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.

We report the shape transformation of gold nanorods to spherical nanoparticles, assisted by cupric ions. The reaction proceeds through a series of structures and could be arrested at any stage to produce particles of desired shape. In the presence of a larger concentration of cetyltrimethylammonium bromide (CTAB), selective etching of the tips of the nanorods occurs to a greater extent. The subsequent transformation is driven by the surface reconstruction of nanorods to generate more stable surfaces. As the stability of various surfaces depends on the protecting agent used, the reactivity is modified by controlling its presence at the surface. We show that the body of the rods is more susceptible for reaction at reduced CTAB concentrations. During the conversion to particles, several anisotropic transient structures were observed and were imaged using high-resolution transmission electron microscopy (HRTEM). The transformation occurs due to the hydroxyl radicals produced by Cu 2+ in the presence of ascorbic acid (AA). A mechanism has been proposed and several control experiments were conducted to test it. The cupric ion induced shape transformations can be extended to other ions, and knowing the mechanism allows the control of the process to stabilize various anisotropic structures.

http://www.dstuns.iitm.ac.in/listpdf/156.pdf

Body- or tip-controlled reactivity of gold nanorods and their conversion to particles through other anisotropic structures

A facile and reversible method for assembling and disassembling gold nanorods (GNRs) using a common chelating agent, ethylenediaminetetraacetic acid (EDTA), is reported. Assembly was induced by the electrostatic interaction between the cetyltrimethylammonium bromide (CTAB) bilayer present on GNRs and EDTA. At lower concentrations of EDTA, end-to-end assembled chains were formed. At higher concentrations of EDTA, these chains come together to form sheet-like structures. The complex of CTAB and EDTA, being labile, disassembles in the presence of stronger chelating agents. Upon addition of metal ions having higher formation constants, EDTA detaches from the GNRs and forms stronger complexes with metal ions, resulting in disassembly. Characteristic changes were observed in the UV/vis spectra. Addition of EDTA resulted in a red shift of longitudinal surface plasmon (LSP) resonance at lower concentrations, indicating an end-to-end assembly. At higher concentrations, the characteristic of side-by-side assembly was seen in the UV/vis spectra. TEM analysis proved the existence of end-to-end chains at lower concentrations of EDTA and side-by-side assembled sheet-like structures at higher concentrations. The addition of metal ions induced disassembly. Even 2 ppb of metal ion was detected using the spectral changes. Disassembly was studied in detail, taking Pb(II) as the model system. Upon addition of Pb(II), TSP showed a blue shift and decreased in intensity while the LSP showed a red shift and increased in intensity. A new peak at a higher wavelength region emerged, pointing to the existence of both side-by-side and end-to-end assembly in the system. TEM analysis showed that the disassembly involves the formation of bundled chains which may be the reason for the observed spectral changes. Surface-enhanced Raman scattering (SERS) activity of the system could be tuned by controlling the concentration of EDTA and the metal ion, Pb(II).

https://www.dstuns.iitm.ac.in/listpdf/228_SI.pdf

Reversible assembly and disassembly of gold nanorods induced by EDTA and its application in SERS tuning.

This paper explores the reduction of water dispersed graphene oxide (GO) by sunlight as an environmentally friendly alternative to conventional methods of reduction of GO. The possible mechanism of the reduction process is delineated. The electrical and thermal conductivity, the degree of reduction and structural defects of sunlight reduced GO (sRGO) are studied thoroughly and compared with RGO samples produced through hydrazine (hRGO) and hydrothermal (hyRGO) reduction routes. The study reveals that the production of sRGO is feasible and its electronic properties are on a par with those of hRGO. Interestingly, sRGO showed the least structural defects, good dispersibility and higher conductivity vis-a-vis its counterparts. This cost effective and environmentally friendly method of reducing GO to RGO with enhanced electronic properties may find applications in bio-sensing and electrochemical energy storage devices.

/pdf/solar-mediated-reduction-of-graphene-oxide-3wodpeqrrv.pdf

Solar mediated reduction of graphene oxide

A new solvothermal method for the synthesis of thiol-protected silver nanoparticles starting from silver thiolates is reported. The method has been tried with thiols of different chain length, such as octane and octadecane thiols, and the particle size was found to be nearly the same for both molecules. The synthesis was dependent on heating conditions and the best results were obtained when the temperature was between 180 and 200 °C. Addition of complexation agents such as acetyl acetone or triethylamine to the solvent did not change the product distribution significantly.

http://www.dstuns.iitm.ac.in/listpdf/112.pdf

Solvothermal synthesis of silver nanoparticles from thiolates

We report the evolution and confinement of atomically precise and luminescent gold clusters in a small protein, lysozyme (Lyz) using detailed mass spectrometric (MS) and other spectroscopic investigations. A maximum of 12 Au0 species could be bound to a single Lyz molecule irrespective of the molar ratio of Lyz : Au3+ used for cluster growth. The cluster-encapsulated protein also forms aggregates similar to the parent protein. Time dependent studies reveal the emergence of free protein and the redistribution of detached Au atoms, at specific Lyz to Au3+ molar ratios, as a function of incubation time, proposing inter-protein metal ion transfer. The results are in agreement with the studies of inter-protein metal transfer during cluster growth in similar systems. We believe that this study provides new insights into the growth of clusters in smaller proteins.

/pdf/protein-encapsulated-gold-cluster-aggregates-the-case-of-4yxaxjb6l2.pdf

Thalappil Pradeep

Papers

Body- or tip-controlled reactivity of gold nanorods and their conversion to particles through other anisotropic structures

Reversible assembly and disassembly of gold nanorods induced by EDTA and its application in SERS tuning.

Solar mediated reduction of graphene oxide

Solvothermal synthesis of silver nanoparticles from thiolates

Protein-encapsulated gold cluster aggregates: the case of lysozyme