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 term photonic crystals appears because of the analogy between electron waves in crystals and the light waves in artificial periodic dielectric structures. During the recent years the investigation of one-, two-and three-dimensional periodic structures has attracted a widespread attention of the world optics community because of great potentiality of such structures in advanced applied optical fields. The interest in periodic structures has been stimulated by the fast development of semiconductor technology that now allows the fabrication of artificial structures, whose period is comparable with the wavelength of light in the visible and infrared ranges.

http://ieeexplore.ieee.org/iel5/6354/16969/00781867.pdf

Photonic crystals

Gold nanoparticles have been used in biomedical applications since their first colloidal syntheses more than three centuries ago. However, over the past two decades, their beautiful colors and unique electronic properties have also attracted tremendous attention due to their historical applications in art and ancient medicine and current applications in enhanced optoelectronics and photovoltaics. In spite of their modest alchemical beginnings, gold nanoparticles exhibit physical properties that are truly different from both small molecules and bulk materials, as well as from other nanoscale particles. Their unique combination of properties is just beginning to be fully realized in range of medical diagnostic and therapeutic applications. This critical review will provide insights into the design, synthesis, functionalization, and applications of these artificial molecules in biomedicine and discuss their tailored interactions with biological systems to achieve improved patient health. Further, we provide a survey of the rapidly expanding body of literature on this topic and argue that gold nanotechnology-enabled biomedicine is not simply an act of ‘gilding the (nanomedicinal) lily’, but that a new ‘Golden Age’ of biomedical nanotechnology is truly upon us. Moving forward, the most challenging nanoscience ahead of us will be to find new chemical and physical methods of functionalizing gold nanoparticles with compounds that can promote efficient binding, clearance, and biocompatibility and to assess their safety to other biological systems and their long-term term effects on human health and reproduction (472 references).

The golden age: gold nanoparticles for biomedicine

基礎講座 電気泳動(Electrophoresis)

https://weitzlab.seas.harvard.edu/files/weitzlab/files/2008_mattoday_shah.pdf

Designer emulsions using microfluidics

All-nanoparticle thin-film coatings that exhibit antireflection, antifogging (superhydrophilicity), and self-cleaning properties have been prepared via layer-by-layer deposition of TiO2 and SiO2 nanoparticles. The porosity and chemical composition of the coatings were determined using a simple method that is based on ellipsometry and does not require any assumptions about the refractive indices of the constituent nanoparticles. The presence of nanopores in the TiO2/SiO2 nanoparticle coatings results in superhydrophilicity as well as antireflection properties. The superhydrophilicity of contaminated coatings could also be readily recovered and retained after ultraviolet irradiation.

https://pubs.acs.org/doi/pdf/10.1021/nl0706796

All-nanoparticle thin-film coatings.

Antibacterial coatings based on hydrogen-bonded multilayers containing in situ synthesized Ag nanoparticles were created on planar surfaces and on magnetic colloidal particles. We report the antibacterial properties of these coatings, determined using a disk-diffusion (Kirby-Bauer) test, as a function of the film thickness and the concentration of Ag nanoparticles in the hydrogen-bonded multilayers. The zone of inhibition (ZoI) determined by the disk-diffusion test increases as the thickness of the multilayer film is increased. Results obtained for the values of the ZoI as a function of film thickness can be described adequately with a simple diffusion model (i.e., the square of the zone of inhibition (ZoI) depended linearly on the logarithm of the thickness of the silver-loaded films). This observation suggests that, in order to incrementally increase the ZoI, an exponentially increasing amount of Ag is required within the multilayers. In general, there was no statistically significant correlation between the zone of inhibition and the number of Ag loading and reduction cycles. The duration of sustained release of antibacterial Ag ions from these coatings, however, could be prolonged by increasing the total supply of zerovalent silver in the films via multiple loading and reduction cycles. These results indicate that the release of silver is controlled by an oxidation mechanism at the surface of the nanoparticles and that repeated loading and reduction of silver leads preferentially to growth of the existing silver nanoparticles in the film as opposed to nucleation of new Ag nanoparticles. We also show that magnetic microspheres coated with silver nanoparticle loaded hydrogen-bonded multilayer thin films can be used to deliver antibacterial agents to specific locations. The minimum inhibitory concentration (MIC) of nanocomposite coated microspheres was determined by the agar dilution technique: antibacterial magnetic microspheres with higher concentrations of Ag nanoparticles exhibited lower MIC values.

Antibacterial properties of Ag nanoparticle loaded multilayers and formation of magnetically directed antibacterial microparticles.

Using a combination of an aqueous layer-by-layer deposition technique, nanoparticle surface modification chemistry, and nanoreactor chemistry, we constructed thin film coatings with two distinct layered functional regions: a reservoir for the loading and release of bactericidal chemicals and a nanoparticle surface cap with immobilized bactericides. This results in dual-functional bactericidal coatings bearing both chemical-releasing bacteria-killing capacity and contact bacteria-killing capacity. These dual-functional coatings showed very high initial bacteria-killing efficiency due to the release of Ag ions and retained significant antibacterial activity after the depletion of embedded Ag because of the immobilized quaternary ammonium salts.

Two-level antibacterial coating with both release-killing and contact-killing capabilities.

We present a novel approach for fabricating monodisperse phospholipid vesicles with high encapsulation efficiency using controlled double emulsions as templates. Glass-capillary microfluidics is used to generate monodisperse double emulsion templates. We show that the high uniformity in size and shape of the templates are maintained in the final phospholipid vesicles after a solvent removal step. Our simple and versatile technique is applicable to a wide range of phospholipids.

/pdf/double-emulsion-templated-monodisperse-phospholipid-vesicles-jjn64aq4s3.pdf

Daeyeon Lee

Papers

Designer emulsions using microfluidics

All-nanoparticle thin-film coatings.

Antibacterial properties of Ag nanoparticle loaded multilayers and formation of magnetically directed antibacterial microparticles.

Two-level antibacterial coating with both release-killing and contact-killing capabilities.

Double emulsion templated monodisperse phospholipid vesicles.