Department of Chemistry

Indian Institute of Technology Palakkad&nbsp;(IIT Palakkad or IIT PKD) is a public autonomous&nbsp;engineering&nbsp;and&nbsp;research&nbsp;institute located in&nbsp;Palakkad,&nbsp;Kerala. It was&nbsp;one of the five new&nbsp;IITs&nbsp;proposed in the&nbsp;2014 Union budget of India. The campus was inaugurated on 3 August 2015. The institute has 94 faculty, 978 students, and 63 non-teaching staffs.

IT Palakkad currently offers four-year Bachelor of Technology (B.Tech) and two years MS programmes in 8 different engineering disciplines including&nbsp;Computer Science, Electrical, Mechanical, Civil among others.

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IIT Palakkad

A harmonic oscillator that evolves under the action of both a systematic time-dependent force and a random time-correlated force can do work w. This work is a random quantity, and Mai and Dhar have recently shown, using the generalized Langevin equation (GLE) for the oscillator's position x, that it satisfies a fluctuation theorem. In principle, the same result could have been derived from the Fokker-Planck equation (FPE) for the probability density function, P(x,w,t), for the oscillator being at x at time t, having done work w. Although the FPE equivalent to the above GLE is easily constructed and solved, one finds, unexpectedly, that its predictions for the mean and variance of w do not agree with the fluctuation theorem. We show that to resolve this contradiction, it is necessary to construct an FPE that includes the velocity of the oscillator, v, as an additional variable. The FPE for P(x,v,w,t) does indeed yield expressions for the mean and variance of w that agree with the fluctuation theorem. © 2008 IOP Publishing Ltd.

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Journal of Statistical Mechanics: Theory and Experiment

Resolving a puzzle concerning fluctuation theorems for forced harmonic oscillators in non-Markovian heat baths

Single system bi-functional inorganic-organic hybrid nanocomposites, PB@SiO2@BTC@Ln (PB = Prussian blue, BTC = benzene tricarboxylate; Ln = Tb(III)/Sm(III)) having a PB magnetic core and a luminescent lanthanide probe, show superparamagnetic behavior and significant enhancement in luminescence intensities. © 2008 The Royal Society of Chemistry.

Journal of Materials Chemistry

Construction of bi-functional inorganic-organic hybrid nanocomposites

In this report, we demonstrate glucose-derived carbon nanospheres to be an emerging class of intracellular carriers. The surfaces of these spheres are highly functionalized and do not need any further modification. Besides, the intrinsic fluorescence property of carbon nanospheres helps in tracking their cellular localization without any additional fluorescent tags. The spheres are found to target the nucleus of the mammalian cells, causing no toxicity. Interestingly, the in vivo experiments show that these nanospheres have an important ability to cross the blood-brain barrier and localize in the brain besides getting localized in the liver and the spleen. There is also evidence to show that they are continuously being removed from these tissues over time. Furthermore, these nanospheres were used as a carrier for the membrane-impermeable molecule CTPB (/V-(4-chloro-3-trifluoromethylphenyl)-2- ethoxybenzamide), the only known small-molecule activator of histone acetyltransferase (HAT) p300.2 Biochemical analyses such as Western blotting, immunohistochemistry, and gene expression analysis show the induction of the hyperacetylation of histone acetyltransferase (HAT) p300 (autoacetylation) as well as histones both in vitro and in vivo and the activation of HAT-dependent transcription upon CTPB delivery. These results establish an alternative path for the activation of gene expression mediated by the induction of HAT activity instead of histone deacetylase (HDAC) inhibition. © 2008 American Chemical.

Nano Letters

Intrinsically fluorescent carbon nanospheres as a nuclear targeting vector: delivery of membrane-impermeable molecule to modulate gene expression in vivo

The utility of an approximate heuristic version of Kramers' theory of reaction rates that was earlier used [Chaudhury and Cherayil, J. Chem. Phys. 125, 024904 (2006)] to successfully describe the nonexponential waiting time distributions of the enzyme Β -galactosidase is reassessed. The original model, based on the Smoluchowski equation, is reformulated in terms of the phase space variables of the reaction coordinate, without neglecting inertial contributions. A new derivation of the Fokker-Planck equation (FPE) that describes the dynamics of this coordinate is presented. This derivation, based on functional methods, provides a more direct alternative to the existing distribution function approach used by Hanggi and Mojtabai [Phys. Rev. A 26, 1168 (1982)]. The time-dependent coefficients in the FPE, when incorporated into the exact expression for the transmission coefficient obtained from a reactive-flux formalism [Kohen and Tannor, J. Chem. Phys. 103, 6013 (1995)], are found to yield virtually the same results as the earlier heuristic model. © 2008 American Institute of Physics.

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Journal of Chemical Physics

The dynamics of single enzyme reactions: A reconsideration of Kramers' model for colored noise processes

BCN nanotube brushes have been obtained by the high temperature reaction of amorphous carbon nanotube (a-CNT) brushes with a mixture of boric acid and urea. The a-CNT brushes themselves were obtained by the pyrolysis of glucose in a polycarbonate membrane. The BCN nanotubes have been characterized by EELS, XPS, electron microscopy, Raman spectroscopy and other techniques. The composition of these nanotubes is found to be BC4N. The nanotubes, which are stable up to 900 °C, are insulating and nonmagnetic. They exhibit a selective uptake of CO2 up to 23.5 wt%. In order to understand the structure and properties, we have carried out first-principles density functional theory based calculations on (6,0), (6,6) and (8,0) nanotubes with the composition BC4N. While (8,0) BC4N nanotubes exhibit a semiconducting gap, the (6,0) BC4N nanotube remains metallic if ordered BN bonds are present in all the six-membered rings. The (6,6) BC 4N nanotubes, however, exhibit a small semiconducting gap unlike the carbon nanotubes. The most stable structure is predicted to be the one where BN3 and NB3 units connected by a B-N bond are present in the graphite matrix, the structure with ordered B-N bonds in the six-membered rings of graphite being less stable. In the former structure, (6,0) nanotubes also exhibit a gap. The calculations predict BC4N nanotubes to be overall nonmagnetic, as is indeed observed. © The Royal Society of Chemistry.

Synthesis, structure and properties of homogeneous BC4N nanotubes

Amorphous carbon nanotube brushes were prepared by a simple method using glucose as the carbon precursor. The functional surfaces of these nanotubes were covered with gallium ions and then calcined to get gallium oxide nanotube brushes. The gallium oxide nanotube brushes were successfully converted to crystalline GaN nanotube brushes by treatment of ammonia at 800°C. The method is applicable to make other nanobrushes as well. © 2007 American Chemical Society.

Journal of Physical Chemistry C

Use of amorphous carbon nanotube brushes as templates to fabricate GaN nanotube brushes and related materials

The transient rupture and reformation of hydrogen bonds between base pairs on distinct chains of double-stranded DNA ("bubble" dynamics) is modeled in terms of the fluctuating distance between the bases. The fluctuations in the distance are assumed to be governed by a simple Langevin equation with a quadratic potential under conditions of high friction. A critical distance of separation L must be achieved before a bubble defect is considered to have been formed. The decay of the dynamic correlations between states of the DNA that have such defects and those that do not has been calculated from the above model and has been found to reproduce the trends in experimental measurements of the same quantity. © 2007 American Institute of Physics.

The dynamics of intermittent strand separation in double-stranded DNA

Pectin is an important structural polysaccharide found in the cell walls of all land plants. While in detail its composition and its organization in muro are complex, it is predominantly a copolymer of galacturonic acid and its methylesterified counterpart. Previous single-molecule stretching studies carried out on a sparsely methylesterified pectin sample indicated the importance of force-induced conformational transitions of the pyranose ring during extension, and the possible biological role of such transitions was discussed. More heavily methylesterified samples are better biomimetic models of the polymeric components as found in the plant cell wall, in particular being less restricted by the shackles of the significant intermolecular interactions expected to constrain the behavior of bare galacturonic acid sequences. Density functional theory calculations revealed that upon extending galacturonic acid monomers, whether methylesterified or not, the initial (C14) chair structure is transformed to a (S53) skew boat and that subsequently upon further elongation, via an intermediate inverted skew boat (S35), the inverted chair (C41) is reached. Experimentally, the force-extension curve of highly methylesterified pectin was found to be solvent dependent in the same manner as the un-esterified sample, indicating that minimal changes in the strength of interring hydrogen bonding result from such a substitution, and finally, as only subtle changes in the force-extension behavior of pectin resulted from changes in the degree of methylesterification, previous speculations about the role of force-induced transformations in vivo are supported. © 2007 The American Physical Society.

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Investigation of the effects of fine structure on the nanomechanical properties of pectin

Modification of important physicochemical properties of aqueous surfactant solutions can be achieved by addition of environmentally benign room temperature ionic liquids (ILs). While low aqueous solubility of "hydrophobic" ILs limits the amount of IL that may be added to achieve desired changes in the physicochemical properties, hydrophilic ILs do not have such restrictions associated to them. Alterations in the key physicochemical properties of aqueous solutions of a common nonionic surfactant Triton X-100 (TX100) on addition of up to 30 wt % hydrophilic IL 1-butyl-3-methylimidazolium tetrafluoroborate ([bmim] [B F4]) are reported. The presence of micellar aggregates in as high as 30 wt % [bmim] [B F4] -added aqueous TX100 solutions is established by dynamic light scattering and fluorescence probe behavior. Increasing the concentration of [bmim] [B F4] results in decrease in average micellar size and aggregation number and increase in critical micelle concentration, indicating an overall unfavorable aggregation process. Increase in the dipolarity and the microfluidity of the probe cybotactic region within the palisade layer of the micellar phase upon [bmim] [B F4] addition implies increased water penetration and the possibility of TX100- [bmim] [B F4] interactions. While the changes in some of the physicochemical properties indicate the role of [bmim] [B F4] to be similar to a cosurfactant, the IL acts like a cosolvent as far as changes in other properties are concerned. Effectiveness of IL [bmim] [B F4] in modifying physicochemical properties of aqueous TX100 is demonstrated. © 2007 American Institute of Physics.

Unique role of hydrophilic ionic liquid in modifying properties of aqueous Triton X-100

Use of vinyl acetate as acyl donor in transesterification of benzyl alcohol catalyzed by a commercially available lipase (Lipozyme® RM IM) gave 100% conversion in 10 min. The excess acyl donor and the enzyme could be recovered and reused. Unlike the chemical catalytic processes, it produced no undesirable side product. © 2006 Elsevier Ltd. All rights reserved.