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Ekta Khurana

Publications and source records attributed to Ekta Khurana.

3 recordsLinked to original sources

Gemini surfactants at the air/water interface: a fully atomistic molecular dynamics study.

Gemini surfactants typically consist of two single-chain surfactants chemically linked by a spacer molecule. We report herein the results of fully atomistic molecular dynamics (MD) simulations of a series of Gemini surfactants: CsH2s-alpha,omega-bis(C12H25N+(CH3)2Cl-), at the air/water interface with s = 3, 4, 6, 12, 14, and 16, at values of the initial surface area per surfactant AS = 70 A2, 77 A2, 95 A2, 151 A2, 133 A2, and 103 A2, respectively. The AS values employed were obtained from surface tension and neutron reflection experiments at the respective cmc of each surfactant. The Gemini surfactant corresponding to s = 3 was also simulated at AS = 105 A2, which is the experimentally derived value of surface area per surfactant at 1/10th of cmc. Only the surfactants with s = 12 and 14 and the surfactant with s = 3 at AS = 105 A2 gave a stable monolayer at the air/water interface. In other cases, we observe movement of some surfactant molecules from the air/water interface into the aqueous phase, resulting in a stable primary monolayer of surfactants at the air/water interface and a small concentration of surfactant molecules below it. The latter form aggregates, with their hydrophobic chains in the core. The density profiles along the normal to the interface are compared with the ones obtained from neutron reflection experiments. The MD simulations confirm the bending of the spacer toward the hydrophobic chains as the spacer length is increased and the spacer becomes more hydrophobic. The simulations have helped to shed light on the low-resolution picture which emerges from experimental analyses.

Air↗

Self-assembling cyclic peptides: molecular dynamics studies of dimers in polar and nonpolar solvents.

The self-assembly of cyclic D,L-alpha-peptides into hollow nanotubes is a crucial mechanistic step in their application as antibacterial and drug-delivery agents. To understand this process, molecular dynamics (MD) simulations were performed on dimers of cyclic peptides formed from cyclo [(-L-Trp-D-N-MeLeu-)4-]2 and cyclo [(-L-Trp-D-Leu-)4-]2 subunits in nonpolar (nonane) and polar (water) solvent. The dimers were observed to be stable only in nonpolar solvent over the full 10 ns length of the MD trajectory. The behavior of the dimers in different solvents is rationalized in terms of the intersubunit hydrogen bonding, hydrogen bonding with the solvent, and planarity of the rings. It is shown that the phi and psi dihedral angles of a single uncapped ring in nonane lie in the beta-sheet region of the Ramachandran plot, and the ring stays in a flat conformation. Steered MD (SMD) simulations based on Jarzynski's equality were performed to obtain the potential of mean force as a function of the distance between the two rings of the capped dimer in nonane. It is also shown that a single peptide subunit prefers to reside close to the nonane/water interface rather than in bulk solvent because of the amphiphilic character of the peptide ring. The present MD results build the foundation for using MD simulations to study the mechanism of the formation of cyclic peptide nanotubes in lipid bilayers.

Dimerization↗

A physicochemical model for analyzing DNA sequences.

In search of an ab initio model to characterize DNA sequences as genes and nongenes, we examined some physicochemical properties of each trinucleotide (codon), which could accomplish this task. We constructed three-dimensional vectors for each double-helical trinucleotide sequence considering hydrogen-bonding energy, stacking energy, and a third parameter, which we provisionally identified with DNA-protein interactions. As this three-dimensional vector moves along any genome, the net orientation of the resultant vector should differ significantly for gene and nongene regions to make a distinction feasible, if the underlying model has some merits. An analysis of 331 prokaryotic genomes comprising a total of 294 786 experimentally verified genes (nonoverlapping) and an equal number of nongenes presents a proof of concept of the model without the need for further parametrization. Also, initial analyses on Saccharomyces cerevisiae and Arabidopsis thaliana suggest that the methodology is extendable to eukaryotes. The physicochemical model (ChemGenome1.0) introduced has the potential to be developed into a gene-finding algorithm and, more pressingly, could be employed for an independent assessment of the annotation of DNA sequences.

Bacteria↗