@article { ISI:000326122800047, title = {Characterization of conformation and interaction of gene delivery vector polyethylenimine with phospholipid bilayer at different protonation state}, journal = {Biomacromolecules}, volume = {14}, number = {10}, year = {2013}, month = {OCT}, pages = {3759-3768}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

Polyethylenimine (PEI) is a pH sensitive polymer possessing stretched and coiled conformation at low and high pH, respectively. It is an efficient gene delivery agent. Thus, the interaction of PEI with the biomembrane is very crucial to understand the gene delivery mechanism. In this report, we have investigated the structural properties of PEI and bilayer due to the interaction of PEI with lipid molecules. PEI has coil structure at high pH while at low pH it is elongated. The neutral PEI chain predominately settles itself at the bilayer water interface. We do not find any disruption or pore formation on the bilayer due to interaction of neutral PEI chain. PEI at low pH gets elongated due to electrostatic interaction between charges of the protonated sites. This protonated PEI chain interacts with bilayer membrane, which leads to formation of water/ion channel through the membrane. We have analyzed the structure of the channel and water dynamics along the channel.

}, issn = {1525-7797}, doi = {10.1021/bm4011408}, author = {Choudhury, Chandan Kumar and Kumar, Abhinaw and Roy, Sudip} } @article { ISI:000313077100009, title = {Characterization of the structures and dynamics of phosphoric acid doped benzimidazole mixtures: a molecular dynamics study}, journal = {Journal of Molecular Modeling}, volume = {19}, number = {1}, year = {2013}, month = {JAN}, pages = {109-118}, publisher = {SPRINGER}, address = {233 SPRING ST, NEW YORK, NY 10013 USA}, abstract = {

Benzimidazole-based polymer membranes like poly(2,5-benzimidazole) (ABPBI) doped with phosphoric acid (PA) are electrolytes that exhibit high proton conductivity in fuel cells at elevated temperatures. The benzimidazole (BI) moiety is an important constituent of these membranes, so the present work was performed in order to achieve a molecular understanding of the BI-PA interactions in the presence of varying levels of the PA dopant, using classical molecular dynamics (MD) simulations. The various hydrogen-bonding interactions, as characterized based on structural properties and hydrogen-bond lifetime calculations, show that both BI and PA molecules exhibit dual proton-acceptor/donor functionality. An examination of diffusion coefficients showed that the diffusion of BI decreases with increasing PA uptake, whereas the diffusion of PA slightly increases. The hydrogen-bond lifetime calculations pointed to the existence of competitive hydrogen bonding between various sites in BI and PA.

}, keywords = {Diffusion coefficient, Hydrogen bond, molecular dynamics, Radial distribution functions}, issn = {1610-2940}, doi = {10.1007/s00894-012-1519-8}, author = {More, Minal and Pahari, Swagata and Roy, Sudip and Venkatnathan, Arun} } @article { ISI:000357192200003, title = {Compact polar moieties induce lipid-water systems to form discontinuous reverse micellar phase}, journal = {Soft Matter}, volume = {11}, number = {27}, year = {2015}, month = {MAY}, pages = {5417-5424}, publisher = {ROYAL SOC CHEMISTRY}, address = {THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND}, abstract = {

The role of molecular interactions in governing lipid mesophase organization is of fundamental interest and has technological implications. Herein, we describe an unusual pathway for monoolein/water reorganization from a bicontinuous mesophase to a discontinuous reverse micellar assembly, directed by the inclusion of polar macromolecules. This pathway is very different from those reported earlier, wherein the Fd3m phase formed only upon addition of apolar oils. Experiments and molecular dynamics simulations indicate that hydrophilic ternary additives capable of inducing discontinuous phase formation must (i) interact strongly with the monoolein head group and (ii) have a compact molecular architecture. We present a detailed investigation that contrasts a monoolein-water system containing polyamidoamine (PAMAM) dendrons with one containing their linear analogs. The Fd3m phase forms only on the addition of PAMAM dendrons but not their linear analogs. Thus, the dendritic architecture of PAMAM plays an important role in determining lipid mesophase behavior. Both dendrons and their linear analogs interact strongly with monoolein through their amine groups. However, while linear polymers adsorb and spread on monoolein, dendrons form aggregates that interact with the lipid. Dendrons induce formation of an intermediate reverse hexagonal phase, which subsequently restructures into the Fd3m phase. Finally, we demonstrate that other additives with compact structures that are known to interact with monoolein, such as branched polyethylenimine and polyhedral silsesquioxane cages, also induce the formation of the Fd3m phase.

}, issn = {1744-683X}, doi = {10.1039/c5sm00854a}, author = {Kumar, Manoj and Patil, Naganath G. and Choudhury, Chandan Kumar and Roy, Sudip and Ambade, Ashootosh V. and Kumaraswamy, Guruswamy} } @article {45521, title = {Comparison of different water models for melting point calculation of methane hydrate using molecular dynamics simulations}, journal = {Chemical Physics}, volume = {516}, year = {2019}, month = {JAN }, pages = {6-14}, type = {Article}, abstract = {

Molecular dynamics simulation is a powerful tool to understand the gas hydrate nucleation, growth, and dissociation at molecular level. Prerequisite of super-cooling during gas hydrate formation and a certain degree of super-healing during melting shows significant hysteresis in the transition between solid and liquid state due to large nucleation barrier. Different water models quantitatively differ in their prediction of thermodynamic and kinetic properties of bulk water, including phase behaviour. The present work carries out a systematic investigation of the effect of the chosen water model on the phase behaviour, in particular, the decomposition of methane hydrate. Void-induced melting has been used to predict the melting point of methane hydrate using TIP4P/Ice, TIP4P/2005, TIP4P, and SPC/E water models. This method avoids the need for a predetermined interface for melting point calculations and thus may have its importance in identifying dissociation kinetics of bulk hydrate.

}, keywords = {decomposition, Gas hydrates, Void-induced melting, Water models}, issn = {0301-0104}, doi = {10.1016/j.chemphys.2018.08.036}, author = {Choudhary, Nilesh and Chakrabarty, Suman and Roy, Sudip and Kumar, Rajnish} }