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

Chemical force microscopy of cellulosic fibers

Mutation or loss of collagen VI has been linked to a variety of musculoskeletal abnormalities, particularly muscular dystrophies, tissue ossification and/or fibrosis, and hip osteoarthritis. However, the role of collagen VI in bone and cartilage structure and function in the knee is unknown. In this study, we examined the role of collagen VI in the morphology and physical properties of bone and cartilage in the knee joint of Col6a1−/− mice by micro-computed tomography (microCT), histology, atomic force microscopy (AFM), and scanning microphotolysis (SCAMP). Col6a1−/− mice showed significant differences in trabecular bone structure, with lower bone volume, connectivity density, trabecular number, and trabecular thickness but higher structure model index and trabecular separation compared to Col6a1+/+ mice. Subchondral bone thickness and mineral content increased significantly with age in Col6a1+/+ mice, but not in Col6a1−/− mice. Col6a1−/− mice had lower cartilage degradation scores, but developed early, severe osteophytes compared to Col6a1+/+mice. In both groups, cartilage roughness increased with age, but neither the frictional coefficient nor compressive modulus of the cartilage changed with age or genotype, as measured by AFM. Cartilage diffusivity, measured via SCAMP, varied minimally with age or genotype. The absence of type VI collagen has profound effects on knee joint structure and morphometry, yet minimal influences on the physical properties of the cartilage. Together with previous studies showing accelerated hip osteoarthritis in Col6a1−/− mice, these findings suggest different roles for collagen VI at different sites in the body, consistent with clinical data.

/pdf/altered-trabecular-bone-structure-and-delayed-cartilage-4oisihcog9.pdf

Altered trabecular bone structure and delayed cartilage degeneration in the knees of collagen VI null mice.

Surfaces with end-grafted, nanopatterned polymer brushes that exhibit well-defined feature dimensions and controlled chemical and physical properties provide versatile platforms not only for investigation of nanoscale phenomena at biointerfaces, but also for the development of advanced devices relevant to biotechnology and electronics applications. In this review, we first give a brief introduction of scaling behavior of nanopatterned polymer brushes and then summarize recent progress in fabrication and application of nanopatterned polymer brushes. Specifically, we highlight applications of nanopatterned stimuli-responsive polymer brushes in the areas of biomedicine and biotechnology.

Nanopatterned polymer brushes: conformation, fabrication and applications

Elastin-like polypeptides (ELPs) are stimulus-responsive polymers that contain repeats of 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. While studying the conformational mechanics of ELPs over a range of solvent conditions by single-molecule force spectroscopy, we noticed that some force-extension curves showed temperature-independent, extensional transitions that could not be fitted with a freely jointed chain or worm-like chain model. Here we show that the observed molecular elongation results from the force-induced peptidyl-prolyl cis-trans isomerization in prolines, which are repeated every fifth residue in the main chain of ELPs. Control experiments with poly(L-proline) demonstrate the similarity of the conformational transition between poly(L-proline) and ELPs. In contrast, the force-extension behavior of poly(L-lysine) showed no deviation in the relevant force range. Force-extension curves in hysteresis experiments showed an elongational difference between extension and relaxation pathways that suggests that the cis conformational state of the prolines could be exhausted on the time scale of the experiment. We present further computational evidence for this mechanism by Monte Carlo simulation of the force-extension behavior using an elastically coupled, two-state model. We believe ours is the first demonstration of force-induced prolyl cis-trans isomerization in proline-containing polypeptides. Our results suggest that single-molecule force spectroscopy could provide an alternate means to assay this important conformational transition in polypeptides.

Force-induced prolyl cis-trans isomerization in elastin-like polypeptides.

Stimulus-responsive elastin-like polypeptides (ELPs) grafted onto surfaces are of significant technical interest because they can be exploited for force generation, in sensing applications, or as molecular switches with tunable properties. Changes in the conformational state of grafted ELPs, induced by a phase transition or changes in osmotic pressure, lead to significant changes in the surface stress in the ELP graft layer and translate into detectable changes in microcantilever deflection. In this study, we investigate the conformational mechanics of ELPs in response to changes in solution pH and ionic strength using atomic force microscopy (AFM) microcantilever deflection and quartz crystal microbalance (QCM) measurements. We show that the use of genetically encoded, surface-grafted ELPs is exciting for cantilever actuation and sensing because commonly available microfabricated cantilever springs offer a simple and nonintrusive way to detect changes in solvent type, temperature, and pH, promising great potential for sensing applications in microfluidic devices.

Stefan Zauscher

Papers

Chemical force microscopy of cellulosic fibers

Altered trabecular bone structure and delayed cartilage degeneration in the knees of collagen VI null mice.

Nanopatterned polymer brushes: conformation, fabrication and applications

Force-induced prolyl cis-trans isomerization in elastin-like polypeptides.

Microcantilever Sensing and Actuation with End-Grafted Stimulus-Responsive Elastin-Like Polypeptides†