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.

/pdf/microfluidics-fluid-physics-at-the-nanoliter-scale-4bpahtd8qa.pdf

Microfluidics: Fluid physics at the nanoliter scale

http://experimentationlab.berkeley.edu/sites/default/files/AFMImages/butt_AFM.pdf

Force measurements with the atomic force microscope: Technique, interpretation and applications

We report gas and water flow measurements through microfabricated membranes in which aligned carbon nanotubes with diameters of less than 2 nanometers serve as pores. The measured gas flow exceeds predictions of the Knudsen diffusion model by more than an order of magnitude. The measured water flow exceeds values calculated from continuum hydrodynamics models by more than three orders of magnitude and is comparable to flow rates extrapolated from molecular dynamics simulations. The gas and water permeabilities of these nanotube-based membranes are several orders of magnitude higher than those of commercial polycarbonate membranes, despite having pore sizes an order of magnitude smaller. These membranes enable fundamental studies of mass transport in confined environments, as well as more energy-efficient nanoscale filtration.

http://science.sciencemag.org/content/sci/312/5776/1034.full.pdf

Fast Mass Transport Through Sub-2-Nanometer Carbon Nanotubes

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

For several centuries fluid dynamics studies have relied upon the assumption that when a liquid flows over a solid surface, the liquid molecules adjacent to the solid are stationary relative to the solid. This no-slip boundary condition (BC) has been applied successfully to model many macroscopic experiments, but has no microscopic justification. In recent years there has been an increased interest in determining the appropriate BCs for the flow of Newtonian liquids in confined geometries, partly due to exciting developments in the fields of microfluidic and microelectromechanical devices and partly because new and more sophisticated measurement techniques are now available. An increasing number of research groups now dedicate great attention to the study of the flow of liquids at solid interfaces, and as a result a large number of experimental, computational and theoretical studies have appeared in the literature. We provide here a review of experimental studies regarding the phenomenon of slip of Newtonian liquids at solid interfaces. We dedicate particular attention to the effects that factors such as surface roughness, wettability and the presence of gaseous layers might have on the measured interfacial slip. We also discuss how future studies might improve our understanding of hydrodynamic BCs and enable us to actively control liquid slip.

https://iopscience.iop.org/article/10.1088/0034-4885/68/12/R05/pdf

Boundary slip in Newtonian liquids: a review of experimental studies

We report direct measurements of hydrodynamic drainage forces, which show clear evidence of boundary slip in a Newtonian liquid. The degree of boundary slip is found to be a function of the liquid viscosity and the shear rate, as characterized by the slip length, and is up to $\ensuremath{\sim}20\mathrm{nm}$. This has implications for confined biological systems, the permeability of microporous media, and for the lubrication of nanomachines, and will be important in the microcontrol of liquid flow. We also show that current theories of slip do not adequately describe the experimental data.

Shear-Dependent Boundary Slip in an Aqueous Newtonian Liquid

The synthesis of biomimetic, micro­patterned surface coatings with topographical and chemical features to capture water from a humid atmosphere is demonstrated. The coatings are prepared by dewetting thin polymer films to create materials consisting of raised hydrophilic bumps on a hydrophobic background. An enhanced rate of water condensation is measured on these surfaces under representative climatic conditions.

Biomimetic surface coatings for atmospheric water capture prepared by dewetting of polymer films.

We studied the synthesis and characterization of Ca(OH)2 colloidal particles and their application to the restoration of wall paintings. Submicrometer Ca(OH)2 crystalline particles have been obtained by mixing equal volumes of NaOH and CaCl2 aqueous solutions with different degrees of supersaturation (from 2 to 10) and in the temperature range 60−90 °C. The Ca(OH)2 particles are crystalline and have the appearance of hexagonal platelets with thicknesses of a few nanometers, as determined by scanning electron microscopy, transmission electron microscopy, X-ray diffractometry, and atomic force microscopy techniques. The kinetic stability of dispersions of Ca(OH)2 particles in water and propan-1-ol has also been studied in view of their possible application in wall painting conservation. A successful example of this application to the restoration of Santi di Tito's wall paintings (16th century) in the Santa Maria del Fiore Cathedral in Florence is also reported.

Colloidal Particles of Ca(OH)2: Properties and Applications to Restoration of Frescoes

Liquid-infused surfaces (or lubricant-infused surfaces) (LIS) are a new class of functional materials introduced in 2011. Their exceptional properties have earned them a place at the forefront of many fields including anti-biofouling, anti-icing, anti-corrosion, drag reduction, droplet manipulation and drop-wise condensation. Integral to their success is the infused lubricant layer which affords them their properties. In this review, we examine the current state of the literature relating to the lubricant layer. We consider the lubricant through all stages in the surface's lifecycle from design, to use, all the way through to depletion and eventual failure. First, we examine trends in lubricant choice and how to choose a lubricant, including environmental and medical considerations. We then look at the different methods used to infuse lubricant into surfaces and how lubricant depletes from the surface. We then report direct and indirect methods to characterise the thickness and distribution of the lubricant layer. Finally, we examine how droplets interact with LIS and the unique properties afforded by the lubricant before providing an outlook into where research centred on understanding the lubricant layer is heading in the new decade.

Chiara Neto

Papers

Boundary slip in Newtonian liquids: a review of experimental studies

Shear-Dependent Boundary Slip in an Aqueous Newtonian Liquid

Biomimetic surface coatings for atmospheric water capture prepared by dewetting of polymer films.

Colloidal Particles of Ca(OH)2: Properties and Applications to Restoration of Frescoes

Life and death of liquid-infused surfaces: a review on the choice, analysis and fate of the infused liquid layer.