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

Cell motility in viscous fluids is ubiquitous and affects many biological processes, including reproduction, infection and the marine life ecosystem. Here we review the biophysical and mechanical principles of locomotion at the small scales relevant to cell swimming, tens of micrometers and below. At this scale, inertia is unimportant and the Reynolds number is small. Our emphasis is on the simple physical picture and fundamental flow physics phenomena in this regime. We first give a brief overview of the mechanisms for swimming motility, and of the basic properties of flows at low Reynolds number, paying special attention to aspects most relevant for swimming such as resistance matrices for solid bodies, flow singularities and kinematic requirements for net translation. Then we review classical theoretical work on cell motility, in particular early calculations of swimming kinematics with prescribed stroke and the application of resistive force theory and slender-body theory to flagellar locomotion. After examining the physical means by which flagella are actuated, we outline areas of active research, including hydrodynamic interactions, biological locomotion in complex fluids, the design of small-scale artificial swimmers and the optimization of locomotion strategies. (Some figures in this article are in colour only in the electronic version) This article was invited by Christoph Schmidt.

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The hydrodynamics of swimming microorganisms

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.

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Active Particles in Complex and Crowded Environments

We review the observations and the basic laws describing the essential aspects of collective motion -- being one of the most common and spectacular manifestation of coordinated behavior Our aim is to provide a balanced discussion of the various facets of this highly multidisciplinary field, including experiments, mathematical methods and models for simulations, so that readers with a variety of background could get both the basics and a broader, more detailed picture of the field The observations we report on include systems consisting of units ranging from macromolecules through metallic rods and robots to groups of animals and people Some emphasis is put on models that are simple and realistic enough to reproduce the numerous related observations and are useful for developing concepts for a better understanding of the complexity of systems consisting of many simultaneously moving entities As such, these models allow the establishing of a few fundamental principles of flocking In particular, it is demonstrated, that in spite of considerable differences, a number of deep analogies exist between equilibrium statistical physics systems and those made of self-propelled (in most cases living) units In both cases only a few well defined macroscopic/collective states occur and the transitions between these states follow a similar scenario, involving discontinuity and algebraic divergences

Collective Motion

The behaviour of dense assemblies of dry grains submitted to continuous shear deformation has been the subject of many experiments and discrete particle simulations. This paper is a collective work carried out among the French research group Groupement de Recherche Milieux Divises (GDR MiDi). It proceeds from the collection of results on steady uniform granular flows obtained by different groups in six different geometries both in experiments and numerical works. The goal is to achieve a coherent presentation of the relevant quantities to be measured i.e. flowing thresholds, kinematic profiles, effective friction, etc. First, a quantitative comparison between data coming from different experiments in the same geometry identifies the robust features in each case. Second, a transverse analysis of the data across the different configurations, allows us to identify the relevant dimensionless parameters, the different flow regimes and to propose simple interpretations. The present work, more than a simple juxtaposition of results, demonstrates the richness of granular flows and underlines the open problem of defining a single rheology.

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On dense granular flows.

Dynamic simulations of the pressure-driven flow in a channel of a non-Brownian suspension at zero Reynolds number were conducted using Stokesian Dynamics. The simulations are for a monolayer of identical particles as a function of the dimensionless channel width and the bulk particle concentration. Starting from a homogeneous dispersion, the particles gradually migrate towards the centre of the channel, resulting in an homogeneous concentration profile and a blunting of the particle velocity profile. The time for achieving steady state scales as (H/a)3a/[left angle bracket]u[right angle bracket], where H is the channel width, a the radii of the particles, and [left angle bracket]u[right angle bracket] the average suspension velocity in the channel. The concentration and velocity profiles determined from the simulations are in qualitative agreement with experiment.

A model for suspension flow has been proposed in which macroscopic mass, momentum and energy balances are constructed and solved simultaneously. It is shown that the requirement that the suspension pressure be constant in directions perpendicular to the mean motion leads to particle migration and concentration variations in inhomogeneous flow. The concept of the suspension ‘temperature’ – a measure of the particle velocity fluctuations – is introduced in order to provide a nonlocal description of suspension behaviour. The results of this model for channel flow are in good agreement with the simulations.

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Pressure-driven flow of suspensions : simulation and theory

Measurements of the relation between mass hold-up and flow rate have been made for glass beads in fully developed flow down an inclined chute, over the whole range of inclinations for which such flows are possible. Velocity profiles in the flowing material have also been measured. For a given inclination it is found that two different flow regimes may exist for each value of the flow rate in a certain interval. One is an ‘energetic’ flow, and is produced when the particles are dropped into the chute from a height, while the other is relatively quiescent and occurs when entry to the chute is regulated by a gate. At some values of the inclination jumps in the flow pattern occur between these branches, and it is even possible for both branches to coexist in the same chute, separated by a shock. A theoretical treatment of chute flow has been based on a rheological model of the material which takes into account both collisional and fractional mechanisms for generating stress. Its predictions include most aspects of the observed behaviour, but quantitative comparison of theory and experiment is difficult because of the uncertain values of some parameters appearing in the theory.

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/S0022112090001380

Frictional-collisional equations of motion for particulate flows and their application to chutes

Preface. 1. Introduction 2. Theory for slow plane flow 3. Flow through hoppers 4. Flow through wedge-shaped bunkers 5. Theory for slow three-dimensional flow 6. Flow through axisymmetric hoppers and bunkers 7. Theory for rapid flow of smooth, inelastic particles 8. Analysis of rapid flow in simple geometries 9. Theory for rapid flow of rough, inelastic particles 10. Hybrid theories A. Operations with vectors and tensors B. The stress tensor C. Hyperbolic partial differential equations of first order D. Jump balances E. Discontinuous solutions of hyperbolic equations F. Proof of the coaxiality condition G. Material frame-indifference H. The evaluation of some integrals I. Linear stability J. Pseudoscalars, vectors, and tensors K. Answers to selected problems References.

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An Introduction to Granular Flow

We present experimental measurements of the normal stresses in sheared Stokesian suspensions. Though the suspending fluid is Newtonian, dispersing rigid non-Brownian particles in it yields a suspension that is non-Newtonian, as it exhibits normal stress differences and an excess isotropic pressure in viscometric flows. At small to moderate concentrations, the normal stresses are very small in magnitude, and hence difficult to measure. This difficulty is compounded by the presence of noise due to unavoidable experimental artifacts. Owing to these limitations, most measurements reported earlier were carried out at relatively high particle concentrations, and some at shear rates large enough that the effects of particle and fluid inertia may have been significant. In our study, we have used a novel technique to measure the small stress levels. This was achieved by applying a sinusoidally varying shear rate with a fixed (low) frequency superimposed on a constant shear rate, and using a lock-in amplifier to measure the Fourier component of the same frequency in the stress signal. We have measured normal stresses in cylindrical-Couette and parallel-plate geometries, and combined these measurements to determine the two normal stress differences for particle volume fractions in the range 0.3–0.45. While the normal stresses are very small at low concentrations, they rise rapidly with increasing concentration. The normal stresses vary linearly with the magnitude of the shear rate, and are independent of its sign. In contrast to polymeric solutions, both normal stress differences are negative, and the first normal stress difference is significantly smaller in magnitude. We compare our data with the results of earlier studies, and observe good agreement.

Experimental measurements of the normal stresses in sheared Stokesian suspensions

This paper addresses a fundamental discrepancy between the suspension balance model and other two-phase flow formulations. The former was proposed to capture the shear-induced migration of particles in Stokesian suspensions, and hinges on the presence of a particle phase stress to drive particle migration. This stress is taken to be the “particle stress,” defined as the particle contribution to the suspension stress. On the other hand, the two-phase flow equations derived in several studies show only a force acting on the particle phase, but no stress. We show that the identification of the particle phase stress with the particle contribution to the suspension stress in the suspension balance model is incorrect, but there exists a well-defined particle phase stress. Following the rigorous method of volume averaging, we show that the force on the particle phase may be written as the sum of an interphase drag and the divergence of the particle phase stress. We derive exact micromechanical relations for thes...

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Prabhu R. Nott

Papers

Pressure-driven flow of suspensions : simulation and theory

Frictional-collisional equations of motion for particulate flows and their application to chutes

An Introduction to Granular Flow

Experimental measurements of the normal stresses in sheared Stokesian suspensions

The suspension balance model revisited