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

Polydopamine and Its Derivative Materials: Synthesis and Promising Applications in Energy, Environmental, and Biomedical Fields

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

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

Colloidal particles act in many ways like surfactant molecules, particularly if adsorbed to a fluid–fluid interface. Just as the water or oil-liking tendency of a surfactant is quantified in terms of the hydrophile–lipophile balance (HLB) number, so can that of a spherical particle be described in terms of its wettability via contact angle. Important differences exist, however, between the two types of surface-active material, due in part to the fact that particles are strongly held at interfaces. This review attempts to correlate the behaviour observed in systems containing either particles or surfactant molecules in the areas of adsorption to interfaces, partitioning between phases and solid-stabilised emulsions and foams.

Particles as surfactants—similarities and differences

Reverse osmosis desalination: Water sources, technology, and today's challenges

Experimental data are presented to show the influence of colloidal particles on the stability of oil-water emulsions. It is shown that these solids stabilize emulsions both by providing steric hindrance to drop-drop coalescence and by modifying the rheological properties of the interfacial region. Coalescence occurs as a result of the displacement of the colloids along the interface. Results are presented on the effects of pH and salt concentration in the aqueous phase, the concentration of surfactant in the oleic phase, and the properties of the solid particles on the type and the stability of emulsions formed.

Factors Controlling the Stability of Colloid-Stabilized Emulsions: I. An Experimental Investigation

Bacterial infection of biomaterial surfaces is an important problem in the biomedical and health industries. The design of materials resistant to infections necessitates an understanding of the forces driving bacterial adhesion. Escherichia coli cells were immobilized onto the tip of a standard atomic force microscope (AFM) cantilever, and force measurements were performed by approaching the modified cantilever onto mica, hydrophilic glass, hydrophobic glass, polystyrene, and Teflon. Consistent with prior qualitative observations, we show that bacterial adhesion is indeed enhanced by the surface hydrophobicity of the substrate. The forces of interaction measured with the AFM are compared to those of model predictions based on an extended-DLVO approach. In this model, short-range acid−base and steric interactions are included with the conventional van der Waals attraction and electrostatic components. The theoretical predictions agree well with experimental data for E. coli D21f2, a strain whose outer surf...

Adhesion Forces between E. coli Bacteria and Biomaterial Surfaces

Microbial surfactants are a structurally diverse group of compounds consisting of hydrophilic and hydrophobic domains and which partition preferentially at interfaces. Biosurfactants are of increasing interest commercially as substitutes for synthetic surfactants particularly for environmental applications. This article discusses recent progress in the genetic and biochemical analysis of biosurfactant synthesis as well as the current status of fermentation technologies.

Surface-active compounds from microorganisms.

Bacterial adhesion and the subsequent formation of biofilm are major concerns in biotechnology and medicine. The initial step in bacterial adhesion is the interaction of cells with a surface, a process governed by long-range forces, primarily van der Waals and electrostatic interactions. The precise manner in which the force of interaction is affected by cell surface components and by the physiochemical properties of materials is not well understood. Here, we show that atomic force microscopy can be used to analyze the initial events in bacterial adhesion with unprecedented resolution. Interactions between the cantilever tip and confluent monolayers of isogenic strains of Escherichia coli mutants exhibiting subtle differences in cell surface composition were measured. It was shown that the adhesion force is affected by the length of core lipopolysaccharide molecules on the E. coli cell surface and by the production of the capsular polysaccharide, colanic acid. Furthermore, by modifying the atomic force microscope tip we developed a method for determining whether bacteria are attracted or repelled by virtually any biomaterial of interest. This information will be critical for the design of materials that are resistant to bacterial adhesion.

https://www.pnas.org/content/pnas/95/19/11059.full.pdf

Mukul M. Sharma

Papers

Factors Controlling the Stability of Colloid-Stabilized Emulsions: I. An Experimental Investigation

Adhesion Forces between E. coli Bacteria and Biomaterial Surfaces

Surface-active compounds from microorganisms.

Molecular determinants of bacterial adhesion monitored by atomic force microscopy

The effect of colloidal particles on fluid-fluid interfacial properties and emulsion stability