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

Hybrid density functionals are very successful in describing a wide range of molecular properties accurately. In large molecules and solids, however, calculating the exact (Hartree–Fock) exchange is computationally expensive, especially for systems with metallic characteristics. In the present work, we develop a new hybrid density functional based on a screened Coulomb potential for the exchange interaction which circumvents this bottleneck. The results obtained for structural and thermodynamic properties of molecules are comparable in quality to the most widely used hybrid functionals. In addition, we present results of periodic boundary condition calculations for both semiconducting and metallic single wall carbon nanotubes. Using a screened Coulomb potential for Hartree–Fock exchange enables fast and accurate hybrid calculations, even of usually difficult metallic systems. The high accuracy of the new screened Coulomb potential hybrid, combined with its computational advantages, makes it widely applicable to large molecules and periodic systems.

Hybrid functionals based on a screened Coulomb potential

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Self-assembled monolayers of thiolates on metals as a form of nanotechnology.

The interest in nanoscale materials stems from the fact that new properties are acquired at this length scale and, equally important, that these properties * To whom correspondence should be addressed. Phone, 404-8940292; fax, 404-894-0294; e-mail, mostafa.el-sayed@ chemistry.gatech.edu. † Case Western Reserve UniversitysMillis 2258. ‡ Phone, 216-368-5918; fax, 216-368-3006; e-mail, burda@case.edu. § Georgia Institute of Technology. 1025 Chem. Rev. 2005, 105, 1025−1102

Chemistry and properties of nanocrystals of different shapes.

Removal of heavy metal ions from wastewaters: A review

This paper describes the application of reduction photolithography, using arrays of microlenses and gray scale masks, to generate arrays of micropatterns having multilevel and curved features in ph...

Reduction photolithography using microlens arrays: applications in gray scale photolithography.

This paper describes how a memory-based, sequential wrinkling process can transform flat polystyrene sheets into multiscale, three-dimensional hierarchical textures. Multiple cycles of plasma-mediated skin growth followed by directional strain relief of the substrate resulted in hierarchical architectures with characteristic generational (G) features. Independent control over wrinkle wavelength and wrinkle orientation for each G was achieved by tuning plasma treatment time and strain-relief direction for each cycle. Lotus-type superhydrophobicity was demonstrated on three-dimensional G1–G2–G3 hierarchical wrinkles as well as tunable superhydrophilicity on these same substrates after oxygen plasma. This materials system provides a general approach for nanomanufacturing based on bottom-up sequential wrinkling that will benefit a diverse range of applications and especially those that require large area (>cm2), multiscale, three-dimensional patterns.

Controlled Three-Dimensional Hierarchical Structuring by Memory-Based, Sequential Wrinkling

Surface plasmon polaritons (SPPs) are responsible for exotic optical phenomena, including negative refraction, surface enhanced Raman scattering, and nanoscale focusing of light. Although many materials support SPPs, the choice of metal for most applications has been based on traditional plasmonic materials (Ag, Au) because there have been no side-by-side comparisons of the different materials on well-defined, nanostructured surfaces. Here, we report a platform that not only enabled rapid screening of a wide range of metals under different excitation conditions and dielectric environments, but also identified new and unexpected materials for biosensing applications. Nanopyramidal gratings were used to generate plasmon dispersion diagrams for Al, Ag, Au, Cu, and Pd. Surprisingly, the SPP coupling efficiencies of Cu and Al exceeded widely used plasmonic materials under certain excitation conditions. Furthermore, grazing angle excitation led to the highest refractive index sensitivities (figure of merit >85) reported at optical frequencies because of extremely narrow SPP resonances (full-width-at-half-minimum <6 nm or 7 meV). Finally, our screening process revealed that Ag, with the highest sensitivity, was not necessarily the preferred material for detecting molecules. We discovered that Au and even Pd, a weak plasmonic material, showed comparable index shifts on formation of a protein monolayer.

https://www.pnas.org/content/pnas/105/51/20146.full.pdf

Screening plasmonic materials using pyramidal gratings

This paper describes how delamination-free, hierarchical patterning of graphene can be achieved on prestrained thermoplastic sheets by surface wrinkling. Conformal contact between graphene and the substrate during strain relief was maintained by the presence of a soft skin layer, resulting in the uniform patterning of three-dimensional wrinkles over large areas (>cm2). The graphene wrinkle wavelength was tuned from the microscale to the nanoscale by controlling the thickness of the skin layer with 1 nm accuracy to realize a degree of control not possible by crumpling, which relies on delamination. Hierarchical patterning of the skin layers with varying thicknesses enabled multiscale graphene wrinkles with predetermined orientations to be formed. Significantly, hierarchical graphene wrinkles exhibited tunable mechanical stiffness at the nanoscale without compromising the macroscale electrical conductivity.

Multiscale, Hierarchical Patterning of Graphene by Conformal Wrinkling

This paper describes a set of design parameters for manipulating the branch length, branch direction, and overall size of gold nanostars (AuNS) synthesized by a seedless process. We controlled the structure of AuNS by varying four different synthetic factors: mechanical agitation, type of Good’s buffer, concentration ratio of precursors, and pH of growth solution. We found that stirring the precursors increased the yield of branched particles. Additionally, the AuNS morphology could be controlled by changing the buffer type and concentration ratio of precursors, which tuned the localized plasmon resonances from the visible to the near-infrared. We determined that performing the synthesis at a pH less than the pKa of the buffer was critical for the stability of the AuNS; when the pH was greater than the pKa, the nanoparticles aggregated in solution. We expanded the library of Good’s buffers able to form AuNS and optimized the mechanical and chemical synthesis conditions, which improved the structural homog...

Teri W. Odom

Papers

Reduction photolithography using microlens arrays: applications in gray scale photolithography.

Controlled Three-Dimensional Hierarchical Structuring by Memory-Based, Sequential Wrinkling

Screening plasmonic materials using pyramidal gratings

Multiscale, Hierarchical Patterning of Graphene by Conformal Wrinkling

Manipulating the Anisotropic Structure of Gold Nanostars using Good’s Buffers