A versatile model for soft patchy particles with various patch arrangements.

We propose a simple and general mesoscale soft patchy particle model, which can felicitously describe the deformable and surface-anisotropic characteristics of soft patchy particles. This model can be used in dynamics simulations to investigate the aggregation behavior and mechanism of various types of soft patchy particles with tunable number, size, direction, and geometrical arrangement of the patches. To improve the computational efficiency of this mesoscale model in dynamics simulations, we give the simulation algorithm that fits the compute unified device architecture (CUDA) framework of NVIDIA graphics processing units (GPUs). The validation of the model and the performance of the simulations using GPUs are demonstrated by simulating several benchmark systems of soft patchy particles with 1 to 4 patches in a regular geometrical arrangement. Because of its simplicity and computational efficiency, the soft patchy particle model will provide a powerful tool to investigate the aggregation behavior of soft patchy particles, such as patchy micelles, patchy microgels, and patchy dendrimers, over larger spatial and temporal scales.

[1]  S. Ghosh,et al.  Self-assembly of Janus nanoparticles in diblock copolymers. , 2010, ACS nano.

[2]  L. An,et al.  A simulation model for soft triblock Janus particles and their ordered packing , 2013 .

[3]  J. Pitera,et al.  Soft patchy nanoparticles from solution-phase self-assembly of binary diblock copolymers. , 2008, Nano letters.

[4]  Phase diagram of patchy colloids: towards empty liquids. , 2006, Physical review letters.

[5]  Qian Chen,et al.  Directed self-assembly of a colloidal kagome lattice , 2014 .

[6]  F. Sciortino,et al.  Observation of empty liquids and equilibrium gels in a colloidal clay. , 2010, Nature materials.

[7]  I. Z. Reguly,et al.  A comparison between parallelization approaches in molecular dynamics simulations on GPUs , 2014, J. Comput. Chem..

[8]  F. Sciortino,et al.  Patchy particle model for vitrimers. , 2013, Physical review letters.

[9]  I. Coluzza,et al.  Telechelic star polymers as self-assembling units from the molecular to the macroscopic scale. , 2012, Physical review letters.

[10]  F. Sciortino,et al.  Two dimensional assembly of triblock Janus particles into crystal phases in the two bond per patch limit , 2011 .

[11]  Xiaoming Mao,et al.  Entropic effects in the self-assembly of open lattices from patchy particles. , 2013, Physical review. E, Statistical, nonlinear, and soft matter physics.

[12]  F. Sciortino,et al.  Phase diagram of Janus particles. , 2009, Physical review letters.

[13]  L. An,et al.  Model, self-assembly structures, and phase diagram of soft Janus particles , 2012 .

[14]  V. Percec,et al.  Predicting the size and properties of dendrimersomes from the lamellar structure of their amphiphilic Janus dendrimers. , 2011, Journal of the American Chemical Society.

[15]  Andreas Walther,et al.  Janus particles: synthesis, self-assembly, physical properties, and applications. , 2013, Chemical reviews.

[16]  Zhong-yuan Lu,et al.  A single-site anisotropic soft-core model for the study of phase behavior of soft rodlike particles , 2011 .

[17]  J. Doye,et al.  Formation of dodecagonal quasicrystals in two-dimensional systems of patchy particles. , 2011, The Journal of chemical physics.

[18]  Limin Wu,et al.  Fabrication, properties and applications of Janus particles. , 2012, Chemical Society reviews.

[19]  F. Schacher,et al.  Guided hierarchical co-assembly of soft patchy nanoparticles , 2013, Nature.

[20]  S. Glotzer,et al.  Anisotropy of building blocks and their assembly into complex structures. , 2007, Nature materials.

[21]  E. Bianchi,et al.  Patchy colloids: state of the art and perspectives. , 2011, Physical chemistry chemical physics : PCCP.

[22]  Chad A. Mirkin,et al.  Materials science: Self-assembly gets new direction , 2012, Nature.

[23]  Martin Stutzmann,et al.  Protein-modified nanocrystalline diamond thin films for biosensor applications , 2004, Nature materials.

[24]  E. Sanz,et al.  Phase diagram of a tetrahedral patchy particle model for different interaction ranges , 2010 .

[25]  P. Charbonneau,et al.  Crystallization of asymmetric patchy models for globular proteins in solution. , 2013, Physical review. E, Statistical, nonlinear, and soft matter physics.

[26]  H. Kawaguchi,et al.  Janus microgels prepared by surfactant-free pickering emulsion-based modification and their self-assembly. , 2007, Journal of the American Chemical Society.

[27]  M. Bradley,et al.  Cluster formation of Janus polymer microgels , 2009 .

[28]  F. Sciortino,et al.  Effects of patch size and number within a simple model of patchy colloids. , 2010, The Journal of chemical physics.

[29]  D. Wales,et al.  Design principles for Bernal spirals and helices with tunable pitch. , 2014, Nanoscale.

[30]  R. Kaner,et al.  Honeycomb carbon: a review of graphene. , 2010, Chemical reviews.

[31]  R. D. Groot,et al.  Equation of state of surface-adsorbing colloids , 2010, 1102.4694.

[32]  M. Klein,et al.  Virgil Percec and Other Complex Architectures Self-Assembly of Janus Dendrimers into Uniform Dendrimersomes , 2014 .

[33]  G. Yi,et al.  Recent progress on patchy colloids and their self-assembly , 2013, Journal of physics. Condensed matter : an Institute of Physics journal.

[34]  F. Sciortino,et al.  Gas–liquid phase coexistence in a tetrahedral patchy particle model , 2007 .

[35]  J. Doye,et al.  Controlling crystallization and its absence: proteins, colloids and patchy models. , 2007, Physical chemistry chemical physics : PCCP.

[36]  M. Hagan,et al.  Self-limited self-assembly of chiral filaments. , 2010, Physical review letters.

[37]  Andreas Walther,et al.  Facile, solution-based synthesis of soft, nanoscale Janus particles with tunable Janus balance. , 2012, Journal of the American Chemical Society.

[38]  J. Banavar,et al.  Computer Simulation of Liquids , 1988 .

[39]  Zhong-yuan Lu,et al.  Soft Janus particles: ideal building blocks for template-free fabrication of two-dimensional exotic nanostructures. , 2014, Soft matter.

[40]  G. A. Chapela,et al.  Self-assembly of kagome lattices, entangled webs and linear fibers with vibrating patchy particles in two dimensions. , 2014, Soft matter.

[41]  I. Kretzschmar,et al.  Fabrication, assembly, and application of patchy particles. , 2010, Macromolecular rapid communications.

[42]  D. Frenkel,et al.  Fluid-fluid coexistence in colloidal systems with short-ranged strongly directional attraction , 2003 .

[43]  F. Sciortino,et al.  Colloidal self-assembly: Patchy from the bottom up. , 2011, Nature materials.

[44]  F. Sciortino,et al.  Liquids more stable than crystals in particles with limited valence and flexible bonds , 2013, Nature Physics.

[45]  H. Lekkerkerker,et al.  Colloidal gels: Clay goes patchy. , 2011, Nature materials.

[46]  Duncan Poole,et al.  Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born , 2012, Journal of chemical theory and computation.

[47]  D. Heyes,et al.  Interactions between microgel particles , 2009 .

[48]  Andreas Stein,et al.  Colloidal assembly: the road from particles to colloidal molecules and crystals. , 2011, Angewandte Chemie.

[49]  Self-assembly of patchy particles into polymer chains: a parameter-free comparison between Wertheim theory and Monte Carlo simulation. , 2007, The Journal of chemical physics.

[50]  Shekhar Garde,et al.  Do Inverse Monte Carlo Algorithms Yield Thermodynamically Consistent Interaction Potentials , 2006 .

[51]  F. Schacher,et al.  Precise hierarchical self-assembly of multicompartment micelles , 2012, Nature Communications.

[52]  Berend Smit,et al.  Understanding Molecular Simulation , 2001 .

[53]  Jaewon Yoon,et al.  Recent advances with anisotropic particles , 2011 .

[54]  E. Sanz,et al.  Crystallization of tetrahedral patchy particles in silico. , 2011, The Journal of chemical physics.

[55]  Orientationally glassy crystals of Janus spheres , 2014, 1406.2625.

[56]  J. Doye,et al.  The stability of a crystal with diamond structure for patchy particles with tetrahedral symmetry. , 2010, The Journal of chemical physics.

[57]  J. Doye,et al.  Computing phase diagrams for a quasicrystal-forming patchy-particle system. , 2013, Physical review letters.

[58]  Erik Luijten,et al.  Triblock colloids for directed self-assembly. , 2011, Journal of the American Chemical Society.

[59]  Hajime Tanaka,et al.  Influence of patch-size variability on the crystallization of tetrahedral patchy particles. , 2014, Physical review letters.

[60]  I. Coluzza,et al.  Hierarchical self-assembly of telechelic star polymers: from soft patchy particles to gels and diamond crystals , 2013 .

[61]  A. Müller,et al.  Amphiphilic Janus micelles with polystyrene and poly(methacrylic acid) hemispheres. , 2003, Journal of the American Chemical Society.

[62]  Flavio Romano,et al.  Patterning symmetry in the rational design of colloidal crystals , 2012, Nature Communications.

[63]  Duncan Poole,et al.  Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald. , 2013, Journal of chemical theory and computation.

[64]  Steve Plimpton,et al.  Fast parallel algorithms for short-range molecular dynamics , 1993 .

[65]  R. D. Groot,et al.  Mesoscopic model for colloidal particles, powders, and granular solids. , 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.

[66]  Jianzhong Du,et al.  Anisotropic particles with patchy, multicompartment and Janus architectures: preparation and application. , 2011, Chemical Society reviews.

[67]  Hongzheng Chen,et al.  Graphene-like two-dimensional materials. , 2013, Chemical reviews.

[68]  E. W. Meijer,et al.  Self-assembly of soft nanoparticles with tunable patchiness. , 2009, Nature nanotechnology.

[69]  Qian Chen,et al.  Staged self-assembly of colloidal metastructures. , 2012, Journal of the American Chemical Society.

[70]  D. Frenkel Playing Tricks with Designer "Atoms" , 2002, Science.

[71]  Christos N Likos,et al.  Soft matter with soft particles. , 2006, Soft matter.

[72]  Jian Mao,et al.  Predictive supracolloidal helices from patchy particles , 2014, Scientific Reports.

[73]  Jing Zhang,et al.  Self-assembly structures of amphiphilic multiblock copolymer in dilute solution , 2013 .

[74]  F. Sciortino,et al.  Phase diagram and structural properties of a simple model for one-patch particles. , 2009, The Journal of chemical physics.

[75]  Qian Chen,et al.  Entropy favours open colloidal lattices. , 2013, Nature materials.

[76]  G. Kahl,et al.  Soft-patchy nanoparticles: modeling and self-organization. , 2015, Faraday discussions.

[77]  P. B. Warren,et al.  DISSIPATIVE PARTICLE DYNAMICS : BRIDGING THE GAP BETWEEN ATOMISTIC AND MESOSCOPIC SIMULATION , 1997 .

[78]  Thomas F. Miller,et al.  Symplectic quaternion scheme for biophysical molecular dynamics , 2002 .

[79]  D. Wales,et al.  A left-handed building block self-assembles into right- and left-handed helices , 2013 .

[80]  Sharon C. Glotzer,et al.  Rigid body constraints realized in massively-parallel molecular dynamics on graphics processing units , 2011, Comput. Phys. Commun..

[81]  S. Glotzer Some Assembly Required , 2004, Science.

[82]  S. Glotzer,et al.  Self-Assembly of Patchy Particles. , 2004, Nano letters.

[83]  Shu Yang,et al.  Patchy and multiregion janus particles with tunable optical properties. , 2010, Nano letters.

[84]  Wataru Shinoda,et al.  Large-Scale Molecular Dynamics Simulations of Self-Assembling Systems , 2008, Science.

[85]  I. Kretzschmar,et al.  Macromol. Rapid commun. 2/2010. , 2010, Macromolecular rapid communications.

[86]  Hong Liu,et al.  GALAMOST: GPU‐accelerated large‐scale molecular simulation toolkit , 2013, J. Comput. Chem..

[87]  Aaron S. Keys,et al.  Self-assembly of patchy particles into diamond structures through molecular mimicry. , 2005, Langmuir : the ACS journal of surfaces and colloids.

[88]  David R M Williams,et al.  Single Chain Asymmetric Block Copolymers in Poor Solvents. Candidates for Patchy Colloids , 2011 .

[89]  C. Angell,et al.  Materials science: Soft is strong , 2009, Nature.

[90]  J. Douglas,et al.  Self-assembly-induced protein crystallization. , 2009, Physical review letters.

[91]  S. Granick,et al.  Supracolloidal Reaction Kinetics of Janus Spheres , 2011, Science.

[92]  F. Sciortino,et al.  A numerical study of one-patch colloidal particles: from square-well to Janus. , 2010, Physical chemistry chemical physics : PCCP.

[93]  D. van der Spoel,et al.  GROMACS: A message-passing parallel molecular dynamics implementation , 1995 .

[94]  Yu Wang,et al.  Colloids with valence and specific directional bonding , 2012, Nature.

[95]  D. Wales,et al.  Designing a Bernal spiral from patchy colloids. , 2013, ACS nano.

[96]  F. Sciortino,et al.  Phase diagram of a reentrant gel of patchy particles. , 2013, The Journal of chemical physics.

[97]  Xinyuan Zhu,et al.  A supramolecular Janus hyperbranched polymer and its photoresponsive self-assembly of vesicles with narrow size distribution. , 2013, Journal of the American Chemical Society.

[98]  Shekhar Garde,et al.  Mesoscale model of polymer melt structure: self-consistent mapping of molecular correlations to coarse-grained potentials. , 2005, The Journal of chemical physics.