Zhan-Wei Li

GALAMOST: GPU-accelerated large-scale molecular simulation toolkit

GALAMOST [graphics processing unit (GPU)‐accelerated large‐scale molecular simulation toolkit] is a molecular simulation package designed to utilize the computational power of GPUs. Besides the common features of molecular dynamics (MD) packages, it is developed specially for the studies of self‐assembly, phase transition, and other properties of polymeric systems at mesoscopic scale by using some lately developed simulation techniques. To accelerate the simulations, GALAMOST contains a hybrid particle‐field MD technique where particle–particle interactions are replaced by interactions of particles with density fields. Moreover, the numerical potential obtained by bottom‐up coarse‐graining methods can be implemented in simulations with GALAMOST. By combining these force fields and particle‐density coupling method in GALAMOST, the simulations for polymers can be performed with very large system sizes over long simulation time. In addition, GALAMOST encompasses two specific models, that is, a soft anisotropic particle model and a chain‐growth polymerization model, by which the hierarchical self‐assembly of soft anisotropic particles and the problems related to polymerization can be studied, respectively. The optimized algorithms implemented on the GPU, package characteristics, and benchmarks of GALAMOST are reported in detail.

Model, self-assembly structures, and phase diagram of soft Janus particles

Janus particles exhibit interesting self-assembly behavior and functional performances. In particular, soft and deformable Janus particles, as diverse as Janus micelles, Janus microgels, and Janus dendrimers, should receive more attention due to their unique chemical and physical properties and enormous potential applications. Gaining control over precise and predictable self-assembled structures and understanding the fundamental details of self-assembly remain a formidable challenge. Here we present a novel mesoscale model for soft Janus particles, which successfully reflects their physical nature by directly mapping onto experimentally measurable particle properties. By properly tuning Janus balance and the strength of attraction between attractive patches, soft Janus particles can reversibly self-assemble into a number of fascinating hierarchical superstructures in dilute solutions, such as micelles, wormlike strings, single helices, double helices, bilayers, tetragonal bilayers, and complex supermicelles. Our work demonstrates that soft Janus particles with deformable and non-centrosymmetric characteristics hide many surprises in the design and fabrication of hierarchically self-assembled superstructures.

A simulation model for soft triblock Janus particles and their ordered packing

We present a mesoscale simulation model that is suitable for describing the deformable and non-centrosymmetric characteristics of soft triblock Janus particles. The model parameters are readily mapped onto experimental systems under different ambient conditions. We examine the influence of Janus balance and the flexibility of Janus particle aggregates on the packing structures. Some ordered structures, such as the hexagonal columnar structure and the body-centered tetragonal structure, are observed in our simulations. Our study demonstrates that the Janus balance and the flexibility of Janus particle aggregates can be tuned to obtain various ordered packing structures. The soft Janus particles with soft and deformable characteristics may bring new excitement to materials science.

Simulation Model for Hierarchical Self-Assembly of Soft Disklike Particles

We develop a novel mesoscale simulation model in order to study the hierarchical self-assembly of soft disklike particles in dilute solutions. In suitable solvent conditions, the soft anisotropic disklike particles first self-assemble into one-dimensional flexible threads, in accord with experiments. Then, intriguingly, the threads reversibly pack into flexible hexagonal bundles by decreasing the solvent quality. Hierarchical self-assembly of this type may be important to provide a strategy to create bundle structures by bottom-up self-assembly with a single type of soft and flexible building block and mimic the bundles commonly found in biological structures.

Hierarchical self-assembly of soft disklike particles under shear flow.

We develop a mesoscale nonequilibrium simulation model to study the effect of steady shear on the hierarchical self-assembly of soft disklike particles in dilute solutions. By properly tuning shear rates and solvent conditions, soft disklike particles can self-assemble into flexible threads and bundle-like structures along the flow direction. Shear flow facilitates the self-assembly of soft disklike particles into one-dimensional long threads along the flow direction; however, it suppresses the formation of flexible bundles from the threads while decreasing the solvent quality. The relatively well-defined bundle structures along the flow direction can only be obtained when the solvent condition becomes even worse. Our study elucidates how the solvent condition and shear rate can be utilized to control the shear-induced self-assembled structures, which would enable designed nanofabrication.

Employing multi-GPU power for molecular dynamics simulation: an extension of GALAMOST

ABSTRACT We describe the algorithm of employing multi-GPU power on the basis of Message Passing Interface (MPI) domain decomposition in a molecular dynamics code, GALAMOST, which is designed for the coarse-grained simulation of soft matters. The code of multi-GPU version is developed based on our previous single-GPU version. In multi-GPU runs, one GPU takes charge of one domain and runs single-GPU code path. The communication between neighbouring domains takes a similar algorithm of CPU-based code of LAMMPS, but is optimised specifically for GPUs. We employ a memory-saving design which can enlarge maximum system size at the same device condition. An optimisation algorithm is employed to prolong the update period of neighbour list. We demonstrate good performance of multi-GPU runs on the simulation of Lennard–Jones liquid, dissipative particle dynamics liquid, polymer and nanoparticle composite, and two-patch particles on workstation. A good scaling of many nodes on cluster for two-patch particles is presented.

Supracolloidal fullerene-like cages: design principles and formation mechanisms

How to create novel desired structures by rational design of building blocks represents a significant challenge in materials science. Here we report a conceptually new design principle for creating supracolloidal fullerene-like cages through the self-assembly of soft patchy particles interacting via directional nonbonded interactions by mimicking non-planar sp2 hybridized carbon atoms in C60. Our numerical investigations demonstrate that the rational design of patch configuration, size, and interaction can drive soft three-patch particles to reversibly self-assemble into a vast collection of supracolloidal fullerene-like cages. We further elucidate the formation mechanisms of supracolloidal fullerene-like cages by analyzing the structural characteristics and the formation process. Our results provide conceptual and practical guidance towards the experimental realization of supracolloidal fullerene-like cages, as well as a new perspective on understanding the fullerene formation mechanisms.

General patchy ellipsoidal particle model for the aggregation behaviors of shape- and/or surface-anisotropic building blocks

We present a general patchy ellipsoidal particle model suitable for conducting dynamics simulations of the aggregation behaviors of various shape- and/or surface-anisotropic colloids, especially patchy ellipsoids with continuously variable shape and tunable patchiness. To achieve higher computational efficiency in dynamics simulations, we employ a multi-GPU acceleration technique based on a domain decomposition algorithm. The validation and performance evaluation of this GPU-assisted model are performed by simulating several typical benchmark systems of non-patchy and patchy ellipsoids. Given the generality and efficiency of our GPU-assisted patchy ellipsoidal particle model, it will provide a highly feasible dynamics simulation framework to investigate the aggregation behaviors of anisotropic soft matter systems comprised of shape- and/or surface-anisotropic building blocks.