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

Deposits of clastic carbonate-dominated (calciclastic) sedimentary slope systems in the rock record have been identified mostly as linearly-consistent carbonate apron deposits, even though most ancient clastic carbonate slope deposits fit the submarine fan systems better. Calciclastic submarine fans are consequently rarely described and are poorly understood. Subsequently, very little is known especially in mud-dominated calciclastic submarine fan systems. Presented in this study are a sedimentological core and petrographic characterisation of samples from eleven boreholes from the Lower Carboniferous of Bowland Basin (Northwest England) that reveals a >250 m thick calciturbidite complex deposited in a calciclastic submarine fan setting. Seven facies are recognised from core and thin section characterisation and are grouped into three carbonate turbidite sequences. They include: 1) Calciturbidites, comprising mostly of highto low-density, wavy-laminated bioclast-rich facies; 2) low-density densite mudstones which are characterised by planar laminated and unlaminated muddominated facies; and 3) Calcidebrites which are muddy or hyper-concentrated debrisflow deposits occurring as poorly-sorted, chaotic, mud-supported floatstones. These

Phd by thesis

Background Since at least 400 C.E., when the Mayans first used layered clays to make dyes, people have been harnessing the properties of layered materials. This gradually developed into scientific research, leading to the elucidation of the laminar structure of layered materials, detailed understanding of their properties, and eventually experiments to exfoliate or delaminate them into individual, atomically thin nanosheets. This culminated in the discovery of graphene, resulting in a new explosion of interest in two-dimensional materials. Layered materials consist of two-dimensional platelets weakly stacked to form three-dimensional structures. The archetypal example is graphite, which consists of stacked graphene monolayers. However, there are many others: from MoS 2 and layered clays to more exotic examples such as MoO 3 , GaTe, and Bi 2 Se 3 . These materials display a wide range of electronic, optical, mechanical, and electrochemical properties. Over the past decade, a number of methods have been developed to exfoliate layered materials in order to produce monolayer nanosheets. Such exfoliation creates extremely high-aspect-ratio nanosheets with enormous surface area, which are ideal for applications that require surface activity. More importantly, however, the two-dimensional confinement of electrons upon exfoliation leads to unprecedented optical and electrical properties. Liquid exfoliation of layered crystals allows the production of suspensions of two-dimensional nanosheets, which can be formed into a range of structures. (A) MoS 2 powder. (B) WS 2 dispersed in surfactant solution. (C) An exfoliated MoS 2 nanosheet. (D) A hybrid material consisting of WS 2 nanosheets embedded in a network of carbon nanotubes. Advances An important advance has been the discovery that layered crystals can be exfoliated in liquids. There are a number of methods to do this that involve oxidation, ion intercalation/exchange, or surface passivation by solvents. However, all result in liquid dispersions containing large quantities of nanosheets. This brings considerable advantages: Liquid exfoliation allows the formation of thin films and composites, is potentially scaleable, and may facilitate processing by using standard technologies such as reel-to-reel manufacturing. Although much work has focused on liquid exfoliation of graphene, such processes have also been demonstrated for a host of other materials, including MoS 2 and related structures, layered oxides, and clays. The resultant liquid dispersions have been formed into films, hybrids, and composites for a range of applications. Outlook There is little doubt that the main advances are in the future. Multifunctional composites based on metal and polymer matrices will be developed that will result in enhanced mechanical, electrical, and barrier properties. Applications in energy generation and storage will abound, with layered materials appearing as electrodes or active elements in devices such as displays, solar cells, and batteries. Particularly important will be the use of MoS 2 for water splitting and metal oxides as hydrogen evolution catalysts. In addition, two-dimensional materials will find important roles in printed electronics as dielectrics, optoelectronic devices, and transistors. To achieve this, much needs to be done. Production rates need to be increased dramatically, the degree of exfoliation improved, and methods to control nanosheet properties developed. The range of layered materials that can be exfoliated must be expanded, even as methods for chemical modification must be developed. Success in these areas will lead to a family of materials that will dominate nanomaterials science in the 21st century.

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Liquid Exfoliation of Layered Materials

About Supramolecular Assemblies of π-Conjugated Systems

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Mechanisms of Nucleation and Growth of Nanoparticles in Solution

We present a theoretical study on continuum percolation of rod-like colloidal particles in the presence of axial and planar quadrupole fields. Our work is based on a self-consistent numerical treatment of the connectedness Ornstein–Zernike equation, in conjunction with the Onsager equation that describes the orientational distribution function of particles interacting via a hard-core repulsive potential. Our results show that axial and planar quadrupole fields both in principle increase the percolation threshold. By how much depends on a combination of the field strength, the concentration, the aspect ratio of the particles, and percolation criterion. We find that the percolated state can form and break down multiple times with increasing concentration, i.e., it exhibits re-entrance behaviour. Finally, we show that planar fields may induce a high degree of triaxiality in the shape of particle clusters that in actual materials may give rise to highly anisotropic conductivity properties.

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Continuum percolation in colloidal dispersions of hard nanorods in external axial and planar fields.

Carbon nanotubes (CNTs) are stiff, all-carbon macromolecules with diameters as small as one nanometer and few microns long. Solutions of CNTs in chlorosulfonic acid (CSA) follow the phase behavior of rigid rod polymers interacting via a repulsive potential and display a liquid crystalline phase at sufficiently high concentration. Here, we show that small-angle X-ray scattering and polarized light microscopy data can be combined to characterize quantitatively the morphology of liquid crystalline phases formed in CNT solutions at concentrations from 3 to 6.5 % by volume. We find that upon increasing their concentration, CNTs self-assemble into a liquid crystalline phase with a pleated texture and with a large inter-particle spacing that could be indicative of a transition to higher-order liquid crystalline phases. We explain how thermal undulations of CNTs can enhance their electrostatic repulsion and increase their effective diameter by an order of magnitude. By calculating the critical concentration, where the mean amplitude of undulation of an unconstrained rod becomes comparable to the rod spacing, we find that thermal undulations start to affect steric forces at concentrations as low as the isotropic cloud point in CNT solutions.

Enhanced ordering in length-polydisperse carbon nanotube solutions at high concentrations as revealed by small angle X-ray scattering

We apply connectedness percolation theory to fractal liquids of hard particles, and make use of a Percus-Yevick liquid state theory combined with a geometric connectivity criterion. We find that in fractal dimensions the percolation threshold interpolates continuously between integer-dimensional values, and that it decreases monotonically with increasing (fractal) dimension. The influence of hard-core interactions is significant only for dimensions below three. Finally, our theory incorrectly suggests that a percolation threshold is absent below about two dimensions, which we attribute to the breakdown of the connectedness Percus-Yevick closure.

Connectedness percolation of fractal liquids

Many single-stranded (ss) RNA viruses self assemble from capsid protein subunits and the nucleic acid to form an infectious virion. It is believed that the electrostatic interactions between the negatively charged RNA and the positively charged viral capsid proteins drive the encapsidation, although there is growing evidence that the sequence of the viral RNA also plays a role in packaging. In particular the sequence will determine the possible secondary structures that the ssRNA will take in solution. In this work, we use a mean field theory to investigate how the secondary structure of the RNA combined with electrostatic interactions affects the efficiency of assembly and stability of the assembled virions. We show that the secondary structure of RNA may result in negative osmotic pressures while a linear polymer causes positive osmotic pressures for the same conditions. This may suggest that the branched structure makes the RNA more effectively packaged and the virion more stable.

Effects of RNA sequence specificity in the electrostatic stabilization of viruses

Liquid crystal networks exploit the coupling between the responsivity of liquid-crystalline mesogens, e.g., to electric fields, and the (visco)elastic properties of a polymer network. Because of this, these materials have been put forward for a wide array of applications, including responsive surfaces such as artificial skins and membranes. For such applications, the desired functional response must generally be realized under strict geometrical constraints, such as provided by supported thin films. To model such settings, we present a dynamical, spatially-heterogeneous Landau-type theory for electrically-actuated liquid crystal network films. We find that the response of the liquid crystal network permeates the film from top to bottom, and illustrate how this affects the time scale associated with macroscopic deformation. Finally, by linking our model parameters to experimental quantities, we suggest that the permeation rate can be controlled by varying the aspect ratio of the mesogens and their degree of orientational order when cross-linked into the polymer network, for which we predict a single optimum. Our results contribute specifically to the rational design of future applications involving transport or on-demand release of molecular cargo in liquid crystal network films.

Paul van der Schoot

Papers

Continuum percolation in colloidal dispersions of hard nanorods in external axial and planar fields.

Enhanced ordering in length-polydisperse carbon nanotube solutions at high concentrations as revealed by small angle X-ray scattering

Connectedness percolation of fractal liquids

Effects of RNA sequence specificity in the electrostatic stabilization of viruses

Controlling permeation in electrically-deforming liquid crystal network films: a dynamical Landau theory