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

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

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.

Nanocrystals are fundamental to modern science and technology. Mastery over the shape of a nanocrystal enables control of its properties and enhancement of its usefulness for a given application. Our aim is to present a comprehensive review of current research activities that center on the shape-controlled synthesis of metal nanocrystals. We begin with a brief introduction to nucleation and growth within the context of metal nanocrystal synthesis, followed by a discussion of the possible shapes that a metal nanocrystal might take under different conditions. We then focus on a variety of experimental parameters that have been explored to manipulate the nucleation and growth of metal nanocrystals in solution-phase syntheses in an effort to generate specific shapes. We then elaborate on these approaches by selecting examples in which there is already reasonable understanding for the observed shape control or at least the protocols have proven to be reproducible and controllable. Finally, we highlight a number of applications that have been enabled and/or enhanced by the shape-controlled synthesis of metal nanocrystals. We conclude this article with personal perspectives on the directions toward which future research in this field might take.

Shape‐Controlled Synthesis of Metal Nanocrystals: Simple Chemistry Meets Complex Physics?

▪ Abstract Solution phase syntheses and size-selective separation methods to prepare semiconductor and metal nanocrystals, tunable in size from ∼1 to 20 nm and monodisperse to ≤5%, are presented. Preparation of monodisperse samples enables systematic characterization of the structural, electronic, and optical properties of materials as they evolve from molecular to bulk in the nanometer size range. Sample uniformity makes it possible to manipulate nanocrystals into close-packed, glassy, and ordered nanocrystal assemblies (superlattices, colloidal crystals, supercrystals). Rigorous structural characterization is critical to understanding the electronic and optical properties of both nanocrystals and their assemblies. At inter-particle separations 5–100 A, dipole-dipole interactions lead to energy transfer between neighboring nanocrystals, and electronic tunneling between proximal nanocrystals gives rise to dark and photoconductivity. At separations <5 A, exchange interactions cause otherwise insulating ass...

Synthesis and Characterization of Monodisperse Nanocrystals and Close-Packed Nanocrystal Assemblies

Addressing an array of bistable [2]rotaxanes through a two-dimensional crossbar arrangement provides the device element of a current-driven molecular electronic circuit. The development of the [2]rotaxane switches through an iterative, evolutionary process is described. The arrangement reported here allows both memory and logic functions to use the same elements.

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Two-dimensional molecular electronics circuits.

Self-propelled jumping drops are continuously removed from a condensing superhydrophobic surface to enable a micrometric steady-state drop size. Here, we report that subcooled condensate on a chilled superhydrophobic surface are able to repeatedly jump off the surface before heterogeneous ice nucleation occurs. Frost still forms on the superhydrophobic surface due to ice nucleation at neighboring edge defects, which eventually spreads over the entire surface via an interdrop frost wave. The growth of this interdrop frost front is shown to be up to 3 times slower on the superhydrophobic surface compared to a control hydrophobic surface, due to the jumping-drop effect dynamically minimizing the average drop size and surface coverage of the condensate. A simple scaling model is developed to relate the success and speed of interdrop ice bridging to the drop size distribution. While other reports of condensation frosting on superhydrophobic surfaces have focused exclusively on liquid–solid ice nucleation for i...

Delayed frost growth on jumping-drop superhydrophobic surfaces.

Three things largely determine the electronic properties of a crystal:  the energy levels of the atoms or lattice sites, the coupling between adjacent sites, and the symmetry of the solid. Imagine being able to control each of these properties separately, and therefore being able to “design” a solid with a prescribed set of electronic properties. For an atomic solid, this would amount to being able to tune the electronegativity of an atom, to control the strength of the covalent interactions within the lattice, and to choose the crystal structure. While the chemistry of the periodic table does not permit such control, the chemistry of “artificial atoms”,1 or quantum dots (QDs), does. In this Account, we will discuss one example of “designing” a unique electronic property into a QD solid. This property, which is the ability of the solid to reversibly pass through a metal−insulator (MI) transition under ambient conditions, is something that has not been previously demonstrated for a more traditional solid. A two-dimensional (2D) hexagonal superlattice of organically passivated silver QDs was fabricated as a Langmuir monolayer. Selecting a particular size of QD controlled the (super)lattice site energies. The coupling between adjacent QDs was coarsely controlled by selection of the organic surface passivant, and precisely controlled by compressing the superlattice using the Langmuir technique. By using the title “Architectonic2 Quantum Dot Solids”, we emphasize that many of the collective properties of the superlattice were rationally designed into the material.

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Architectonic Quantum Dot Solids

Solid-state tunnel junction devices were fabricated from Langmuir Blodgett molecular monolayers of a bistable [2]catenane, a bistable [2]pseudorotaxane, and a single-station [2]rotaxane. All devices exhibited a (noncapacitive) hysteretic current−voltage response that switched the device between high- and low-conductivity states, although control devices exhibited no such response. Correlations between the structure and solution-phase dynamics of the molecular and supramolecular systems, the crystallographic domain structure of the monolayer film, and the room-temperature device performance characteristics are reported.

http://pubs.acs.org/doi/pdf/10.1021/ja0114456

Molecular-based electronically switchable tunnel junction devices.

We have employed water-soluble porphyrin molecules [meso-(tetrakis-4-sulfonatophenyl) porphine dihydrochloride] to solubilize single-walled carbon nanotubes (SWNTs), resulting in aqueous solutions that are stable for several weeks. The porphyrin-nanotube complexes have been characterized with absorption and fluorescence spectroscopy and with AFM. We find that the porphyrin/SWNT interaction is selective for the free base form, and that this interaction stabilizes the free base against protonation to the diacid. Under mildly acidic conditions nanotube-mediated J-aggregates form, which are unstable in solution and result in precipitation of the nanotubes over the course of a few days. Porphyrin-coated SWNTs can be precisely aligned on hydrophilic poly(dimethylsiloxane) (PDMS) surfaces by combing SWNT solution along a desired direction and then transferred to silicon substrates by stamping. Parallel SWNT patterns have been fabricated in this manner.

C. Patrick Collier

Papers

Two-dimensional molecular electronics circuits.

Delayed frost growth on jumping-drop superhydrophobic surfaces.

Architectonic Quantum Dot Solids

Molecular-based electronically switchable tunnel junction devices.

Noncovalent functionalization of single-walled carbon nanotubes with water-soluble porphyrins.