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

Responsive polymer materials can adapt to surrounding environments, regulate transport of ions and molecules, change wettability and adhesion of different species on external stimuli, or convert chemical and biochemical signals into optical, electrical, thermal and mechanical signals, and vice versa. These materials are playing an increasingly important part in a diverse range of applications, such as drug delivery, diagnostics, tissue engineering and 'smart' optical systems, as well as biosensors, microelectromechanical systems, coatings and textiles. We review recent advances and challenges in the developments towards applications of stimuli-responsive polymeric materials that are self-assembled from nanostructured building blocks. We also provide a critical outline of emerging developments.

Emerging applications of stimuli-responsive polymer materials

http://experimentationlab.berkeley.edu/sites/default/files/AFMImages/butt_AFM.pdf

Force measurements with the atomic force microscope: Technique, interpretation and applications

Coinage metals, such as Au, Ag, and Cu, have been important materials throughout history.1 While in ancient cultures they were admired primarily for their ability to reflect light, their applications have become far more sophisticated with our increased understanding and control of the atomic world. Today, these metals are widely used in electronics, catalysis, and as structural materials, but when they are fashioned into structures with nanometer-sized dimensions, they also become enablers for a completely different set of applications that involve light. These new applications go far beyond merely reflecting light, and have renewed our interest in maneuvering the interactions between metals and light in a field known as plasmonics.2–6

In plasmonics, the metal nanostructures can serve as antennas to convert light into localized electric fields (E-fields) or as waveguides to route light to desired locations with nanometer precision. These applications are made possible through a strong interaction between incident light and free electrons in the nanostructures. With a tight control over the nanostructures in terms of size and shape, light can be effectively manipulated and controlled with unprecedented accuracy.3,7 While many new technologies stand to be realized from plasmonics, with notable examples including superlenses,8 invisible cloaks,9 and quantum computing,10,11 conventional technologies like microprocessors and photovoltaic devices could also be made significantly faster and more efficient with the integration of plasmonic nanostructures.12–15 Of the metals, Ag has probably played the most important role in the development of plasmonics, and its unique properties make it well-suited for most of the next-generation plasmonic technologies.16–18

1.1. What is Plasmonics?
Plasmonics is related to the localization, guiding, and manipulation of electromagnetic waves beyond the diffraction limit and down to the nanometer length scale.4,6 The key component of plasmonics is a metal, because it supports surface plasmon polariton modes (indicated as surface plasmons or SPs throughout this review), which are electromagnetic waves coupled to the collective oscillations of free electrons in the metal.

While there are a rich variety of plasmonic metal nanostructures, they can be differentiated based on the plasmonic modes they support: localized surface plasmons (LSPs) or propagating surface plasmons (PSPs).5,19 In LSPs, the time-varying electric field associated with the light (Eo) exerts a force on the gas of negatively charged electrons in the conduction band of the metal and drives them to oscillate collectively. At a certain excitation frequency (w), this oscillation will be in resonance with the incident light, resulting in a strong oscillation of the surface electrons, commonly known as a localized surface plasmon resonance (LSPR) mode.20 This phenomenon is illustrated in Figure 1A. Structures that support LSPRs experience a uniform Eo when excited by light as their dimensions are much smaller than the wavelength of the light.



Figure 1

Schematic illustration of the two types of plasmonic nanostructures discussed in this article as excited by the electric field (Eo) of incident light with wavevector (k). In (A) the nanostructure is smaller than the wavelength of light and the free electrons ...



In contrast, PSPs are supported by structures that have at least one dimension that approaches the excitation wavelength, as shown in Figure 1B.4 In this case, the Eo is not uniform across the structure and other effects must be considered. In such a structure, like a nanowire for example, SPs propagate back and forth between the ends of the structure. This can be described as a Fabry-Perot resonator with resonance condition l=nλsp, where l is the length of the nanowire, n is an integer, and λsp is the wavelength of the PSP mode.21,22 Reflection from the ends of the structure must also be considered, which can change the phase and resonant length. Propagation lengths can be in the tens of micrometers (for nanowires) and the PSP waves can be manipulated by controlling the geometrical parameters of the structure.23

/pdf/controlling-the-synthesis-and-assembly-of-silver-1ktlgomyt6.pdf

Controlling the synthesis and assembly of silver nanostructures for plasmonic applications

Atomic Force Microscopes (AFM) can measure the force between a surface and the tip of a cantilever as a junction of separation with great precision. For example, van der Waals type forces and electrostatic repulsive forces can easily be measured in aqueous solutions using an AFM. The complex, pyramidal shape of the typical AFM cantilever is, however, not well suited for quantitative measurements. It is thus desirable to attach particles of known geometry (usually spheres) to the tip of a cantilever. This technique, pioneered by Ducker ef at. in 1992, has led to a number of investigations where particle modified cantilevers were used (for example, refs. 2-4), and has led to the publication of a support note addressing the procedure of how to attach particles to cantilevers. The adhesive of choice seems to be an epoxy resin solid (Epon 1004) manufactured by Shell, Epon 1004 is used as a hot melt adhesive and requires heating the cantilevers on a hotstage. This can lead to warping of (especially metal coated) cantilevers. In my work, I also need to attach spherical particles (cellulose beads) onto standard silicone nitride AFM cantilevers, but I need to avoid excessive heat. I found that an optical adhesive which cures in seconds when exposed to ultraviolet light, and thus does not need heat treatment for crosslinking, works very well. Norland's optical adhesive #81 (NOA #81) is designed for bonding applications where low strain, optical clarity and low outgassing are required. NOA #81 has a viscosity of 300 cp at 25°C, which allows dispensing the adhesive from a micro-pipette with a tip diameter of less than 0.2 [i<n\\. The adhesive has a modulus of 1.4 GPa (about 200,000 psi), a Shore D hardness of 90, and cures extremely fast (within 60 seconds) when exposed to longwave (320 to 380 nm) UV light, A small hand held or desk top UV light source can be used. Cantilevers deflect (droop and twist) under the weight of the object attached to the free end. A nice way to observe the distortion in a lever (Figure) is to use a light microscope equipped with Nomarski interference, This differential contrast technique is used in light microscopy to emphasize surface structure. Using this observation method, I find that cantilevers are sometimes already distorted when new and I usually discard these levers, The Nomarski technique may also offer a non-destructive way to calibrate the lever for stiffness by placing particles of known mass on the end of the lever and observing the color change with deflection. Color video images of the deflected lever could easily be analyzed with image analysis software and, once a color deflection calibration has been performed,-the lever stiffness can be inferred. (I haven't investigated the feasibility of this yet), It is imperative when attaching particles to make sure that the particle is absolutely centered on the lever to minimize twisting of the lever under contact pressure or in a strong force field. The twisting motion of a cantilever is usually coupled to the deflection motion of the cantilever, and thus twisting can give rise to an undesirable deflection, The strength of this coupling and any unusual twist while the cantilever is brought into contact with the surface can be observed with an AFM where both horizontal and vertical deflection signal of the lever can be accessed simultaneously. For example, with Digital Instruments' MultiMode AFM and Software version 4,22, turn on Channel 2 in the force calibration mode and set it to friction. The lateral force signal should not change dramatically upon engaging the tip. •

Putting a Sphere on an Atomic Force Microscope Cantilever Tip

DNA Brushes: Advances in Synthesis and Applications

: Our research provides a first step towards a systematic, cell-level study of the effects of shock waves on the mechanical and biochemical properties of cells on solid supports. Motivated to better understand the relationship between shock exposure and heterotopic ossification (HO), a type of soft tissue injury, we designed an experimental setup to expose cell sheets of adipose derived stem cells to shock waves. A key guideline in the experimental design was to suppress cavitation. To this end we built a spark transducer and used a pressurized sample chamber. Cell viability tests and cytoskeletal staining showed little difference between shock-exposed cells and controls. We attribute this to the absence of cavitation. Time-resolved gene expression revealed that a large number of genes were affected by the shock wave exposure. Importantly, the experimental setup and the procedures we developed provide a basis for further studies of shock wave effects on a broad range of other cells. Specifically, they could be adopted to gain further understanding of cellular level causes of traumatic brain injury.

Biomechanical and Biochemical Cellular Response Due to Shock Waves

or pH. 1 ELPs contain repeats of the five amino acids Val-Pro-Gly-Xaa-Gly (VPGXG), where Xaa is a guest residue that can be any amino acid with the exception of proline. 1 While the behavior of molecular ensembles of ELPs in solutions was the main focus of previous studies, 1,3 an understanding of the conformational mechanics of end grafted ELP is still lacking. ELPs are of particular interest because they can potentially be exploited for force generation, 1 or as molecular switches with tunable properties. 4 In this study, we measured deflection and resonance characteristics of micro-cantilevers decorated with ELPs on one side. Our measurements showed how environmental stimuli influence the conformation of ELPs with different guest residues. Conformational transitions in ELPs were also utilized to design micro-cantilever based miniaturized sensors and actuators with tunable properties. Experimental Materials. ELPs were synthesized using methods described previously.

Stefan Zauscher

Papers

Putting a Sphere on an Atomic Force Microscope Cantilever Tip

DNA Brushes: Advances in Synthesis and Applications

Biomechanical and Biochemical Cellular Response Due to Shock Waves

Stimulus-responsive elastin-like polypetides as coatings for microcantilevers: applications for sensing and actuation

Self-Assembled Single-Stranded DNA Nano-Networks in Solution and at Surfaces.