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

Differently from passive Brownian particles, active particles, also known as self-propelled Brownian particles or microswimmers and nanoswimmers, are capable of taking up energy from their environment and converting it into directed motion. Because of this constant flow of energy, their behavior can be explained and understood only within the framework of nonequilibrium physics. In the biological realm, many cells perform directed motion, for example, as a way to browse for nutrients or to avoid toxins. Inspired by these motile microorganisms, researchers have been developing artificial particles that feature similar swimming behaviors based on different mechanisms. These man-made micromachines and nanomachines hold a great potential as autonomous agents for health care, sustainability, and security applications. With a focus on the basic physical features of the interactions of self-propelled Brownian particles with a crowded and complex environment, this comprehensive review will provide a guided tour through its basic principles, the development of artificial self-propelling microparticles and nanoparticles, and their application to the study of nonequilibrium phenomena, as well as the open challenges that the field is currently facing.

/pdf/active-particles-in-complex-and-crowded-environments-4pyirdi1aj.pdf

Active Particles in Complex and Crowded Environments

Monthly Notices is one of the three largest general primary astronomical research publications. It is an international journal, published by the Royal Astronomical Society. This article 1 describes its publication policy and practice.

Monthly Notices of the Royal Astronomical Society

Active Brownian particles, also referred to as microswimmers and nanoswimmers, are biological or manmade microscopic and nanoscopic particles that can self-propel. Because of their activity, their behavior can only be explained and understood within the framework of nonequilibrium physics. In the biological realm, many cells perform active Brownian motion, for example, when moving away from toxins or towards nutrients. Inspired by these motile microorganisms, researchers have been developing artificial active particles that feature similar swimming behaviors based on different mechanisms; these manmade micro- and nanomachines hold a great potential as autonomous agents for healthcare, sustainability, and security applications. With a focus on the basic physical features of the interactions of active Brownian particles with a crowded and complex environment, this comprehensive review will put the reader at the very forefront of the field of active Brownian motion, providing a guided tour through its basic principles, the development of artificial self-propelling micro- and nanoparticles, and their application to the study of nonequilibrium phenomena, as well as the open challenges that the field is currently facing.

/pdf/active-brownian-particles-in-complex-and-crowded-3ym4we2m8l.pdf

Active Brownian Particles in Complex and Crowded Environments

Complex (dusty) plasmas: current status, open issues, perspectives

Complex (dusty) plasmas are composed of a weakly ionized gas and charged microparticles and represent the plasma state of soft matter. Complex plasmas have several remarkable features: Dynamical time scales associated with microparticles are ``stretched'' to tens of milliseconds, yet the microparticles themselves can be easily visualized individually. Furthermore, since the background gas is dilute, the particle dynamics in strongly coupled complex plasmas is virtually undamped, which provides a direct analogy to regular liquids and solids in terms of the atomistic dynamics. Finally, complex plasmas can be easily manipulated in different ways---also at the level of individual particles. Altogether, this gives us a unique opportunity to go beyond the limits of continuous media and study---at the kinetic level---various generic processes occurring in liquids or solids, in regimes ranging from the onset of cooperative phenomena to large strongly coupled systems. In the first part of the review some of the basic and new physics are highlighted which complex plasmas enable us to study, and in the second (major) part strong coupling phenomena in an interdisciplinary context are examined. The connections with complex fluids are emphasized and a number of generic liquid and solid-state issues are addressed. In summary, application oriented research is discussed.

Complex plasmas: An interdisciplinary research field

Experiments under microgravity conditions were carried out to study 'condensed' (liquid and crystalline) states of a colloidal plasma (ions, electrons, and charged microspheres). Systems with approximately 10(exp 6) microspheres were produced. The observed systems represent new forms of matter--quasineutral, self-organized plasmas--the properties of which are largely unexplored. In contrast to laboratory measurements, the systems under microgravity are clearly three dimensional (as expected); they exhibit stable vortex flows, sometimes adjacent to crystalline regions, and a central 'void,' free of microspheres.

/pdf/condensed-plasmas-under-microgravity-3n537zzoue.pdf

Condensed Plasmas under Microgravity

The problem of calculating the ion drag force in complex plasmas is considered. It is shown that the standard theory of Coulomb scattering usually fails for the ion-dust elastic collisions. A simple approach to extend this theory is proposed. This leads to a considerable enhancement in the ion-dust elastic scattering cross section and, hence, increases the ion drag force in comparison with the previous analytical results. Analysis shows that the ion drag usually exceeds the electrostatic force in the limit of weak electric field. We suggest that this is the cause of the central "void" observed in microgravity complex plasma experiments.

Ion drag force in complex plasmas.

The plasma crystal experiment PKE-Nefedov, the first basic science experiment on the International Space Station (ISS), was installed in February 2001 by the first permanent crew. It is designed for long-term investigations of complex plasmas under microgravity conditions. `Complex plasmas' contain ions, electrons, neutrals and small solid particles - normally in the micrometre range. These microparticles obtain thousands of elementary charges and interact with each other via a `screened' Coulomb potential. Complex plasmas are of special interest, because they can form liquid and crystalline states (Thomas et al 1994 Phys. Rev. Lett. 73 652-5, Chu and I 1994 Phys. Rev. Lett. 72 4009-12) and are observable at the kinetic level. In experiments on Earth the microparticles are usually suspended against gravity in strong electric fields. This creates asymmetries, stresses and pseudo-equilibrium states with sufficient free energy to readily become unstable. Under microgravity conditions the microparticles move into the bulk of the plasma (Morfill et al 1999 Phys. Rev. Lett. 83 1598), experiencing much weaker volume forces than on Earth. This allows investigations of the thermodynamics of strongly coupled plasma states under substantially stress-free conditions. In this first paper we report our results on plasma crystals, in particular the first experimental observations of bcc lattice structures.

/pdf/pke-nefedov-plasma-crystal-experiments-on-the-international-2wab3xuxh2.pdf

Alexei V. Ivlev

Papers

Complex (dusty) plasmas: current status, open issues, perspectives

Complex plasmas: An interdisciplinary research field

Condensed Plasmas under Microgravity

Ion drag force in complex plasmas.

PKE-Nefedov : plasma crystal experiments on the International Space Station