Molecular dynamics in arbitrary geometries : parallel evaluation of pair forces

A new algorithm for calculating intermolecular pair forces in molecular dynamics (MD) simulations on a distributed parallel computer is presented. The arbitrary interacting cells algorithm (AICA) is designed to operate on geometrical domains defined by an unstructured, arbitrary polyhedral mesh that has been spatially decomposed into irregular portions for parallelisation. It is intended for nano scale fluid mechanics simulation by MD in complex geometries, and to provide the MD component of a hybrid MD/continuum simulation. The spatial relationship of the cells of the mesh is calculated at the start of the simulation and only the molecules contained in cells that have part of their surface closer than the cut-off radius of the intermolecular pair potential are required to interact. AICA has been implemented in the open source C++ code OpenFOAM, and its accuracy has been indirectly verified against a published MD code. The same system simulated in serial and in parallel on 12 and 32 processors gives the same results. Performance tests show that there is an optimal number of cells in a mesh for maximum speed of calculating intermolecular forces, and that having a large number of empty cells in the mesh does not add a significant computational overhead

Surface tension of the isotropic-nematic interface

We present the first calculations of the pressure tensor profile in the vicinity of the planar interface between isotropic liquid and nematic liquid crystal, using Onsager's density functional theory and computer simulation. When the liquid crystal director is aligned parallel to the interface, the situation of lowest free energy, there is a large tension on the nematic side of the interface and a small compressive region on the isotropic side. By contrast, for perpendicular alignment, the tension is on the isotropic side. There is excellent agreement between theory and simulation both in the forms of the pressure tensor profiles, and the values of the surface tension.Comment: Minor changes; to appear in Phys. Rev.

Self-assembly of twisted, multi-sheet aggregates

Hierarchical self-assembly underpins much of the diversity of form and function seen in soft systems, yet the pathways by which they achieve their final form are not always straightforward – intermediate steps, kinetic effects and finite sizes of aggregates all influence the self-assembly pathways of these systems. In this paper, we use molecular dynamics simulations of binary mixtures of spheres and ellipsoidal discs to investigate the self-assembly of anisotropic aggregates with internal structures. Through this, the full aggregation pathways of spontaneously chiral, multi-bilayer and multi-layer assemblies have been tracked and characterised via a semi-qualitative analysis. This includes the unambiguous identification of first-, second- and third-generation hierarchical assemblies within a single simulation. Given the significant challenge of tracking full aggregation pathways in experimental systems, our findings strongly support the notion that molecular simulation has much to contribute to improving our understanding of hierarchical self-assembling systems

Evolution of Non-Equilibrium Profile in Adsorbate Layer under Compressive Strain

We investigate the time evolution of an initial step profile separating a bare substrate region from the rest of the compressively strained adsorbate layer near a commensurate to incommensurate transition. The rate of profile evolution as a function of the mismatch, coverage and the strength of the substrate potential are determined by Brownian molecular dynamics simulations. We find that the results are qualitatively similar to those observed for the Pb/Si(111) system. The anomalously fast time evolution and sharpness of the non-equilibrium profile can be understood through the domain wall creation at the boundary and its subsequent diffusion into the interior of the adsorbate layer.Comment: 6 pages, 7 figures, Tribology Letter

Equivalent thermo-mechanical parameters for perfect crystals

Thermo-elastic behavior of perfect single crystal is considered. The crystal is represented as a set of interacting particles (atoms). The approach for determination of equivalent continuum values for the discrete system is proposed. Averaging of equations of particles' motion and long wave approximation are used in order to make link between the discrete system and equivalent continuum. Basic balance equations for equivalent continuum are derived from microscopic equations. Macroscopic values such as Piola and Cauchy stress tensors and heat flux are represented via microscopic parameters. Connection between the heat flux and temperature is discussed. Equation of state in Mie-Gruneisen form connecting Cauchy stress tensor with deformation gradient and thermal energy is obtained from microscopic considerations.Comment: To be published in proceedings of IUTAM Simposium on "Vibration Analysis of Structures with Uncertainties", 2009; 14 pages

Penentration of dynamic localized states in DC-driven Josephson junction ladders by discrete jumps

We give a theoretical study of unusual resistive (dynamic) localized states in anisotropic Josephson junction ladders, driven by a DC current at one edge. These states comprise nonlinearly coupled rotating Josephson phases in adjacent cells, and with increasing current they are found to expand into neighboring cells by a sequence of sudden jumps. We argue that the jumps arise from instabilities in the ladder's superconducting part, and our analytic expressions for the peculiar voltage (rotational frequency) ratios and I-V curves are in very good agreement with direct numerical simulations.Comment: Accepted, Physical Review E. 5 pages, 5 figures. Revtex, with postscript figure

Forces between elongated particles in a nematic colloid

Using molecular dynamics simulations we study the interactions between elongated colloidal particles (length to breath ratio ≫1) in a nematic host. The simulation results are compared to the results of a Landau–de Gennes elastic free energy. We find that depletion forces dominate for the sizes of the colloidal particles studied. The tangential component of the force, however, allows us to resolve the elastic contribution to the total interaction. We find that this contribution differs from the quadrupolar interaction predicted at large separations. The difference is due to the presence of nonlinear effects, namely, the change in the positions and structure of the defects and their annihilation at small separations

Structure, Stresses and Local Dynamics in Glasses

The interrelations between short range structural and elastic aspects in glasses and glass forming liquids pose important and yet unresolved questions. In this paper these relations are analyzed for mono-atomic glasses and stressed liquids with a short range repulsive-attractive pair potentials. Strong variations of the local pressure are found even in a zero temperature glass, whereas the largest values of pressure are the same in both glasses and liquids. The coordination number z(J) and the effective first peak radius depend on the local pressures J's. A linear relation was found between components of site stress tensor and the local elastic constants. A linear relation was also found between the trace of the squares of the local frequencies and the local pressures. Those relations hold for glasses at zero temperature and for liquids. We explain this by a relation between the structure and the potential terms. A structural similarity between liquids and solids is manifested by similar dependencies of the coordination number on the pressures.Comment: 7 pages, 11 figure

Computer simulations of hard pear-shaped particles

We report results obtained from Monte Carlo simulations investi- gating mesophase formation in two model systems of hard pear-shaped particles. The first model considered is a hard variant of the trun- cated Stone-Expansion model previously shown to form nematic and smectic mesophases when embedded within a 12-6 Gay-Berne-like po- tential [1]. When stripped of its attractive interactions, however, this system is found to lose its liquid crystalline phases. For particles of length to breadth ratio k = 3, glassy behaviour is seen at high pressures, whereas for k = 5 several bi-layer-like domains are seen, with high intradomain order but little interdomain orientational correlation. For the second model, which uses a parametric shape parameter based on the generalised Gay-Berne formalism, results are presented for particles with elongation k = 3; 4 and 5. Here, the systems with k = 3 and 4 fail to display orientationally ordered phases, but that with k = 5 shows isotropic, nematic and, unusually for a hard-particle model, interdigitated smectic A2 phases.</p