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

Microfabricated integrated circuits revolutionized computation by vastly reducing the space, labor, and time required for calculations. Microfluidic systems hold similar promise for the large-scale automation of chemistry and biology, suggesting the possibility of numerous experiments performed rapidly and in parallel, while consuming little reagent. While it is too early to tell whether such a vision will be realized, significant progress has been achieved, and various applications of significant scientific and practical interest have been developed. Here a review of the physics of small volumes (nanoliters) of fluids is presented, as parametrized by a series of dimensionless numbers expressing the relative importance of various physical phenomena. Specifically, this review explores the Reynolds number Re, addressing inertial effects; the Peclet number Pe, which concerns convective and diffusive transport; the capillary number Ca expressing the importance of interfacial tension; the Deborah, Weissenberg, and elasticity numbers De, Wi, and El, describing elastic effects due to deformable microstructural elements like polymers; the Grashof and Rayleigh numbers Gr and Ra, describing density-driven flows; and the Knudsen number, describing the importance of noncontinuum molecular effects. Furthermore, the long-range nature of viscous flows and the small device dimensions inherent in microfluidics mean that the influence of boundaries is typically significant. A variety of strategies have been developed to manipulate fluids by exploiting boundary effects; among these are electrokinetic effects, acoustic streaming, and fluid-structure interactions. The goal is to describe the physics behind the rich variety of fluid phenomena occurring on the nanoliter scale using simple scaling arguments, with the hopes of developing an intuitive sense for this occasionally counterintuitive world.

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Microfluidics: Fluid physics at the nanoliter scale

Block copolymer (BCP) self-assembly has attracted considerable attention for many decades because it can yield ordered structures in a wide range of morphologies, including spheres, cylinders, bicontinuous structures, lamellae, vesicles, and many other complex or hierarchical assemblies. These aggregates provide potential or practical applications in many fields. The present tutorial review introduces the primary principles of BCP self-assembly in bulk and in solution, by describing experiments, theories, accessible morphologies and morphological transitions, factors affecting the morphology, thermodynamics and kinetics, among others. As one specific example at a more advanced level, BCP vesicles (polymersomes) and their potential applications are discussed in some detail.

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Self-assembly of block copolymers

Wetting phenomena are ubiquitous in nature and technology. A solid substrate exposed to the environment is almost invariably covered by a layer of fluid material. In this review, the surface forces that lead to wetting are considered, and the equilibrium surface coverage of a substrate in contact with a drop of liquid. Depending on the nature of the surface forces involved, different scenarios for wetting phase transitions are possible; recent progress allows us to relate the critical exponents directly to the nature of the surface forces which lead to the different wetting scenarios. Thermal fluctuation effects, which can be greatly enhanced for wetting of geometrically or chemically structured substrates, and are much stronger in colloidal suspensions, modify the adsorption singularities. Macroscopic descriptions and microscopic theories have been developed to understand and predict wetting behavior relevant to microfluidics and nanofluidics applications. Then the dynamics of wetting is examined. A drop, placed on a substrate which it wets, spreads out to form a film. Conversely, a nonwetted substrate previously covered by a film dewets upon an appropriate change of system parameters. The hydrodynamics of both wetting and dewetting is influenced by the presence of the three-phase contact line separating "wet" regions from those that are either dry or covered by a microscopic film only. Recent theoretical, experimental, and numerical progress in the description of moving contact line dynamics are reviewed, and its relation to the thermodynamics of wetting is explored. In addition, recent progress on rough surfaces is surveyed. The anchoring of contact lines and contact angle hysteresis are explored resulting from surface inhomogeneities. Further, new ways to mold wetting characteristics according to technological constraints are discussed, for example, the use of patterned surfaces, surfactants, or complex fluids.

/pdf/wetting-and-spreading-56ditqbfmj.pdf

Wetting and Spreading

Recent years have brought exciting theoretical advances to understanding the behavior of macromolecular systems under nonequilibrium conditions. Developments in diffusion-controlled reactions of polymers are bringing molecular insights to reactive blending technologies, and improved theories relating to associating polymers should aid in the design of thickening agents and coatings. Recent progress in molecular theories of flow and deformation may facilitate the design of branched polymers with tailored rheological properties and improved adhesives.

The theory of polymer dynamics

The first € price and the £ and $ price are net prices, subject to local VAT. Prices indicated with * include VAT for books; the €(D) includes 7% for Germany, the €(A) includes 10% for Austria. Prices indicated with ** include VAT for electronic products; 19% for Germany, 20% for Austria. All prices exclusive of carriage charges. Prices and other details are subject to change without notice. All errors and omissions excepted. P.-G. de Gennes, F. Brochard-Wyart, D. Quere Capillarity and Wetting Phenomena

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Capillarity and Wetting Phenomena

Films of silicone oils (or alkanes) deposited on low-energy surfaces (grafted silicone wafers) are metastable. We nucleate a dry spot at the center of the wafer and observe the rate of growth V=dR/dt of the dry patch of radius R. We find that V is (a) independent of R, (b) independent of the film thickness, (c) inversely proportional to the oil viscosity, and (d) very sensitive to the value of ${\mathrm{\ensuremath{\theta}}}_{\mathit{e}}$, the equilibrium contact angle between oil and wafer. At small ${\mathrm{\ensuremath{\theta}}}_{\mathit{e}}$, V\ensuremath{\approxeq}${\mathrm{\ensuremath{\theta}}}_{\mathit{e}}^{3}$. All these features are in agreement with a recent hydrodynamic theory.

Dynamics of dewetting.

https://www.cell.com/biophysj/pdf/S0006-3495(03)74981-9.pdf

Cascades of Transient Pores in Giant Vesicles: Line Tension and Transport

We image macroscopic transient pores in mechanically stretched giant vesicles. Holes open above a critical radius rc1, grow up to a radius rc2, and close. We interpret the upper limit rc2 by a relaxation of the membrane tension as the holes expand. The closing of the holes is caused by a further relaxation of the surface tension when the internal liquid leaks out. A dynamic model fits our data for the growth and closure of pores.

https://www.pnas.org/content/pnas/96/19/10591.full.pdf

Dynamics of transient pores in stretched vesicles

We discuss wetting criteria for solid/liquid pairs where the long-range interaction is not oscillating and is described by a Hamaker constant A. The key parameters are then A and the spreading coefficient S. Since S contains contributions from short range interactions, S and A are independent variables and can be of either sign. Discussing the resulting four possibilities, we expect three fundamental regimes: (1) complete wetting, a small droplet spreads to become a flat “pancake” surrounded by a dry solid; (2) pseudo partial wetting, a droplet forms a spherical cap with a finite contact angle but the surrounding solid is wet, the drop is in equilibrium with a molecular film; (3) partial wetting, the contact angle is nonzero and now the solid around the drop is dry. The pseudo partial wetting regime may explain some surprising observations concerning the spreading of silicone droplets.

Françoise Brochard-Wyart

Papers

Capillarity and Wetting Phenomena

Dynamics of dewetting.

Cascades of Transient Pores in Giant Vesicles: Line Tension and Transport

Dynamics of transient pores in stretched vesicles

Spreading of nonvolatile liquids in a continuum picture