title = {Particle mesh Ewald: An $N \log N$ method for Ewald sums in large systems},
# Line 1853 | Line 2261
2261  
2262   @article{Marrink03,
2263          Author = {S.~J. Marrink and A.~E. Mark},
2264 <        Date-Modified = {2006-02-15 10:28:41 -0500},
2264 >        Date-Modified = {2006-03-16 09:54:52 -0500},
2265          Journal = {J. Am. Chem. Soc.},
2266          Pages = {15233-15242},
2267 <        Title = {Molecular Dynaimcs Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles},
2267 >        Title = {Molecular Dynamics Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles},
2268          Volume = 125,
2269          Year = 2003}
2270  

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