Thalappil Pradeep

Bio: Thalappil Pradeep is an academic researcher from Indian Institute of Technology Madras. The author has contributed to research in topics: Cluster (physics) & Mass spectrometry. The author has an hindex of 76, co-authored 581 publications receiving 24664 citations. Previous affiliations of Thalappil Pradeep include DST Systems & Lawrence Berkeley National Laboratory.

Polymorphism of Ag29(BDT)12(TPP)43− cluster: interactions of secondary ligands and their effect on solid state luminescence

Abstract: We present the first example of polymorphism (cubic & trigonal) in single crystals of an atomically precise monolayer protected cluster, Ag29(BDT)12(TPP)43-. We demonstrate that C-Hπ interactions of the secondary ligands (TPP) are dominant in a cubic lattice compared to a trigonal lattice, resulting in a greater rigidity of the structure, which in turn, results in a higher luminescence efficiency in it.

Pristine and Hybrid Nickel Nanowires: Template-, Magnetic Field-, and Surfactant-Free Wet Chemical Synthesis and Raman Studies

Abstract: Nickel nanowires of high purity and various aspect ratios were synthesized by a wet chemical reduction method without the assistance of surfactants, templates, and external magnetic field. The observed unique optical absorption features of nickel nanowires are highly dependent on the nanowire dimensions. In order to tailor the physical and chemical properties of the nanowires, we have incorporated functionalities in the form of tellurium and zinc oxide coating on them by overgrowth processes using simple wet chemical reactions. The pristine and functional nanowires were characterized by different microscopic and spectroscopic techniques such as scanning electron microscopy (SEM), transmission electron microscopy (TEM), confocal Raman microscopy, X-ray diffraction spectroscopy (XRD), and UV−visible spectroscopy. Our system provides additional details into the growth of anisotropic Ni nanowires, especially in the absence of surfactants, templates, and external magnetic field. We have also demonstrated surfa...

Enhancement in the efficiency of polymerase chain reaction by TiO2 nanoparticles: crucial role of enhanced thermal conductivity.

Abstract: Improvement of the specificity and efficiency of the polymerase chain reaction (PCR) by nanoparticles is an emerging area of research. We observed that TiO2 nanoparticles of ∼25 nm diameter caused significant enhancement of PCR efficiency for various types of templates (namely plasmid DNA, genomic DNA and complementary DNA). By a series of experiments, the optimal TiO2 concentration was determined to be 0.4 nM, which resulted in up to a seven-fold increase in the amount of PCR product. As much as 50% reduction in overall reaction time (by reduction of the number of cycles and the time periods of cycles) was also achieved by utilizing TiO2 nanoparticles without compromising the PCR yield. Investigations of the mechanism of such PCR enhancement by simulations using the ‘Fluent K epsilon turbulent model’ provided evidence of faster heat transfer in the presence of TiO2 nanoparticles. Consistent with these findings, TiO2 nanoparticles were observed to augment the denaturation of genomic DNA, indicating more efficient thermal conductivity through the reaction buffer. TiO2 nanoparticle-assisted PCR may be useful for profound reduction of the overall PCR reaction period and for enhanced amplification of DNA amplicons from a variety of samples, including GC-rich templates that are often observed to yield unsatisfactory results. (Some figures in this article are in colour only in the electronic version)

Au22Ir3(PET)18: An Unusual Alloy Cluster through Intercluster Reaction

Abstract: An intercluster reaction between Au25(PET)18 and Ir9(PET)6 producing the alloy cluster, Au22Ir3(PET)18 exclusively, is demonstrated where the ligand PET is 2-phenylethanethiol. Typical reactions of this kind between Au25(PET)18 and Ag25(SR)18, and other clusters reported previously, produce mixed cluster products. The cluster composition was confirmed by detailed high-resolution electrospray ionization mass spectrometry (ESI MS) and other spectroscopic techniques. This is the first example of Ir metal incorporation in a monolayer-protected noble metal cluster. The formation of a single product was confirmed by thin layer chromatography (TLC). Density functional theory (DFT) calculations suggest that the most favorable geometry of the Au22Ir3(PET)18 cluster is one wherein the three Ir atoms are arranged triangularly with one Ir atom at the icosahedral core and the other two on the icosahedral shell. Significant contraction of the metal core was observed due to strong Ir–Ir interactions.

I and i

Abstract: 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 …

Fast parallel algorithms for short-range molecular dynamics

Abstract: 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.

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

Abstract: 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。

Gold nanoparticles in chemical and biological sensing.

Abstract: 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.