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.

Nucleolin-aptamer therapy in retinoblastoma: molecular changes and mass spectrometry–based imaging

Abstract: Retinoblastoma (RB) is an intraocular childhood tumor which, if left untreated, leads to blindness and mortality. Nucleolin (NCL) protein which is differentially expressed on the tumor cell surface, binds ligands and regulates carcinogenesis and angiogenesis. We found that NCL is over expressed in RB tumor tissues and cell lines compared to normal retina. We studied the effect of nucleolin-aptamer (NCL-APT) to reduce proliferation in RB tumor cells. Aptamer treatment on the RB cell lines (Y79 and WERI-Rb1) led to significant inhibition of cell proliferation. Locked nucleic acid (LNA) modified NCL-APT administered subcutaneously (s.c.) near tumor or intraperitoneally (i.p.) in Y79 xenografted nude mice resulted in 26 and 65% of tumor growth inhibition, respectively. Downregulation of inhibitor of apoptosis proteins, tumor miRNA-18a, altered serum cytokines, and serum miRNA-18a levels were observed upon NCL-APT treatment. Desorption electrospray ionization mass spectrometry (DESI MS)-based imaging of cell lines and tumor tissues revealed changes in phosphatidylcholines levels upon treatment. Thus, our study provides proof of concept illustrating NCL-APT-based targeted therapeutic strategy and use of DESI MS-based lipid imaging in monitoring therapeutic responses in RB.

Manifestation of the Difference in Reactivity of Silver Clusters in Contrast to Its Ions and Nanoparticles: The Growth of Metal Tipped Te Nanowires

Abstract: Reactivity of two different nanosystems of silver, namely nanoparticles and atomically precise clusters, toward 1D tellurium nanowires (NWs) was probed and compared with the reaction of silver ions. While the reaction of nanoparticles and ions led to silver telluride nanowires, a different reactivity was exhibited by clusters which resulted in silver islands at different positions on the Te NWs. These hybrid Ag nodule-decorated Te NWs are sensitive to temperature, and they transform to dumbbell-shaped silver-tipped Te NWs upon solution phase annealing. Differences in chemical reactivity of nanoparticles of two different size regimes with nanowires are demonstrated. Synthetic methods of this kind will be useful in creating complex nanostructures which are difficult to be made in the solution phase.

Interconversions of Structural Isomers of [PdAu8(PPh3)8]2+ and [Au9(PPh3)8]3+ Revealed by Ion Mobility Mass Spectrometry

Abstract: Collision cross sections (CCSs) of ligand-protected metal clusters were evaluated using ion mobility mass spectrometry The targets used in this study were phosphine-protected clusters [PdAu8(PPh3)8]2+ and [Au9(PPh3)8]3+, for which the total structures have been resolved by single-crystal X-ray analysis The arrival time distributions of [PdAu8(PPh3)8]2+ as a function of the He flow rate in a cell located just in front of a traveling wave ion mobility cell filled with N2 buffer gas demonstrated that it got converted to another structural isomer having a smaller CCS, with the increase in the nominal collision energy A similar phenomenon was observed for [Au9(PPh3)8]3+ These results were explained by the collisional excitation and cooling with the buffer gas inducing the conversion of the packing arrangement of the ligands rather than the atomic structure of the metallic core: the ligand layer was converted from disordered to the closely packed arrangement found in a single crystal during this process Th

Chemical interactions at noble metal nanoparticle surfaces — catalysis, sensors and devices

Abstract: In this paper, a summary of some of the recent research efforts in our laboratory on chemical interactions at noble metal nanoparticle surfaces is presented. The article is divided into five sections, detailing with (i) interactions of simple halocarbons with gold and silver nanoparticle surfaces at room temperature by a new chemistry and the exploitation of this chemistry in the extraction of pesticides from drinking water, (ii) interaction of biologically important proteins such as Cyt c, hemoglobin and myoglobin as well as a model system, hemin with gold and silver nanoparticles and nanorods forming nano–bio conjugates and their surface binding chemistry, (iii) formation of polymer–nano composites with tunable optical properties and temperature sensing characteristics by single and multi-step methodologies, (iv) nanomaterials-based flow sensors and (v) composites of noble metal nanoparticles and metallic carbon nanotubes showing visible fluorescence induced by metal–semiconductor transition.

Covalent chemical modification of self‐ assembled fluorocarbon monolayers by low‐ energy CH2Br2+· ions: a combined ion/surface scattering and X‐ray photoelectron spectroscopic investigation

Abstract: Specific covalent chemical modification at the outermost atomic layers of fluorinated self-assembled monolayers (F-SAMs) on gold is achieved by bombardment with low-energy polyatomic ions ( 2 Br 2 +· (m/z 172), mass and energy selected using a hybrid ion/surface scattering mass spectrometer and scattered from the F-SAM surface, CF 3 (CF 2 ) 7 (CH 2 ) 2 -S-Au, undergoes ion/surface reactions evident from the nature of the scattered ions, CH 2 F + (m/z 33), CHBrF + (m/z 111), and CF 2 Br + (m/z 129). The chemical transformation of the reactive F-SAM surface was independently monitored by in situ chemical sputtering with the projectile Xe +· . Representative species sputtered from the modified surface include CF 2 Br + , an indicator of terminal CF 3 to CF 2 Br conversion. X-ray photoelectron spectroscopy (XPS) was used to confirm the presence of organic bromine at the surface; Br ( 3 P 3/2 ) and Br ( 3 P ½ ) peaks were present at binding energies of 182 and 190 eV, respectively. XPS analysis also revealed increased surface modification at higher collision energies in these reactive ion bombardment experiments, as exemplified by the increased hydrocarbon/fluorocarbon peak ratio in the C(1s) region and incorporation of oxygen in the surface seen in the observation of an O(1s) peak.

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.