Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

Multiscale modeling and simulation of polymer nanocomposites

Due to their atomically precise structures and intriguing chemical/physical properties, metal nanoclusters are an emerging class of modular nanomaterials. Photo-luminescence (PL) is one of their most fascinating properties, due to the plethora of promising PL-based applications, such as chemical sensing, bio-imaging, cell labeling, phototherapy, drug delivery, and so on. However, the PL of most current nanoclusters is still unsatisfactory-the PL quantum yield (QY) is relatively low (generally lower than 20%), the emission lifetimes are generally in the nanosecond range, and the emitted color is always red (emission wavelengths of above 630 nm). To address these shortcomings, several strategies have been adopted, and are reviewed herein: capped-ligand engineering, metallic kernel alloying, aggregation-induced emission, self-assembly of nanocluster building blocks into cluster-based networks, and adjustments on external environment factors. We further review promising applications of these fluorescent nanoclusters, with particular focus on their potential to impact the fields of chemical sensing, bio-imaging, and bio-labeling. Finally, scope for improvements and future perspectives of these novel nanomaterials are highlighted as well. Our intended audience is the broader scientific community interested in the fluorescence of metal nanoclusters, and our review hopefully opens up new horizons for these scientists to manipulate PL properties of nanoclusters. This review is based on publications available up to December 2018.

Tailoring the photoluminescence of atomically precise nanoclusters.

ConspectusThe vast amount of plastic waste emitted into the environment and the increasing concern of potential harm to wildlife has made microplastic and nanoplastic pollution a growing environmental concern. Plastic pollution has the potential to cause both physical and chemical harm to wildlife directly or via sorption, concentration, and transfer of other environmental contaminants to the wildlife that ingest plastic. Small particles of plastic pollution, termed microplastics (>100 nm and <5 mm) or nanoplastics (<100 nm), can form through fragmentation of larger pieces of plastic. These small particles are especially concerning because of their high specific surface area for sorption of contaminants as well as their potential to translocate in the bodies of organisms. These same small particles are challenging to separate and identify in environmental samples because their size makes handling and observation difficult. As a result, our understanding of the environmental prevalence of nanoplastics and ...

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Separation and Analysis of Microplastics and Nanoplastics in Complex Environmental Samples

The surge of interest in and scientific publications on the structure and properties of nanocomposites has made it rather difficult for the novice to comprehend the physical structure of these new materials and the relationship between their properties and those of the conventional range of composite materials. Some of the questions that arise are: How should the reinforcement volume fraction be calculated? How can the clay gallery contents be assessed? How can the ratio of intercalate to exfoliate be found? Does polymerization occur in the clay galleries? How is the crystallinity of semi-crystalline polymers affected by intercalation? What role do the mobilities of adsorbed molecules and clay platelets have? How much information can conventional X-ray diffraction offer? What is the thermodynamic driving force for intercalation and exfoliation? What is the elastic modulus of clay platelets? The growth of computer simulation techniques applied to clay materials has been rapid, with insight gained into the structure, dynamics and reactivity of polymer–clay systems. However these techniques operate on the basis of approximations, which may not be clear to the non-specialist. This critical review attempts to assess these issues from the viewpoint of traditional composites thereby embedding these new materials in a wider context to which conventional composite theory can be applied. (210 references)

A critical appraisal of polymer-clay nanocomposites.

Molecular interactions in intercalated organically modified clay and clay–polycaprolactam nanocomposites: Experiments and modeling

Pyrophyllite is the precursor to other smectite-group minerals which exhibit swelling. The mineral structure of pyrophyllite can lead to other minerals in the smectite group, including montmorillonite, through appropriate isomorphous substitutions. In this work, an atomic model of the pyrophyllite interlayer was constructed. The response of the interlayer was evaluated using steered molecular dynamics simulations. In steered molecular dynamics, external forces were applied to individual atoms to study the response of the model to applied forces. In this work, forces are applied to the surface clay atoms to evaluate the displacement vs. applied stress in the interlayer between clay layers. This paper describes the construction of the model, the simulation procedure, and the results of the simulations which show that under the applied loading, deformation occurs mainly in the interlayer. The clay layers show relatively little deformation. The results show that the relationship between applied stress and displacement of the interlayer is linear. The stress-deformation relationship for the interlayer is presented.

Modeling the response of pyrophyllite interlayer to applied stress using steered molecular dynamics

Mineral proximity influences mechanical response of proteins in biological mineral-protein hybrid systems.

The mechanical response of the interlayer of hydrated montmorillonite was evaluated using steered molecular dynamics. An atomic model of the sodium montmorillonite was previously constructed. In the current study, the interlayer of the model was hydrated with multiple layers of water. Using steered molecular dynamics, external forces were applied to individual atoms of the clay surface, and the response of the model was studied. The displacement versus applied stress and stress versus strain relationships of various parts of the interlayer were studied. The paper describes the construction of the model, the simulation procedure, and results of the simulations. Some results of the previous work are further interpreted in the light of the current research. The simulations provide quantitative stress deformation relationships as well as an insight into the molecular interactions taking place between the clay surface and interlayer water and cations.

Pijush Ghosh

Papers

Molecular interactions in intercalated organically modified clay and clay–polycaprolactam nanocomposites: Experiments and modeling

Modeling the response of pyrophyllite interlayer to applied stress using steered molecular dynamics

Mineral proximity influences mechanical response of proteins in biological mineral-protein hybrid systems.

Evolution of Mechanical Response of Sodium Montmorillonite Interlayer with Increasing Hydration by Molecular Dynamics

Mechanical properties of the sodium montmorillonite interlayer intercalated with amino acids.