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

Fabrication of Gold Nanowires by Electric‐Field‐Induced Scanning Probe Lithography and In Situ Chemical Development

A massively parallel magnetic tweezer system has been constructed that utilizes the self-repulsion of colloidal beads from a planar interface via a magnetic dipole image force. Self-repulsion enables the application of a uniform magnetic force to thousands of beads simultaneously, which permits the measurement of unbinding histograms at the lowest loading rates ever tested. The adhesion of 9.8 μm polystyrene beads to a fluorocarbon, PEG, and UV-irradiated PEG surfaces were measured between 10−3−100 pN/s force loading rates, revealing the presence of both kinetic and quasi-equilibrium unbinding regimes.

Imaginary Magnetic Tweezers for Massively Parallel Surface Adhesion Spectroscopy

For decades ferroelectric thin films (FETFs) have been the focus of research and development for next-generation memory and semiconductor devices. FETFs are attractive because their polarization states are highly localized, stable, and switchable. These unique properties are also attractive for (bio)molecular sensing and separation applications. Polarization of both polymer and ceramic FETF results in the expression of a sustained high, non-Faradaic, surface charge density. If these surface charges are maintained in aqueous environments, then the resulting electrostatic forces should induce the formation of electrolyte gradients and aid in the localization of charged species to the surface. Recently, there has been a growing interest in the interfacial properties of FETFs, specifically how they interact with liquid or gaseous phases. Recent work has shown that the FETF polarization state affects adsorption from the gaseous phase, surface catalysis, and cell growth. Encouraged by these findings, the use of FETFs in aqueous environments is explored. After an introduction to FETFs, the growing body of literature on the FETF interface is reviewed, along with the limited number of studies demonstrating FETF function in gas and liquid environments. Finally, the exciting possibilities that FETFs could bring to interfacial engineering and lab-on-chip (LOC) device design is reviewed.

Ferroelectric thin films in fluidic environments: a new interface for sensing and manipulation of matter.

Contact resonance AFM (CR-AFM) is a scanning probe microscopy technique that utilizes the contact resonances of the AFM cantilever for concurrent imaging of topography and surface stiffness. The technique has not been used in liquid until recently due to analytical and experimental difficulties, associated with viscous damping of cantilever vibrations and fluid loading effects. To address these difficulties, (i) an analytical approach for contact resonances in liquid is developed, and (ii) direct excitation of the contact resonances is demonstrated by actuating the cantilever directly in a magnetic field. By implementing the analytical approach and the direct actuation through magnetic particles, quantitative stiffness imaging on surfaces with a wide range of stiffness can be achieved in liquid with soft cantilevers and low contact forces.

https://iopscience.iop.org/article/10.1088/0957-4484/25/44/445703/pdf

Liquid contact resonance AFM: analytical models, experiments, and limitations

High molecular weight ssDNA amphiphiles are synthesized by enzymatic polymerization. These highly asymmetric diblock DNA copolymers self-assemble into "hairy", star-like micelles, shown in the AFM image and the DPD snapshot.

Stefan Zauscher

Papers

Fabrication of Gold Nanowires by Electric‐Field‐Induced Scanning Probe Lithography and In Situ Chemical Development

Imaginary Magnetic Tweezers for Massively Parallel Surface Adhesion Spectroscopy

Ferroelectric thin films in fluidic environments: a new interface for sensing and manipulation of matter.

Liquid contact resonance AFM: analytical models, experiments, and limitations

Enzymatic polymerization of high molecular weight DNA amphiphiles that self-assemble into star-like micelles.