-
Notifications
You must be signed in to change notification settings - Fork 183
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Replace hardcoded literature references by BibTeX
The citations were obtained from icp.bib.
- Loading branch information
Showing
29 changed files
with
417 additions
and
160 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,323 @@ | ||
| @Article{usta05a, | ||
| title = {{Lattice-Boltzmann simulations of the dynamics of polymer solutions in periodic and confined geometries}}, | ||
| author = {Usta, O. B. and Ladd, A. J. C. and Butler, J. E.}, | ||
| journal = {Journal of Chemical Physics}, | ||
| year = {2005}, | ||
| pages = {094902}, | ||
| volume = {122}, | ||
| doi = {10.1063/1.1854151}, | ||
| } | ||
| @Article{ladd94a, | ||
| title = {{Numerical simulations of particulate suspensions via a discretized Boltzmann equation. Part 1. Theoretical foundation}}, | ||
| author = {Ladd, A. J. C.}, | ||
| journal = {Journal of Fluid Mechanics}, | ||
| year = {1994}, | ||
| pages = {285--309}, | ||
| volume = {271}, | ||
| doi = {10.1017/S0022112094001771}, | ||
| } | ||
| @article{sonnenschein85a, | ||
| author = {Sonnenschein, Roland}, | ||
| title = {{An improved algorithm for molecular dynamics simulation of rigid molecules}}, | ||
| journal = {Journal of Computational Physics}, | ||
| volume = {59}, | ||
| number = {2}, | ||
| pages = {347-350}, | ||
| year = {1985}, | ||
| doi = {10.1016/0021-9991(85)90151-2}, | ||
| } | ||
| @article{neumann85b, | ||
| author = {Neumann, Martin}, | ||
| title = {{The dielectric constant of water. Computer simulations with the {MCY} potential}}, | ||
| journal = {The Journal of Chemical Physics}, | ||
| volume = {82}, | ||
| number = {12}, | ||
| pages = {5663-5672}, | ||
| year = {1985}, | ||
| doi = {10.1063/1.448553}, | ||
| } | ||
| @Article{wang01a, | ||
| author = {Wang, Zuowei and Holm, Christian}, | ||
| title = {{Estimate of the cutoff errors in the Ewald summation for dipolar systems}}, | ||
| journal = {The Journal of Chemical Physics}, | ||
| year = {2001}, | ||
| volume = {115}, | ||
| pages = {6351--6359}, | ||
| doi = {10.1063/1.1398588}, | ||
| } | ||
| @Article{brodka04a, | ||
| author = {Br\'{o}dka, A.}, | ||
| title = {{Ewald summation method with electrostatic layer correction for interactions of point dipoles in slab geometry}}, | ||
| journal = {Chemical Physics Letters}, | ||
| year = {2004}, | ||
| volume = {400}, | ||
| number = {1-3}, | ||
| pages = {62--67}, | ||
| doi = {10.1016/j.cplett.2004.10.086}, | ||
| } | ||
| @Article{dhumieres09a, | ||
| title = {{Viscosity independent numerical errors for lattice Boltzmann models: from recurrence equations to ``magic'' collision numbers}}, | ||
| author = {d'Humi\`{e}res, Dominique and Ginzburg, Irina}, | ||
| journal = {Computers \& Mathematics with Applications}, | ||
| year = {2009}, | ||
| number = {5}, | ||
| pages = {823--840}, | ||
| volume = {58}, | ||
| doi = {10.1016/j.camwa.2009.02.008} | ||
| } | ||
| @Article{dunweg07a, | ||
| author = {D\"{u}nweg, Burkhard and Schiller, Ulf D. and Ladd, Anthony J. C.}, | ||
| title = {{Statistical mechanics of the fluctuating lattice Boltzmann equation}}, | ||
| journal = {Physical Review E}, | ||
| year = {2007}, | ||
| volume = {76}, | ||
| number = {3}, | ||
| pages = {036704}, | ||
| doi = {10.1103/PhysRevE.76.036704}, | ||
| } | ||
| @Article{soddemann03a, | ||
| title = {{Dissipative particle dynamics: A useful thermostat for equilibrium and nonequilibrium molecular dynamics simulations}}, | ||
| author = {Soddemann, T. and D\"{u}nweg, B. and Kremer, K.}, | ||
| journal = {Physical Review E}, | ||
| year = {2003}, | ||
| number = {4}, | ||
| pages = {46702}, | ||
| volume = {68}, | ||
| doi = {10.1103/PhysRevE.68.046702}, | ||
| } | ||
| @Article{ahlrichs99a, | ||
| title = {{Simulation of a single polymer chain in solution by combining lattice Boltzmann and molecular dynamics}}, | ||
| author = {Ahlrichs, P. and D\"{u}nweg, B.}, | ||
| journal = {Journal of Chemical Physics}, | ||
| year = {1999}, | ||
| number = {17}, | ||
| pages = {8225--8239}, | ||
| volume = {111}, | ||
| doi = {10.1063/1.480156}, | ||
| } | ||
| @InCollection{duenweg09a, | ||
| title = {{Lattice Boltzmann simulations of soft matter systems}}, | ||
| author = {D\"{u}nweg, B. and Ladd, A. J. C.}, | ||
| booktitle = {{Advanced Computer Simulation Approaches for Soft Matter Sciences III}}, | ||
| publisher = {Springer-Verlag Berlin}, | ||
| year = {2009}, | ||
| address = {Berlin, Germany}, | ||
| pages = {89--166}, | ||
| series = {Advances in Polymer Science}, | ||
| type = {Review}, | ||
| volume = {221}, | ||
| doi = {10.1007/12_2008_4}, | ||
| issn = {0065-3195}, | ||
| } | ||
| @Article{arnold13c, | ||
| title = {{Efficient algorithms for electrostatic interactions including dielectric contrasts}}, | ||
| author = {Arnold, Axel and Breitsprecher, Konrad and Fahrenberger, Florian and Kesselheim, Stefan and Lenz, Olaf and Holm, Christian}, | ||
| journal = {Entropy}, | ||
| year = {2013}, | ||
| number = {11}, | ||
| pages = {4569--4588}, | ||
| volume = {15}, | ||
| doi = {10.3390/e15114569}, | ||
| issn = {1099-4300}, | ||
| } | ||
| @Article{essmann95a, | ||
| title = {{A smooth Particle Mesh Ewald method}}, | ||
| author = {Essmann, U. and Perera, L. and Berkowitz, M. L. and Darden, T. and Lee, H. and Pedersen, L.}, | ||
| journal = {Journal of Chemical Physics}, | ||
| year = {1995}, | ||
| pages = {8577}, | ||
| volume = {103}, | ||
| doi = {10.1063/1.470117}, | ||
| } | ||
| @Article{tyagi10a, | ||
| author = {Tyagi, Sandeep and S\"{u}zen, Mehmet and Sega, Marcello and Barbosa, Marcia C. and Kantorovich, Sofia S. and Holm, Christian}, | ||
| title = {{An iterative, fast, linear-scaling method for computing induced charges on arbitrary dielectric boundaries}}, | ||
| journal = {The Journal of Chemical Physics}, | ||
| year = {2010}, | ||
| volume = {132}, | ||
| pages = {154112}, | ||
| doi = {10.1063/1.3376011}, | ||
| } | ||
| @Article{arnold02a, | ||
| author = {Arnold, Axel and Holm, Christian}, | ||
| title = {{{MMM2D}: A fast and accurate summation method for electrostatic interactions in {2D} slab geometries}}, | ||
| journal = {Computer Physics Communications}, | ||
| year = {2002}, | ||
| volume = {148}, | ||
| number = {3}, | ||
| pages = {327--348}, | ||
| doi = {10.1016/s0010-4655(02)00586-6}, | ||
| } | ||
| @article{marsili10a, | ||
| author = {Marsili, Simone and Signorini, Giorgio Federico and Chelli, Riccardo and Marchi, Massimo and Procacci, Piero}, | ||
| title = {{{ORAC}: A molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level}}, | ||
| journal = {Journal of Computational Chemistry}, | ||
| volume = {31}, | ||
| number = {5}, | ||
| pages = {1106-1116}, | ||
| doi = {10.1002/jcc.21388}, | ||
| year = {2010}, | ||
| } | ||
| @Article{andersen83a, | ||
| title = {{Rattle: A "velocity" version of the shake algorithm for molecular dynamics calculations}}, | ||
| author = {Andersen, Hans C.}, | ||
| journal = {Journal of Computational Physics}, | ||
| year = {1983}, | ||
| pages = {24--34}, | ||
| volume = {52}, | ||
| doi = {10.1016/0021-9991(83)90014-1}, | ||
| } | ||
| @Article{guo02a, | ||
| title = {{Discrete lattice effects on the forcing term in the lattice Boltzmann method}}, | ||
| author = {Guo, Zhaoli and Zheng, Chuguang and Shi, Baochang}, | ||
| journal = {Physical Review E}, | ||
| year = {2002}, | ||
| number = {4}, | ||
| pages = {046308}, | ||
| volume = {65}, | ||
| doi = {10.1103/PhysRevE.65.046308}, | ||
| } | ||
| @incollection{burtscher11a, | ||
| author = {Burtscher, Martin and Pingali, Keshav}, | ||
| chapter = {6}, | ||
| title = {{An efficient CUDA implementation of the tree-based Barnes Hut n-body algorithm}}, | ||
| editor = {Hwu, Wen-mei W.}, | ||
| booktitle = {{GPU Computing Gems Emerald Edition}}, | ||
| publisher = {Morgan Kaufmann}, | ||
| address = {Boston}, | ||
| pages = {75-92}, | ||
| year = {2011}, | ||
| series = {Applications of GPU Computing Series}, | ||
| isbn = {978-0-12-384988-5}, | ||
| doi = {10.1016/B978-0-12-384988-5.00006-1}, | ||
| } | ||
| @Article{reed92a, | ||
| title = {{Monte Carlo study of titration of linear polyelectrolytes}}, | ||
| author = {Reed, C. E. and Reed, W. F.}, | ||
| journal = {Journal of Chemical Physics}, | ||
| year = {1992}, | ||
| pages = {1609}, | ||
| volume = {96}, | ||
| doi = {10.1063/1.462145}, | ||
| } | ||
| @Article{ladd01a, | ||
| title = {{Lattice-Boltzmann simulations of particle-fluid suspensions}}, | ||
| author = {Ladd, A. J. C. and Verberg, R.}, | ||
| journal = {Journal of Statistical Physics}, | ||
| year = {2001}, | ||
| number = {5/6}, | ||
| pages = {1191--1251}, | ||
| volume = {104}, | ||
| doi = {10.1023/A:1010414013942}, | ||
| } | ||
| @article{dupin08a, | ||
| author = {Dupin, M. M. and Halliday, I. and Care, C. M. and Munn, L. L.}, | ||
| title = {{Lattice Boltzmann modelling of blood cell dynamics}}, | ||
| journal = {International Journal of Computational Fluid Dynamics}, | ||
| volume = {22}, | ||
| number = {7}, | ||
| pages = {481-492}, | ||
| year = {2008}, | ||
| doi = {10.1080/10618560802238242}, | ||
| } | ||
| @inproceedings{zhang01b, | ||
| author={Zhang, Cha and Chen, Tsuhan}, | ||
| booktitle={{Proceedings 2001 International Conference on Image Processing (Cat. No.01CH37205)}}, | ||
| title={{Efficient feature extraction for {2D/3D} objects in mesh representation}}, | ||
| year={2001}, | ||
| volume={3}, | ||
| pages={935-938}, | ||
| doi={10.1109/ICIP.2001.958278}, | ||
| } | ||
| @book{kruger12a, | ||
| author={Kr\"{u}ger, Timm}, | ||
| title={{Computer simulation study of collective phenomena in dense suspensions of red blood cells under shear}}, | ||
| year={2012}, | ||
| publisher={Vieweg+Teubner Verlag}, | ||
| address={Wiesbaden}, | ||
| isbn={978-3-8348-2376-2}, | ||
| doi={10.1007/978-3-8348-2376-2}, | ||
| } | ||
| @article{gompper96a, | ||
| author={Gompper, G. and Kroll, D. M.}, | ||
| journal={Journal de Physique I France}, | ||
| number={10}, | ||
| pages={1305-1320}, | ||
| title={{Random surface discretizations and the renormalization of the bending rigidity}}, | ||
| volume={6}, | ||
| year={1996}, | ||
| doi={10.1051/jp1:1996246}, | ||
| } | ||
| @article{moss96a, | ||
| author={Moss, G. P.}, | ||
| journal={Pure and Applied Chemistry}, | ||
| number={12}, | ||
| pages={2193-2222}, | ||
| title={{Basic terminology of stereochemistry}}, | ||
| volume={68}, | ||
| year={1996}, | ||
| doi={10.1351/pac199668122193}, | ||
| } | ||
| @Article{cerda08d, | ||
| author = {Cerd\`{a}, Juan J. and Ballenegger, Vincent and Lenz, Olaf and Holm, Christian}, | ||
| title = {{{P3M} algorithm for dipolar interactions}}, | ||
| journal = {Journal of Chemical Physics}, | ||
| year = {2008}, | ||
| volume = {129}, | ||
| pages = {234104}, | ||
| doi = {10.1063/1.3000389}, | ||
| } | ||
| @PhdThesis{deserno00b, | ||
| author = {Deserno, Markus}, | ||
| title = {Counterion condensation for rigid linear polyelectrolytes}, | ||
| year = {2000}, | ||
| month = FEB, | ||
| url = {http://archimed.uni-mainz.de/pub/2000/0018}, | ||
| school = {Universit\"{a}t Mainz}, | ||
| } | ||
| @Article{ewald21a, | ||
| title = {{Die Berechnung optischer und elektrostatischer Gitterpotentiale}}, | ||
| author = {Ewald, P. P.}, | ||
| journal = {Annales de Physique}, | ||
| year = {1921}, | ||
| number = {3}, | ||
| pages = {253--287}, | ||
| volume = {369}, | ||
| doi = {10.1002/andp.19213690304}, | ||
| } | ||
| @Book{hockney88a, | ||
| title = {{Computer simulation using particles}}, | ||
| author = {Hockney, R. W. and Eastwood, J. W.}, | ||
| publisher = {CRC Press}, | ||
| year = {1988}, | ||
| isbn = {9780852743928}, | ||
| url = {https://www.crcpress.com/Computer-Simulation-Using-Particles/Hockney-Eastwood/p/book/9780852743928}, | ||
| } | ||
| @Article{deserno98a, | ||
| author = {Deserno, Markus and Holm, Christian}, | ||
| title = {{How to mesh up Ewald sums. I. A theoretical and numerical comparison of various particle mesh routines}}, | ||
| journal = {Journal of Chemical Physics}, | ||
| year = {1998}, | ||
| volume = {109}, | ||
| pages = {7678}, | ||
| doi = {10.1063/1.477414}, | ||
| } | ||
| @Article{deserno98b, | ||
| author = {Deserno, Markus and Holm, Christian}, | ||
| title = {{How to mesh up Ewald sums. II. An accurate error estimate for the Particle-Particle-Particle-Mesh algorithm}}, | ||
| journal = {Journal of Chemical Physics}, | ||
| year = {1998}, | ||
| volume = {109}, | ||
| pages = {7694}, | ||
| doi = {10.1063/1.477415}, | ||
| } | ||
| @InProceedings{deserno00e, | ||
| author = {Deserno, Markus and Holm, Christian and Limbach, Hans J\"{o}rg}, | ||
| title = {{How to mesh up Ewald sums}}, | ||
| booktitle = {{Molecular Dynamics on Parallel Computers}}, | ||
| year = {2000}, | ||
| editor = {Esser, R. and Grassberger, P. and Grotendorst, J. and Lewerenz, M.}, | ||
| pages = {319}, | ||
| doi = {10.1142/9789812793768_0023}, | ||
| address = {Singapore}, | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.