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

The interfacial gelation of proteins at metallic surfaces was investigated with an electrochemical quartz crystal microbalance (QCM). When Cr electrodes were corroded in proteinaceous solutions, it was found that gels will form at the Cr surfaces if molybdate ions are also present in the solution. Gelation is reversible and can also be controlled with the electrochemical potential at the electrode. Further, a method was developed to characterize the viscoelastic properties of thin films in liquid media using the QCM as a high-frequency rheometer. By measuring the frequency and dissipation at multiple harmonics of the resonance frequency, the viscoelastic phase angle, density–modulus product, and areal mass of a film can be determined. The method was applied to characterize the protein films, demonstrating that they have a phase angle near 55° and a density-modulus product of ≈107 Pa·g/cm3. Data imply that the gels are composed of a weakly cross-linked proteinaceous network with properties similar to album...

Viscoelastic properties of electrochemically deposited protein/metal complexes.

A contact mechanics methodology utilizing the quartz crystal microbalance (QCM) has been applied to study the spreading behavior of polymer solutions and gels. Changes in the resonant frequency and in the dissipation are monitored as these materials are brought into contact with the electrode surface of the QCM. The primary application is in studies of elastic polymer gels, where spreading over the surface of the QCM is limited by the elasticity of the gel. Simultaneous measurement of the applied loads and displacements, along with measurement of the QCM/gel contact area, the frequency shift, and the dissipation, enable us to calibrate the QCM as a contact sensor. While changes in the frequency and dissipation both depend linearly on the contact area, measurements of the dissipation provide a more reliable indicator. The relationship between the dissipation and the contact area is determined by the solvent viscosity and by the high-frequency intrinsic viscosity of the system of interest. This result is consistent with previous results on the high-frequency rheological behavior of polymer solutions.

/pdf/contact-mechanics-studies-with-the-quartz-crystal-20mipdalvu.pdf

Contact Mechanics Studies with the Quartz Crystal Microbalance

Poly(methyl methacrylate)–poly(methacrylic acid)–poly(methyl methacrylate) (PMMA–PMAA–PMMA) triblock copolymers can self-assemble into well-defined elastic hydrogels in water by forming glassy PMMA micelle cores connected with PMAA bridges. The stiffness and toughness of these hydrogels are enhanced substantially by introducing partially quaternized poly(4-vinylpyridine) (QVP) into the system. Interactions between the QVP and PMAA molecules provide an energy dissipation mechanism, with fracture energies in excess of 1000 J/m2 obtained in some cases. The materials are fully self-assembled and are formed by exposing liquid solutions in DMSO to small amounts of water. The simplicity of gel formation, and the ability to adjust the chemical and physical characteristics of these materials over a wide range, make them excellent model systems for fundamental investigations of the mechanical response of ion-containing gels.

High-Toughness Polycation Cross-Linked Triblock Copolymer Hydrogels

A method of producing an acrylic block copolymer comprising hydrophobic poly (lower alkyl methoacrylate), hydrophilic poly (lower alkyl methacrylic acid), and hydrophobic poly (lower alkyl methacrylate).

Modified Acrylic Block Copolymers For Hydrogels and Pressure Sensitive Wet Adhesives

A recently developed conductive atomic force microscopy (cAFM) technique, nanoscale impedance microscopy (NIM), is presented as a characterization strategy for nanoelectronic devices and circuits. NIM concurrently monitors the amplitude and phase response of the current through a cAFM tip in response to a temporally periodic applied bias. By varying the frequency of the driving potential, the resistance and reactance of conductive pathways can be quantitatively determined. Proof-of-principle experiments show 10-nm spatial resolution and ideal frequency-dependent impedance spectroscopy behavior for test circuits connected to electron beam lithographically patterned electrode arrays. Possible applications of NIM include defect detection and failure analysis testing for nanoscale integrated circuits.

Kenneth R. Shull

Papers

Viscoelastic properties of electrochemically deposited protein/metal complexes.

Contact Mechanics Studies with the Quartz Crystal Microbalance

High-Toughness Polycation Cross-Linked Triblock Copolymer Hydrogels

Modified Acrylic Block Copolymers For Hydrogels and Pressure Sensitive Wet Adhesives

Nanoscale impedance microscopy-a characterization tool for nanoelectronic devices and circuits