And80

Andersen. Molecular-Dynamics Simulations At Constant Pressure And/Or Temperature. J. Chem. Phys, 72(4):2384-2393, 1980.

And83

Hans C. Andersen. Rattle: a “velocity” version of the shake algorithm for molecular dynamics calculations. J. Comp. Phys., 51:24–34, 1983.

AH05

A. Arnold and C. Holm. MMM1D: A method for calculating electrostatic interactions in 1D periodic geometries. J. Chem. Phys., 123(12):144103, 2005.

AH02a

Axel Arnold and Christian Holm. A novel method for calculating electrostatic interactions in 2D periodic slab geometries. Chem. Phys. Lett., 354:324–330, 2002.

AH02b

Axel Arnold and Christian Holm. MMM2D: a fast and accurate summation methodlimnb for electrostatic interactions in 2d slab geometries. Comput. Phys. Commun., 148(3):327–348, 2002. arXiv:cond-mat/0202265.

ALK+ed

Axel Arnold, Olaf Lenz, Stefan Kesselheim, Rudolf Weeber, Florian Fahrenberger, Dominic Roehm, Peter Kosovan, and Christian Holm. ESPResSo 3.1 – molecular dynamics software for coarse-grained models. In Michael Griebel, Christian Rieger, and Marc Alexander Schweitzer, editors, Proceedings of the Sixth International Workshop on Meshfree Methods for Partial Differential Equations, Lecture Notes in Computational Science and Engineering. Springer, Berlin, Germany, submitted.

AdeJoannisH02

Axel Arnold, Jason de Joannis, and Christian Holm. Electrostatics in Periodic Slab Geometries I+II. J. Chem. Phys., 117:2496–2512, 2002. arXiv:cond-mat/0202399 and cond-mat/0202400.

BAC09

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. URL: http://link.aip.org/link/?JCP/131/094107/1, doi:10.1063/1.3216473.

BP07

RE Belardinelli and VD Pereyra. Fast algorithm to calculate density of states. Physical Review E, 75(4):046701, 2007.

Bro04

A. Brodka. Ewald summation method with electrostatic layer correction for interactions of point dipoles in slab geometry. Chem. Phys. Lett., 400:62–67, 2004.

BN95

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

CerdaBLH08

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

CBLCHolm08

Juan J. Cerda, V. Ballenegger, O. Lenz, and C.Holm. P3M algorithm for dipolar interactions. J. Chem. Phys., 129:234104, 2008. arXiv:cond-mat/????

CimrakGJanvcigova14

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.

CimrakGS12

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.

CF10

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. Engng., 26(3-4):471–487, 2010.

dGMM+16

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.

Des00

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

DH98a

M. Deserno and C. Holm. How to mesh up Ewald sums. i. J. Chem. Phys., 109:7678, 1998.

DH98b

M. Deserno and C. Holm. How to mesh up Ewald sums. ii. J. Chem. Phys., 109:7694, 1998.

DHL00

M. Deserno, C. Holm, and H. J. Limbach. Molecular Dynamics on Parallel Computers, chapter How to mesh up Ewald sums. World Scientific, Singapore, 2000.

DE86

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

DHCA07

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 Stat Nonlin Soft Matter Phys., 75:066707, 2007.

DunwegL08

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. URL: http://dx.doi.org/10.1007/12_2008_4, doi:10.1007/12_2008_4.

EPB+95

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.

Ewa21

P.P. Ewald. Die berechnung optischer und elektrostatischer gitterpotentiale. Ann. Phys., 64:253–287, 1921.

FS02

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

GK86

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.

HTBL+08

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.

HHHS10

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}.

HE88

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

HDS96

W. Humphrey, A. Dalke, and K. Schulten. VMD: visual molecular dynamics. J. Mol. Graphics, 14:33–38, 1996.

KSH11

Stefan Kesselheim, Marcello Sega, and Christian Holm. Applying to dna translocation: effect of dielectric boundaries. Computer Physics Communications, 182(1):33 – 35, 2011. <ce:title>Computer Physics Communications Special Edition for Conference on Computational Physics Kaohsiung, Taiwan, Dec 15-19, 2009</ce:title>. URL: http://www.sciencedirect.com/science/article/pii/S001046551000305X, doi:10.1016/j.cpc.2010.08.014.

KP92

Jiri Kolafa and John W. Perram. Cutoff errors in the ewald summation formulae for point charge systems. Molecular Simulation, 9(5):351–368, 1992.

Kruger11

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

LHS17a

Jonas Landsgesell, Christian Holm, and Jens Smiatek. Simulation of weak polyelectrolytes: a comparison between the constant ph and the reaction ensemble method. The European Physical Journal Special Topics, 2017. doi:10.1140/epjst/e2016-60324-3.

LHS17b

Jonas Landsgesell, Christian Holm, and Jens Smiatek. Wang-landau reaction ensemble method: simulation of weak polyelectrolytes and general acid-base reactions. Journal of Chemical Theory and Computation, 13(2):852–862, 2017. doi:10.1021/acs.jctc.6b00791.

MF01

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}.

Man05

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

Pes03

Charles S Peskin. The immersed boundary method. Acta Numerica, 11:479–517, 2003.

PLD+13

A.Yu. Polyakov, T.V. Lyutyy, S. Denisov, V.V. Reva, and P. Hänggi. Large-scale ferrofluid simulations on graphics processing units. Computer Physics Communications, 184:1483–1489, 2013.

RSVL10

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, OCT 21 2010. doi:{10.1063/1.3491098}.

RR92

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

RA12

D. Roehm and A. Arnold. Lattice boltzmann simulations on GPUs with ESPResSo. Eur. Phys. J. ST, 210:73–88, 2012.

RC03

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

SchatzelDS88

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, APR 1988. doi:{10.1080/09500348814550731}.

Smi81

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

ST94

WR 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.

SDunwegK01

T. Soddemann, B. Dünweg, and K. Kremer. A generic computer model for amphiphilic systems. Eur. Phys. J. E, 6:409, 2001.

Str99

R. Strebel. Pieces of software for the Coulombic $m$ body problem. PhD thesis, ETH Zürich, 1999. URL: http://e-collection.ethbib.ethz.ch/show?type=diss\&nr=13504.

Suc01

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

TPM09

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. Journal of Chemical Physics, 131:154107, 2009.

TSuzenS+10

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.

TAH07

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.

TAH08

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.

WP02

Alexander J. Wagner and Ignacio Pagonabarraga. Lees–edwards boundary conditions for lattice boltzmann. Journal of statistical physics, 107:521–537, 2002. doi:10.1023/A:1014595628808.

WL01

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