Hu-Jun Qian

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.

Dissipative particle dynamics simulation study on the binary mixture phase separation coupled with polymerization.

The influence of polymerization on the phase separation of binary immiscible mixtures has been investigated by the dissipative particle dynamics simulations in two dimensions. During polymerization, the bulk viscosity increases, which consequently slows down the spinodal decomposition process. The domain size growth is monitored in the simulations. The absence of 23 exponent for inertial hydrodynamic mechanism clearly reflects the suppressing effect of polymerization on the phase separation. Due to the increasing viscosity, the individual phase may be trapped in a metastable stage instead of the lamellar morphology identified for symmetric mixtures. Moreover, the polymerization induced phase separation in the binary miscible mixture has been studied. The domain growth is strongly dependent on the polymerization probability, which is naturally related to the activation energy for polymerization. The observed complex phase separation behavior is attributed to the interplay between the increasing thermodynamic driving force for phase separation and the increasing viscosity that suppresses phase separation as the polymerization proceeds.

IBIsCO: A molecular dynamics simulation package for coarse‐grained simulation

IBIsCO is a parallel molecular dynamics simulation package developed specially for coarse‐grained simulations with numerical potentials derived by the iterative Boltzmann inversion (IBI) method (Reith et al., J Comput Chem 2003, 24, 1624). In addition to common features of molecular dynamics programs, the techniques of dissipative particle dynamics (Groot and Warren, J Chem Phys 1997, 107, 4423) and Lowe–Andersen dynamics (Lowe, Europhys Lett 1999, 47, 145) are implemented, which can be used both as thermostats and as sources of friction to compensate the loss of degrees of freedom by coarse‐graining. The reverse nonequilibrium molecular dynamics simulation method (Müller‐Plathe, Phys Rev E 1999, 59, 4894) for the calculation of viscosities is also implemented. Details of the algorithms, functionalities, implementation, user interfaces, and file formats are described. The code is parallelized using PE_MPI on PowerPC architecture. The execution time scales satisfactorily with the number of processors.

Crack healing and reclaiming of vulcanized rubber by triggering the rearrangement of inherent sulfur crosslinked networks

CuCl2 has been shown to effectively catalyze reshuffling of the inherent sulfur crosslinked networks of vulcanized rubber. Once activated, CuCl2-based complex catalysis enables disulfide metathesis through circulated crossover reactions among disulfide and polysulfide bonds without forming radicals and ionic intermediates. By taking advantage of this mechanism, the model material of this study, vulcanized polybutadiene rubber, acquires thermal remendability as characterized by repeated restoration of mechanical properties. Moreover, it can be reprocessed like thermoplastics. The compositions and fabrication of the model material simulate those of industrial vulcanized rubber, so as to facilitate formulation optimization under the circumstances close to the actual situation for possible future practical applications. It is hoped that the results of the present preliminary exploration would provide the basis for extending the service life and developing new recycling techniques of vulcanized rubber, which is produced, used and scrapped in large quantities every day.

Molecular simulation of water and hydration effects in different environments: challenges and developments for DFTB based models.

We discuss the description of water and hydration effects that employs an approximate density functional theory, DFTB3, in either a full QM or QM/MM framework. The goal is to explore, with the current formulation of DFTB3, the performance of this method for treating water in different chemical environments, the magnitude and nature of changes required to improve its performance, and factors that dictate its applicability to reactions in the condensed phase in a QM/MM framework. A relatively minor change (on the scale of kBT) in the O–H repulsive potential is observed to substantially improve the structural properties of bulk water under ambient conditions; modest improvements are also seen in dynamic properties of bulk water. This simple change also improves the description of protonated water clusters, a solvated proton, and to a more limited degree, a solvated hydroxide. By comparing results from DFTB3 models that differ in the description of water, we confirm that proton transfer energetics are adequately described by the standard DFTB3/3OB model for meaningful mechanistic analyses. For QM/MM applications, a robust parametrization of QM-MM interactions requires an explicit consideration of condensed phase properties, for which an efficient sampling technique was developed recently and is reviewed here. The discussions help make clear the value and limitations of DFTB3 based simulations, as well as the developments needed to further improve the accuracy and transferability of the methodology.

Reactive Molecular Dynamics Simulation of Fullerene Combustion Synthesis: ReaxFF vs DFTB Potentials

The dynamic fullerene self-assembly process during benzene combustion was studied using classical Reactive Force Field (ReaxFF) nonequilibrium molecular dynamics (MD) simulations. In order to drive the combustion process, the hydrogen to carbon (H/C) ratio was gradually reduced during the course of the MD simulations. Target temperatures of 2500 and 3000 K were maintained by using a Berendsen thermostat. Simulation conditions and hydrogen removal strategies were chosen to match closely a previous quantum chemical MD (QM/MD) study based on the density-functional tight-binding (DFTB) potential ( Saha et al. ACS Nano 2009 , 3 , 2241 ) to allow a comparison between the two different potentials. Twenty trajectories were computed at each target temperature, and hydrocarbon cluster size, CxHy composition, average carbon cluster curvature, carbon hybridization type, and ring count statistics were recorded as a function of time. Similarly as in the QM/MD simulations, only giant fullerene cages in the range from 155 to 212 carbon atoms self-assembled, and no C60 cages were observed. The most notable difference concerned the time required for completing cage self-assembly: Depending on temperature, it takes between 50 and 150 ps in DFTB/MD simulations but never less than 100 ps and frequently several 100s ps in ReaxFF/MD simulations. In the present system, the computational cost of ReaxFF/MD is about 1 order of magnitude lower than that of the corresponding DFTB/MD. Overall, the ReaxFF/MD simulations method paints a qualitatively similar picture of fullerene formation in benzene combustion when compared to direct MD simulations based on the DFTB potential.

Coupled cluster and density functional theory calculations of atomic hydrogen chemisorption on pyrene and coronene as model systems for graphene hydrogenation.

Ab initio coupled cluster and density functional theory studies of atomic hydrogen addition to the central region of pyrene and coronene as molecular models for graphene hydrogenation were performed. Fully relaxed potential energy curves (PECs) were computed at the spin-unrestricted B3LYP/cc-pVDZ level of theory for the atomic hydrogen attack of a center carbon atom (site A), the midpoint of a neighboring carbon bond (site B), and the center of a central hexagon (site C). Using the B3LYP/cc-pVDZ PEC geometries, we evaluated energies at the PBE density functional, as well as ab initio restricted open-shell ROMP2, ROCCSD, and ROCCSD(T) levels of theory, employing cc-pVDZ and cc-pVTZ basis sets, and performed a G2MS extrapolation to the ROCCSD(T)/cc-pVTZ level of theory. In agreement with earlier studies, we find that only site A attack leads to chemisorption. The G2MS entrance channel barrier heights, binding energies, and PEC profiles are found to agree well with a recent ab initio multireference wave function theory study (Bonfanti et al. J. Chem. Phys.2011, 135, 164701), indicating that single-reference open-shell methods including B3LYP are sufficient for the theoretical treatment of the interaction of graphene with a single hydrogen atom.

Effective control of the transport coefficients of a coarse-grained liquid and polymer models using the dissipative particle dynamics and Lowe-Andersen equations of motion.

The dynamics of coarse-grained models obtained through iterative Boltzmann inversion [J. Comput. Chem., 2003, 24, 1624] is always faster than that of the parent atomistic models. In this work, the dissipative particle dynamics (DPD) and Lowe-Andersen (LA) equations of motion are applied in coarse-grained simulations to slow down the coarse-grained dynamics. Both methods provide effective friction and both conserve the linear momentum locally, so that they can be used for the calculation of viscosities. Coarse-grained models of liquid ethylbenzene and of short-chain polystyrene melts are studied. Based on the simulation of ethylbenzene at four different temperatures, empirical rules are proposed for choosing the noise strength in DPD or the bath collision frequency in LA dynamics to reproduce the diffusion coefficients of the fully atomistic simulation. The rules developed using the ethylbenzene system are finally tested on the polystyrene melt where they lead to a close reproduction of the experimental diffusion coefficient.

The effects of Lowe–Andersen temperature controlling method on the polymer properties in mesoscopic simulations

Lowe-Andersen (LA) temperature controlling method [C. P. Lowe, Europhys. Lett. 47, 145 (1999)] is applied in a series of mesoscopic polymer simulations to test its validity and efficiency. The method is an alternative for dissipative particle dynamics simulation (DPD) technique which is also Galilean invariant. It shows excellent temperature control and gives correct radial distribution function as that from DPD simulation. The efficiency of LA method is compared with other typical DPD integration schemes and is proved to be moderately efficient. Moreover, we apply this approach to diblock copolymer microphase separation simulations. With LA method, we are able to reproduce all the results from the conventional DPD simulations. The calculated structure factors of the microphases are consistent with the experiments. We also study the microphase evolution dynamics with increasing chiN and find that the bath collision frequency Gamma does not affect the order of appearing phases. Although the thermostat does not affect the surface tension, the order-disorder transition (ODT) is somewhat sensitive to the values of Gamma, i.e., the ODT is nonmonotonic with increasing Gamma. The dynamic scaling law is also tested, showing that the relation obeys the Rouse theory with various Gamma.

Dissipative particle dynamics study on the interfaces in incompatible A∕B homopolymer blends and with their block copolymers

Dissipative particle dynamics, a simulation technique appropriate at mesoscopic scales, has been applied to investigate the interfaces in immiscible binary A/B homopolymer blends and in the ternary systems with their block copolymers. For the binary blends, the interfacial tension increases and the interface thickness decreases with increasing Flory-Huggins interaction parameter chi while the homopolymer chain length is fixed. However, when the chi parameter and one of the homopolymer chain length is fixed, increasing another homopolymer chain length will induce only a small increase on interfacial tension and slight decrease on interface thickness. For the ternary blends, adding the A-b-B block copolymer will reduce the interfacial tension. When the mole number of the block copolymer is fixed, longer block chains have higher efficiency on reducing the interfacial tension than the shorter ones. But for the block copolymers with fixed volume fraction, shorter chains will be more efficient than the longer ones on reducing the interfacial tension. Increasing the block copolymer concentration reduces interfacial tension. This effect is more prominent for shorter block copolymer chains.