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

Self-assembly is the autonomous organization of components into patterns or structures without human intervention. Self-assembling processes are common throughout nature and technology. They involve components from the molecular (crystals) to the planetary (weather systems) scale and many different kinds of interactions. The concept of self-assembly is used increasingly in many disciplines, with a different flavor and emphasis in each.

http://science.sciencemag.org/content/sci/295/5564/2418.full.pdf

Self-assembly at all scales.

A family of highly ordered mesoporous (20−300 A) silica structures have been synthesized by the use of commercially available nonionic alkyl poly(ethylene oxide) (PEO) oligomeric surfactants and poly(alkylene oxide) block copolymers in acid media. Periodic arrangements of mescoscopically ordered pores with cubic Im3m, cubic Pm3m (or others), 3-d hexagonal (P63/mmc), 2-d hexagonal (p6mm), and lamellar (Lα) symmetries have been prepared. Under acidic conditions at room temperature, the nonionic oligomeric surfactants frequently form cubic or 3-d hexagonal mesoporous silica structures, while the nonionic triblock copolymers tend to form hexagonal (p6mm) mesoporous silica structures. A cubic mesoporous silica structure (SBA-11) with Pm3m diffraction symmetry has been synthesized in the presence of C16H33(OCH2CH2)10OH (C16EO10) surfactant species, while a 3-d hexagonal (P63/mmc) mesoporous silica structure (SBA-12) results when C18EO10 is used. Surfactants with short EO segments tend to form lamellar mesost...

Nonionic Triblock and Star Diblock Copolymer and Oligomeric Surfactant Syntheses of Highly Ordered, Hydrothermally Stable, Mesoporous Silica Structures

As a fascinating conjugated polymer, graphitic carbon nitride (g-C3N4) has become a new research hotspot and drawn broad interdisciplinary attention as a metal-free and visible-light-responsive photocatalyst in the arena of solar energy conversion and environmental remediation. This is due to its appealing electronic band structure, high physicochemical stability, and “earth-abundant” nature. This critical review summarizes a panorama of the latest progress related to the design and construction of pristine g-C3N4 and g-C3N4-based nanocomposites, including (1) nanoarchitecture design of bare g-C3N4, such as hard and soft templating approaches, supramolecular preorganization assembly, exfoliation, and template-free synthesis routes, (2) functionalization of g-C3N4 at an atomic level (elemental doping) and molecular level (copolymerization), and (3) modification of g-C3N4 with well-matched energy levels of another semiconductor or a metal as a cocatalyst to form heterojunction nanostructures. The constructi...

Graphitic Carbon Nitride (g-C3N4)-Based Photocatalysts for Artificial Photosynthesis and Environmental Remediation: Are We a Step Closer To Achieving Sustainability?

Self-assembling Nanostructures to Deliver Angiogenic Factors to Pancreatic Islets

Peptidic oligothiophene derivatives self-assemble into 1D nanostructures in aqueous solution.

Self-assembling quinquethiophene–oligopeptide hydrogelators

This article reports on the reaction of bone to a new family of nanocrystalline hydroxyapatite biomaterials with crystal sizes similar to those of human bone. Pure nanoapatite cylinders and organoapatite cylinders containing a synthetic nanopeptide were analyzed 28 days after implantation into the spongy bone of Chinchilla rabbits. The experimental techniques used for analysis were light microscopy, scanning electron microscopy, and transmission electron microscopy. Both implant types were well incorporated, and interface events were found to be similar to those observed on human bone surfaces with regard to resorption by osteoclast-like cells and bone formation by osteoblasts. Different types of giant cells were observed resorbing the outermost surfaces of implants. There seemed to be both dissolution of the implant and particulate biodegradation leading to less dense implant regions near the interface, whereas the bulk of the implants remained denser. Transmission electron micrographs revealed that bone bonding occurred with and without an afibrillar intervening layer. Given the biologic reaction observed, these implant materials should be suitable for bone replacement and the organoapatite form could be useful for additional functions such as the release of drugs and optimized release of antibiotics, growth factors, or other substances. The organic component can also be used to control physical properties in a bony implantation bed. © 1995 John Wiley & Sons, Inc.

Nanoapatite and organoapatite implants in bone: Histology and ultrastructure of the interface

1.1. Biomineralization
The study of biomineralization is not only important to gain an understanding of how mineral-rich tissues are created in vivo but also because it is a great source of inspiration for the design of advanced materials.1-7 Mineralized tissues have remarkable hierarchical structures that have evolved over time to achieve great functions in a large variety of organisms. Organic phases play a key role in templating the structure of mineralized tissues; therefore, their matrices are often hybrid in composition, varying widely in the relative content of organic and inorganic substances. Understanding the complex integration of hard and soft phases that biology achieves in mineralized matrices across scales and its link to properties is knowledge of great value to materials chemistry. At the same time, the synthetic mechanisms used by biology to create mineralized matrices could also offer some useful strategies to create synthetic hybrid materials. Often, the amount of organic material utilized by Nature to modify mechanical properties of mineralized structures is vanishingly small. One example is the role of occluded proteins in the toughness of biogenic calcite.8 The study of mammalian bone and teeth in the biomineralization and biomimetic context is particularly interesting since the information derived could contribute a significant biomedical impact on therapies and strategies to repair or regenerate human mineralized tissues. This is an important area given the continually rising average life span of humans. The materials of interest could be highly sophisticated bioactive scaffolds to regenerate bone and possibly dental tissues as well. This review focuses on the formation of hydroxyapatite (HA) in synthetic systems designed primarily in the biomimetic context of bone or enamel mineralization for therapeutic approaches in repair of human tissues. Bone and enamel share the same mineral composition, HA, but have different morphologies and organic content. Enamel is almost entirely inorganic in composition, and bone has a relatively high organic composition. Knowledge acquired in this field may inspire the chemical synthesis of novel hybrid materials, including apatite-based structures for the regeneration of human bone and dental tissues.

Biomimetic Systems for Hydroxyapatite Mineralization Inspired by Bone and Enamel

TThe synthesis and properties of a novel set of building blocks for the preparation of self-assembling biomaterials are described. These molecules consist of a relatively short oligo(L-lactic acid)n segment (n = 10-40) that is substituted with a cholesterol moiety as an end group and in some cases has a second biofunctional substituent at its other terminus. The cholesterol moiety not only serves to induce liquid crystalline properties and drive the self-assembly of these oligomers, but also is expected to have an effect on the interaction of cells with these materials. The cholesteryl-(L-lactic acid)n (CLAn) oligomers form thermotropic liquid crystals and self-assemble into lamellar structures consisting of interdigitated bilayers. In addition, the CLAn oligomers can be homogeneously blended with poly(L-lactic acid), thereby offering the possibility to improve the cell interaction properties of this common surgical biomaterial. Furthermore, the secondary alcohol terminus of the CLAn oligomers allows the opportunity to introduce additional bioactive substituents such as cholesterol, indomethacin (an antiinflammatory drug), and pyrene and rhodamine B (which can act as fluorescent labels for bioimaging purposes) and various α-amino acids. These biofunctional CLAn oligomers can also be homogeneously mixed with the unsubstituted CLAn oligomers and thus could enable a further noncovalent functionalization of self-assembling biomaterials.

Samuel I. Stupp

Papers

Self-assembling Nanostructures to Deliver Angiogenic Factors to Pancreatic Islets

Self-assembling quinquethiophene–oligopeptide hydrogelators

Nanoapatite and organoapatite implants in bone: Histology and ultrastructure of the interface

Biomimetic Systems for Hydroxyapatite Mineralization Inspired by Bone and Enamel

Cholesteryl-(L-lactic acid)n building blocks for self-assembling biomaterials