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

The stability of two-dimensional (2D) layers and membranes is subject of a long standing theoretical debate. According to the so called Mermin-Wagner theorem, long wavelength fluctuations destroy the long-range order for 2D crystals. Similarly, 2D membranes embedded in a 3D space have a tendency to be crumpled. These dangerous fluctuations can, however, be suppressed by anharmonic coupling between bending and stretching modes making that a two-dimensional membrane can exist but should present strong height fluctuations. The discovery of graphene, the first truly 2D crystal and the recent experimental observation of ripples in freely hanging graphene makes these issues especially important. Beside the academic interest, understanding the mechanisms of stability of graphene is crucial for understanding electronic transport in this material that is attracting so much interest for its unusual Dirac spectrum and electronic properties. Here we address the nature of these height fluctuations by means of straightforward atomistic Monte Carlo simulations based on a very accurate many-body interatomic potential for carbon. We find that ripples spontaneously appear due to thermal fluctuations with a size distribution peaked around 70 \AA which is compatible with experimental findings (50-100 \AA) but not with the current understanding of stability of flexible membranes. This unexpected result seems to be due to the multiplicity of chemical bonding in carbon.

Intrinsic ripples in graphene

Kepa Ruiz-Mirazo,†,∥ Carlos Briones,‡,∥ and Andreś de la Escosura* †Biophysics Unit (CSIC-UPV/EHU), Leioa, and Department of Logic and Philosophy of Science, University of the Basque Country, Avenida de Tolosa 70, 20080 Donostia−San Sebastiań, Spain ‡Department of Molecular Evolution, Centro de Astrobiología (CSIC−INTA, associated to the NASA Astrobiology Institute), Carretera de Ajalvir, Km 4, 28850 Torrejoń de Ardoz, Madrid, Spain Organic Chemistry Department, Universidad Autońoma de Madrid, Cantoblanco, 28049 Madrid, Spain

Prebiotic systems chemistry: new perspectives for the origins of life.

Multiscale modeling and simulation of polymer nanocomposites

Nanofilled polymeric matrices have demonstrated remarkable mechanical, electrical, and thermal properties. In this article we review the processing of carbon nanotube, graphene, and clay montmorillonite platelet as potential nanofillers to form nanocomposites. The various functionalization techniques of modifying the nanofillers to enable interaction with polymers are summarized. The importance of filler dispersion in the polymeric matrix is highlighted. Finally, the challenges and future outlook for nanofilled polymeric composites are presented.

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Polymer nanocomposites-A comparison between carbon nanotubes, graphene, and clay as nanofillers

Large-scale atomistic simulations, which we define as containing more than 100 000 atoms, are becoming more commonplace as computational resources increase and efficient classical molecular dynamics algorithms are developed. With the advent of grid-computing methods, it is now possible to simulate even larger systems efficiently. Using this new technology, we have simulated montmorillonite clay systems containing up to approximately ten million atoms whose dimensions approach those of a realistic clay platelet. This considerably extends the spatial dimensions of microscopic simulation into a domain normally encountered in mesoscopic simulation. The simulations exhibit emergent behavior with increasing size, manifesting collective thermal motion of clay sheet atoms over lengths greater than 150 A. This motion produces low-amplitude, long-wavelength undulations of the clay sheets, implicitly inhibited by the small system sizes normally encountered in atomistic simulation. The thermal bending fluctuations al...

Large-scale molecular dynamics study of montmorillonite clay : Emergence of undulatory fluctuations and determination of material properties

The intercalation of DNA into layered double hydroxides (LDHs) has various applications, including drug delivery for gene therapy and origins of life studies. The nanoscale dimensions of the interlayer region make the exact conformation of the intercalated DNA difficult to elucidate experimentally. We use molecular dynamics techniques, performed on high performance supercomputing grids, to carry out large-scale simulations of double stranded, linear and plasmid DNA up to 480 base pairs in length intercalated within a magnesium−aluminum LDH. Currently only limited experimental data have been reported for these systems. Our models are found to be in agreement with experimental observations, according to which hydration is a crucial factor in determining the structural stability of DNA. Phosphate backbone groups are found to align with aluminum lattice positions. At elevated temperatures and pressures, relevant to origins of life studies which maintain that the earliest life forms originated around deep ocea...

Computer simulation study of the structural stability and materials properties of DNA-intercalated layered double hydroxides.

Graphite's lubricating properties due to the "weak" interactions between individual layers have long been known. However, these interactions are not weak enough to allow graphite to readily exfoliate into graphene on a large scale. Separating graphite layers down to a single sheet is an intense area of research as scientists attempt to utilize graphene's superlative properties. The exfoliation and processing of layered materials is governed by the friction between layers. Friction on the macroscale can be intuitively understood, but there is little understanding of the mechanisms involved in nanolayered materials. Using molecular dynamics and a new forcefield, graphene's unusual behavior in a superlubric state is examined, and the energy dissipated between two such surfaces sliding past each other is shown. The dependence of friction on temperature and surface roughness is described, and agreement with experiment is reported. The accuracy of the simulated behavior enables the processes that drive exfoliation of graphite into individual graphene sheets to be described. Taking into account the friction between layers, a peeling mechanism of exfoliation is predicted to be of lower energy cost than shearing.

https://www.onlinelibrary.wiley.com/doi/epdf/10.1002/adma.201705791

Graphene-Graphene Interactions: Friction, Superlubricity and Exfoliation

This work was funded in part by the EU FP7 MAPPER project (grant number RI-261507) and the Qatar National Research Fund (grant number 09–260–1–048). Supercomputing time was provided by PRACE on JUGENE (project PRA044), the Hartree Centre (Daresbury Laboratory) on BlueJoule and BlueWonder via the CGCLAY project, and on HECToR and ARCHER, the UK national supercomputing facility at the University of Edinburgh, via EPSRC through grants EP/F00521/1, EP/E045111/1, EP/I017763/1 and the UK Consortium on Mesoscopic Engineering Sciences (EP/L00030X/1). The authors are grateful to Professor Julian Evans for stimulating discussions during the course of this project. Data-storage and management services were provided by EUDAT (grant number 283304).

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Chemically Specific Multiscale Modeling of Clay–Polymer Nanocomposites Reveals Intercalation Dynamics, Tactoid Self‐Assembly and Emergent Materials Properties

In oil and gas drilling operations, drilling fluids perform essential tasks such as lubricating the drill bit, providing hydrostatic pressure and removing drill cuttings. One important function of the drilling fluid is to stop compacted clay minerals, commonly encountered in drilling operations, from taking up water from the drilling fluids and consequently swelling. Such a scenario can have an adverse impact on drilling operations and may lead to significantly increased oil well construction costs. With increasingly stringent environmental guidelines determining which swelling inhibitors are available for use in the oilfield as drilling fluid additives, there is a need to fully understand the mechanisms of clay hydration in order to design new swelling inhibitors which conform to evolving regulations. Using a range of computational techniques and analysis, combined with known experimental results, we have devised a set of “rule-based” design criteria for clay-swelling inhibitors. To achieve this, we have formulated a hydration energy parameter, which assesses the changes in energy during the step-wise progression from mono- to bi- to trilayers of water in the clay sheet galleries. This parameter can be used to rationalise and predict the swelling profiles for clays containing both cationic and neutral clay swelling inhibitors. The rules we have devised are as follows: (i) Cationic inhibitors should be able to replace sodium ions in the interlayer. (ii) Cationic inhibitors should possess a water soluble, hydrophobic backbone. (iii) Cationic inhibitors should have primary di-amine or mono-quaternary amine functionality. (iv) Cationic inhibitors should have little alcohol functionality. (v) The hydrophobic backbone of the cationic inhibitor should be long enough to form a dense monolayer in the interlayer. (vi) For neutral inhibitors, the inhibitor should be a water soluble organic molecule of low molecular weight with well defined domains of relatively high hydrophobicity and small domains of hydrophobicity. Our “rule-based” criteria will facilitate the rational design of improved—and more environmentally acceptable—clay swelling inhibitors for oilfield drilling operations.

James L. Suter

Papers

Large-scale molecular dynamics study of montmorillonite clay : Emergence of undulatory fluctuations and determination of material properties

Computer simulation study of the structural stability and materials properties of DNA-intercalated layered double hydroxides.

Graphene-Graphene Interactions: Friction, Superlubricity and Exfoliation

Chemically Specific Multiscale Modeling of Clay–Polymer Nanocomposites Reveals Intercalation Dynamics, Tactoid Self‐Assembly and Emergent Materials Properties

Rule based design of clay-swelling inhibitors