Santosh Mogurampelly

Computer Simulations of Ion Transport in Polymer Electrolyte Membranes

Understanding the mechanisms and optimizing ion transport in polymer membranes have been the subject of active research for more than three decades. We present an overview of the progress and challenges involved with the modeling and simulation aspects of the ion transport properties of polymer membranes. We are concerned mainly with atomistic and coarser level simulation studies and discuss some salient work in the context of pure binary and single ion conducting polymer electrolytes, polymer nanocomposites, block copolymers, and ionic liquid-based hybrid electrolytes. We conclude with an outlook highlighting future directions.

Engagement of CF3 group in N-H···F-C hydrogen bond in the solution state: NMR spectroscopy and MD simulation studies.

Unambiguous evidence for the engagement of CF(3) group in N-H···F-C hydrogen bond in a low polarity solvent, the first observation of its kind, is reported. The presence of such weak molecular interactions in the solution state is convincingly established by one and two-dimensional (1)H, (19)F, and natural abundant (15)N NMR spectroscopic studies. The strong and direct evidence is derived by the observation of through-space couplings, such as, (1h)J(FH), (1h)J(FN), and (2h)J(FF), where the spin polarization is transmitted through hydrogen bond. In an interesting example of a molecule containing two CF(3) groups getting simultaneously involved in hydrogen bond, where hydrogen bond mediated couplings are not reflected in the NMR spectrum, (19)F-(19)F NOESY experiment yielded confirmatory evidence. Significant deviations in the strengths of (1)J(NH), variable temperature, and the solvent induced perturbations yielded additional support. The NMR results are corroborated by both DFT calculations and MD simulations, where the quantitative information on different ways of involvement of fluorine in two and three centered hydrogen bonds, their percentage of occurrences, and geometries have been obtained. The hydrogen bond interaction energies have also been calculated.

Unraveling siRNA unzipping kinetics with graphene.

Using all atom molecular dynamics simulations, we report spontaneous unzipping and strong binding of small interfering RNA (siRNA) on graphene. Our dispersion corrected density functional theory based calculations suggest that nucleosides of RNA have stronger attractive interactions with graphene as compared to DNA residues. These stronger interactions force the double stranded siRNA to spontaneously unzip and bind to the graphene surface. Unzipping always nucleates at one end of the siRNA and propagates to the other end after few base-pairs get unzipped. While both the ends get unzipped, the middle part remains in double stranded form because of torsional constraint. Unzipping probability distributions fitted to single exponential function give unzipping time (τ) of the order of few nanoseconds which decrease exponentially with temperature. From the temperature variation of unzipping time we estimate the energy barrier to unzipping.

Translocation and encapsulation of siRNA inside carbon nanotubes

We report spontaneous translocation of small interfering RNA (siRNA) inside carbon nanotubes (CNTs) of various diameters and chirality using all atom molecular dynamics simulations with explicit solvent. We use umbrella sampling method to calculate the free energy landscape of the siRNA entry and translocation event. Free energy profiles show that siRNA gains free energy while translocating inside CNT, and barrier for siRNA exit from CNT ranges from 40 to 110 kcal/mol depending on CNT chirality and salt concentration. The translocation time τ decreases with the increase of CNT diameter with a critical diameter of 24 Å for the translocation. In contrast, double strand DNA of the same sequence does not translocate inside CNT due to large free energy barrier for the translocation. This study helps in understanding the nucleic acid transport through nanopores at microscopic level and may help designing carbon nanotube based sensor for siRNA.

Mechanisms Underlying Ion Transport in Polymerized Ionic Liquids

We report the results of atomistic molecular dynamics simulations informed by quantum-mechanically parametrized force fields, which identify the mechanisms underlying ion motion and diffusivities in poly(1-butyl-3-vinylimidazolium-hexafluorophosphate) polymerized ionic liquid (polyIL) electrolytes. Our results demonstrate that anion transport in polyILs occurs through a mechanism involving intra- and intermolecular ion hopping through formation and breaking of ion-associations involving four polymerized cationic monomers bonded to two different polymer chains. The resulting ion mobilities are directly correlated to the average lifetimes of the ion-associations. Such a trend is demonstrated to contrast with the behavior in pure ILs, wherein structural relaxations and the associated times are dominant mechanism. Our results establish the basis for experimental findings that reported ion transport in polyILs to be decoupled from polymer segmental relaxations.

Elasticity of DNA and the effect of dendrimer binding

Abstract.Negatively charged DNA can be compacted by positively charged dendrimers and the degree of compaction is a delicate balance between the strength of the electrostatic interaction and the elasticity of DNA. We report various elastic properties of short double-stranded DNA (dsDNA) and the effect of dendrimer binding using fully atomistic molecular dynamics and numerical simulations. In equilibrium at room temperature, the contour length distribution P(L) and the end-to-end distance distribution P(R) are nearly Gaussian, the former gives an estimate of the stretch modulus

Influence of nanoparticle-ion and nanoparticle-polymer interactions on ion transport and viscoelastic properties of polymer electrolytes

\gamma_{1}

Structure and mechanisms underlying ion transport in ternary polymer electrolytes containing ionic liquids

of dsDNA in quantitative agreement with the literature value. The bend angle distribution

Phonons and thermal conducting properties of borocarbonitride (BCN) nanosheets

P(\theta)

Particle-Based Modeling of Living Actin Filaments in an Optical Trap

of the dsDNA also has a Gaussian form and allows to extract a persistence length, Lp of 43nm. When the dsDNA is compacted by positively charged dendrimer, the stretch modulus stays invariant but the effective bending rigidity estimated from the end-to-end distance distribution decreases dramatically due to backbone charge neutralization of dsDNA by dendrimer. We support our observations with numerical solutions of the worm-like-chain (WLC) model as well as using non-equilibrium dsDNA stretching simulations. These results are helpful in understanding the dsDNA elasticity at short length scales as well as how the elasticity is modulated when dsDNA binds to a charged object such as a dendrimer or protein.Graphical abstract