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1 gezelter 3897 %% This BibTeX bibliography file was created using BibDesk.
2     %% http://bibdesk.sourceforge.net/
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5 gezelter 3945 %% Created for Dan Gezelter at 2013-09-03 16:58:47 -0400
6 gezelter 3897
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11    
12 gezelter 3945 @article{OOPSE,
13     Author = {Meineke, Matthew A. and Vardeman, Charles F. and Lin, Teng and Fennell, Christopher J. and Gezelter, J. Daniel},
14     Date-Added = {2013-09-03 20:42:45 +0000},
15     Date-Modified = {2013-09-03 20:42:45 +0000},
16     Doi = {10.1002/jcc.20161},
17     Issn = {1096-987X},
18     Journal = {Journal of Computational Chemistry},
19     Keywords = {OOPSE, molecular dynamics},
20     Number = {3},
21     Pages = {252--271},
22     Publisher = {Wiley Subscription Services, Inc., A Wiley Company},
23     Title = {OOPSE: An object-oriented parallel simulation engine for molecular dynamics},
24     Url = {http://dx.doi.org/10.1002/jcc.20161},
25     Volume = {26},
26     Year = {2005},
27     Bdsk-Url-1 = {http://dx.doi.org/10.1002/jcc.20161}}
28    
29     @article{Ewald,
30     Author = {C. J. Fennell and J. D. Gezelter},
31     Date-Added = {2013-09-03 20:42:37 +0000},
32     Date-Modified = {2013-09-03 20:42:37 +0000},
33     Journal = {J. Chem. Phys.},
34     Keywords = {Ewald and OpenMD},
35     Month = {June},
36     Pages = {234104},
37     Title = {Is the Ewald summation still necessary? Pairwise alternatives to the accepted standard for long-range electrostatics},
38     Volume = {124},
39     Year = {2006}}
40    
41     @misc{openmd,
42     Author = {J. Daniel Gezelter and Joseph Michalka and Shenyu Kuang and James Marr and Kelsey Stocker and Chunlei Li and Charles F. Vardeman and Teng Lin and Christopher J. Fennell and Xiuquan Sun and Kyle Daily and Yang Zheng and Matthew A. Meineke},
43     Date-Added = {2013-09-03 20:42:37 +0000},
44     Date-Modified = {2013-09-03 20:42:37 +0000},
45     Howpublished = {Available at {\tt http://openmd.org}},
46     Title = {{OpenMD, an Open Source Engine for Molecular Dynamics}}}
47    
48     @article{Buch:2008fk,
49     Abstract = {The physics of the ice crystal surface and its interaction with adsorbates are not only of fundamental interest but also of considerable importance to terrestrial and planetary chemistry. Yet the atomic-level structure of even the pristine ice surface at low temperature is still far from well understood. This computational study focuses on the pattern of dangling H and dangling O (lone pairs) atoms at the basal ice surface. Dangling atoms serve as binding sites for adsorbates capable of hydrogen- and electrostatic bonding. Extension of the well known orientational disorder (``proton disorder'') of bulk crystal ice to the surface would naturally suggest a disordered dangling atom pattern; however, extensive computer simulations employing two different empirical potentials indicate significant free energy preference for a striped phase with alternating rows of dangling H and dangling O atoms, as suggested long ago by Fletcher [Fletcher NH (1992) Philos Mag 66:109--115]. The presence of striped phase domains within the basal surface is consistent with the hitherto unexplained minor fractional peaks in the helium diffraction pattern observed 10 years ago. Compared with the disordered model, the striped model yields improved agreement between computations and experimental ppp-polarized sum frequency generation spectra.},
50     Author = {Buch, V. and Groenzin, H. and Li, I. and Shultz, M. J. and Tosatti, E.},
51     Date-Added = {2013-09-03 20:15:03 +0000},
52     Date-Modified = {2013-09-03 20:15:11 +0000},
53     Doi = {10.1073/pnas.0710129105},
54     Eprint = {http://www.pnas.org/content/105/16/5969.full.pdf+html},
55     Journal = {Proceedings of the National Academy of Sciences},
56     Number = {16},
57     Pages = {5969-5974},
58     Title = {Proton order in the ice crystal surface},
59     Url = {http://www.pnas.org/content/105/16/5969.abstract},
60     Volume = {105},
61     Year = {2008},
62     Bdsk-Url-1 = {http://www.pnas.org/content/105/16/5969.abstract},
63     Bdsk-Url-2 = {http://dx.doi.org/10.1073/pnas.0710129105}}
64    
65     @article{Wilson08,
66     Author = {Wilson, P. W. and Haymet, A. D. J.},
67     Date-Added = {2013-09-03 20:09:39 +0000},
68     Date-Modified = {2013-09-03 20:09:47 +0000},
69     Doi = {10.1021/jp804047x},
70     Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp804047x},
71     Journal = {The Journal of Physical Chemistry B},
72     Note = {PMID: 18720967},
73     Number = {37},
74     Pages = {11750-11755},
75     Title = {Workman−Reynolds Freezing Potential Measurements between Ice and Dilute Salt Solutions for Single Ice Crystal Faces},
76     Url = {http://pubs.acs.org/doi/abs/10.1021/jp804047x},
77     Volume = {112},
78     Year = {2008},
79     Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp804047x},
80     Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp804047x}}
81    
82     @article{Nada12,
83     Author = {Nada, Hiroki and Furukawa, Yoshinori},
84     Date = {2012/07//print},
85     Date-Added = {2013-09-03 20:08:08 +0000},
86     Date-Modified = {2013-09-03 20:08:14 +0000},
87     Isbn = {0032-3896},
88     Journal = {Polym J},
89     Month = {07},
90     Number = {7},
91     Pages = {690--698},
92     Publisher = {The Society of Polymer Science, Japan},
93     Title = {Antifreeze proteins: computer simulation studies on the mechanism of ice growth inhibition},
94     Ty = {JOUR},
95     Url = {http://dx.doi.org/10.1038/pj.2012.13},
96     Volume = {44},
97     Year = {2012},
98     Bdsk-Url-1 = {http://dx.doi.org/10.1038/pj.2012.13}}
99    
100     @article{Smith05,
101     Author = {E. J. Smith and T. Bryk and A. D. J. Haymet},
102     Date-Added = {2013-09-03 20:03:24 +0000},
103     Date-Modified = {2013-09-03 20:03:30 +0000},
104     Doi = {10.1063/1.1953578},
105     Eid = {034706},
106     Journal = {The Journal of Chemical Physics},
107     Keywords = {chlorine; sodium; ice; water; positive ions; negative ions; free energy; solvation; molecular dynamics method; interface phenomena; melting point},
108     Number = {3},
109     Numpages = {16},
110     Pages = {034706},
111     Publisher = {AIP},
112     Title = {Free energy of solvation of simple ions: Molecular-dynamics study of solvation of Cl[sup -] and Na[sup +] in the ice/water interface},
113     Url = {http://link.aip.org/link/?JCP/123/034706/1},
114     Volume = {123},
115     Year = {2005},
116     Bdsk-Url-1 = {http://link.aip.org/link/?JCP/123/034706/1},
117     Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.1953578}}
118    
119     @article{Chapsky97,
120     Author = {Chapsky, Lars and Rubinsky, Boris},
121     Date = {1997/07/21},
122     Date-Added = {2013-09-03 20:02:20 +0000},
123     Date-Modified = {2013-09-03 20:02:28 +0000},
124     Id = {S0014-5793(97)00787-4},
125     Isbn = {0014-5793},
126     Journal = {FEBS letters},
127     Journal1 = {FEBS letters},
128     Journal2 = {FEBS Lett},
129     Keywords = {Antifreeze proteins; Protein adsorption; Temperature gradient thermometry; Ice},
130     Month = {07},
131     Number = {1},
132     Pages = {241--244},
133     Publisher = {Elsevier Science B.V.},
134     Title = {Kinetics of antifreeze protein-induced ice growth inhibition},
135     Ty = {ABST},
136     Url = {http://linkinghub.elsevier.com/retrieve/pii/S0014579397007874?showall=true},
137     Volume = {412},
138     Year = {1997},
139     Bdsk-Url-1 = {http://linkinghub.elsevier.com/retrieve/pii/S0014579397007874?showall=true}}
140    
141     @article{Sakai96,
142     Author = {Hideki Sakai},
143     Date-Added = {2013-09-03 20:01:26 +0000},
144     Date-Modified = {2013-09-03 20:01:36 +0000},
145     Doi = {http://dx.doi.org/10.1016/0039-6028(96)01033-3},
146     Issn = {0039-6028},
147     Journal = {Surface Science},
148     Keywords = {Surface melting},
149     Number = {3},
150     Pages = {387 - 392},
151     Title = {How does a slab-shaped solid melt?},
152     Url = {http://www.sciencedirect.com/science/article/pii/0039602896010333},
153     Volume = {348},
154     Year = {1996},
155     Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/0039602896010333},
156     Bdsk-Url-2 = {http://dx.doi.org/10.1016/0039-6028(96)01033-3}}
157    
158     @article{Sakai96B,
159     Author = {Hideki Sakai},
160     Date-Added = {2013-09-03 20:00:35 +0000},
161     Date-Modified = {2013-09-03 20:01:43 +0000},
162     Doi = {http://dx.doi.org/10.1016/0039-6028(95)01263-X},
163     Issn = {0039-6028},
164     Journal = {Surface Science},
165     Keywords = {Surface melting},
166     Number = {1--3},
167     Pages = {285 - 291},
168     Title = {Surface-induced melting of small particles},
169     Url = {http://www.sciencedirect.com/science/article/pii/003960289501263X},
170     Volume = {351},
171     Year = {1996},
172     Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/003960289501263X},
173     Bdsk-Url-2 = {http://dx.doi.org/10.1016/0039-6028(95)01263-X}}
174    
175     @article{Vanfleet95,
176     Author = {Richard R. Vanfleet and J.M. Mochel},
177     Date-Added = {2013-09-03 19:59:42 +0000},
178     Date-Modified = {2013-09-03 19:59:51 +0000},
179     Doi = {http://dx.doi.org/10.1016/0039-6028(95)00728-8},
180     Issn = {0039-6028},
181     Journal = {Surface Science},
182     Keywords = {Wetting},
183     Number = {1--2},
184     Pages = {40 - 50},
185     Title = {Thermodynamics of melting and freezing in small particles},
186     Url = {http://www.sciencedirect.com/science/article/pii/0039602895007288},
187     Volume = {341},
188     Year = {1995},
189     Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/0039602895007288},
190     Bdsk-Url-2 = {http://dx.doi.org/10.1016/0039-6028(95)00728-8}}
191    
192     @article{Granasy95,
193     Author = {Granasy, Laszlo},
194     Date-Added = {2013-09-03 19:58:11 +0000},
195     Date-Modified = {2013-09-03 19:58:23 +0000},
196     Doi = {10.1021/j100038a061},
197     Eprint = {http://pubs.acs.org/doi/pdf/10.1021/j100038a061},
198     Journal = {The Journal of Physical Chemistry},
199     Number = {38},
200     Pages = {14182-14187},
201     Title = {Diffuse Interface Analysis of Ice Nucleation in Undercooled Water},
202     Url = {http://pubs.acs.org/doi/abs/10.1021/j100038a061},
203     Volume = {99},
204     Year = {1995},
205     Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/j100038a061},
206     Bdsk-Url-2 = {http://dx.doi.org/10.1021/j100038a061}}
207    
208     @article{Han92,
209     Author = {Han, K. and Hale, B. N.},
210     Date-Added = {2013-09-03 19:57:15 +0000},
211     Date-Modified = {2013-09-03 19:57:24 +0000},
212     Doi = {10.1103/PhysRevB.45.29},
213     Issue = {1},
214     Journal = {Phys. Rev. B},
215     Month = {Jan},
216     Pages = {29--35},
217     Publisher = {American Physical Society},
218     Title = {Monte Carlo study of a simple model bulk-ice-Ih system: \textit{P} - \textit{T} melting behavior at constant volume},
219     Url = {http://link.aps.org/doi/10.1103/PhysRevB.45.29},
220     Volume = {45},
221     Year = {1992},
222     Bdsk-Url-1 = {http://link.aps.org/doi/10.1103/PhysRevB.45.29},
223     Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevB.45.29}}
224    
225     @article{Duman:2001qy,
226     Author = {Duman, J. G.},
227     Date-Added = {2013-09-03 19:23:31 +0000},
228     Date-Modified = {2013-09-03 19:23:31 +0000},
229     Isi = {Isi:000168071900015},
230     Issn = {0066-4278},
231     Journal = {Ann. Rev. Physiology},
232     Pages = {327--357},
233     Publication-Type = {J},
234     Title = {Antifreeze and Ice Nucleator Proteins in Terrestrial Arthropods},
235     Volume = {63},
236     Year = {2001}}
237    
238     @article{Meister29012013,
239     Abstract = {Antifreeze proteins (AFPs) are specific proteins that are able to lower the freezing point of aqueous solutions relative to the melting point. Hyperactive AFPs, identified in insects, have an especially high ability to depress the freezing point by far exceeding the abilities of other AFPs. In previous studies, we postulated that the activity of AFPs can be attributed to two distinct molecular mechanisms: (i) short-range direct interaction of the protein surface with the growing ice face and (ii) long-range interaction by protein-induced water dynamics extending up to 20 {\AA} from the protein surface. In the present paper, we combine terahertz spectroscopy and molecular simulations to prove that long-range protein--water interactions make essential contributions to the high antifreeze activity of insect AFPs from the beetle Dendroides canadensis. We also support our hypothesis by studying the effect of the addition of the osmolyte sodium citrate.},
240     Author = {Meister, Konrad and Ebbinghaus, Simon and Xu, Yao and Duman, John G. and DeVries, Arthur and Gruebele, Martin and Leitner, David M. and Havenith, Martina},
241     Date-Added = {2013-09-03 19:22:18 +0000},
242     Date-Modified = {2013-09-03 19:22:18 +0000},
243     Doi = {10.1073/pnas.1214911110},
244     Eprint = {http://www.pnas.org/content/110/5/1617.full.pdf+html},
245     Journal = {Proceedings of the National Academy of Sciences},
246     Number = {5},
247     Pages = {1617-1622},
248     Title = {Long-range protein--water dynamics in hyperactive insect antifreeze proteins},
249     Url = {http://www.pnas.org/content/110/5/1617.abstract},
250     Volume = {110},
251     Year = {2013},
252     Bdsk-Url-1 = {http://www.pnas.org/content/110/5/1617.abstract},
253     Bdsk-Url-2 = {http://dx.doi.org/10.1073/pnas.1214911110}}
254    
255 plouden 3942 @article{Nada05,
256     Author = {H. Nada and Y. Furukawa},
257     Date-Added = {2013-08-30 00:03:37 +0000},
258 gezelter 3945 Date-Modified = {2013-09-03 19:53:16 +0000},
259 plouden 3942 Journal = {Journal of Crystal Growth},
260     Pages = {242-256},
261 gezelter 3945 Title = {Anisotropy in growth kinetics at interfaces between proton-disordered hexagonal ice and water: A molecular dynamics study using the six-site model of \ce{H2O}},
262 plouden 3942 Volume = {283},
263     Year = {2005}}
264    
265     @article{Pit99,
266     Author = {R. Pitt and H. Hervet and L. L{\'e}ger},
267     Date-Added = {2013-08-29 23:04:53 +0000},
268     Date-Modified = {2013-08-29 23:06:52 +0000},
269     Journal = {Tribology Letters},
270     Pages = {147-152},
271     Title = {Friction and slip of a simple liquid at a solid surface},
272     Volume = {7},
273     Year = {1999}}
274    
275 plouden 3941 @article{Laage08,
276     Author = {D. Laage and J. T. Hynes},
277     Date-Added = {2013-08-25 18:29:26 +0000},
278     Date-Modified = {2013-08-25 18:30:32 +0000},
279     Journal = {J. Chem. Phys. B},
280     Pages = {14230-14242},
281     Title = {On the Molecular Mechanism of Water Reorientation},
282     Volume = {112},
283     Year = {2008}}
284    
285     @article{Laage11,
286     Author = {D. Laage and G. Stirnemann and F. Sterpone and R. Rey and J. T. Hynes},
287     Date-Added = {2013-08-25 18:27:56 +0000},
288     Date-Modified = {2013-08-25 18:29:23 +0000},
289     Journal = {Annu. Rev. Phys. Chem.},
290     Pages = {395-416},
291     Title = {Reorientation and Allies Dynamics in Water and Aqueous Solutions},
292     Volume = {62},
293     Year = {2011}}
294    
295     @article{Furse08,
296     Author = {K. E. Furse and S. A. Corcelli},
297     Date-Added = {2013-08-25 18:26:35 +0000},
298     Date-Modified = {2013-08-25 18:27:51 +0000},
299     Journal = {JACS},
300     Pages = {13103-13109},
301     Title = {The Dynamics of Water at DNA Interfaces: Computational Studies of Hoechst 33258 Bound to DNA},
302     Volume = {130},
303     Year = {2008}}
304    
305 plouden 3924 @article{Bresme08,
306     Author = {F. Bresme and A. Lervik and D. Bedeaux and Signe Kjelstrup},
307     Date-Added = {2013-07-16 15:35:54 +0000},
308     Date-Modified = {2013-07-16 15:36:46 +0000},
309     Journal = {Physical Review Letters},
310     Pages = {020602},
311     Volume = {101},
312     Year = {2008}}
313 gezelter 3915
314 plouden 3924 @article{Bryk04,
315     Author = {T. Bryk and A. D. J. Haymet},
316     Date-Added = {2013-07-15 18:33:15 +0000},
317     Date-Modified = {2013-07-15 18:34:17 +0000},
318     Journal = {Journal of Molecular Liquids},
319     Pages = {47-50},
320     Title = {Charge separation at the ice/water interface: a molecular dynamics simulation study of solute ions at the ice basal plane},
321     Volume = {112},
322     Year = {2004}}
323 gezelter 3915
324 plouden 3924 @article{Wilson10,
325     Author = {P. W. Wilson and A. D. J. Haymet},
326     Date-Added = {2013-07-15 18:25:02 +0000},
327     Date-Modified = {2013-07-15 18:26:04 +0000},
328     Journal = {J. Phys. Chem.},
329     Pages = {12585},
330     Title = {Effect of Ice Growth on the Measured WOrkman-Reynolds Freezing Potential between Ice and Dilute NaCl Soltutions},
331     Volume = {114},
332     Year = {2010}}
333 gezelter 3918
334 plouden 3924 @article{Wierzbicki07,
335     Author = {A. Wierzbicki and P. Dalal and T. E. Cheatham III and J. E. Knickelbein and A. D. J. Haymet and J. D. Madura},
336     Date-Added = {2013-07-15 18:19:56 +0000},
337     Date-Modified = {2013-07-15 18:21:13 +0000},
338     Journal = {Biophysical Journal},
339     Pages = {1442-1451},
340     Volume = {93},
341     Year = {2007}}
342 plouden 3899
343 plouden 3924 @article{Rick03,
344     Author = {S. W. Rick and A. D. J. Haymet},
345     Date-Added = {2013-07-15 16:05:32 +0000},
346     Date-Modified = {2013-07-15 16:06:41 +0000},
347     Journal = {J. Chem. Phys.},
348     Number = {20},
349     Pages = {9291-9296},
350     Title = {Dielectric constant and proton order and disorder in ice Ih: Monte Carlo computer simulations},
351     Volume = {118},
352     Year = {2003}}
353    
354 gezelter 3918 @article{Davidchack12,
355 plouden 3924 Author = {Davidchack, Ruslan L. and Handel, Richard and Anwar, Jamshed and Brukhno, Andrey V.},
356     Date-Added = {2013-07-11 21:25:47 +0000},
357     Date-Modified = {2013-07-11 21:34:56 +0000},
358     Doi = {10.1021/ct300193e},
359     Eprint = {http://pubs.acs.org/doi/pdf/10.1021/ct300193e},
360 gezelter 3918 Journal = {Journal of Chemical Theory and Computation},
361 plouden 3924 Number = {7},
362     Pages = {2383-2390},
363     Title = {Ice Ih--Water Interfacial Free Energy of Simple Water Models with Full Electrostatic Interactions},
364     Url = {http://pubs.acs.org/doi/abs/10.1021/ct300193e},
365 gezelter 3918 Volume = {8},
366     Year = {2012},
367 plouden 3924 Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/ct300193e},
368     Bdsk-Url-2 = {http://dx.doi.org/10.1021/ct300193e}}
369 gezelter 3918
370 plouden 3924 @article{Armstrong13,
371     Author = {J. A. Armstrong and F. Bresme},
372     Date-Added = {2013-07-11 19:35:13 +0000},
373     Date-Modified = {2013-07-12 19:40:42 +0000},
374     Journal = {J. Chem. Phys.},
375     Pages = {014504},
376     Title = {Water polarization induced by thermal gradients: Te extended simple point charge model (SPC/E)},
377     Volume = {139},
378     Year = {2013}}
379    
380     @article{Smith93,
381     Author = {P. E. Smith and W F. van Gunsteren},
382     Date-Added = {2013-06-19 17:39:04 +0000},
383     Date-Modified = {2013-07-12 19:44:47 +0000},
384     Journal = {Chem. Phys. Letters},
385     Number = {4},
386     Pages = {315-318},
387     Title = {The viscosity of SPC and SPC/E water at 277 and 300 K},
388     Volume = {215},
389     Year = {1993}}
390    
391     @article{Gonzalez10,
392     Author = {M. A. Gonzalez and J. L. F. Abascal},
393     Date-Added = {2013-06-19 17:30:15 +0000},
394     Date-Modified = {2013-07-12 19:42:54 +0000},
395     Journal = {J. Chem. Phys.},
396     Pages = {096101-1},
397     Title = {The shear viscosity of rigid water models},
398     Volume = {132},
399     Year = {2010}}
400    
401     @article{Balasubramanian96,
402     Author = {S. Balasubramanian and C. J. Mundy and M. L. Klein},
403     Date-Added = {2013-06-19 17:28:24 +0000},
404     Date-Modified = {2013-07-12 19:41:03 +0000},
405     Journal = {J. Chem. Phys.},
406     Number = {24},
407     Pages = {11190-11195},
408     Title = {Shear viscosity of polar fluids: Molecular dynamics calculations of water},
409     Volume = {105},
410     Year = {1996}}
411    
412     @article{Guo01,
413     Author = {G. Guo and Y. Zhang},
414     Date-Added = {2013-06-19 17:27:08 +0000},
415     Date-Modified = {2013-07-12 19:43:00 +0000},
416 plouden 3898 Journal = {Molecular Physics},
417 plouden 3924 Number = {4},
418     Pages = {283-289},
419     Title = {Equilibrium molecular dynamics calculation of the bulk viscosity of liquid water},
420     Volume = {99},
421     Year = {2001}}
422 plouden 3898
423 plouden 3924 @article{Hess02,
424     Author = {B. Hess},
425     Date-Added = {2013-06-19 17:19:04 +0000},
426     Date-Modified = {2013-06-19 17:20:27 +0000},
427     Journal = {J. Chem. Phys.},
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