There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality.

Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

I and i

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

Silver nanoparticles as a new generation of antimicrobials.

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.

Copper(I) n-alkane thiolate systems have been characterized using powder X-ray diffraction, IR spectroscopy, X-ray photoelectron spectroscopy and thermal analyses. The diffraction pattern is composed of a series of peaks, which are indexed to (0k0) reflections of a layered structure. The tilt angle, θ, of the alkyl chains is estimated to be 13°, distinctly different from the silver thiolates, where the chains are near normal to the silver plane. The layers interpenetrate to a small (or negligible) extent. The alkyl chain assembly is different from that of crystalline alkanes. An increase in the alkyl chain order with increase in chain length is evident in the infrared spectra. The chains are essentially all-trans, but gauche conformations are seen near the sulfur end. Upon cooling, an orientational transition occurs resulting in the freezing of the local symmetry around the methyl group. The materials show high thermal stability and desorption is seen only above 500 K. High temperature phase transitions of the materials have been studied by variable temperature powder XRD, variable temperature IR and differential scanning calorimetry. Two distinct transitions; one from an original gauche–trans
(g–t) to a gauche
(g) phase and another subsequent one, to a columnar mesophase, have been identified. The transitions are not fully reversible, conformational changes are observed upon heating and cooling. Thiolates appear to be model systems for the investigation of molecular self-assembly on copper surfaces.

http://www.dstuns.iitm.ac.in/listpdf/95.pdf

An investigation of the structure and properties of layered copper thiolates

https://www.dstuns.iitm.ac.in/listpdf/211.pdf

Manganese dioxide nanowhiskers: A potential adsorbent for the removal of Hg(II) from water

Visible light-active carbon-loaded anatase TiO2 (C-TiO2) nanocrystals of spherical, distorted spherical, rice grain and hexagonal morphologies, with a particle size range of 50–70 nm, have been synthesized by a rapid microwave-assisted route in the solution state. The morphology of these materials is greatly tuned at low concentrations of the precursors used. The absorption band gaps (Egap) are shifted to the visible region due to C loading, and the distorted spherical C-TiO2 exhibits a maximum energy shift relative to pure TiO2. Carbon gets deposited predominantly on the surface as graphitic carbon, in the preparative conditions, as confirmed by X-ray photoelectron, scanning electron microscopy elemental mapping and Raman spectroscopic studies. The rapid degradation of an endocrine disrupting agent and a persistent pollutant in wastewater, carbamazepine, by the rice grain shaped C-TiO2 is attributed to the large surface area (229 m2/g) of the particles and coexposure of the high surface energy and more r...

https://www.dstuns.iitm.ac.in/listpdf/331.pdf

Rapid Synthesis of C-TiO2: Tuning the Shape from Spherical to Rice Grain Morphology for Visible Light Photocatalytic Application

https://www.dstuns.iitm.ac.in/listpdf/205.pdf

Optical limiting properties of Te and Ag2Te nanowires

A method is described for assembling gold nanorods into one-, two-, and three-dimensional superstructures. The addition of dimercaptosuccinic acid (DMSA) into the nanorod solution was found to induce self-assembly of the latter to one-dimensional "tapelike", two-dimensional "sheetlike" and three-dimensional "superlattice-like" structures depending on the DMSA concentration. The assembly was found to follow a smectic structure, where the nanorod long axes are parallel to each other. The rods are spaced 8.5 +/- 0.3 nm apart in the resulting structures, which extend over several micrometers in length. Organizations perpendicular to the grid were also found. The nanorod tapes were found to bend, and they form circular assemblies as well. The assembly and morphology of the nanorod structures were characterized by transmission electron microscopy and UV-vis spectroscopy. The effect of the DMSA concentration as well as the pH of the medium was also studied. On the basis of several control experiments utilizing similar molecules, charge neutralization of the nanorods by the carboxylic group of DMSA was found to be the principal reason for such an assembly, while the mercapto groups render additional stability to its structure. A mechanistic model of the assembly is proposed. This type of assembly would plausibly function as a plasmonic waveguide in potential nanodevices.

Thalappil Pradeep

Papers

An investigation of the structure and properties of layered copper thiolates

Manganese dioxide nanowhiskers: A potential adsorbent for the removal of Hg(II) from water

Rapid Synthesis of C-TiO2: Tuning the Shape from Spherical to Rice Grain Morphology for Visible Light Photocatalytic Application

Optical limiting properties of Te and Ag2Te nanowires

One-, two-, and three-dimensional superstructures of gold nanorods induced by dimercaptosuccinic acid.