20. Bibliography


Hans C. Andersen. Molecular dynamics simulations at constant pressure and/or temperature. J. Chem. Phys., 72(4):2384-2393, 1980. doi:10.1063/1.439486.


Hans C. Andersen. Rattle: a “velocity” version of the shake algorithm for molecular dynamics calculations. J. Comput. Phys., 51:24–34, 1983. doi:10.1016/0021-9991(83)90014-1.


A. Arnold, J. de Joannis, and C. Holm. Electrostatics in periodic slab geometries II. J. Chem. Phys., 117:2503–2512, 2002. doi:10.1063/1.1491954.


A. Arnold, J. de Joannis, and C. Holm. Electrostatics in periodic slab geometries I. J. Chem. Phys., 117:2496–2502, 2002. doi:10.1063/1.1491955.


A. Arnold and C. Holm. MMM1D: A method for calculating electrostatic interactions in one-dimensional periodic geometries. J. Chem. Phys., 123(12):144103, 2005. doi:10.1063/1.2052647.


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.


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


Axel Arnold and Christian Holm. MMM2D: a fast and accurate summation method for electrostatic interactions in 2D slab geometries. Comput. Phys. Commun., 148(3):327–348, 2002. doi:10.1016/S0010-4655(02)00586-6.


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. J. Chem. Phys., 131(9):094107, 2009. doi:10.1063/1.3216473.


R. E. Belardinelli and V. D. Pereyra. Fast algorithm to calculate density of states. Phys. Rev. E, 75(4):046701, 2007. doi:10.1103/PhysRevE.75.046701.


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


A. Bródka. Ewald summation method with electrostatic layer correction for interactions of point dipoles in slab geometry. Chem. Phys. Lett., 400:62–67, 2004. doi:10.1016/j.cplett.2004.10.086.


Juan J. Cerdà, V. Ballenegger, O. Lenz, and Ch. Holm. P3M algorithm for dipolar interactions. J. Chem. Phys., 129:234104, 2008. doi:10.1063/1.3000389.


I. Cimrák, M. Gusenbauer, and I. Jančigová. An ESPResSo implementation of elastic objects immersed in a fluid. Comput. Phys. Commun., 185(3):900 – 907, 2014. doi:10.1016/j.cpc.2013.12.013.


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.


Lindsay M Crowl and Aaron L Fogelson. Computational model of whole blood exhibiting lateral platelet motion induced by red blood cells. Int. J. Numer. Meth. Biomed. Eng., 26(3-4):471–487, 2010. doi:10.1002/cnm.1274.


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. J. Chem. Phys., 144:134106, 2016. doi:10.1063/1.4944962.


M. Deserno. Counterion condensation for rigid linear polyelectrolytes. PhD thesis, Universität Mainz, 2000.


M. Deserno and C. Holm. How to mesh up Ewald sums. I. A theoretical and numerical comparison of various particle mesh routines. J. Chem. Phys., 109:7678, 1998. doi:10.1063/1.477414.


M. Deserno and C. Holm. How to mesh up Ewald sums. II. An accurate error estimate for the Particle-Particle-Particle-Mesh algorithm. J. Chem. Phys., 109:7694, 1998. doi:10.1063/1.477415.


M. Deserno, C. Holm, and H. J. Limbach. How to mesh up Ewald sums. World Scientific, Singapore, 2000. doi:10.1142/9789812793768_0023.


M Doi and S F Edwards. The theory of polymer dynamics. Oxford Science Publications, 1986.


M.M. Dupin, I. Halliday, C.M. Care, and L. Alboul. Modeling the flow of dense suspensions of deformable particles in three dimensions. Phys. Rev. E, 75:066707, 2007. doi:10.1103/PhysRevE.75.066707.


Burkhard Dünweg and Anthony J.C. Ladd. Lattice Boltzmann Simulations of Soft Matter Systems. In Lattice Boltzmann Simulations of Soft Matter Systems, Advances in Polymer Science, pages 1–78. Springer Berlin Heidelberg, 2008. doi:10.1007/978-3-540-87706-6_2.


Ulrich Essmann, Lalith Perera, Max L Berkowitz, Tom Darden, Hsing Lee, and Lee G Pedersen. A smooth particle mesh ewald method. J. Chem. Phys., 103(19):8577–8593, 1995. doi:10.1063/1.470117.


P.P. Ewald. Die Berechnung optischer und elektrostatischer Gitterpotentiale. Ann. Phys., 64:253–287, 1921. doi:10.1002/andp.19213690304.


Daan Frenkel and Berend Smit. Understanding Molecular Simulation. Academic Press, San Diego, second edition, 2002.


Gary S. Grest and Kurt Kremer. Molecular dynamics simulation for polymers in the presence of a heat bath. Phys. Rev. A, 33(5):3628–31, 1986. doi:10.1103/PhysRevA.33.3628.


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.


C Heath Turner, John K Brennan, Martin Lisal, 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.


Owen A. Hickey, Christian Holm, James L. Harden, and Gary W. Slater. Implicit Method for Simulating Electrohydrodynamics of Polyelectrolytes. Phys. Rev. Lett., SEP 29 2010. doi:10.1103/PhysRevLett.105.148301.


R. W. Hockney and J. W. Eastwood. Computer Simulation Using Particles. IOP, 1988.


W. Humphrey, A. Dalke, and K. Schulten. VMD: visual molecular dynamics. J. Mol. Graph., 14:33–38, 1996. doi:10.1016/0263-7855(96)00018-5.


Stefan Kesselheim, Marcello Sega, and Christian Holm. Applying ICC* to DNA translocation. Effect of dielectric boundaries. Comput. Phys. Commun., 182(1):33 – 35, 2011. doi:10.1016/j.cpc.2010.08.014.


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.


Timm Krüger. Computer simulation study of collective phenomena in dense suspensions of red blood cells under shear. PhD thesis, Universität Bochum, 2011.


Jonas Landsgesell, Christian Holm, and Jens Smiatek. Simulation of weak polyelectrolytes: A comparison between the constant pH and the reaction ensemble method. Eur. Phys. J. Special Topics, 2017. doi:10.1140/epjst/e2016-60324-3.


Jonas Landsgesell, Christian Holm, and Jens Smiatek. Wang-Landau reaction ensemble method: Simulation of weak polyelectrolytes and general acid-base reactions. J. Chem. Theory Comput., 13(2):852–862, 2017. doi:10.1021/acs.jctc.6b00791.


D Magatti and F Ferri. Fast multi-tau real-time software correlator for dynamic light scattering. Applied Optics, 40(24):4011–4021, AUG 20 2001. doi:10.1364/AO.40.004011.


Bernward A. Mann. The Swelling Behaviour of Polyelectrolyte Networks. PhD thesis, Johannes Gutenberg-University, Mainz, Germany, December 2005.


Charles S Peskin. The immersed boundary method. Acta Numer., 11:479–517, 2003. doi:10.1017/S0962492902000077.


A. Yu. Polyakov, T. V. Lyutyy, S. Denisov, V. V. Reva, and P. Hänggi. Large-scale ferrofluid simulations on graphics processing units. Comput. Phys. Commun., 184:1483–1489, 2013. doi:10.1016/j.cpc.2013.01.016.


Jorge Ramirez, Sathish K. Sukumaran, Bart Vorselaars, and Alexei E. Likhtman. Efficient on the fly calculation of time correlation functions in computer simulations. J. Chem. Phys., 133(15):154103, October 2010. doi:10.1063/1.3491098.


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


D. Roehm and A. Arnold. Lattice Boltzmann simulations on GPUs with ESPResSo. Eur. Phys. J. Special Topics, 210:89–100, 2012. doi:10.1140/epjst/e2012-01639-6.


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


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, April 1988. doi:10.1080/09500348814550731.


E. R. Smith. Electrostatic energy in ionic crystals. Proc. R. Soc. Lond. A, 375:475–505, 1981. doi:10.1098/rspa.1981.0064.


WR Smith and B Triska. The reaction ensemble method for the computer simulation of chemical and phase equilibria. I. Theory and basic examples. J. Chem. Phys., 100(4):3019–3027, 1994. doi:10.1063/1.466443.


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


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


S. Succi. The lattice Boltzmann equation for fluid dynamics and beyond. Oxford University Press, USA, 2001.


A. P. Thompson, S. J. Plimpton, and W. Mattson. General formulation of pressure and stress tensor for arbitrary many-body interaction potentials under periodic boundary conditions. J. Chem. Phys., 131(15):154107, 2009. doi:10.1063/1.3245303.


C. Tyagi, M. Süzen, M. Sega, M. Barbosa, S. Kantorovich, and C. Holm. An iterative, fast, linear-scaling method for computing induced charges on arbitrary dielectric boundaries. J. Chem. Phys., 132:154112, 2010. doi:10.1063/1.3376011.


S. Tyagi, A. Arnold, and C. Holm. ICMMM2D: an accurate method to include planar dielectric interfaces via image charge summation. J. Chem. Phys., 127:154723, 2007. doi:10.1063/1.2790428.


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. J. Chem. Phys., 129(20):204102, 2008. doi:10.1063/1.3021064.


Alexander J. Wagner and Ignacio Pagonabarraga. Lees–Edwards boundary conditions for lattice Boltzmann. J. Stat. Phys., 107:521–537, 2002. doi:10.1023/A:1014595628808.


Fugao Wang and David P Landau. Efficient, multiple-range random walk algorithm to calculate the density of states. Phys. Rev. Lett., 86(10):2050, 2001.