-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathbibliography.bib
302 lines (264 loc) · 14 KB
/
bibliography.bib
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
Quantum computing for chemical and biomolecular product design@article{feynman_1982,
title = {\href{https://link.springer.com/article/10.1007/BF02650179}{Simulating physics with computers - International Journal of Theoretical Physics}},
url = {\url{https://link.springer.com/article/10.1007/BF02650179}},
journal = {SpringerLink},
publisher = {Kluwer Academic Publishers-Plenum Publishers},
author = {Feynman, Richard P.},
year = {1982},
month = {Jun},
doi = {https://doi.org/10.1007/BF02650179}
}
@misc{bit_definition,
author = {Wikipedia},
title = {\href{https://en.wikipedia.org/wiki/Bit}{Bit}},
url = {\url{https://en.wikipedia.org/wiki/Bit}},
journal = {Wikipedia}
}
@misc{logic_gate_definition,
author = {Wikipedia},
title = {\href{https://en.wikipedia.org/wiki/Logic_gate}{Logic Gate}},
url = {\url{https://en.wikipedia.org/wiki/Logic_gate}},
journal = {Wikipedia}
}
@misc{dirac_notation,
author = {Wikipedia},
title = {\href{https://en.wikipedia.org/wiki/Bra-ket_notation}{Dirac Notation}}
}
@misc{quantum_spin,
author = {Wikipedia},
title = {\href{https://en.wikipedia.org/wiki/Spin_(physics)}{Spin}}
}
@article{present_landscape_q,
author = {Hassija, Vikas and Chamola, Vinay and Saxena, Vikas and Chanana, Vaibhav and Parashari, Prakhar and Mumtaz, Shahid and Guizani, Mohsen},
title = {\href{https://doi.org/10.1049/iet-qtc.2020.0027}{Present landscape of quantum computing}},
journal = {IET Quantum Communication},
volume = {1},
number = {2},
pages = {42-48},
keywords = {quantum computing, cloud computing, quantum computers, quantum computing},
doi = {https://doi.org/10.1049/iet-qtc.2020.0027},
url = {https://ietresearch.onlinelibrary.wiley.com/doi/abs/10.1049/iet-qtc.2020.0027},
eprint = {https://ietresearch.onlinelibrary.wiley.com/doi/pdf/10.1049/iet-qtc.2020.0027},
abstract = {Quantum computing is currently a topic of interest that harnesses the phenomena of quantum mechanics. It can address several scientific challenges and generate new business opportunities. Recently, for the first time in the history of quantum computing, the authors are starting to see practical applications. Keeping this in mind, this article is designed to explore the field without any required prerequisites. The authors start with a brief overview of the fundamentals of quantum computing and also outline several applications. The timeline for widespread adoption cannot be predicted, but quite a few organisations have built the first generation of quantum computers using various hardware technologies. The authors have briefly covered the wide landscape of hardware technologies. The first generation of quantum computers can be programmed using available software development kits and accessed using online cloud services. Furthermore, the growing trend in investments and patents in the field of quantum computing is also presented. A major reason for this trend is the threat that quantum computers pose against cryptography.},
year = {2020}
}
@misc{superposition,
author = {Wikipedia},
title = {\href{https://en.wikipedia.org/wiki/Quantum_superposition}{Quantum Superposition}}
}
@misc{bloch_sphere,
author = {Wikipedia},
title = {\href{https://en.wikipedia.org/wiki/Bloch_sphere}{Bloch Sphere}}
}
@misc{laplace_eq,
author = {Wikipedia},
title = {\href{https://en.wikipedia.org/wiki/Laplace%27s_equation}{Laplace's Equation}}
}
@article{biom12111665,
author = {Bhowmick, Sumana and Jing, Tim and Wang, Wei and Zhang, Elena Y. and Zhang, Frank and Yang, Yanmin},
title = {In Silico Protein Folding Prediction of COVID-19 Mutations and Variants},
journal = {Biomolecules},
volume = {12},
year = {2022},
number = {11},
article-number = {1665},
url = {https://www.mdpi.com/2218-273X/12/11/1665},
pubmedid = {36359015},
issn = {2218-273X},
doi = {10.3390/biom12111665}
}
@article{modern_techniques_cov,
title = {A review of modern technologies for tackling COVID-19 pandemic},
journal = {Diabetes \& Metabolic Syndrome: Clinical Research \& Reviews},
volume = {14},
number = {4},
pages = {569-573},
year = {2020},
issn = {1871-4021},
doi = {https://doi.org/10.1016/j.dsx.2020.05.008},
url = {https://www.sciencedirect.com/science/article/pii/S1871402120301272},
author = {Aishwarya Kumar and Puneet Kumar Gupta and Ankita Srivastava}
}
@inbook{hager2010introduction,
title = {Introduction to high performance computing for scientists and engineers},
author = {Hager, Georg and Wellein, Gerhard},
year = {2010},
pages = {xvii},
publisher = {CRC Press}
}
@misc{frontier,
author = {TOP500},
title = {\href{https://www.top500.org/system/180047/}{Frontier} },
year = {2022}
}
@inbook{first_super,
author = {Eric Gottfrid Swedin},
chapter = {3},
pages = {57},
publisher = {Greenwood Press},
title = {Computers : the life story of a technology},
year = {2005}
}
@misc{supercomputer-power-flops,
author = {\textnormal{Our World In Data}},
title = {\href{ https://ourworldindata.org/grapher/supercomputer-power-flops}{ https://ourworldindata.org/grapher/supercomputer-power-flops}},
year = {2021}
}
@inbook{sciences1989supercomputers,
title = {Supercomputers: Directions in Technology and Applications},
author = {\textnormal{National Academy of Sciences} and Allan R. Hoffman and Joseph Frederick Traub and \textnormal{Academy Industry Program} and \textnormal{National Research Council}},
isbn = {9780309040884},
lccn = {89062945},
url = {https://books.google.co.uk/books?id=oqdiSfup-0UC},
year = {1989},
pages = {35-47},
publisher = {National Academies Press}
}
@article{Quantum-assisted,
issn = {1364503X},
url = {http://www.jstor.org/stable/25699187},
abstract = {Our understanding of the physics of biological molecules, such as proteins and DNA, is limited because the approximations we usually apply to model inert materials are not, in general, applicable to soft, chemically inhomogeneous systems. The configurational complexity of biomolecules means the entropic contribution to the free energy is a significant factor in their behaviour, requiring detailed dynamical calculations to fully evaluate. Computer simulations capable of taking all interatomic interactions into account are therefore vital. However, even with the best current supercomputing facilities, we are unable to capture enough of the most interesting aspects of their behaviour to properly understand how they work. This limits our ability to design new molecules, to treat diseases, for example. Progress in biomolecular simulation depends crucially on increasing the computing power available. Faster classical computers are in the pipeline, but these provide only incremental improvements. Quantum computing offers the possibility of performing huge numbers of calculations in parallel, when it becomes available. We discuss the current open questions in biomolecular simulation, how these might be addressed using quantum computation and speculate on the future importance of quantum-assisted biomolecular modelling.},
author = {Sarah A. Harris and Vivien M. Kendon},
journal = {Philosophical Transactions: Mathematical, Physical and Engineering Sciences},
number = {1924},
pages = {3581--3592},
publisher = {The Royal Society},
title = {Quantum-assisted biomolecular modelling},
urldate = {2023-02-07},
volume = {368},
year = {2010}
}
@article{MDsim,
author = {Peter L Freddolino and Feng Liu and Martin Gruebele and Klaus Schulten},
journal = {Biophys},
title = {Ten-microsecond molecular dynamics simulation of a fast-folding WW domain},
volume = {94},
pages = {L75-77},
year = {2008}
}
@article{Sanbonmatsu_2006,
doi = {10.1088/1742-6596/46/1/047},
url = {https://dx.doi.org/10.1088/1742-6596/46/1/047},
year = {2006},
month = {sep},
publisher = {},
volume = {46},
number = {1},
pages = {334},
author = {K Y Sanbonmatsu and C-S Tung},
title = {Large-scale simulations of the ribosome: a new landmark in computational biology},
journal = {Journal of Physics: Conference Series},
abstract = {Within computational biology, all-atom simulation is the most computationally demanding field, in terms of compute load, communication speed, and memory load. Here, we report molecular dynamics simulation results for the ribosome, using 2.64 × 106 atoms, the largest all-atom biomolecular simulation published to date. The ribosome is the largest asymmetric biological structure solved to date to atomic resolution (2.8 Å). While simulations requiring long-range electrostatic forces have been previously restricted to much smaller systems, breakthroughs in electrostatic force calculation and dynamic load balancing have enabled molecular dynamics simulations of large biomolecular complexes. The LANL Q Machine played a key role in enabling such large simulations to be performed. The LANL Q machine displays approximately 85% parallel scaling efficiency for the ribosome system on 1024 CPUs. Using the targeted molecular dynamics algorithm, we have simulated the ratelimiting step in genetic decoding by the ribosome. The simulations use experimentally determined ribosome structures in different functional states as the initial and final conditions, making our simulations entirely and rigorously consistent with these experimental data. The simulations have identified candidate 23S rRNA nucleotides important for the accommodation of tRNA into the ribosome during protein synthesis.}
}
@misc{complexity,
author = {Qef and Wikipedia},
title = {\href{https://commons.wikimedia.org/wiki/File:Complexity_subsets_pspace.svg}{Wikimedia Commons}}
}
@article{doi:10.1137/S0097539796300921,
author = {Bernstein, Ethan and Vazirani, Umesh},
title = {Quantum Complexity Theory},
journal = {SIAM Journal on Computing},
volume = {26},
number = {5},
pages = {1411-1473},
year = {1997},
doi = {10.1137/S0097539796300921},
url = {
https://doi.org/10.1137/S0097539796300921
},
eprint = {
https://doi.org/10.1137/S0097539796300921
}
}
@inproceedings{365700,
author = {Shor, P.W.},
booktitle = {Proceedings 35th Annual Symposium on Foundations of Computer Science},
title = {Algorithms for quantum computation: discrete logarithms and factoring},
year = {1994},
volume = {},
number = {},
pages = {124-134},
doi = {10.1109/SFCS.1994.365700}
}
@inbook{10.5555/270146,
author = {Knuth, Donald E.},
title = {The Art of Computer Programming, Volume 2 (3rd Ed.): Seminumerical Algorithms},
year = {1997},
isbn = {0201896842},
publisher = {Addison-Wesley Longman Publishing Co., Inc.},
pages = {403}
}
@article{Vandersypen_2001,
doi = {10.1038/414883a},
url = {https://doi.org/10.1038%2F414883a},
year = 2001,
month = {dec},
publisher = {Springer Science and Business Media {LLC}
},
volume = {414},
number = {6866},
pages = {883--887},
author = {Lieven M. K. Vandersypen and Matthias Steffen and Gregory Breyta and Costantino S. Yannoni and Mark H. Sherwood and Isaac L. Chuang},
title = {Experimental realization of Shor{\textquotesingle}s quantum factoring algorithm using nuclear magnetic resonance},
journal = {Nature}
}
@article{10.48550/arxiv.2011.06571,
doi = {10.48550/ARXIV.2011.06571},
url = {https://arxiv.org/abs/2011.06571},
author = {Lloyd, Seth and De Palma, Giacomo and Gokler, Can and Kiani, Bobak and Liu, Zi-Wen and Marvian, Milad and Tennie, Felix and Palmer, Tim},
keywords = {Quantum Physics (quant-ph), Chaotic Dynamics (nlin.CD), FOS: Physical sciences, FOS: Physical sciences},
title = {Quantum algorithm for nonlinear differential equations},
publisher = {arXiv},
year = {2020},
copyright = {Creative Commons Attribution 4.0 International}
}
@article{Berry_2014,
doi = {10.1088/1751-8113/47/10/105301},
url = {https://doi.org/10.1088%2F1751-8113%2F47%2F10%2F105301},
year = 2014,
month = {feb},
publisher = {{IOP} Publishing},
volume = {47},
number = {10},
pages = {105301},
author = {Dominic W Berry},
title = {High-order quantum algorithm for solving linear differential equations},
journal = {Journal of Physics A: Mathematical and Theoretical}
}
@article{10.48550/arxiv.0812.4423,
doi = {10.48550/ARXIV.0812.4423},
url = {https://arxiv.org/abs/0812.4423},
author = {Leyton, Sarah K. and Osborne, Tobias J.},
keywords = {Quantum Physics (quant-ph), FOS: Physical sciences, FOS: Physical sciences},
title = {A quantum algorithm to solve nonlinear differential equations},
publisher = {arXiv},
year = {2008},
copyright = {arXiv.org perpetual, non-exclusive license}
}
@article{5217220,
author = {Brigham, E. O. and Morrow, R. E.},
journal = {IEEE Spectrum},
title = {The fast Fourier transform},
year = {1967},
volume = {4},
number = {12},
pages = {63-70},
doi = {10.1109/MSPEC.1967.5217220}
}
@article{cooley_tukey_1965,
title = {An algorithm for the machine calculation of complex Fourier series},
url = {https://www.ams.org/journals/mcom/1965-19-090/S0025-5718-1965-0178586-1/},
journal = {Mathematics of Computation},
author = {Cooley, James W. and Tukey, John W.},
year = {1965},
month = {Jan}
}
@article{asaka_sakai_yahagi_2020,
title = {Quantum circuit for the fast fourier transform - quantum information processing},
url = {https://link.springer.com/article/10.1007/s11128-020-02776-5#citeas},
journal = {SpringerLink},
publisher = {Springer US},
author = {Asaka, Ryo and Sakai, Kazumitsu and Yahagi, Ryoko},
year = {2020},
month = {Aug}
}