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.

In vitro colocalization of plasmonic nano-biolabels and biomolecules using plasmonic and Raman scattering microspectroscopy

Abstract: An insight into the intracellular fate of theranostics is important for improving their potential in biological applications. In vivo efficacy of plasmonic theranostics depends on our ability to monitor temporal changes in their size, shape, and state of aggregation, and the identification of molecules adsorbed on their surfaces. We develop a technique which combines plasmonic and Raman scattering microspectroscopy to colocalize plasmonic scattering from metallic nanoparticles with the Raman signatures of biomolecules adsorbed on the surface of the former. Using this technique, we have colocalized biomolecules with the plasmonic scattering from silver nanoparticles in the vicinity of Escherichia coli bacteria. To prove the applicability of this setup for the measurements on mammalian cells, imaging of HEK293 cells treated with gold nanoparticles was per- formed. We discuss the importance of such correlated measurements over individual techniques, although the latter may lead to misinterpretation of results. Finally, with the above-mentioned examples, we have given criteria to improve the specificity of theranostics. We believe that this methodology will be considered as a prime development in the assessment of theranostics. © 2015 Society of Photo-Optical Instrumentation Engineers

Molecular Engineering of Atomically Precise Silver Clusters into 2D and 3D Framework Solids

Abstract: : Two- and three-dimensional (2D and 3D) atomically precise nanocluster (NC)-based metal − organic frameworks (MOFs) with properties richer than those of NCs themselves are emerging materials. However, fabricating such materials with good stability has not been easy. In this work, a facile synthetic strategy was employed for t h e c r e a t i o n o f s i l v e r N C − M O F s s t a r t i n g f r o m [Ag 12 (TBT) 7 (TFA) 4 (CH 3 CN) 6 ] + , facilitated by heterocyclic amines, 4,4 ′ -bipyridine (bpy) and pyrazine (pyz), via metal − metal and metal-sul fi de rearrangement reactions, where TBT and TFA are tertiar-ybutylthiolate and tri fl uoroacetate, respectively. In one of the reactions, the pyz ligand facilitates the formation of a 2D framework with a trigonal crystal system, which exhibits high stability and emits bright green luminescence at low temperatures. Owing to its facile synthesis, good stability, e ffi cient luminescence, uniform porosity, and layered structure, the resultant hexagonal 2D nanosheets can be e ffi ciently exfoliated from parent crystals. The 2D nanosheets are structurally similar to graphene. A top-down approach was employed for the exfoliation of stable 2D nanosheets with lateral dimensions in the range of 0.156 μ m. In another case, the bpy ligand induces the construction of a 3D framework with an orthorhombic crystal system. Owing to its interpenetrated AB ··· AB structure, robustness, and e ffi cient green luminescence at room temperature, the resultant 3D MOF is capable of functioning as a high-performance luminescent sensor for selective detection of explosive analogues, 2-nitrotoluene and 2,4-dinitrotoluene, with excellent recyclability. However, in the absence of the heterocyclic amines, a pristine AgNC was formed. Time-dependent density functional theory calculations were employed to understand the mechanism of energy transfer in AgNC-MOFs. Our strategy o ff ers an unprecedented approach in which heterocyclic amines facilitate intramolecular rearrangement reactions, resulting in 2D and 3D atomically precise NC framework materials. This work not only demonstrates the creation of 2D and 3D materials but also provides new insights into the critical surface coordination chemistry controlled by heterocyclic amines for de fi ning the morphology and properties of cluster frameworks. were collected in a low-dose mode on a JEM-3200FSC fi eld-emission cryo-electron microscope (JEOL Ltd.) with an Omega-type zero-loss energy fi lter operated at 300 kV. The images were acquired with Gatan DigitalMicrograph software, maintaining the specimen temper- ature at − 187 ° C to minimize beam-induced damage. Thin-Film Preparation. Quartz (or glass) slides with a dimension of 16 mm × 16 mm were rinsed with acetone and kept in an oven for 1 h at 80 ° C to remove any traces of impurities. Thin fi lms were prepared using a drop-casting method at room temperature. For this, a solution containing ( 2 ) was fi ltered to obtain a clear solution. A few droplets of this transparent solution were slowly dropped at the four vertices of the slide until the solution was spread to cover the entire slide. These were left for air drying to obtain a thin coating of AgNC- MOF, which was used to detect nitroaromatics.

Growth of anisotropic gold nanostructures on conducting glass surfaces

Abstract: In this paper, we describe a method for the growth of gold nanowires and nanoplates starting from a bilayer array of gold seeds, anchored on electrically conducting indium tin oxide (ITO) substrates. This is based on a seed-mediated growth approach, where the nanoparticles attached on the substrate through molecular linkages are converted to nanowires and nanoplates at certain cetyltrimethylammonium bromide (CTAB) concentration. Our modified approach can be used to make nanowires of several tens of micrometers length at a lower CTAB concentration of 0.1 M. The length of the nanowires can be varied by adjusting the time of the reaction. As the concentration of CTAB was increased to 0.25 M, the nanoparticles got converted to nanoplates. These Au nanoplates are (111) oriented and are aligned parallel to the substrate.

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.