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.

Unprecedented inhibition of tubulin polymerization directed by gold nanoparticles inducing cell cycle arrest and apoptosis

Abstract: The effect of gold nanoparticles (AuNPs) on the polymerization of tubulin has not been examined till now. We report that interaction of weakly protected AuNPs with microtubules (MTs) could cause inhibition of polymerization and aggregation in the cell free system. We estimate that single citrate capped AuNPs could cause aggregation of ∼105 tubulin heterodimers. Investigation of the nature of inhibition of polymerization and aggregation by Raman and Fourier transform-infrared (FTIR) spectroscopies indicated partial conformational changes of tubulin and microtubules, thus revealing that AuNP-induced conformational change is the driving force behind the observed phenomenon. Cell culture experiments were carried out to check whether this can happen inside a cell. Dark field microscopy (DFM) combined with hyperspectral imaging (HSI) along with flow cytometric (FC) and confocal laser scanning microscopic (CLSM) analyses suggested that AuNPs entered the cell, caused aggregation of the MTs of A549 cells, leading to cell cycle arrest at the G0/G1 phase and concomitant apoptosis. Further, Western blot analysis indicated the upregulation of mitochondrial apoptosis proteins such as Bax and p53, down regulation of Bcl-2 and cleavage of poly(ADP-ribose) polymerase (PARP) confirming mitochondrial apoptosis. Western blot run after cold-depolymerization revealed an increase in the aggregated insoluble intracellular tubulin while the control and actin did not aggregate, suggesting microtubule damage induced cell cycle arrest and apoptosis. The observed polymerization inhibition and cytotoxic effects were dependent on the size and concentration of the AuNPs used and also on the incubation time. As microtubules are important cellular structures and target for anti-cancer drugs, this first observation of nanoparticles-induced protein's conformational change-based aggregation of the tubulin–MT system is of high importance, and would be useful in the understanding of cancer therapeutics and safety of nanomaterials.

Clean Water through Nanotechnology: Needs, Gaps, and Fulfillment

Abstract: Sustainable nanotechnology has made substantial contributions in providing contaminant-free water to humanity. In this Review, we present the compelling need for providing access to clean water through nanotechnology-enabled solutions and the large disparities in ensuring their implementation. We also discuss the current nanotechnology frontiers in diverse areas of the clean water space with an emphasis on applications in the field and provide suggestions for future research. Extending the vision of sustainable and affordable clean water to environment in general, we note that cities can live and breathe well by adopting such technologies. By understanding the global environmental challenges and exploring remedies from emerging nanotechnologies, sustainability in clean water can be realized. We suggest specific pointers and quantify the impact of such technologies.

The Superstable 25 kDa Monolayer Protected Silver Nanoparticle: Measurements and Interpretation as an Icosahedral

Abstract: A cluster obtained in high yield from the reduction of a silver-thiolate precursor, Ag-SCH2CH2Ph, exhibited a single sharp peak near 25 kDa in the matrix-assisted laser desorption mass spectrum (MALDI MS) and a well- defined metal core of ∼2 nm measured with transmission electron microscopy (TEM). The cluster yields a single fraction in high-performance liquid chromatography (HPLC). Increased laser fluence fragments the cluster until a new peak near 19 kDa predominates, suggesting that the parent cluster Ag152(SCH2CH2Ph)60evolves into a stable inorganic core Ag152S60. Exploiting combined insights from investigations of clusters and surface science, a core−shell structure model was developed, with a 92-atom silver core having icosahedral- dodecahedral symmetry and an encapsulating protective shell containing 60 Ag atoms and 60 thiolates arranged in a network of six-membered rings resembling the geometry found in self-assembled monolayers on Ag(111). The structure is in agreement with small-angle X-ray scattering (SAXS) data. The protective layer encapsulating this silver cluster may be the smallest known three-dimensional self-assembled monolayer. First-principles electronic structure calculations show, for the geometry-optimized structure, the development of a ∼0.4 eV energy gap between the highest-occupied and lowest-unoccupied states, originating from a superatom 90-electron shell-closure and conferring stability to the cluster. The optical absorption spectrum of the cluster resembles that of plasmonic silver nanoparticles with a broad single feature peaking at 460 nm, but the luminescence spectrum shows two maxima with one attributed to the ligated shell and the other to the core.

Structure-conserving spontaneous transformations between nanoparticles.

Abstract: Ambient, structure- and topology-preserving chemical reactions between two archetypal nanoparticles, Ag25(SR)18 and Au25(SR)18, are presented. Despite their geometric robustness and electronic stability, reactions between them in solution produce alloys, AgmAun(SR)18 (m+n=25), keeping their M25(SR)18 composition, structure and topology intact. We demonstrate that a mixture of Ag25(SR)18 and Au25(SR)18 can be transformed to any arbitrary alloy composition, AgmAun(SR)18 (n=1-24), merely by controlling the reactant compositions. We capture one of the earliest events of the process, namely the formation of the dianionic adduct, (Ag25Au25(SR)36)2-, by electrospray ionization mass spectrometry. Molecular docking simulations and density functional theory (DFT) calculations also suggest that metal atom exchanges occur through the formation of an adduct between the two clusters. DFT calculations further confirm that metal atom exchanges are thermodynamically feasible. Such isomorphous transformations between nanoparticles imply that microscopic pieces of matter can be transformed completely to chemically different entities, preserving their structures, at least in the nanometric regime.

Low-energy ionic collisions at molecular solids.

Abstract: ion mechanism, discussed in section 1.1.2. Figure 27 illustrates the reactive scattering mechanism with four representative snapshots of a Cs scattering trajectory in a classical MD simulation. The abstraction reaction is driven by the ion−dipole attraction force between the Cs ion and an adsorbate molecule. The impinging projectile first releases part of its initial energy to the surface (Figure 27b) even without direct collision with the adsorbate. Subsequently, the projectile pulls the adsorbate gently away from the surface in its outgoing trajectory (parts c and d of Figures 27 in sequence), leading to the formation of a Cs−molecule complex. The velocity of the outgoing Cs must be slow enough to accommodate the inertia of the adsorbate. As a result, adsorbates of low mass and small binding energy are efficiently abstracted. A heavier projectile like Cs transfers more energy to the target surface, and its lower velocity in the outgoing trajectory enhances the efficiency of reactive scattering events. Detailed aspects of Cs reactive scattering and its application for surface analysis have been reviewed. Table 9. Hyperthermal Energy Collisions at Condensed Molecular Solids method (projectile ion) system aim/observations refs reactive scattering and LES (Cs) H2O−D2O rate and activation energy of self-diffusion and H/D exchange of water 462, 476, 479, 496 H3O −water ice affinity of protons for the ice surface and proton transfer mechanism 478−480 H3O −H2O−D2O hydronium ion-mediated proton transfer at the ice surface 495 OH−H2O−D2O hydroxide ion-mediated proton transfer at the ice surface 497 HCl−water ice molecular and ionized states of HCl on ice 457, 477 Na−water ice hydrolysis of Na 484 H3O −NH3−water ice incomplete proton transfer from H3O to NH3 on the ice surface 454, 458 H3O −amine−water ice proton transfer efficiency on ice is reversed from the order of amine basicity 502 CO2−Na−water ice CO2 hydrolysis is not facilitated by a hydroxide ion 463 NO2−water ice NO2 hydrolysis produces nitrous acid 465 SO2−water ice SO2 hydrolysis occurs through various intermediates 511 C2H4−HCl−water ice electrophilic addition reaction mechanism at the condensed molecular surface 466 ethanol/2-methylpropan-2-ol−water ice SN1 and SN2 mechanisms at the condensed molecular surface 505 NH3−water ice and UV irradiation ammonium ion formation 608 CH3NH2−water ice and UV irradiation protonated methylamine formation 483 CH3NH2−CO2−water ice and UV irradiation glycine and carbamic acid formation 464 NaX−water ice (X = F, Cl, Br) surface/bulk segregation and transport properties of electrolyte ions 472−474 reactive scattering (Cs) CO and CO2 on Pt(111) mechanism of Cs + reactive ion scattering 89 Ar, Kr, Xe, and N2 on Pt(111) adsorbate mass effect on the reactive ion scattering cross-section 609 C2H4 on Pt(111) dehydrogenation mechanism of ethylene to ethylidyne 459, 610 C2D4 and H on Pt(111) ethylidene intermediate in H/D exchange reaction with ethylene 80, 610 reactive scattering (H) water ice and alcohol H2 + formation 469 CS (Ar) water ice−chloromethanes (CCl4, CHCl3, CH2Cl2) except CCl4, others undergo diffusive mixing 174 water ice−simple carboxylic acids structural reorganization on the ice film 175 water ice micropore collapse in the top layers of the ice film 176 water ice−butanol 494 Figure 27. Illustration of the reactive scattering mechanism of a Cs ion in four snapshots of a scattering trajectory from a Pt(111) surface: (a) initial positions before impact, (b) impact of the Cs and energy release to the surface, (c) Cs pulling the adsorbate away in its outgoing trajectory, (d) slow outgoing Cs dragging the adsorbate along and forming a Cs−molecule association product. Reprinted with permission from ref 88. Copyright 2004 John Wiley and Sons, Inc. Chemical Reviews Review dx.doi.org/10.1021/cr200384k | Chem. Rev. 2012, 112, 5356−5411 5388 Figure 28 shows an example of reactive collision mass spectra, which were obtained on a D2O ice film exposed first to 0.5 L of HCl gas and then to varying amounts of NH3 gas at 140 K. The spectra show peaks at higher masses than Cs (m/z 133), viz., CsNH3 + at m/z 150, Cs(D2O)n + (n = 1, 2) at m/z 153 and 173, and CsHCl at m/z 168, indicating the presence of the corresponding molecules on the surface. The intensities of H/D-exchanged species represent their original concentrations on the surface, because H/D isotopic scrambling does not occur during the ion/surface collision time (<1 × 10−12 s). The conversion efficiency of a neutral adsorbate (X) into a gaseous ion (CsX) ranges from ∼10−4 for chemisorbed species to ∼0.1 for physisorbed small molecules. Typical product ion signal intensities for ice film surfaces are much stronger than those for chemisorbed species. Also, it is worthwhile to point out that reactive collisions of Cs are ineffective for detecting large molecules such as polymers or long-chain SAM molecules. The mass spectra in Figure 28 also show LES signals corresponding to pre-existing ions on the surface. The hydronium ions seen are produced by the spontaneous ionization of HCl on the ice surface, and they undergo proton transfer reactions with NH3 to generate ammonium ions. The spectra show characteristic H/D isotopomers of each species produced by H/D exchange reactions with D2O molecules. The LES signals due to preformed hydronium and ammonium ions exhibited sputtering thresholds at Cs impact energies of 17 and 19 eV, respectively. On the other hand, on pure H2O and NH3 surfaces, these ions were emitted only above ∼60 eV due to their formation during secondary ion emission. It was also found that ultra-low-energy (a few electronvolts) collision of H with the ice surface can produce H2 +. The reaction proceeds more efficiently on amorphous solid water than crystalline water, reflecting differences in the surface concentration of dangling O−H bonds. Simple alkanols also behave in the same manner. The combined occurrence of reactive scattering and LES provides a powerful means to probe both neutral molecules and ions on surfaces and, therefore, to follow reactions on ice surfaces such as the ionization of electrolytes and acid−base reactions, which are described below. 7.2. Surface Composition and Structure Impurities in ice become concentrated in the quasi-liquid layers in the surface and at grain boundary regions due to the “freeze concentration effect”, and this has important consequences for atmospheric reactions on ice surfaces. However, there appear to be numerous exceptions to this general trend, where the surface segregation behavior of the dissolving species and their bulk solubility are determined by thermodynamic factors specific to individual chemical species. A good example is the formation of stable bulk phases of clathrate hydrates. Chemical specificity in the segregation phenomena can be studied by monitoring the surface populations of the dissolving species during the slow annealing of ice samples. Kang and coworkers examined these propensities in Na and halide ions at the surface and in the interior of ice films. They ionized NaF, NaCl, and NaBr molecules on ice films by the vapor deposition of the salts, and the variation in the surface population of the ions was monitored as a function of the ice temperature for 100−140 K by using LES. As shown in Figure 29, the LES intensities of Na and F− ions decrease with an increase in temperature above ∼120 K, whereas the Cl− and Br− intensities remain unchanged. The results indicate that Na and F− ions migrate from the ice surface to the interior at the elevated temperatures. The migration process is driven Figure 28. Cs reactive scattering and LES spectra monitoring the H3O −NH3 reaction on ice. The D2O film [3−4 bilayers (BLs), 1 BL = 1.1 × 10 water molecules cm−2] was exposed first to 0.5 L of HCl to generate hydronium ions and then to NH3 at varying exposures: (a) 0.02 L, (b) 0.3 L, (c) 0.7 L. The sample temperature was 100 K. The Cs collision energy was 30 eV. Reprinted with permission from ref 454. Copyright 2001 John Wiley and Sons, Inc. Figure 29. Surface populations of Na (□), F− (▲), Cl− (◇), and Br− (●) ions as a function of the ice film temperature measured from LES intensities of the ions. NaF, NaCl, and NaBr were deposited for a coverage of 0.8 ML for each salt on a D2O ice film grown at 130 K. The LES signals were measured at the indicated temperatures of salt adsorption. The LES intensities are shown on the normalized scale with the intensity at 100−105 K as a reference. The Cs beam energy was 35 eV. The figure is drawn on the basis of the data in refs 473 and 474. Chemical Reviews Review dx.doi.org/10.1021/cr200384k | Chem. Rev. 2012, 112, 5356−5411 5389 by the ion solvation energy, and it requires that surface water molecules have enough mobility to facilitate ion passage at temperatures above 120 K. It is worth noting that such a segregation behavior for ice agrees with the negative adsorption energy of these ions at water surfaces predicted by the Gibbs surface tension equation and MD simulations. An interesting property of hydronium ions observed in recent studies is that they preferentially reside at the surface of ice rather than in its interior. Evidence of this property has come from a variety of experimental observations over the past decade. The adsorption and ionization of HCl on an ice film promotes H/D exchange on the surface. However, vertical proton transfer to the film interior is inefficient. Continuous exposure of HCl gas on the ice film led to saturation in the hydronium ion population at the surface, and the amount of HCl uptake required for this saturation was independent of the thickness of the ice film. These observations suggest that protons stay at the ice surface and hardly migrate to the interior. This behavior can be attributed either to the active trapping of protons at the surface or to the lack of proton mobility to the ice interior. The observation of asymmetric

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.