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

Although gold is the subject of one of the most ancient themes of investigation in science, its renaissance now leads to an exponentially increasing number of publications, especially in the context of emerging nanoscience and nanotechnology with nanoparticles and self-assembled monolayers (SAMs). We will limit the present review to gold nanoparticles (AuNPs), also called gold colloids. AuNPs are the most stable metal nanoparticles, and they present fascinating aspects such as their assembly of multiple types involving materials science, the behavior of the individual particles, size-related electronic, magnetic and optical properties (quantum size effect), and their applications to catalysis and biology. Their promises are in these fields as well as in the bottom-up approach of nanotechnology, and they will be key materials and building block in the 21st century. Whereas the extraction of gold started in the 5th millennium B.C. near Varna (Bulgaria) and reached 10 tons per year in Egypt around 1200-1300 B.C. when the marvelous statue of Touthankamon was constructed, it is probable that “soluble” gold appeared around the 5th or 4th century B.C. in Egypt and China. In antiquity, materials were used in an ecological sense for both aesthetic and curative purposes. Colloidal gold was used to make ruby glass 293 Chem. Rev. 2004, 104, 293−346

Gold nanoparticles: assembly, supramolecular chemistry, quantum-size-related properties, and applications toward biology, catalysis, and nanotechnology.

Hydrogels with improved mechanical properties, made by combining polymer networks with ionic and covalent crosslinks, should expand the scope of applications, and may serve as model systems to explore mechanisms of deformation and energy dissipation. Hydrogels are used in flexible contact lenses, as scaffolds for tissue engineering and in drug delivery. Their poor mechanical properties have so far limited the scope of their applications, but new strong and stretchy materials reported here could take hydrogels into uncharted territories. The new system involves a double-network gel, with one network forming ionic crosslinks and the other forming covalent crosslinks. The fracture energy of these materials is very high: they can stretch to beyond 17 times their own length even when containing defects that usually initiate crack formation in hydrogels. The materials' toughness is attributed to crack bridging by the covalent network accompanied by energy dissipation through unzipping of the ionic crosslinks in the second network. Hydrogels are used as scaffolds for tissue engineering1, vehicles for drug delivery2, actuators for optics and fluidics3, and model extracellular matrices for biological studies4. The scope of hydrogel applications, however, is often severely limited by their mechanical behaviour5. Most hydrogels do not exhibit high stretchability; for example, an alginate hydrogel ruptures when stretched to about 1.2 times its original length. Some synthetic elastic hydrogels6,7 have achieved stretches in the range 10–20, but these values are markedly reduced in samples containing notches. Most hydrogels are brittle, with fracture energies of about 10 J m−2 (ref. 8), as compared with ∼1,000 J m−2 for cartilage9 and ∼10,000 J m−2 for natural rubbers10. Intense efforts are devoted to synthesizing hydrogels with improved mechanical properties11,12,13,14,15,16,17,18; certain synthetic gels have reached fracture energies of 100–1,000 J m−2 (refs 11, 14, 17). Here we report the synthesis of hydrogels from polymers forming ionically and covalently crosslinked networks. Although such gels contain ∼90% water, they can be stretched beyond 20 times their initial length, and have fracture energies of ∼9,000 J m−2. Even for samples containing notches, a stretch of 17 is demonstrated. We attribute the gels’ toughness to the synergy of two mechanisms: crack bridging by the network of covalent crosslinks, and hysteresis by unzipping the network of ionic crosslinks. Furthermore, the network of covalent crosslinks preserves the memory of the initial state, so that much of the large deformation is removed on unloading. The unzipped ionic crosslinks cause internal damage, which heals by re-zipping. These gels may serve as model systems to explore mechanisms of deformation and energy dissipation, and expand the scope of hydrogel applications.

/pdf/highly-stretchable-and-tough-hydrogels-4ocu3amojx.pdf

Highly stretchable and tough hydrogels

Since the discovery of mechanically exfoliated graphene in 2004, research on ultrathin two-dimensional (2D) nanomaterials has grown exponentially in the fields of condensed matter physics, material science, chemistry, and nanotechnology. Highlighting their compelling physical, chemical, electronic, and optical properties, as well as their various potential applications, in this Review, we summarize the state-of-art progress on the ultrathin 2D nanomaterials with a particular emphasis on their recent advances. First, we introduce the unique advances on ultrathin 2D nanomaterials, followed by the description of their composition and crystal structures. The assortments of their synthetic methods are then summarized, including insights on their advantages and limitations, alongside some recommendations on suitable characterization techniques. We also discuss in detail the utilization of these ultrathin 2D nanomaterials for wide ranges of potential applications among the electronics/optoelectronics, electrocat...

Recent Advances in Ultrathin Two-Dimensional Nanomaterials

Adhesion between a model acrylic elastomer and a glassy polymeric substrate has been investigated by the JKR technique. Hemispherical lenses of lightly cross-linked poly(n-butyl acrylate) (PNBA) were subjected to loading/unloading cycles on flat poly(methyl methacrylate) (PMMA) substrates. Significant adhesion hysteresis is observed at all accessible rates of unloading. The amount of hysteresis is seen to increase systematically with unloading rate and is characterized by the measured energy release rate (G). The presence of free PNBA chains, whether in the elastomer or applied directly to the interface, significantly reduces adhesion of the elastomer to the glassy substrate. Unloading profiles of the crack growth rate dependence of G yield a threshold value (G(0) = 70 ± 30 mJ/m2) which is close to the expected thermodynamic work of adhesion (W) between PNBA and PMMA. However, fits of the JKR model to loading data result in values of G which are significantly lower than W. We also examine the underlying a...

JKR Studies of Acrylic Elastomer Adhesion to Glassy Polymer Substrates

We have shown that the addition of polyisoprene (PI) tethered chains to a polystyrene (PS) substrate produces a large increase in its adhesion to a PI cross-linked lens over the whole range of crack speeds (10 -10 -10 -7 m/s) that the have investigated. Such an increase cannot be explained by the rate dependence of bulk viscoelastic losses and is believed to be due to the viscous pullout of the PI chains from the network. At low crack speeds the fracture toughness of the interface G c was found to increase linearly with velocity from a threshold value G 0

Molecular Weight Effects in Chain Pullout

The effects of molecular weight and acrylic acid content on the adhesive properties of a series of monodisperse poly(n-butyl acrylate) materials have been investigated. The short-time adhesion, or ...

Influence of Molecular Features on the Tackiness of Acrylic Polymer Melts

Fingering instabilities similar to those commonly observed in viscous systems have been observed in purely elastic layers that are strained in tension. The instability is driven by the release of lateral constraints within a confined elastic layer and is observed when the lateral confinement significantly exceeds the thickness of the elastic layer. Our results show convincingly that yielding or flow of a material is not required in order for fingering to be initiated in a confined material.

/pdf/fingering-instabilities-of-confined-elastic-layers-in-1zhle4pgsk.pdf

Fingering Instabilities of Confined Elastic Layers in Tension

A combination of methods has been used to study the dynamic properties of a nanocomposite consisting of evaporated gold particles embedded in poly(tert-butyl acrylate). Rutherford backscattering spectrometry was used to measure the diffusion coefficients of the gold particles and of the polymer molecules; dewetting experiments were used to probe the viscosity of thin films with and without gold particles. The gold particles diffused with a temperature dependence similar to the temperature dependence of the polymer viscosity, but with hydrodynamic radii that greatly exceeded the actual radii of the gold particles. The gold particles also increased the viscosity of a low molecular weight polymer film by a factor of 4. Our interpretation of these results is that long-lived polymer bridges between individual gold particles stabilize clusters with dimensions of approximately 50 nm. A geometrical model of the bridging process was also developed. Results from this model can readily be applied to homogeneous nano...

Kenneth R. Shull

Papers

JKR Studies of Acrylic Elastomer Adhesion to Glassy Polymer Substrates

Molecular Weight Effects in Chain Pullout

Influence of Molecular Features on the Tackiness of Acrylic Polymer Melts

Fingering Instabilities of Confined Elastic Layers in Tension

Dynamic properties of a model polymer/metal nanocomposite : gold particles in poly (tert-butyl acrylate).