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

Stimulus-responsive biomolecules have attracted a large research interest because of their potential application in various areas such as drug delivery, actuators and sensing devices at the nanoscale. Using single-molecule force spectroscopy (SMFS) we studied elastin-like polypeptides (ELPs). These stimulus-responsive polypeptides undergo an inverse temperature transition, accompanied by a large conformational change, when the solvent quality is changed by increasing the temperature or by addition of salt. Understanding the relationship between peptide sequence and mechanisms of force generation can provide a route to engineer ELPs with desirable mechano-chemical properties. Here we studied the effect of solvent quality and type of guest residue on the mechanical properties of ELPs on the single-molecule level. We used a statistical approach to estimate polymer elasticity parameters from model fits to the data. With this approach we were able to resolve small changes in the Kuhn segment length distributions associated with different molecular architectures. We then show that these mechanical differences likely arise from differences in the hydrophobic hydration of sidegoups, in line with recent predictions from molecular dynamics simulations.

Polypeptide-Solvent Interactions Measured by Single Molecule Force Spectroscopy

Pulp extrusion at ultra-high consistency ( 30% solids) has been shown to be a viable process for converting recovered paper, wastepaper, and papermill residues into solid sheets and profiles. We have previously shown that extrusion of ultra-high consistency pulps and “model” sludges requires the addition of a water-soluble polymer (WSP) to alter the rheological properties of the pulp such that an homogenous “pulp paste” can be formed and extruded. This paper discusses our attempts to evaluate the viability of extruding a variety of papermill sludges. Several sludges were acquired from various mills and classified by ash content, contaminant level, and biological activity. Various blends of sludge, newsprint (ONP), and WSP were prepared and extruded into continuous sheets. The sheets were then cut into strips for consolidation by press drying. These strips were further cut into coupons for tensile testing. The results showed that a variety of sludges could be successfully extruded with adequate tensile strength. However, the presence of contaminants (e.g., chips, staples, plastics, silica) and interfering chemistries posed some difftculties in processing these residues.

https://www.fpl.fs.fed.us/documnts/pdf2000/scott00b.pdf

Pulp extrusions incorporating sludge from the pulp and paper industry

Stimulus-responsive polymers and polypeptides (SRPs) experience a significant entropic response when exposed to an environemental stimulus, such as a change in temperature. This phase transition directly affects polymer conformation and can potentially be harnessed for force generation in actuation devices on nano- and micro-scales. While interfacial applications of SRPs have been prototypically demonstrated, a systematic investigation of the phase transition behavior at the solid-liquid interface and on the single-molecule level is lacking. In this paper we present results from force-spectroscopy measurements probing the force-extension and conformational behavior of one SRP, elastin-like polypeptides (ELP), below and above their transition temperature. The results indicate that there is no signficant difference in the force extension behavior at intermediate and large extensions, but the behavior is dramatically different at small extensions. Results also demonstrated that above the phase transition temperature large, unspecific adhesion forces often gave way to constant force steps upon extension, indicating a collapsed, potentially entangled, hydrophobic state of the ELP. The extension behavior below the phase transition temperature, however, closely followed that of random polymer coil, without any significant unspecific adhesion forces. The excellent fit of a simple extended freely jointed chain model to the data at intermediate and large extension suggests that the ELP is in a random conformational state without significant secondary structure. Forces associated with a phase transition therefore arise likely from entropic conformational changes associated with a hydrophobic collapse.

Conformational mechanics of stimulus-responsive polypeptides

Throughout a lifetime, articular joints experience many loading cycles and are prone to mechanical degradation. To safeguard the cartilage in these joints, synovial fluid acts as a natural lubricant. However, degenerative joint diseases, like osteoarthritis, alter the composition of synovial fluid, diminishing its protective properties. In such cases, exogenous lubricants or viscosupplements can be injected to enhance the compromised synovial fluid's function. Scientists are now developing next-generation viscosupplements, based on hyaluronic acid (HA), that can better bind to and adhere to cartilage. Additionally, non-HA-based viscosupplements offer benefits over HA-based ones, as they possess more intricate molecular architectures, such as dendrimer or bottlebrush-like structures. These viscosupplements draw inspiration from natural molecules present in synovial fluid, providing them with a distinct advantage. 

Progress in the design and synthesis of viscosupplements for articular joint lubrication

(2) The first demonstration of the in situ fabrication of stimuli responsive polypeptide nanostructures [2]. We have demonstrated that a genetically engineered stimuli responsive Elastin-like polypeptide (ELP) can be nanopatterned by DPN and that these biopolymer nanostructures exhibit a “smart” hydrophilic-hydrophobic phase transition at the surface. ELP nanopatterns with feature sizes ranging from 200 nm to 2.5 mm were fabricated by this method on gold surfaces. We also demonstrated that these smart nanostructures could reversibly bind a target protein of interest from solution by triggering the phase transition of the ELP on the surface. Nanopatterning with stimulusresponsive -smartbiopolymers holds significant promise for the fabrication of devices for biotechnology applications that require the capture of a target protein directly from a complex mixture and for devices where the transport, separation and detection of many biomacromolecules must be performed in aqueous solutions, with applications in biosensors and proteomic chips, and nanofluidic devices.

/pdf/fabrication-of-biomolecular-and-polymeric-nanostructures-by-17iuyadmtg.pdf

Stefan Zauscher

Papers

Polypeptide-Solvent Interactions Measured by Single Molecule Force Spectroscopy

Pulp extrusions incorporating sludge from the pulp and paper industry

Conformational mechanics of stimulus-responsive polypeptides

Progress in the design and synthesis of viscosupplements for articular joint lubrication

Fabrication of Biomolecular and Polymeric Nanostructures by Proximal Probes