Gaurav Arya

Rapid self-healing hydrogels

Synthetic materials that are capable of autonomous healing upon damage are being developed at a rapid pace because of their many potential applications. Despite these advancements, achieving self-healing in permanently cross-linked hydrogels has remained elusive because of the presence of water and irreversible cross-links. Here, we demonstrate that permanently cross-linked hydrogels can be engineered to exhibit self-healing in an aqueous environment. We achieve this feature by arming the hydrogel network with flexible-pendant side chains carrying an optimal balance of hydrophilic and hydrophobic moieties that allows the side chains to mediate hydrogen bonds across the hydrogel interfaces with minimal steric hindrance and hydrophobic collapse. The self-healing reported here is rapid, occurring within seconds of the insertion of a crack into the hydrogel or juxtaposition of two separate hydrogel pieces. The healing is reversible and can be switched on and off via changes in pH, allowing external control over the healing process. Moreover, the hydrogels can sustain multiple cycles of healing and separation without compromising their mechanical properties and healing kinetics. Beyond revealing how secondary interactions could be harnessed to introduce new functions to chemically cross-linked polymeric systems, we also demonstrate various potential applications of such easy-to-synthesize, smart, self-healing hydrogels.

Engineering the cell-material interface for controlling stem cell adhesion, migration, and differentiation.

The effective utilization of stem cells in regenerative medicine critically relies upon our understanding of the intricate interactions between cells and their extracellular environment. While bulk mechanical and chemical properties of the matrix have been shown to influence various cellular functions, the role of matrix interfacial properties on stem cell behavior is unclear. Here, we report the striking effect of matrix interfacial hydrophobicity on stem cell adhesion, motility, cytoskeletal organization, and differentiation. This is achieved through the development of tunable, synthetic matrices with control over their hydrophobicity without altering the chemical and mechanical properties of the matrix. The observed cellular responses are explained in terms of hydrophobicity-driven conformational changes of the pendant side chains at the interface leading to differential binding of proteins. These results demonstrate that the hydrophobicity of the extracellular matrix could play a considerably larger role in dictating cellular behaviors than previously anticipated. Additionally, these tunable matrices, which introduce a new control feature for regulating various cellular functions offer a platform for studying proliferation and differentiation of stem cells in a controlled manner and would have applications in regenerative medicine.

Self-orienting nanocubes for the assembly of plasmonic nanojunctions

Plasmonic hot spots are formed when metal surfaces with high curvature are separated by nanoscale gaps and an electromagnetic field is localized within the gaps. These hot spots are responsible for phenomena such as subwavelength focusing, surface-enhanced Raman spectroscopy and electromagnetic transparency, and depend on the geometry of the nanojunctions between the metal surfaces. Direct-write techniques such as electron-beam lithography can create complex nanostructures with impressive spatial control but struggle to fabricate gaps on the order of a few nanometres or manufacture arrays of nanojunctions in a scalable manner. Self-assembly methods, in contrast, can be carried out on a massively parallel scale using metal nanoparticle building blocks of specific shape. Here, we show that polymer-grafted metal nanocubes can be self-assembled into arrays of one-dimensional strings that have well-defined interparticle orientations and tunable electromagnetic properties. The nanocubes are assembled within a polymer thin film and we observe unique superstructures derived from edge-edge or face-face interactions between the nanocubes. The assembly process is strongly dependent on parameters such as polymer chain length, rigidity or grafting density, and can be predicted by free energy calculations.

Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions

The architecture of the chromatin fiber, which determines DNA accessibility for transcription and other template-directed biological processes, remains unknown. Here we investigate the internal organization of the 30-nm chromatin fiber, combining Monte Carlo simulations of nucleosome chain folding with EM-assisted nucleosome interaction capture (EMANIC). We show that at physiological concentrations of monovalent ions, linker histones lead to a tight 2-start zigzag dominated by interactions between alternate nucleosomes (i ± 2) and sealed by histone N-tails. Divalent ions further compact the fiber by promoting bending in some linker DNAs and hence raising sequential nucleosome interactions (i ± 1). Remarkably, both straight and bent linker DNA conformations are retained in the fully compact chromatin fiber as inferred from both EMANIC and modeling. This conformational variability is energetically favorable as it helps accommodate DNA crossings within the fiber axis. Our results thus show that the 2-start zigzag topology and the type of linker DNA bending that defines solenoid models may be simultaneously present in a structurally heteromorphic chromatin fiber with uniform 30 nm diameter. Our data also suggest that dynamic linker DNA bending by linker histones and divalent cations in vivo may mediate the transition between tight nucleosome packing within discrete 30-nm fibers and self-associated higher-order chromosomal forms.

A critical comparison of equilibrium, non-equilibrium and boundary-driven molecular dynamics techniques for studying transport in microporous materials

Transport in an idealized model with variable pore diameter as well as an AlPO4-5 zeolite is examined using three different molecular dynamics techniques: (1) equilibrium molecular dynamics (EMD); (2) external field nonequilibrium molecular dynamics (EF–NEMD); and (3) dual control volume grand canonical molecular dynamics (DCV–GCMD). The EMD and EF–NEMD methods yield identical transport coefficients for all the systems studied. The transport coefficients calculated using the DCV–GCMD method, however, tend to be lower than those obtained from the EMD and EF–NEMD methods unless a large ratio of stochastic to dynamic moves is used for each control volume, and a streaming velocity is added to all inserted molecules. Through development and application of a combined reaction–diffusion–convection model, this discrepancy is shown to be due to spurious mass and momentum transfers caused by the control volume equilibration procedure. This shortcoming can be remedied with a proper choice of streaming velocity in co...

Role of histone tails in chromatin folding revealed by a mesoscopic oligonucleosome model

The role of each histone tail in regulating chromatin structure is elucidated by using a coarse-grained model of an oligonucleosome incorporating flexible histone tails that reproduces the conformational and dynamical properties of chromatin. Specifically, a tailored configurational-bias Monte Carlo method that efficiently samples the possible conformational states of oligonucleosomes yields positional distributions of histone tails around nucleosomes and illuminates the nature of tail/core/DNA interactions at various salt milieus. Analyses indicate that the H4 histone tails are most important in terms of mediating internucleosomal interactions, especially in highly compact chromatin with linker histones, followed by H3, H2A, and H2B tails in decreasing order of importance. In addition to mediating internucleosomal interactions, the H3 histone tails crucially screen the electrostatic repulsion between the entering/exiting DNA linkers. The H2A and H2B tails distribute themselves along the periphery of chromatin fibers and are important for mediating fiber/fiber interactions. A delicate balance between tail-mediated internucleosomal attraction and repulsion among linker DNAs allows the entering/exiting linker DNAs to align perpendicular to each other in linker-histone deficient chromatin, leading to the formation of an irregular zigzag-folded fiber with dominant pair-wise interactions between nucleosomes i and i ± 4.

Molecular Simulations of Knudsen Wall-slip: Effect of Wall Morphology

This work involves a molecular simulation study of the phenomena of wall slip occurring in rarefied gases flowing through micro- and nano-channels. A simulation strategy that mimics a scattering experiment is developed in order to compute the tangential momentum accommodation coefficient (f) which governs the degree of slip at the wall surface. Noninteracting gas molecules are bombarded at an atomic wall composed of rigid atoms with suitably distributed velocities and a tangential drift velocity that simulates flow. The accommodation coefficient is computed from the loss in the tangential momentum of these molecules. The accommodation coefficient is observed to be strongly dependent on the physical roughness of the wall, as characterized by the parameter sgr wg/L, and the attractiveness of the wall to the fluid, as characterized by the parameter ε wg/k B T, where sgr wg and ε wg are the Lennard–Jones interaction parameters of the wall and gas atoms while L is the lattice unit length. The accommodation coefficient is found to be independent of the tangential drift velocity at small drift velocities commensurate to those observed in micro devices. The accommodation coefficient is also found to be independent of the inertial mass of the gas molecules. The dependence of f on the two main governing factors has been presented in convenient “phase diagrams” plots. We also show a means of separating gases based on the differences in the accommodation coefficients of the various components in the mixture. Using molecular dynamics simulations, we show that separation factors higher than 20 are achieved for gases flowing through nanometer wide channels in the Knudsen regime. We also present a simple analytical model to determine the lower bound on the separation factor of the two gases.

Dynamic Electromechanical Hydrogel Matrices for Stem Cell Culture

Hydrogels have numerous biomedical applications including synthetic matrices for cell culture and tissue engineering. Here we report the development of hydrogel based multifunctional matrices that not only provide three-dimensional structural support to the embedded cells but also can simultaneously provide potentially beneficial dynamic mechanical and electrical cues to the cells. A unique aspect of these matrices is that they undergo reversible, anisotropic bending dynamics in an electric field. The direction and magnitude of this bending can be tuned through the hydrogel crosslink density while maintaining the same electric potential gradient, allowing control over the mechanical strain imparted to the cells in a three-dimensional environment. The conceptual design of these hydrogels was motivated through theoretical modeling of the osmotic pressure changes occurring at the gel-solution interfaces in an electric field. These electro-mechanical matrices support survival, proliferation, and differentiation of stem cells. Thus, these new three-dimensional in vitro synthetic matrices, which mimic multiple aspects of the native cellular environment, take us one step closer to in vivo systems.

A structural perspective on the where, how, why, and what of nucleosome positioning.

Abstract The DNA in eukaryotic chromatin is packed by histones into arrays of repeating units called nucleosomes. Each nucleosome contains a nucleosome core, where the DNA is wrapped around a histone octamer, and a stretch of relatively unconstrained DNA called the linker DNA. Since nucleosome cores occlude the DNA from many DNA-binding factors, their positions provide important clues for understanding chromatin packing and gene regulation. Here we review the recent advances in the genome-wide mapping of nucleosome positions, the molecular and structural determinants of nucleosome positioning, and the importance of nucleosome positioning in chromatin higher order folding and transcriptional regulation.

Heparin mimicking polymer promotes myogenic differentiation of muscle progenitor cells.

Heparin and heparan sulfate mediated basic fibroblast growth factor (bFGF) signaling plays an important role in skeletal muscle homeostasis by maintaining a balance between proliferation and differentiation of muscle progenitor cells. In this study we investigate the role of a synthetic mimic of heparin, poly(sodium-4-styrenesulfonate) (PSS), on myogenic differentiation of C2C12 cells. Exogenous supplementation of PSS increased the differentiation of C2C12 cells in a dose-dependent manner, while the formation of multinucleated myotubes exhibited a nonmonotonic dependence with the concentration of PSS. Our results further suggest that one possible mechanism by which PSS promotes myogenic differentiation is by downregulating the mitogen activated extracellular regulated signaling kinase (MAPK/ERK) pathway. The binding ability of PSS to bFGF was found to be comparable to heparin through molecular docking calculations and by native PAGE. Such synthetic heparin mimics could offer a cost-effective alternative to heparin and also reduce the risk associated with batch-to-batch variation and contamination of heparin.