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 Science Publications. Oxford University Press, Oxford, 2nd edition, 2017. ISBN 978-0-19-880319-5. doi:10.1093/oso/9780198803195.001.0001.

[3]

Hans C. Andersen. Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations. Journal of Computational Physics, 52(1):24–34, 1983. doi:10.1016/0021-9991(83)90014-1.

[4]

Axel Arnold, Jason de Joannis, and Christian Holm. Electrostatics in periodic slab geometries. I. The Journal of Chemical Physics, 117:2496–2502, 2002. doi:10.1063/1.1491955.

[5]

Axel Arnold and Christian Holm. A novel method for calculating electrostatic interactions in 2D periodic slab geometries. Chemical Physics Letters, 354(3–4):324–330, 2002. doi:10.1016/S0009-2614(02)00131-8.

[6]

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.

[7]

Axel Arnold and Christian 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.

[8]

Axel Arnold, Olaf Lenz, Stefan Kesselheim, Rudolf Weeber, Florian Fahrenberger, Dominic Röhm, Peter Košovan, and Christian Holm. ESPResSo 3.1 – molecular dynamics software for coarse-grained models. In Michael Griebel and Marc Alexander 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.

[9]

Vincent Ballenegger, Axel Arnold, and Joan J. Cerdà. 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, September 2009. doi:10.1063/1.3216473.

[10]

Josep Batle and Orion Ciftja. Minimum and maximum energy for crystals of magnetic dipoles. Scientific Reports, 10(1):19113, 2020. doi:10.1038/s41598-020-76029-x.

[11]

Martin Bauer, Sebastian Eibl, Christian Godenschwager, Nils Kohl, Michael Kuron, Christoph Rettinger, Florian Schornbaum, Christoph Schwarzmeier, Dominik Thönnes, Harald Köstler, and Ulrich Rüde. waLBerla: a block-structured high-performance framework for multiphysics simulations. Computers & Mathematics with Applications, 81:478–501, 2021. doi:10.1016/j.camwa.2020.01.007.

[12]

Martin Bauer, Johannes Hötzer, Dominik Ernst, Julian Hammer, Marco Seiz, Henrik Hierl, Jan Hönig, Harald Köstler, Gerhard Wellein, Britta Nestler, and Ulrich Rüde. Code generation for massively parallel phase-field simulations. In Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis. New York, 2019. Association for Computing Machinery. doi:10.1145/3295500.3356186.

[13]

Martin Bauer, Harald Köstler, and Ulrich Rüde. lbmpy: automatic code generation for efficient parallel lattice Boltzmann methods. Journal of Computational Science, 49:101269, 2021. doi:10.1016/j.jocs.2020.101269.

[14]

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.

[15]

David Boehme, Todd Gamblin, David Beckingsale, Peer-Timo Bremer, Alfredo Gimenez, Matthew LeGendre, Olga Pearce, and Martin Schulz. Caliper: performance introspection for HPC software stacks. In SC '16: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, 550–560. IEEE Press, November 2016. LLNL-CONF-699263.

[16]

David Brown and Sylvie Neyertz. A general pressure tensor calculation for molecular dynamics simulations. Molecular Physics, 84(3):577–595, 1995. doi:10.1080/00268979500100371.

[17]

A. Bródka. Ewald summation method with electrostatic layer correction for interactions of point dipoles in slab geometry. Chemical Physics Letters, 400(1–3):62–67, 2004. doi:10.1016/j.cplett.2004.10.086.

[18]

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.

[19]

Orion Ciftja. Equivalence of an infinite one-dimensional ionic crystal to a simple electrostatic model. Results in Physics, 13:102325, 2019. doi:10.1016/j.rinp.2019.102325.

[20]

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.

[21]

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.

[22]

Lindsay M. Crowl and Aaron L. Fogelson. Computational model of whole blood exhibiting lateral platelet motion induced by red blood cells. International Journal for Numerical Methods in Biomedical Engineering, 26(3–4):471–487, 2010. doi:10.1002/cnm.1274.

[23]

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.

[24]

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.

[25]

Jason de Joannis, Axel Arnold, and Christian Holm. Electrostatics in periodic slab geometries. II. The Journal of Chemical Physics, 117:2503–2512, 2002. doi:10.1063/1.1491954.

[26]

Markus Deserno. Counterion condensation for rigid linear polyelectrolytes. PhD thesis, Universität Mainz, February 2000. doi:10.25358/openscience-1411.

[27]

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.

[28]

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.

[29]

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.

[30]

Masao Doi and Samuel Frederick Edwards. The Theory of Polymer Dynamics. Clarendon Press: Oxford, 1986. ISBN 9780198519768.

[31]

Michael M. Dupin, Ian Halliday, Chris M. Care, Lyuba Alboul, and Lance L. Munn. Modeling the flow of dense suspensions of deformable particles in three dimensions. Physical Review E, 75(6):066707, 2007. doi:10.1103/PhysRevE.75.066707.

[32]

L. Durlofsky, J. F. Brady, and G. Bossis. Dynamic simulation of hydrodynamically interacting particles. Journal of Fluid Mechanics, 180:21–49, 1987. doi:10.1017/S002211208700171X.

[33]

Burkhard Dünweg and Anthony J. C. Ladd. Lattice Boltzmann simulations of soft matter systems. In Christian Holm and Kurt Kremer, editors, Advanced Computer Simulation Approaches for Soft Matter Sciences III, volume 221 of Advances in Polymer Science, pages 89–166. Springer Berlin Heidelberg, 2009. doi:10.1007/978-3-540-87706-6_2.

[34]

Rokas Elijošius, Fabian Zills, Ilyes Batatia, Sam Walton Norwood, Dávid Péter Kovács, Christian Holm, and Gábor Csányi. Zero shot molecular generation via similarity kernels. Preprint arXiv:2402.08708, arXiv, 2024. doi:10.48550/arXiv.2402.08708.

[35]

Donald L. Ermak and J. A. McCammon. Brownian dynamics with hydrodynamic interactions. The Journal of Chemical Physics, 69(4):1352–1360, 1978. doi:10.1063/1.436761.

[36]

Ulrich Essmann, Lalith Perera, Max L. Berkowitz, Tom Darden, Hsing Lee, and Lee G. Pedersen. A smooth particle mesh Ewald method. The Journal of Chemical Physics, 103(19):8577–8593, 1995. doi:10.1063/1.470117.

[37]

H. M. Evjen. On the stability of certain heteropolar crystals. Physical Review, 39(4):675–687, 1932. doi:10.1103/PhysRev.39.675.

[38]

P. P. Ewald. Die Berechnung optischer und elektrostatischer Gitterpotentiale. Annalen der Physik, 369(3):253–287, 1921. doi:10.1002/andp.19213690304.

[39]

Daan Frenkel and Berend Smit. Understanding Molecular Simulation: From Algorithms to Applications. Volume 1 of Computational Science. Academic Press, San Diego, 2nd edition, 2002. ISBN 978-0-12-267351-1. doi:10.1016/B978-0-12-267351-1.X5000-7.

[40]

J. G. Gay and B. J. Berne. Modification of the overlap potential to mimic a linear site-site potential. The Journal of Chemical Physics, 74(6):3316–3319, 1981. doi:10.1063/1.441483.

[41]

Christian Godenschwager, Florian Schornbaum, Martin Bauer, Harald Köstler, and Ulrich Rüde. A framework for hybrid parallel flow simulations with a trillion cells in complex geometries. In Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis. New York, 2013. Association for Computing Machinery. doi:10.1145/2503210.2503273.

[42]

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.

[43]

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.

[44]

R. W. Hockney and J. W. Eastwood. Computer Simulation Using Particles. CRC Press, 1988. ISBN 9780852743928. URL: https://www.routledge.com/Computer-Simulation-Using-Particles/Hockney-Eastwood/p/book/9780852743928.

[45]

William Humphrey, Andrew Dalke, and Klaus Schulten. VMD: visual molecular dynamics. Journal of Molecular Graphics, 14(1):33–38, 1996. doi:10.1016/0263-7855(96)00018-5.

[46]

Felix Höfling, Karl-Ulrich Bamberg, and Thomas Franosch. Anomalous transport resolved in space and time by fluorescence correlation spectroscopy. Soft Matter, 7(4):1358–1363, 2011. doi:10.1039/C0SM00718H.

[47]

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.

[48]

Robert Kern, Jon Crall, Brett Olsen, and OpenPyUtils community contributors. line_profiler and kernprof. 2008. URL: https://github.com/pyutils/line_profiler.

[49]

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.

[50]

Thomas Kluyver, Benjamin Ragan-Kelley, Fernando Pérez, Brian E Granger, Matthias Bussonnier, Jonathan Frederic, Kyle Kelley, Jessica B Hamrick, Jason Grout, Sylvain Corlay, Paul Ivanov, Damián Avila, Safia Abdalla, Carol Willing, and Jupyter Development Team. Jupyter Notebooks—a publishing format for reproducible computational workflows. In Fernando Loizides and Birgit Schmidt, editors, Positioning and Power in Academic Publishing: Players, Agents and Agendas, 87–90. IOS Press, 2016. doi:10.3233/978-1-61499-649-1-87.

[51]

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.

[52]

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.

[53]

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.

[54]

Timm Krüger, Halim Kusumaatmaja, Alexandr Kuzmin, Orest Shardt, Goncalo Silva, and Erlend Magnus Viggen. The Lattice Boltzmann Method: Principles and Practice. Springer International Publishing, Cham, 2017. ISBN 978-3-319-44649-3. doi:10.1007/978-3-319-44649-3.

[55]

Pijush K. Kundu, Ira M. Cohen, and Howard Hu. Fluid Mechanics. Elsevier Science, 2nd edition, 2002. ISBN 978-0-12-178251-1. doi:10.1016/C2009-0-20716-1.

[56]

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.

[57]

A. W. Lees and S. F. Edwards. The computer study of transport processes under extreme conditions. Journal of Physics C: Solid State Physics, 1972. doi:10.1088/0022-3719/5/15/006.

[58]

H. J. Limbach, A. Arnold, B. A. Mann, and C. Holm. ESPResSo – an extensible simulation package for research on soft matter systems. Computer Physics Communications, 174(9):704–727, 2006. doi:10.1016/j.cpc.2005.10.005.

[59]

Davide Magatti and Fabio Ferri. Fast multi-tau real-time software correlator for dynamic light scattering. Applied Optics, 40(24):4011–4021, 2001. doi:10.1364/ao.40.004011.

[60]

Nicholas Nethercote and Julian Seward. Valgrind: a program supervision framework. Electronic Notes in Theoretical Computer Science, 89(2):44–66, October 2003. doi:10.1016/S1571-0661(04)81042-9.

[61]

Nicholas Nethercote and Julian Seward. Valgrind: a framework for heavyweight dynamic binary instrumentation. In Proceedings of the 28th ACM SIGPLAN Conference on Programming Language Design and Implementation, 89–100. New York, New York, USA, June 2007. Association for Computing Machinery. doi:10.1145/1250734.1250746.

[62]

Igor P. Omelyan. On the numerical integration of motion for rigid polyatomics: the modified quaternion approach. Computers in Physics, 12(1):97–103, 1998. doi:10.1063/1.168642.

[63]

Charles S. Peskin. The immersed boundary method. Acta Numerica, 11:479–517, 2002. doi:10.1017/S0962492902000077.

[64]

Steve J. Plimpton. Fast parallel algorithms for short-range molecular dynamics. Journal of Computational Physics, 117(1):1–19, 1995. doi:10.1006/jcph.1995.1039.

[65]

Jorge Ramírez, Sathish K. Sukumaran, Bart Vorselaars, and Alexei E. Likhtman. Efficient on the fly calculation of time correlation functions in computer simulations. The Journal of Chemical Physics, 133(15):154103, 2010. doi:10.1063/1.3491098.

[66]

D. C. Rapaport. The Art of Molecular Dynamics Simulation. Cambridge University Press, New York, NY, USA, 2nd edition, 2004. ISBN 9780511816581. doi:10.1017/CBO9780511816581.

[67]

Christopher E. Reed and Wayne F. Reed. Monte Carlo study of titration of linear polyelectrolytes. The Journal of Chemical Physics, 96(2):1609–1620, 1992. doi:10.1063/1.462145.

[68]

Matthew Rocklin. Dask: parallel computation with blocked algorithms and task scheduling. In Kathryn Huff and James Bergstra, editors, Proceedings of the 14th Python in Science Conference, 126–132. 2015. doi:10.25080/Majora-7b98e3ed-013.

[69]

Michael Rubinstein and Ralph H. Colby. Polymer Physics. Oxford University Press, Oxford, UK, 2003.

[70]

Klaus Schätzel, Martin Drewel, and Sven Stimac. Photon correlation measurements at large lag times: improving statistical accuracy. Journal of Modern Optics, 35(4):711–718, 1988. doi:10.1080/09500348814550731.

[71]

Tamar Schlick. Molecular Modeling and Simulation: An Interdisciplinary Guide. Volume 21 of Interdisciplinary Applied Mathematics. Springer New York, New York, New York, USA, 2010. ISBN 978-1-4419-6350-5. doi:10.1007/978-1-4419-6351-2.

[72]

Konstantin Serebryany, Derek Bruening, Alexander Potapenko, and Dmitry Vyukov. AddressSanitizer: a fast address sanity checker. In USENIX Annual Technical Conference. Berkeley, California, USA, June 2012. USENIX Association. URL: https://www.usenix.org/conference/atc12/addresssanitizer-fast-address-sanity-checker.

[73]

E. R. Smith. Electrostatic energy in ionic crystals. Proceedings of the Royal Society of London A: Mathematical and Physical Sciences, 375:475–505, 1981. doi:10.1098/rspa.1981.0064.

[74]

W. R. Smith and B. Triska. The reaction ensemble method for the computer simulation of chemical and phase equilibria. I. Theory and basic examples. The Journal of Chemical Physics, 100(4):3019–3027, 1994. doi:10.1063/1.466443.

[75]

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.

[76]

T. Soddemann, B. Dünweg, and K. Kremer. A generic computer model for amphiphilic systems. European Physical Journal E, 6:409–419, 2001. doi:10.1007/s10189-001-8054-4.

[77]

Richard Stallman, Roland Pesch, and Stan Shebs. Debugging with GDB: The GNU source-level debugger. GNU Press, 10th edition, 2011. ISBN 978-0-9831592-3-0.

[78]

Rolf Strebel. Pieces of software for the Coulombic m body problem. Dissertation, ETH Zürich, 1999. doi:10.3929/ethz-a-003856704.

[79]

Aidan P. Thompson, Steven J. Plimpton, and William Mattson. General formulation of pressure and stress tensor for arbitrary many-body interaction potentials under periodic boundary conditions. The Journal of Chemical Physics, 131(15):154107, 2009. doi:10.1063/1.3245303.

[80]

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.

[81]

Linus Torvalds. perf: Linux profiling with performance counters. 2009. URL: https://perf.wiki.kernel.org/index.php/Main_Page.

[82]

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.

[83]

Sandeep Tyagi, Axel Arnold, and Christian Holm. ICMMM2D: an accurate method to include planar dielectric interfaces via image charge summation. The Journal of Chemical Physics, 127(15):154723, 2007. doi:10.1063/1.2790428.

[84]

Sandeep Tyagi, Axel Arnold, and Christian Holm. Electrostatic layer correction with image charges: A linear scaling method to treat slab 2D + h systems with dielectric interfaces. The Journal of Chemical Physics, 129(20):204102, 2008. doi:10.1063/1.3021064.

[85]

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(15):154112, 2010. doi:10.1063/1.3376011.

[86]

Alexander J. Wagner and Ignacio Pagonabarraga. Lees–Edwards boundary conditions for lattice Boltzmann. Journal of Statistical Physics, 107(112):521–537, 2002. doi:10.1023/A:1014595628808.

[87]

Josef Weidendorfer, Markus Kowarschik, and Carsten Trinitis. A tool suite for simulation based analysis of memory access behavior. In Marian Bubak, Geert Dick van Albada, Peter M. A. Sloot, and Jack Dongarra, editors, Computational Science - ICCS 2004, volume 3038 of Lecture Notes in Computer Science, 440–447. Berlin, Heidelberg, 2004. Springer Berlin Heidelberg. doi:10.1007/978-3-540-24688-6_58.

[88]

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.

[89]

B. Widom. Some topics in the theory of fluids. The Journal of Chemical Physics, 39(11):2802–2812, 1963. doi:10.1063/1.1734110.

[90]

S. Yaghoubi, E. Shirani, A. R. Pishevar, and Y. Afshar. New modified weight function for the dissipative force in the DPD method to increase the Schmidt number. EPL (Europhysics Letters), 110(2):24002, 2015. doi:10.1209/0295-5075/110/24002.

[91]

LLVM Developers. Undefined behavior sanitizer. 2017. URL: https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html.

[92]

NVIDIA. COMPUTE SANITIZER. User manual v2023.2.0, NVIDIA, June 2023. URL: https://docs.nvidia.com/compute-sanitizer/pdf/ComputeSanitizer.pdf.

[93]

NVIDIA. CU-GDB. User manual Release 12.1, NVIDIA, April 2023. URL: https://docs.nvidia.com/cuda/pdf/cuda-gdb.pdf.