Anirban Sain

Plasticization of Poly(vinylpyrrolidone) Thin Films under Ambient Humidity: Insight from Single-Molecule Tracer Diffusion Dynamics

Studies on diffusion dynamics of single molecules (SMs) have been useful in revealing inhomogeneity of polymer thin films near and above the glass-transition temperature (T(g)). However, despite several applications of polymer thin films where exposure to solvent (or vapor) is common, the effect of absorbed solvent molecules on local morphology and rigidity of polymer matrices is yet to be explored in detail. High-T(g) hydrophilic polymers such as poly(vinylpyrrolidone) (PVP) are used as pharmaceutical coatings for drug release in aqueous medium, as they readily absorb moisture, which results in effective lowering of the T(g) and thereby leads to plasticization. The effect of moisture absorption on swelling and softening of PVP thin films was investigated by visualizing the diffusion dynamics of rhodamine 6G (Rh6G) tracer molecules at various ambient relative humidities (RH). Wide-field epifluorescence microscopy, in conjunction with high-resolution SM tracking, was used to monitor the spatiotemporal evolution of individual tracers under varied moisture contents of the matrix. In the absence of atmospheric moisture, Rh6G molecules in dry PVP films are translationally inactive, suggestive of rigid local environments. Under low moisture contents (RH 30-50%), translational mobility remains arrested but rotational motion is augmented, indicating slight swelling of the polymer network which marks the onset of plasticization. The translational mobility of Rh6G was found to be triggered only at a threshold ambient RH, beyond which a large proportion of tracers exhibit extensive diffusion dynamics. Interestingly, SM tracking data at higher moisture contents of the film (RH ≥ 60%) reveal that the distributions of dynamic parameters (such as diffusivity) are remarkably broad, spanning several orders of magnitude. Furthermore, Rh6G molecules display a wide variety of translational motion even at a fixed ambient RH, clearly pointing out the extremely inhomogeneous environment of plasticized PVP network. Intriguingly, it is observed that a majority of tracers undergo anomalous subdiffusion even under high moisture contents of the matrix. Analyses of SM trajectories using velocity autocorrelation function reveal that subdiffusive behaviors of Rh6G are likely to originate from fractional Brownian motion, a signature of tracer dynamics in viscoelastic medium.

High electron mobility through the edge states in random networks of c-axis oriented wedge-shaped GaN nanowalls grown by molecular beam epitaxy

Transport and optical properties of random networks of c-axis oriented wedge-shaped GaN nanowalls grown spontaneously on c-plane sapphire substrates through molecular beam epitaxy are investigated. Our study suggests a one dimensional confinement of carriers at the top edges of these connected nanowalls, which results in a blue shift of the band edge luminescence, a reduction of the exciton-phonon coupling, and an enhancement of the exciton binding energy. Not only that, the yellow luminescence in these samples is found to be completely suppressed even at room temperature. All these changes are highly desirable for the enhancement of the luminescence efficiency of the material. More interestingly, the electron mobility through the network is found to be significantly higher than that is typically observed for GaN epitaxial films. This dramatic improvement is attributed to the transport of electrons through the edge states formed at the top edges of the nanowalls.

Micromechanics of emergent patterns in plastic flows

Crystalline solids undergo plastic deformation and subsequently flow when subjected to stresses beyond their elastic limit. In nature most crystalline solids exist in polycrystalline form. Simulating plastic flows in polycrystalline solids has wide ranging applications, from material processing to understanding intermittency of earthquake dynamics. Using phase field crystal (PFC) model we show that in sheared polycrystalline solids the atomic displacement field shows spatio-temporal heterogeneity spanning over several orders of length and time scales, similar to that in amorphous solids. The displacement field also exhibits localized quadrupolar patterns, characteristic of two dislocations of the opposite sign approaching each other. This is a signature of crystallinity at microscopic scale. Polycrystals being halfway between single crystals and amorphous solids, in terms of the degree of structural order, descriptions of solid mechanics at two widely different scales, namely continuum plastic flow and discrete dislocation dynamics turns out to be necessary here.

Persistency of single-stranded DNA: The interplay between base sequences and base stacking

The chain persistency of single-stranded (ss) DNA at a high-salt limit mainly arises from the so-called base-stacking interaction between consecutive bases along the strand. Stacking is appreciable for purine–purine (e.g., A–A) and purine–pyrimidine stacks (e.g., A–T), but it is weak for pyrimidine stacks (i.e., T–T, T–C, and C–C). We study how base stacking can stiffen the strand by classifying bases into two subclasses: stacking pairs (i.e., purine–purine and purine–pyrimidine) and non-stacking (i.e., pyrimidine–pyrimidine) pairs. With this simplification, we develop an exactly solvable model for calculating the stacking-induced persistence length lstack of heterogeneous ssDNA. It is shown that lstack is mainly determined by the occurrence rate of purines; intrinsic correlations in real DNA sequences barely influence lstack. Our approach leads to a reasonable estimate of lstack≈2b–3b (under typical conditions), where b is the inter-base distance.

Stuttering Min oscillations within E. coli bacteria: a stochastic polymerization model.

We have developed a 3D off-lattice stochastic polymerization model to study the subcellular oscillation of Min proteins in the bacteria Escherichia coli, and used it to investigate the experimental phenomenon of Min oscillation stuttering. Stuttering was affected by the rate of immediate rebinding of MinE released from depolymerizing filament tips (processivity), protection of depolymerizing filament tips from MinD binding and fragmentation of MinD filaments due to MinE. Processivity, protection and fragmentation each reduce stuttering, speed oscillations and MinD filament lengths. Neither processivity nor tip protection were, on their own, sufficient to produce fast stutter-free oscillations. While filament fragmentation could, on its own, lead to fast oscillations with infrequent stuttering; high levels of fragmentation degraded oscillations. The infrequent stuttering observed in standard Min oscillations is consistent with short filaments of MinD, while we expect that mutants that exhibit higher stuttering frequencies will exhibit longer MinD filaments. Increased stuttering rate may be a useful diagnostic to find observable MinD polymerization under experimental conditions.

Effect of intrinsic curvature on semiflexible polymers

Recently many important biopolymers have been found to possess intrinsic curvature. Tubulin protofilaments in animal cells, FtsZ filaments in bacteria and double stranded DNA are examples. We examine how intrinsic curvature influences the conformational statistics of such polymers. We give exact results for the tangent-tangent spatial correlation function C(r)=, both in two and three dimensions. Contrary to expectation, C(r) does not show any oscillatory behavior, rather decays exponentially and the effective persistence length has strong length dependence for short polymers. We also compute the distribution function P(R) of the end to end distance R and show how curved chains can be distinguished from wormlike chains using loop formation probability.

Stretching-force–dependent transitions in single stranded DNA

Mechanical properties of DNA, in particular their stretch dependent extension and their loop formation characteristics, have been recognized as an effective probe for understanding the possible biochemical role played by them in a living cell. Single stranded DNA (ssDNA), which, till recently was presumed to be an simple flexible polymer continues to spring surprises. Synthetic ssDNA, like polydA (polydeoxyadenosines) has revealed an intriguing force-extension (FX) behavior exhibiting two plateaus, absent in polydT (polydeoxythymidines) for example. Loop closing time in polydA had also been found to scale exponentially with inverse temperature, unexpected from generic models of homopolymers. Here we present a new model for polydA which incorporates both a helix-coil transition and a over-stretching transition, accounting for the two plateaus. Using transfer matrix calculation and Monte-Carlo simulation we show that the model reproduces different sets of experimental observations, quantitatively. It also predicts interesting reentrant behavior in the temperature-extension characteristics of polydA, which is yet to be verified experimentally.

Predicting the coherence resonance curve using a semianalytical treatment.

Emergence of noise-induced regularity or coherence resonance in nonlinear excitable systems is well known. We explain theoretically why the normalized variance (V(N)) of interspike time intervals, which is a measure of regularity in such systems, has a unimodal profile. Our semianalytic treatment of the associated spiking process produces a general yet simple formula for V(N) , which we show is in very good agreement with numerics in two test cases, namely, the FitzHugh-Nagumo model and the chemical oscillator model.

Curvature instability of chiral colloidal membranes on crystallization

Buckling and wrinkling instabilities are failure modes of elastic sheets that are avoided in the traditional material design. Recently, a new paradigm has appeared where these instabilities are instead being utilized for high-performance applications. Multiple approaches such as heterogeneous gelation, capillary stresses, and confinement have been used to shape thin macroscopic elastic sheets. However, it remains a challenge to shape two-dimensional self-assembled monolayers at colloidal or molecular length scales. Here, we show the existence of a curvature instability that arises during the crystallization of finite-sized monolayer membranes of chiral colloidal rods. While the bulk of the membrane crystallizes, its edge remains fluid like and exhibits chiral ordering. The resulting internal stresses cause the flat membrane to buckle macroscopically and wrinkle locally. Our results demonstrate an alternate pathway based on intrinsic stresses instead of the usual external ones to assemble non-Euclidean sheets at the colloidal length scale.Buckling and wrinkling are instabilities which involve thin elastic sheets and are well-investigated phenomena at the macroscale. Here Saikia et al. investigate curvature instabilities at the colloidal lengthscale in quasi-2D monolayers of rod-like viruses across the fluid-crystal phase transition.

How helix-coil transition influences translocation of a single-stranded DNA and kinetics of its fluctuation inside the channel

Many biopolymers like proteins, RNA, single-stranded DNA form secondary structures, namely helices and loops. These polymers often get transported from one compartment of the cell to another through narrow protein channels. Motivated by recent experimental results on translocation of polymers through channels and helix-coil transition inside the channel, we have constructed a two-dimensional toy model to study how secondary structures influence such processes. Through a Langevin dynamics simulation we investigated the statistics of translocation as well as how channel width, force and temperature affect the helix-coil transition inside a channel. Our results are in qualitative agreement with experimental data.