S K Nath

Ambient and Elevated Temperature Geopolymerization Behaviour of Class F Fly Ash

Geopolymerization is the process, where synthetic alkali activated alumino-silicate material is produced by reaction of a solid alumino-silicate with a highly concentrated aqueous alkali hydroxide or silicate solution. Depending on the raw material selection and processing conditions, geopolymers can exhibit a wide variety of properties and characteristics, including high compressive strength, fast or slow setting, acid resistance, and fire resistance. Fly ash, a by-product of coal fired power plant, is produced during combustion of coal. Fly ash is a powdery, aluminosilicate material along with minor impurities which is suitable for geopolymer reaction. The geopolymerization behaviour of class F fly ash has been studied in a temperature range of 27°-55°C using isothermal conduction calorimeter with different alkali concentrations. It was observed that the rate of reaction got intensified and increased with temperature. Compressive strength of the resulting geopolymer was also found to increase with temperature more significantly during early days. Attempt has been made to correlate the reaction with structure and properties.

Statistical mechanics of DNA rupture: Theory and simulations

We study the effects of the shear force on the rupture mechanism on a double stranded DNA. Motivated by recent experiments, we perform the atomistic simulations with explicit solvent to obtain the distributions of extension in hydrogen and covalent bonds below the rupture force. We obtain a significant difference between the atomistic simulations and the existing results in the literature based on the coarse-grained models (theory and simulations). We discuss the possible reasons and improve the coarse-grained model by incorporating the consequences of semi-microscopic details of the nucleotides in its description. The distributions obtained by the modified model (simulations and theoretical) are qualitatively similar to the one obtained using atomistic simulations.

Statistical mechanics of a polymer chain attached to the interface of a cone-shaped channel

A polymer chain confined in nano-scale geometry has been used to investigate the underlying mechanism of Nuclear Pore Complex (NPC), where transport of cargoes is directional. It was shown here that depending on the solvent quality (good or poor) across the channel, a polymer chain can be either inside or outside the channel or both. Exact results based on the short chain revealed that a slight variation in the solvent quality can drag polymer chain inside the pore and {it vice versa} similar to one seen in NPC. Furthermore, we also report the absence of crystalline (highly dense) state when the pore-size is less than the certain value, which may have potential application in packaging of DNA inside the preformed viral proheads.

Rupture of DNA aptamer: New insights from simulations

Base-pockets (non-complementary base-pairs) in a double-stranded DNA play a crucial role in biological processes. Because of thermal fluctuations, it can lower the stability of DNA, whereas, in case of DNA aptamer, small molecules, e.g., adenosinemonophosphate and adenosinetriphosphate, form additional hydrogen bonds with base-pockets termed as binding-pockets, which enhance the stability. Using the Langevin dynamics simulations of coarse grained model of DNA followed by atomistic simulations, we investigated the influence of base-pocket and binding-pocket on the stability of DNA aptamer. Striking differences have been reported here for the separation induced by temperature and force, which require further investigation by single molecule experiments.

Force-induced rupture of double-stranded DNA in the absence and presence of covalently bonded anti-tumor drugs: Insights from molecular dynamics simulations

DNA intra-strand cross-link (ICL) agents are widely used in the treatment of cancer. ICLs are thought to form a link between the same strand (intra-strand) or complimentary strand (inter-strand) and thereby increase the stability of DNA, which forbids the processes like replication and transcription. As a result, cell death occurs. In this work, we have studied the enhanced stability of a double stranded DNA in the presence of ICLs and compared our findings with the results obtained in the absence of these links. Using atomistic simulations with explicit solvent, a force is applied along and perpendicular to the direction of the helix and we measured the rupture force and the unzipping force of DNA-ICL complexes. Our results show that the rupture and the unzipping forces increase significantly in the presence of these links. The ICLs bind to the minor groove of DNA, which enhance the DNA stabilisation. Such information may be used to design alternative drugs that can stall replication and transcription that are critical to a growing number of anticancer drug discovery efforts.

Single polymer gating of channels under a solvent gradient.

We study the effect of a gradient of solvent quality on the coil-globule transition for a polymer in a narrow pore. A simple self-attracting, self-avoiding walk model of a polymer in solution shows that the variation in the strength of the interaction across the pore leads the system to go from one regime (good solvent) to the other (poor solvent) across the channel. This may be thought to be analogous to thermophoresis, where the polymer goes from the hot region to the cold region under the temperature gradient. The behavior of short chains is studied using exact enumeration while the behavior of long chains is studied using transfer matrix techniques. The distribution of the monomer density across the layer suggests that a gatelike effect can be created, with potential applications as a sensor.