24. Bibliography¶

1: Patrick Ahlrichs and Burkhard Dünweg. Simulation of a single polymer chain in solution by combining lattice Boltzmann and molecular dynamics. The Journal of Chemical Physics, 111(17):8225–8239, 1999. doi:10.1063/1.480156.
2: Michael P. Allen and Dominic J. Tildesley. Computer simulation of liquids. Oxford University Press, 2nd edition, 2017. ISBN 9780198803195. doi:10.1093/oso/9780198803195.001.0001.
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4: A. Arnold, J. de Joannis, and C. Holm. Electrostatics in periodic slab geometries II. The Journal of Chemical Physics, 117:2503–2512, 2002. doi:10.1063/1.1491954.
5: A. Arnold, J. de Joannis, and C. Holm. Electrostatics in periodic slab geometries I. The Journal of Chemical Physics, 117:2496–2502, 2002. doi:10.1063/1.1491955.
6: A. Arnold and C. Holm. MMM1D: A method for calculating electrostatic interactions in one-dimensional periodic geometries. The Journal of Chemical Physics, 123(12):144103, 2005. doi:10.1063/1.2052647.
7: A. Arnold, O. Lenz, S. Kesselheim, R. Weeber, F. Fahrenberger, D. Röhm, P. Košovan, and C. Holm. ESPResSo 3.1 — molecular dynamics software for coarse-grained models. In M. Griebel and M. A. Schweitzer, editors, Meshfree Methods for Partial Differential Equations VI, volume 89 of Lecture Notes in Computational Science and Engineering, pages 1–23. Springer Berlin Heidelberg, 2013. doi:10.1007/978-3-642-32979-1_1.
8: Axel Arnold and Christian Holm. A novel method for calculating electrostatic interactions in 2D periodic slab geometries. Chemical Physics Letters, 354:324–330, 2002. doi:10.1016/S0009-2614(02)00131-8.
9: Axel Arnold and Christian Holm. MMM2D: a fast and accurate summation method for electrostatic interactions in 2D slab geometries. Computer Physics Communications, 148(3):327–348, 2002. doi:10.1016/S0010-4655(02)00586-6.
10: V. Ballenegger, A. Arnold, and J. J. Cerda. Simulations of non-neutral slab systems with long-range electrostatic interactions in two-dimensional periodic boundary conditions. The Journal of Chemical Physics, 131(9):094107, 2009. doi:10.1063/1.3216473.
11: Sebastian Bindgen, Florian Weik, Rudolf Weeber, Erin Koos, and Pierre de Buyl. Lees-edwards boundary conditions for translation invariant shear flow: implementation and transport properties. Physics of Fluids, 33(8):083615, 2021. doi:10.1063/5.0055396.
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14: Juan J. Cerdà, Vincent Ballenegger, Olaf Lenz, and Christian Holm. P3M algorithm for dipolar interactions. The Journal of Chemical Physics, 129:234104, 2008. doi:10.1063/1.3000389.
15: I. Cimrák, M. Gusenbauer, and I. Jančigová. An ESPResSo implementation of elastic objects immersed in a fluid. Computer Physics Communications, 185(3):900–907, 2014. doi:10.1016/j.cpc.2013.12.013.
16: I. Cimrák, M. Gusenbauer, and T. Schrefl. Modelling and simulation of processes in microfluidic devices for biomedical applications. Computers & Mathematics with Applications, 64(3):278–288, 2012. doi:10.1016/j.camwa.2012.01.062.
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18: Pierre de Buyl. tidynamics: A tiny package to compute the dynamics of stochastic and molecular simulations. Journal of Open Source Software, 3(28):877, 2018. doi:10.21105/joss.00877.
19: Joost de Graaf, Henri Menke, Arnold J.T.M. Mathijssen, Marc Fabritius, Christian Holm, and Tyler N. Shendruk. Lattice-Boltzmann hydrodynamics of anisotropic active matter. The Journal of Chemical Physics, 144:134106, 2016. doi:10.1063/1.4944962.
20: Markus Deserno. Counterion condensation for rigid linear polyelectrolytes. PhD thesis, Universität Mainz, February 2000. doi:10.25358/openscience-1411.
21: Markus Deserno and Christian Holm. How to mesh up Ewald sums. I. A theoretical and numerical comparison of various particle mesh routines. The Journal of Chemical Physics, 109:7678, 1998. doi:10.1063/1.477414.
22: Markus Deserno and Christian Holm. How to mesh up Ewald sums. II. An accurate error estimate for the Particle-Particle-Particle-Mesh algorithm. The Journal of Chemical Physics, 109:7694, 1998. doi:10.1063/1.477415.
23: Markus Deserno, Christian Holm, and Hans Jörg Limbach. How to mesh up Ewald sums. In R. Esser, P. Grassberger, J. Grotendorst, and M. Lewerenz, editors, Molecular Dynamics on Parallel Computers, 319–320. World Scientific, Singapore, 2000. doi:10.1142/9789812793768_0023.
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33: Achim Guckenberger and Stephan Gekle. Theory and algorithms to compute Helfrich bending forces: A review. Journal of Physics: Condensed Matter, 29(20):203001, 2017. doi:10.1088/1361-648x/aa6313.
34: Felix Höfling, Karl-Ulrich Bamberg, and Thomas Franosch. Anomalous transport resolved in space and time by fluorescence correlation spectroscopy. Soft Matter, 7:1358, 2011. doi:10.1039/C0SM00718H.
35: Owen A. Hickey, Christian Holm, James L. Harden, and Gary W. Slater. Implicit method for simulating electrohydrodynamics of polyelectrolytes. Physical Review Letters, 2010. doi:10.1103/PhysRevLett.105.148301.
36: R. W. Hockney and J. W. Eastwood. Computer Simulation Using Particles. CRC Press, 1988. ISBN 9780852743928.
37: W. Humphrey, A. Dalke, and K. Schulten. VMD: visual molecular dynamics. Journal of Molecular Graphics, 14:33–38, 1996. doi:10.1016/0263-7855(96)00018-5.
38: J. Karl Johnson, Athanassios Z. Panagiotopoulos, and Keith E. Gubbins. Reactive canonical Monte Carlo: A new simulation technique for reacting or associating fluids. Molecular Physics, 81(3):717–733, 1994. doi:10.1080/00268979400100481.
39: Stefan Kesselheim, Marcello Sega, and Christian Holm. Applying ICC* to DNA translocation. Effect of dielectric boundaries. Computer Physics Communications, 182(1):33–35, 2011. doi:10.1016/j.cpc.2010.08.014.
40: Jiri Kolafa and John W. Perram. Cutoff errors in the Ewald summation formulae for point charge systems. Molecular Simulation, 9(5):351–368, 1992. doi:10.1080/08927029208049126.
41: A. Kolb and B. Dünweg. Optimized constant pressure stochastic dynamics. The Journal of Chemical Physics, 111(10):4453–59, 1999. doi:10.1063/1.479208.
42: Timm Krüger. Computer simulation study of collective phenomena in dense suspensions of red blood cells under shear. PhD thesis, Universität Bochum, 2011.
43: Timm Krüger. Computer simulation study of collective phenomena in dense suspensions of red blood cells under shear. Vieweg+Teubner Verlag, Wiesbaden, 2012. ISBN 978-3-8348-2376-2. doi:10.1007/978-3-8348-2376-2.
44: Timm Krüger, Halim Kusumaatmaja, Alexandr Kuzmin, Orest Shardt, Goncalo Silva, and Erlend Magnus Viggen. The Lattice Boltzmann Method. Springer International Publishing, 2017. ISBN 978-3-319-44649-3. doi:10.1007/978-3-319-44649-3.
45: Pijush K. Kundu, Ira M. Cohen, and Howard Hu. Fluid Mechanics. Elsevier Science, 2nd edition, 2001. ISBN 9780080545585.
46: Jonas Landsgesell, Christian Holm, and Jens Smiatek. Simulation of weak polyelectrolytes: A comparison between the constant pH and the reaction ensemble method. European Physical Journal Special Topics, 226(4):725–736, 2017. doi:10.1140/epjst/e2016-60324-3.
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56: D. Roehm and A. Arnold. Lattice Boltzmann simulations on GPUs with ESPResSo. European Physical Journal Special Topics, 210:89–100, 2012. doi:10.1140/epjst/e2012-01639-6.
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58: K. Schätzel, M. Drewel, and S Stimac. Photon correlation measurements at large lag times: improving statistical accuracy. Journal of Modern Optics, 35(4):711–718, 1988. doi:10.1080/09500348814550731.
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63: T. Soddemann, B. Dünweg, and K. Kremer. Dissipative particle dynamics: a useful thermostat for equilibrium and nonequilibrium molecular dynamics simulations. Physical Review E, 68(4):046702, 2003. doi:10.1103/PhysRevE.68.046702.
64: R. Strebel. Pieces of software for the Coulombic m body problem. Dissertation, ETH Zürich, 1999. doi:10.3929/ethz-a-003856704.
65: S. Succi. The lattice Boltzmann equation for fluid dynamics and beyond. Oxford University Press, USA, 2001.
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67: Ilario G. Tironi, René Sperb, Paul E. Smith, and Wilfred F. van Gunsteren. A generalized reaction field method for molecular-dynamics simulations. The Journal of Chemical Physics, 102(13):5451–5459, 1995. doi:10.1063/1.469273.
68: C. Heath Turner, John K. Brennan, Martin Lísal, William R. Smith, J. Karl Johnson, and Keith E. Gubbins. Simulation of chemical reaction equilibria by the reaction ensemble Monte Carlo method: A review. Molecular Simulation, 34(2):119–146, 2008. doi:10.1080/08927020801986564.
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71: Sandeep Tyagi, Mehmet Süzen, Marcello Sega, Marcia C. Barbosa, Sofia S. Kantorovich, and Christian Holm. An iterative, fast, linear-scaling method for computing induced charges on arbitrary dielectric boundaries. The Journal of Chemical Physics, 132:154112, 2010. doi:10.1063/1.3376011.
72: Florian Weik, Rudolf Weeber, Kai Szuttor, Konrad Breitsprecher, Joost de Graaf, Michael Kuron, Jonas Landsgesell, Henri Menke, David Sean, and Christian Holm. ESPResSo 4.0 – an extensible software package for simulating soft matter systems. The European Physical Journal Special Topics, 227(14):1789–1816, 2019. doi:10.1140/epjst/e2019-800186-9.
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