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

HIV-1 Antibodies and Vaccine Antigen Selectively Interact with Lipid Domains

Candida albicans is a leading cause of catheter-associated urinary tract infections and elimination of these biofilm-based infections without antifungal agents would constitute a significant medical advance. A novel urinary catheter prototype that utilizes on-demand surface deformation is effective at eliminating bacterial biofilms and here the broader applicability of this prototype to remove fungal biofilms has been demonstrated. C. albicans biofilms were debonded from prototypes by selectively inflating four additional intralumens surrounding the main lumen of the catheters to provide the necessary surface strain to remove the adhered biofilm. Deformable catheters eliminated significantly more biofilm than the controls (>90% eliminated vs 10% control; p < 0.001). Mechanical testing revealed that fungal biofilms have an elastic modulus of 45 ± 6.7 kPa with a fracture energy of 0.4-2 J m-2. This study underscores the potential of mechanical disruption as a materials design strategy to combat fungal device-associated infections.

https://www.tandfonline.com/doi/pdf/10.1080/08927014.2018.1474461

On-demand release of Candida albicans biofilms from urinary catheters by mechanical surface deformation.

Polymer brushes are polymer coatings in which polymer chains are tethered on one end to a surface at sufficiently high grafting density such that steric repulsion between the chains causes chain stretching. The polymer coating thickness is typically dictated by both the polymer chain length and surface graft density, and ranges from a few nanometers to several hundred nanometers. Thus, polymer brushes occupy a unique interfacial niche between self-assembled monolayers that are typically only a few nanometers thick and spin-cast polymer films that are typically thicker than several hundred nanometers. The synthesis of ultrathin, dense polymeric films and structures on surfaces has been a long standing challenge in interface science because packing polymer chains at high density onto a surface is difficult to achieve via methods that involve grafting polymers from the vapor or solution phase on to a surface, due to the intrinsic thermodynamic penalty for additional surface grafting that arises from size exclusion. The recent development of highly controlled polymer synthesis techniques largely based on controlled radical polymerizations that can be carried out from surface-tethered polymerization initiators, has allowed this thermodynamic constraint to be circumvented, and enables the facile, surface-initiated synthesis of polymer brushes with a broad range of chemical and structural properties. In reviewing the field, we have come to the conclusion and one that may excite raucous debate that the most promising technical advances in using polymer brushes have been associated with their biointerfacial applications, as defined by the interaction of these brushes with biological macromolecules, supramolecular assemblies, and cells. This InFocus section contains a set of papers that provides the reader with an idea of the breadth of the field associated with polymer brushes at biointerfaces, ranging from robust methods of brush synthesis and patterning, their use for protein imprinting, to the design of sophisticated macromolecular architectures to control protein and cell adhesion. Surprisingly, despite the wealth of approaches for polymer brush synthesis that are now available, the substrates used to grow polymer brushes have been largely confined to glass and gold. Similarly, methods to pattern polymer brushes over large, e.g., wafer-scale, areas are also scant. Hucknall et al. address these challenges, and demonstrate the synthesis of protein and cell-resistant poly oligo ethylene glycol methyl methacrylate POEGMA brushes over large areas on a range of substrate materials via simple and versatile methods. Furthermore, they present complementary approaches to pattern these polymer brushes with high fidelity and reliability on the wafer-scale for device production. There has been a proliferation of methods to grow stimulus-responsive polymer brush coatings that can be suitably functionalized to regulate biological function in response to an external stimulus. These methods enable the design of polymeric interfaces that can dynamically control the presentation of regulatory signals with applications that span the modulation of biomolecule activity, coatings that dynamically control drug permeation through nanoporous membranes, and substrates that control cell and protein adhesion. Here, Ionov et al. report on a novel approach that uses mixed polymer brushes with gradually changing charge composition to fabricate pH-sensitive surfaces that produce reversible gradients in protein adsorption. The paper by Arifuzzaman et al. describes amphiphilic polymer brush coatings whose chemistry and stimulus responsiveness can be tailored to protect against marine biofouling –a particularly vexing biointerfacial problem and one for which a solution has so far proved elusive. Their innovative approach, using amphiphilic copolymers comprising EG and fluorinated groups, stemmed from the crucial insight that a polymer brush that presents only a single chemical moiety was likely to be insufficient to prevent marine fouling. Control over cell adhesion is an important goal in the design of biomedical implants to improve their biocompatibility and integration with surrounding tissue. Raynor et al. show that titanium implants, modified with POEGMA brushes that present a bioactive peptide, promote osteoblast differentiation and enhance osseointegration. The function of bioanalytical devices, such as biosensors, heterogeneous immunoassays and microarrays, depends critically on generating a sufficiently large signal-to-noise ratio in response to the presence of an analyte of interest, so that minimizing nonspecific binding to reduce noise and maximizing specific binding between the analyte and a capture agent on the surface the receptor is a critical requirement. The immobilization of poly ethylene glycol PEG is the most commonly employed approach to render surfaces resistant to the adventitious and undesirable adsorption of proteins, cells and other biological components. However, synthetic polymer brushes, such as POEGMA as described by Hucknall et al., or polypeptoid brushes, such as described by Statz et al., have marked advantages over simple PEG coatings. In comparison with linear or branched PEGs that are grafted to a surface either by physisorption or covalent attachment and whose surface density cannot be increased

https://avs.scitation.org/doi/pdf/10.1116/1.3149787

Biological applications of polymer brushes

Convergent advances in the field of soft matter, macromolecular chemistry, and engineering have led to the development of biomaterials that possess autonomous, adaptive, and self-healing characteristics similar to living systems. These rationally designed biomaterials can surpass the capabilities of their parent material. Herein, the modification of hyaluronic acid (HA) to exhibit self-healing properties is described, and its physical and biological function both in vitro and in vivo is studied. The in vitro findings showed that self-healing HA designed to undergo self-repair improves lubrication, enhances free radical scavenging, and attenuates enzymatic degradation compared to unmodified HA. Longitudinal imaging following intraarticular injection of self-healing HA shows improved in vivo retention despite its low molecular weight. Concomitant with these functions, intraarticular injection of self-healing HA mitigates anterior cruciate ligament injury-mediated cartilage degeneration in rodents. This proof-of-concept study shows how incorporation of functional properties such as self-healing can be used to surpass the existing capabilities of biolubricants.

Self-Healing of Hyaluronic Acid to Improve In Vivo Retention and Function.

This paper discusses efforts to characterize the rheological properties of pulps that include low-grade wastepapers and papermill sludges to determine their potential for extrusion and conversion into useful products. We investigated apparent changes in viscosity associated with the addition of typical inorganic paper fillers (calcium carbonate, kaolin clay, and titanium dioxide) to “clean” pulps. Addition of calcium carbonate significantly increased apparent pulp viscosity, but clay and titanium dioxide had minimal effects. When high molecular weight sodium carboxymethyl cellulose (CMC) was added to the pulps, fillers had a minimal effect on viscosity. We determined that a non-cleaned recycled magazine pulp (OMG) makes a suitable model sludge for extrusion purposes. Various levels of OMG were added to a variety of clean pulps and the pulps were extruded. As the ratio of OMG in the feed composition increased, the extrusion conditions (screw torque and die pressure) were reduced significantly, as were tensile properties.

https://www.fpl.fs.fed.us/documnts/pdf1999/scott99b.pdf

Stefan Zauscher

Papers

HIV-1 Antibodies and Vaccine Antigen Selectively Interact with Lipid Domains

On-demand release of Candida albicans biofilms from urinary catheters by mechanical surface deformation.

Biological applications of polymer brushes

Self-Healing of Hyaluronic Acid to Improve In Vivo Retention and Function.

Rheology and extrusion of low-grade paper and sludge