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

J. Appl. Cryst.の発刊に際して

We present an approach to fabricate solid capsules with precise control of size, permeability, mechanical strength, and compatibility. The capsules are fabricated by the self-assembly of colloidal particles onto the interface of emulsion droplets. After the particles are locked together to form elastic shells, the emulsion droplets are transferred to a fresh continuous-phase fluid that is the same as that inside the droplets. The resultant structures, which we call "colloidosomes," are hollow, elastic shells whose permeability and elasticity can be precisely controlled. The generality and robustness of these structures and their potential for cellular immunoisolation are demonstrated by the use of a variety of solvents, particles, and contents.

/pdf/colloidosomes-selectively-permeable-capsules-composed-of-147a06bk70.pdf

Colloidosomes: Selectively Permeable Capsules Composed of Colloidal Particles

General purpose molecular dynamics simulations fully implemented on graphics processing units

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

We describe experimental investigations of the structure of two-dimensional spherical crystals. The crystals, formed by beads self-assembled on water droplets in oil, serve as model systems for exploring very general theories about the minimum-energy configurations of particles with arbitrary repulsive interactions on curved surfaces. Above a critical system size we find that crystals develop distinctive high-angle grain boundaries, or scars, not found in planar crystals. The number of excess defects in a scar is shown to grow linearly with the dimensionless system size. The observed slope is expected to be universal, independent of the microscopic potential.

https://arxiv.org/pdf/cond-mat/0303289.pdf

Grain Boundary Scars and Spherical Crystallography

We propose and analyze an effective free energy describing the physics of disclination defects in particle arrays constrained to move on an arbitrary two-dimensional surface. At finite temperature the physics of interacting disclinations is mapped to a Laplacian sine-Gordon Hamiltonian suitable for numerical simulations. We discuss general features of the ground state and thereafter specialize to the spherical case. The ground state is analyzed as a function of the ratio of the defect core energy to the Young's modulus. We argue that the core energy contribution becomes less and less important in the limit $R\ensuremath{\gg}a,$ where R is the radius of the sphere and a is the particle spacing. For large core energies there are 12 disclinations forming an icosahedron. For intermediate core energies unusual finite-length grain boundaries are preferred. The complicated regime of small core energies, appropriate to the limit $R/\stackrel{\ensuremath{\rightarrow}}{a}\ensuremath{\infty},$ is also addressed. Finally we discuss the application of our results to the classic Thomson problem of finding the ground state of electrons distributed on a two sphere.

/pdf/interacting-topological-defects-on-frozen-topographies-2piezaqgfl.pdf

Interacting topological defects on frozen topographies

We attack the generalized Thomson problem, i.e., determining the ground state energy and configuration of many particles interacting via an arbitrary repulsive pairwise potential on a sphere via a continuum mapping onto a universal long range interaction between angular disclination defects parametrized by the elastic (Young) modulus Y of the underlying lattice and the core energy E(core) of an isolated disclination. Predictions from the continuum theory for the ground state energy agree with numerical simulations of long range power law interactions of the form 1/r(gamma) (0<gamma<2) to four significant figures. The generality of our approach is illustrated by a study of grain boundary proliferation for tilted crystalline order and square lattices on the sphere.

/pdf/crystalline-order-on-a-sphere-and-the-generalized-thomson-5i2r62y19t.pdf

Crystalline order on a sphere and the generalized Thomson problem.

https://surface.syr.edu/cgi/viewcontent.cgi?article=1160&context=phy

Alex Travesset

Papers

General purpose molecular dynamics simulations fully implemented on graphics processing units

Grain Boundary Scars and Spherical Crystallography

Interacting topological defects on frozen topographies

Crystalline order on a sphere and the generalized Thomson problem.

The statistical mechanics of membranes