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

Detection of chemical and biological agents plays a fundamental role in biomedical, forensic and environmental sciences1–4 as well as in anti bioterrorism applications.5–7 The development of highly sensitive, cost effective, miniature sensors is therefore in high demand which requires advanced technology coupled with fundamental knowledge in chemistry, biology and material sciences.8–13

In general, sensors feature two functional components: a recognition element to provide selective/specific binding with the target analytes and a transducer component for signaling the binding event. An efficient sensor relies heavily on these two essential components for the recognition process in terms of response time, signal to noise (S/N) ratio, selectivity and limits of detection (LOD).14,15 Therefore, designing sensors with higher efficacy depends on the development of novel materials to improve both the recognition and transduction processes. Nanomaterials feature unique physicochemical properties that can be of great utility in creating new recognition and transduction processes for chemical and biological sensors15–27 as well as improving the S/N ratio by miniaturization of the sensor elements.28

Gold nanoparticles (AuNPs) possess distinct physical and chemical attributes that make them excellent scaffolds for the fabrication of novel chemical and biological sensors (Figure 1).29–36 First, AuNPs can be synthesized in a straightforward manner and can be made highly stable. Second, they possess unique optoelectronic properties. Third, they provide high surface-to-volume ratio with excellent biocompatibility using appropriate ligands.30 Fourth, these properties of AuNPs can be readily tuned varying their size, shape and the surrounding chemical environment. For example, the binding event between recognition element and the analyte can alter physicochemical properties of transducer AuNPs, such as plasmon resonance absorption, conductivity, redox behavior, etc. that in turn can generate a detectable response signal. Finally, AuNPs offer a suitable platform for multi-functionalization with a wide range of organic or biological ligands for the selective binding and detection of small molecules and biological targets.30–32,36 Each of these attributes of AuNPs has allowed researchers to develop novel sensing strategies with improved sensitivity, stability and selectivity. In the last decade of research, the advent of AuNP as a sensory element provided us a broad spectrum of innovative approaches for the detection of metal ions, small molecules, proteins, nucleic acids, malignant cells, etc. in a rapid and efficient manner.37



Figure 1

Physical properties of AuNPs and schematic illustration of an AuNP-based detection system.



In this current review, we have highlighted the several synthetic routes and properties of AuNPs that make them excellent probes for different sensing strategies. Furthermore, we will discuss various sensing strategies and major advances in the last two decades of research utilizing AuNPs in the detection of variety of target analytes including metal ions, organic molecules, proteins, nucleic acids, and microorganisms.

/pdf/gold-nanoparticles-in-chemical-and-biological-sensing-5e2qojkdzn.pdf

Gold nanoparticles in chemical and biological sensing.

Metal–organic frameworks (MOFs) are a unique class of crystalline solids comprised of metal cations (or metal clusters) and organic ligands that have shown promise for a wide variety of applications Over the past 15 years, research and development of these materials have become one of the most intensely and extensively pursued areas A very interesting and well-investigated topic is their optical emission properties and related applications Several reviews have provided a comprehensive overview covering many aspects of the subject up to 2011 This review intends to provide an update of work published since then and focuses on the photoluminescence (PL) properties of MOFs and their possible utility in chemical and biological sensing and detection The spectrum of this review includes the origin of luminescence in MOFs, the advantages of luminescent MOF (LMOF) based sensors, general strategies in designing sensory materials, and examples of various applications in sensing and detection

Luminescent metal–organic frameworks for chemical sensing and explosive detection

http://users.encs.concordia.ca/~mojtaba/elec6271/silver%20nanoparticles.pdf

Silver nanoparticles: green synthesis and their antimicrobial activities.

Fluorescent carbon-based materials have drawn increasing attention in recent years owing to exceptional advantages such as high optical absorptivity, chemical stability, biocompatibility, and low toxicity. These materials primarily include carbon dots (CDs), nanodiamonds, carbon nanotubes, fullerene, and fluorescent graphene. The superior properties of fluorescent carbon-based materials distinguish them from traditional fluorescent materials, and make them promising candidates for numerous exciting applications, such as bioimaging, medical diagnosis, catalysis, and photovoltaic devices. Among all of these materials, CDs have drawn the most extensive notice, owing to their early discovery and adjustable parameters. However, many scientific issues with CDs still await further investigation. Currently, a broad series of methods for obtaining CD-based materials have been developed, but efficient one-step strategies for the fabrication of CDs on a large scale are still a challenge in this field. Current synthetic methods are mainly deficient in accurate control of lateral dimensions and the resulting surface chemistry, as well as in obtaining fluorescent materials with high quantum yields (QY). Moreover, it is important to expand these kinds of materials to novel applications. Herein, a facile and highoutput strategy for the fabrication of CDs, which is suitable for industrial-scale production (yield is ca. 58%), is discussed. The QY was as high as ca. 80%, which is the highest value recorded for fluorescent carbon-based materials, and is almost equal to fluorescent dyes. The polymer-like CDs were converted into carbogenic CDs by a change from low to high synthesis temperature. The photoluminescence (PL) mechanism (high QY/PL quenching) was investigated in detail by ultrafast spectroscopy. The CDs were applied as printing ink on the macro/micro scale and nanocomposites were also prepared by polymerizing CDs with certain polymers. Additionally, the CDs could be utilized as a biosensor reagent for the detection of Fe in biosystems. The CDs were prepared by a hydrothermal method, which is described in the Supporting Information (Figure 1a; see also the Supporting Information, Figure S1). The reaction was conducted by first condensing citric acid and ethylenediamine, whereupon they formed polymer-like CDs, which were then carbonized to form the CDs. The morphology and structure of CDs were confirmed by analysis. Figure 1b shows transmission electron microscopy (TEM) images of the CDs, which can be seen to have a uniform dispersion without apparent aggregation and particle diameters of 2–6 nm. The sizes of CDs were also measured by atomic force microscopy (AFM; Figure S2), and the average height was 2.81 nm. From the high-resolution TEM, most particles are observed to be amorphous carbon particles without any lattices; rare particles possess well-resolved lattice fringes. With such a low carbon-lattice-structure content, no obvious D or G bands were detected in the Raman spectra of the CDs (Figure S3). The XRD patterns of the CDs (Figure 1c) also displayed a broad peak centered at 258 (0.34 nm), which is also attributed to highly disordered carbon atoms. Moreover, NMR spectroscopy (H and C) was employed to distinguish sp-hybridized carbon atoms from sp-hybridized carbon atoms (Figure S4). In the H NMR spectrum, sp carbons were detected. In the C NMR spectrum, signals in the range of 30–45 ppm, which correspond to aliphatic (sp) carbon atoms, and signals from 100–185 ppm, which are indicative of sp carbon atoms, were observed. Signals in the range of 170– 185 ppm, which correspond to carboxyl/amide groups, were also present. In the FTIR analysis of CDs, the following were observed: stretching vibrations of C OH at 3430 cm 1 and C H at 2923 cm 1 and 2850 cm , asymmetric stretching vibrations of C-NH-C at 1126 cm , bending vibrations of N H at 1570 cm , and the vibrational absorption band of C=O at 1635 cm 1 (Figure S5). Moreover, the surface groups were also investigated by XPS analysis (Figure 1d). C1s analysis revealed three different types of carbon atoms: graphitic or aliphatic (C=C and C C), oxygenated, and nitrous (Table S1). In the UV/Vis spectra, the peak was focused on 344 nm in an aqueous solution of CDs. In the fluorescence spectra, CDs have optimal excitation and emission wavelengths at 360 nm and 443 nm, and show a blue color under a hand-held UV lamp (Figure 2a). Excitation-dependent PL behavior was [*] S. Zhu, Q. Meng, Prof. J. Zhang, Y. Song, Prof. K. Zhang, Prof. B. Yang State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University Changchun, 130012 (P. R. China) E-mail: byangchem@jlu.edu.cn

Highly Photoluminescent Carbon Dots for Multicolor Patterning, Sensors, and Bioimaging

Photoluminescent Graphene Oxide Ink to Print Sensors onto Microporous Membranes for Versatile Visualization Bioassays

Analytical techniques based on surface-enhanced Raman scattering (SERS) suffer from a lack of reproducibility and reliability, thus hampering their practical applications. Herein, we have developed a SERS-active substrate based on a graphene oxide embedded sandwich nanostructure for ultrasensitive Raman signal readout. By using this novel Au@Ag NPs/GO/Au@Ag NPs sandwich nanostructure as a SERS substrate, the Raman signals of analytes were dramatically enhanced due to having plenty of hot spots on their surfaces and the unique structure of the graphene oxide sheets. These features make the sandwich nanostructured film an ideal SERS substrate to improve the sensitivity, reproducibility and reliability of the Raman readout. The sandwich nanostructure film can be applied to detect rhodamine-6G (R6G) with an enhancement factor (EF) of ∼7.0 × 107 and the pesticide thiram in commercial grape juice with a detection limit of as low as 0.1 μM (0.03 ppm), which is much lower than the maximal residue limit (MRL) of 7 ppm in fruit prescribed by the U.S. Environmental Protection Agency (EPA). The GO embedded sandwich nanostructure also has the ability to selectively detect dithiocarbamate compounds over other types of agricultural chemical. Furthermore, spiked tests show that the sandwich nanostructure can be used to monitor thiram in natural lake water and commercial grape juice without further treatment. In addition, the GO enhanced Raman spectroscopic technique offers potential practical applications for the on-site monitoring and assessment of pesticide residues in agricultural products and environments.

Graphene oxide embedded sandwich nanostructures for enhanced Raman readout and their applications in pesticide monitoring

The white backlight in displays is generated by optimizing the proportions of individual emitters with different wavelengths by variations in materials composition, phase, and structure. Color pixels usually result from the separation of white light or the excitation with multiwavelength or multipulse sources. However, it is a challenge to develop a material that comprises a single structure and emits over the full visible spectrum, but where the emission wavelengths can be controlled by a simple excitation source. Herein, we report an upconversion nanostructure that incorporates several lanthanide ions in the same core@shell@shell structure. The combination of multiple narrow spectral bands results in the emission of white light. The emission colors can be tuned by changing the excitation power density, which manipulates the photon transfer pathways. Applications such as flat-panel displays and imaging have been demonstrated.

White-Light Emission from an Integrated Upconversion Nanostructure: Toward Multicolor Displays Modulated by Laser Power

A new “turn on” fluorescence nanosensor for selective Hg2+ determination is reported based on bis(dithiocarbamato)copper(II) functionalized carbon nanodots (CuDTC2-CDs). The CuDTC2 complex was conjugated to the prepared amine-coated CDs by the condensation of carbon disulfide onto the nitrogen atoms in the surface amine groups, followed by the coordination of copper(II) to the resulting dithiocarbamate groups (DTC) and finally by the additional coordination of ammonium N-(dithicarbaxy) sarcosine (DTCS) to form the CuDTC2-complexing CDs. The CuDTC2 complex at surface strongly quenched the bright-blue fluorescence of the CDs by a combination of electron transfer and energy transfer mechanism. Hg2+ could immediately switch on the fluorescence of the CuDTC2-CDs by promptly displacing the Cu2+ in the CuDTC2 complex and thus shutting down the energy transfer pathway, in which the sensitive limit for Hg2+ as low as 4 ppb was reached. Moreover, a paper-based sensor has been fabricated by printing the CuDTC2-CDs p...

Zhongping Zhang

Papers

Photoluminescent Graphene Oxide Ink to Print Sensors onto Microporous Membranes for Versatile Visualization Bioassays

Graphene oxide embedded sandwich nanostructures for enhanced Raman readout and their applications in pesticide monitoring

White-Light Emission from an Integrated Upconversion Nanostructure: Toward Multicolor Displays Modulated by Laser Power

Fluorescence “Turn On” Detection of Mercuric Ion Based on Bis(dithiocarbamato)copper(II) Complex Functionalized Carbon Nanodots

Single‐Hole Hollow Polymer Microspheres toward Specific High‐Capacity Uptake of Target Species