% Encoding: US-ASCII

@Book{abramowitz65a,
  title                    = {Handbook of mathematical functions: With formulas, graphs, and mathematical tables},
  author                   = {Abramowitz, M. and Stegun, I.},
  publisher                = {Dover Publications Inc.},
  year                     = {1965},
  address                  = {New York},
  edition                  = {9th},
  isbn                     = {9780486612720},
  url                      = {https://store.doverpublications.com/0486612724.html},
}

@article{ahlrichs99a,
author = {Ahlrichs, Patrick and D\"{u}nweg, Burkhard},
title = {Simulation of a single polymer chain in solution by combining lattice {B}oltzmann and molecular dynamics},
journal = {The Journal of Chemical Physics},
volume = {111},
number = {17},
pages = {8225--8239},
year = {1999},
doi = {10.1063/1.480156}
}

@book{allen17a,
  title={Computer simulation of liquids},
  author={Allen, Michael P. and Tildesley, Dominic J.},
  year={2017},
  publisher={Oxford University Press},
  doi={10.1093/oso/9780198803195.001.0001},
  isbn={9780198803195},
  edition={2nd},
}

@ARTICLE{andersen83a,
  author = {Andersen, Hans C.},
  title = {Rattle: A "Velocity" Version of the Shake Algorithm for Molecular Dynamics Calculations},
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  year = {1983},
  volume = {52},
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  pages = {24--34}
}

@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},
  pages = {327--348},
  number = {3},
  doi = {10.1016/S0010-4655(02)00586-6},
}

@ARTICLE{arnold02b,
  author = {Axel Arnold and Christian Holm},
  title = {A novel method for calculating electrostatic interactions in 2{D} periodic slab geometries},
  journal = {Chemical Physics Letters},
  year = {2002},
  volume = {354},
  pages = {324--330},
  doi = {10.1016/S0009-2614(02)00131-8},
}

@ARTICLE{arnold02c,
  author = {A. Arnold and J. de Joannis and C. Holm},
  title = {Electrostatics in Periodic Slab Geometries {I}},
  journal = {The Journal of Chemical Physics},
  year = {2002},
  volume = {117},
  pages = {2496--2502},
  doi = {10.1063/1.1491955},
}

@ARTICLE{arnold02d,
  title = {Electrostatics in Periodic Slab Geometries {II}},
  author = {A. Arnold and J. de Joannis and C. Holm},
  journal = {The Journal of Chemical Physics},
  year = {2002},
  volume = {117},
  pages = {2503--2512},
  doi = {10.1063/1.1491954},
}

@ARTICLE{arnold05a,
  author = {A. Arnold and C. Holm},
  title = {{MMM1D}: {A} method for calculating electrostatic interactions in one-dimensional periodic geometries},
  journal = {The Journal of Chemical Physics},
  year = {2005},
  volume = {123},
  pages = {144103},
  doi = {10.1063/1.2052647},
  number = {12}
}

@INCOLLECTION{arnold13a,
  author = {A. Arnold and O. Lenz and S. Kesselheim and R. Weeber and F. Fahrenberger and D. R\"{o}hm and P. Ko\v{s}ovan and C. Holm},
  title = {{ESPResSo}~3.1 --- Molecular Dynamics Software for Coarse-Grained Models},
  booktitle = {Meshfree Methods for Partial Differential Equations {VI}},
  publisher = {Springer Berlin Heidelberg},
  year = {2013},
  editor = {M. Griebel and M. A. Schweitzer},
  series = {Lecture Notes in Computational Science and Engineering},
  pages = {1--23},
  volume = {89},
  doi = {10.1007/978-3-642-32979-1_1},
}

@ARTICLE{ballenegger09a,
  author = {V. Ballenegger and A. Arnold and J. J. Cerda},
  title = {Simulations of non-neutral slab systems with long-range electrostatic interactions in two-dimensional periodic boundary conditions},
  journal = {The Journal of Chemical Physics},
  year = {2009},
  volume = {131},
  pages = {094107},
  number = {9},
  eid = {094107},
  doi = {10.1063/1.3216473},
  numpages = {10},
  publisher = {AIP},
}

@Article{banchio03a,
  author  = {Adolfo J. Banchio and John F. Brady},
  title   = {Accelerated Stokesian dynamics: Brownian motion},
  journal = {Journal of Chemical Physics},
  year    = {2003},
  volume  = {118},
  number  = {22},
  pages   = {10323},
  doi     = {10.1063/1.1571819},
}

@Article{bindgen21a,
  author = {Bindgen, Sebastian and Weik, Florian and Weeber, Rudolf and Koos, Erin and de Buyl, Pierre},
  title = {Lees-Edwards boundary conditions for translation invariant shear flow: implementation and transport properties},
  journal = {Physics of Fluids},
  year = {2021},
  volume = {33},
  number = {8},
  doi = {10.1063/5.0055396},
  pages = {083615},
}

@Article{brady88a,
  author  = {J. F. Brady and G. Bossis},
  title   = {Stokesian Dynamics},
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  year    = {1988},
  volume  = {20},
  pages   = {111--157},
  doi     = {10.1146/annurev.fl.20.010188.000551},
}

@ARTICLE{brodka04a,
  author = {Br\'{o}dka, A.},
  title = {{E}wald summation method with electrostatic layer correction for interactions of point dipoles in slab geometry},
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  year = {2004},
  number = {1--3},
  volume = {400},
  doi = {10.1016/j.cplett.2004.10.086},
  pages = {62--67}
}

@article{brown95a,
  title={A general pressure tensor calculation for molecular dynamics simulations},
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  journal={Molecular Physics},
  volume={84},
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  year={1995},
  doi={10.1080/00268979500100371},
  publisher={Taylor \&{} Francis}
}

@InCollection{burtscher11a,
author = {Burtscher, Martin and Pingali, Keshav},
chapter = {6},
title = {An efficient {CUDA} implementation of the tree-based {B}arnes {H}ut 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{cerda08d,
  title                    = {{P3M} algorithm for dipolar interactions},
  author                   = {Cerd\`{a}, Juan J. and Ballenegger, Vincent and Lenz, Olaf and Holm, Christian},
  journal                  = {The Journal of Chemical Physics},
  year                     = {2008},
  pages                    = {234104},
  volume                   = {129},
  doi                      = {10.1063/1.3000389},
}

@ARTICLE{cimrak12a,
author = {Cimr\'{a}k, I. and Gusenbauer, M. and Schrefl, T.},
title = {Modelling and simulation of processes in microfluidic devices for biomedical applications},
journal = {Computers \&{} Mathematics with Applications},
year = {2012},
number = {3},
volume = {64},
doi = {10.1016/j.camwa.2012.01.062},
pages = {278--288}
}

@ARTICLE{cimrak14a,
  author = {I. Cimr\'{a}k and M. Gusenbauer and I. Jan\v{c}igov\'{a}},
  title = {An {ESPResSo} implementation of elastic objects immersed in a fluid},
  journal = {Computer Physics Communications},
  year = {2014},
  volume = {185},
  pages = {900--907},
  doi = {10.1016/j.cpc.2013.12.013},
  number = {3}
}

@article{crowl10a,
author = {Crowl, Lindsay M. and Fogelson, Aaron L.},
title = {Computational model of whole blood exhibiting lateral platelet motion induced by red blood cells},
journal = {International Journal for Numerical Methods in Biomedical Engineering},
year = {2010},
volume = {26},
number = {3--4},
pages = {471--487},
doi = {10.1002/cnm.1274},
}

@article{debuyl18a,
  author = {de Buyl, Pierre},
  title = {{tidynamics}: {A} tiny package to compute the dynamics of stochastic and molecular simulations},
  journal = {Journal of Open Source Software},
  volume = {3},
  number = {28},
  pages = {877},
  year = {2018},
  doi = {10.21105/joss.00877},
}

@ARTICLE{degraaf16a,
  author = {de Graaf, Joost and Menke, Henri and Mathijssen, Arnold J.T.M. and Fabritius, Marc and Holm, Christian and Shendruk, Tyler N.},
  title = {Lattice-{B}oltzmann Hydrodynamics of Anisotropic Active Matter},
  journal = {The Journal of Chemical Physics},
  volume = {144},
  pages = {134106},
  year = {2016},
  doi = {10.1063/1.4944962},
}

@PHDTHESIS{deserno00b,
  author = {Deserno, Markus},
  title = {Counterion condensation for rigid linear polyelectrolytes},
  school = {Universit\"{a}t Mainz},
  year = {2000},
  month = feb,
  doi = {10.25358/openscience-1411},
}

@InProceedings{deserno00e,
  title = {How to mesh up {E}wald sums.},
  booktitle = {Molecular Dynamics on Parallel Computers},
  publisher = {World Scientific, Singapore},
  year = {2000},
  author = {Deserno, Markus and Holm, Christian and Limbach, Hans J\"{o}rg},
  editor = {Esser, R. and Grassberger, P. and Grotendorst, J. and Lewerenz, M.},
  pages = {319--320},
  doi = {10.1142/9789812793768_0023},
}

@ARTICLE{deserno98a,
  author = {Deserno, Markus and Holm, Christian},
  title = {How to mesh up {E}wald sums. {I.} {A} theoretical and numerical comparison of various particle mesh routines},
  journal = {The Journal of Chemical Physics},
  year = {1998},
  pages = {7678},
  volume = {109},
  doi = {10.1063/1.477414},
}

@ARTICLE{deserno98b,
  author = {Deserno, Markus and Holm, Christian},
  title = {How to mesh up {E}wald sums. {II.} {A}n accurate error estimate for the {P}article-{P}article-{P}article-{M}esh algorithm},
  journal = {The Journal of Chemical Physics},
  year = {1998},
  pages = {7694},
  volume = {109},
  doi = {10.1063/1.477415},
}

@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}
}

@BOOK{doi86a,
  title = {The Theory of Polymer Dynamics},
  author = {Doi, Masao and Edwards, Samuel Frederick},
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  year = {1986},
  isbn = {9780198519768},
}

@Article{dunweg07a,
  author    = {D\"{u}nweg, Burkhard and Schiller, Ulf D. and Ladd, Anthony J. C.},
  title     = {Statistical mechanics of the fluctuating lattice {B}oltzmann equation},
  journal   = {Physical Review E},
  year      = {2007},
  volume    = {76},
  number    = {3},
  pages     = {036704},
  doi       = {10.1103/PhysRevE.76.036704},
}

@InCollection{dunweg09a,
  author    = {D{\"u}nweg, Burkhard and Ladd, Anthony J. C.},
  editor    = {Holm, Christian and Kremer, Kurt},
  title     = {Lattice {B}oltzmann Simulations of Soft Matter Systems},
  booktitle = {Advanced Computer Simulation Approaches for Soft Matter Sciences {III}},
  publisher = {Springer Berlin Heidelberg},
  year      = {2009},
  series    = {Advances in Polymer Science},
  volume    = {221},
  pages     = {89--166},
  doi       = {10.1007/978-3-540-87706-6_2},
  isbn      = {978-3-540-87706-6},
}

@ARTICLE{dupin07a,
  author = {Dupin, Michael M. and Halliday, Ian and Care, Chris M. and Alboul, Lyuba and Munn, Lance L.},
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  year = {2007},
  volume = {75},
  number = {6},
  pages = {066707},
  publisher = {American Physical Society},
  doi = {10.1103/PhysRevE.75.066707},
}

@Article{dupin08a,
author = {Dupin, M. M. and Halliday, I. and Care, C. M. and Munn, L. L.},
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journal = {International Journal of Computational Fluid Dynamics},
volume = {22},
number = {7},
pages = {481--492},
year  = {2008},
doi = {10.1080/10618560802238242},
}

@Article{durlofsky87a,
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  year    = {1987},
  volume  = {180},
  pages   = {21--49},
  doi     = {10.1017/S002211208700171X},
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@article{ermak78a,
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@article{essmann95a,
  title={A smooth particle mesh {E}wald method},
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  doi={10.1063/1.470117},
  publisher={AIP}
}

@ARTICLE{ewald21a,
  author = {Ewald, P. P.},
  title = {Die {B}erechnung optischer und elektrostatischer {G}itterpotentiale},
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  doi = {10.1002/andp.19213690304},
}

@Book{frenkel02b,
  author     = {Frenkel, Daan and Smit, Berend},
  title      = {Understanding molecular simulation: {F}rom algorithms to applications},
  year       = {2002},
  edition    = {2nd},
  publisher  = {Academic Press},
  isbn       = {978-0-12-267351-1},
  doi        = {10.1016/B978-0-12-267351-1.X5000-7},
  address    = {San Diego},
}

@Article{gay81a,
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@Article{gompper96a,
author={Gompper, G. and Kroll, D. M.},
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@article{guckenberger17a,
author = {Achim Guckenberger and Stephan Gekle},
title = {Theory and Algorithms to Compute {H}elfrich Bending Forces: {A} Review},
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doi = {10.1088/1361-648x/aa6313},
year = {2017},
volume = {29},
number = {20},
pages = {203001},
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@Article{guo02a,
  title                    = {Discrete lattice effects on the forcing term in the lattice {B}oltzmann 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},
}

@ARTICLE{hickey10a,
  author = {Hickey, Owen A. and Holm, Christian and Harden, James L. and Slater, Gary W.},
  title = {Implicit Method for Simulating Electrohydrodynamics of Polyelectrolytes},
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  number = {14},
  doi = {10.1103/PhysRevLett.105.148301}
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@Book{hockney88a,
  title     = {Computer Simulation Using Particles},
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  isbn      = {9780852743928},
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@Article{hofling11a,
  title = {Anomalous transport resolved in space and time by fluorescence correlation spectroscopy},
  author = {Felix H\"{o}fling and Karl-Ulrich Bamberg and Thomas Franosch},
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  doi = {10.1039/C0SM00718H},
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@ARTICLE{humphrey96a,
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@Article{jancigova16a,
author = {Jan\v{c}igov\'{a}, Iveta and Cimr\'{a}k, Ivan},
title = {Non-uniform force allocation for area preservation in spring network models},
journal = {International Journal for Numerical Methods in Biomedical Engineering},
volume = {32},
number = {10},
pages = {e02757},
year = {2016},
doi = {10.1002/cnm.2757},
}

@Article{johnson94a,
  author    = {Johnson, J. Karl and Panagiotopoulos, Athanassios Z. and Gubbins, Keith E.},
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  volume    = {81},
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}

@ARTICLE{kesselheim11a,
  author = {Stefan Kesselheim and Marcello Sega and Christian Holm},
  title = {Applying {ICC}* to {DNA} translocation. {E}ffect of dielectric boundaries},
  journal = {Computer Physics Communications},
  year = {2011},
  volume = {182},
  pages = {33--35},
  number = {1},
  doi = {10.1016/j.cpc.2010.08.014},
  issn = {0010-4655},
}

@ARTICLE{kolafa92a,
  author = {Kolafa, Jiri and Perram, John W.},
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@ARTICLE{kolb99a,
  author = {A. Kolb and B. D\"{u}nweg},
  title = {Optimized constant pressure stochastic dynamics},
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  volume = {111},
  pages = {4453--59},
  number = {10},
  doi = {10.1063/1.479208},
}

@PHDTHESIS{kruger11a,
author = {Kr\"{u}ger, Timm},
title = {Computer simulation study of collective phenomena in dense suspensions of red blood cells under shear},
school = {Universit\"{a}t Bochum},
year = {2011}
}

@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},
}

@Book{kruger17a,
author={Kr{\"u}ger, Timm and Kusumaatmaja, Halim and Kuzmin, Alexandr and Shardt, Orest and Silva, Goncalo and Viggen, Erlend Magnus},
title={The Lattice Boltzmann Method},
subtitle={Principles and Practice},
year={2017},
publisher={Springer International Publishing},
isbn={978-3-319-44649-3},
doi={10.1007/978-3-319-44649-3},
}

@Book{kundu01a,
author    = {Kundu, Pijush K. and Cohen, Ira M. and Hu, Howard},
title     = {Fluid Mechanics},
year      = {2001},
edition   = {2nd},
publisher = {Elsevier Science},
isbn      = {9780080545585},
}

@Article{ladd01a,
  title                    = {Lattice-{B}oltzmann 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{ladd94a,
  title                    = {Numerical simulations of particulate suspensions via a discretized {B}oltzmann 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},
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@Article{landsgesell17b,
title                      = {Simulation of weak polyelectrolytes: {A} comparison between the constant p{H} and the reaction ensemble method},
author                     = {Landsgesell, Jonas and Holm, Christian and Smiatek, Jens},
journal                    = {European Physical Journal Special Topics},
year                       = {2017},
volume                     = {226},
number                     = {4},
pages                      = {725--736},
doi                        = {10.1140/epjst/e2016-60324-3}
}

@Article{lees72a,
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@ARTICLE{limbach06a,
  author = {H. J. Limbach and A. Arnold and B. A. Mann and C. Holm},
  title = {{ESPResSo} -- An Extensible Simulation Package for Research on Soft Matter Systems},
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  year = {2006},
  volume = {174},
  pages = {704--727},
  number = {9},
  doi = {10.1016/j.cpc.2005.10.005},
}

@ARTICLE{magatti01a,
  author = {Magatti, D and Ferri, F},
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}

@article{martys99a,
  title = {Velocity {V}erlet algorithm for dissipative-particle-dynamics-based models of suspensions},
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  doi = {10.1103/PhysRevE.59.3733},
}

@book{moshier89a,
  title={Methods and Programs for Mathematical Functions},
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  publisher={Ellis Horwood},
}

@Article{moss96a,
author={Moss, G. P.},
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@Article{neumann85b,
author = {Neumann, Martin},
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