Sachin Shanbhag

Inverted colloidal crystals as three-dimensional microenvironments for cellular co-cultures

Cellular scaffolds made on the basis of inverted colloidal crystals (ICC) provide a unique system for investigation of cell–cell interactions and their mathematical description due to highly controllable and ordered 3D geometry. Here, we describe three new steps in the development of ICC cell scaffolds. First, it was demonstrated that layer-by-layer (LBL) assembly with clay/PDDA multilayers can be used to modify the surface of ICC scaffolds and to enhance cell adhesion. Second, a complex cellular system made from adherent and non-adherent cells co-existing was created. Third, the movement of non-adherent cells inside the scaffold was simulated. It was found that floating cells are partially entrapped in spherical chambers and spend most of their time in the close vicinity of the matrix and cells adhering to the walls of the ICC. Using this approach one can efficiently simulate differentiation niches for different components of hematopoietic systems, such as T-, B- and stem cells.

A Temperature‐Driven Reversible Phase Transfer of 2‐(Diethylamino)ethanethiol‐Stabilized CdTe Nanoparticles

Nanoparticles (NPs) play an important role in applications such as biological imaging, energy conversion, and environmental remediation due to their unique optical and electrical properties. The chemical synthesis of NPs is usually conducted in the presence of either hydrophilic stabilizers in aqueous solution or hydrophobic ligands in an organic solvent. However, the distinct solubility differences of NPs in media with different polarities limit their broader application. For instance, NPs capped with hydrophobic stabilizers can be dispersed and used in organic solvents but not in aqueous solutions, and vice versa. 6] Much effort has therefore been devoted to understanding and controlling the phase-transfer behavior of NPs. The successful strategies reported to date can be classified into two types: 1) changing the wettability characteristics of the stabilizers, and 2) changing the composition of the medium. Both these methods involve altering the hydrophobic/hydrophilic properties of NPs by changing the nature of either the stabilizers or the medium to realize repetitive transfers between the immiscible phases. Herein we report a reversible phase transfer of 2-(diethylamino)ethanethiol (DEAET)-stabilized CdTe NPs in water/toluene which is driven solely by temperature. The mechanism of this phase transfer between the two immiscible phases is investigated in detail. The DEAET-stabilized CdTe NPs were prepared as reported in the literature. DEAET molecules (molecular formula: (CH3CH2)2NCH2CH2SH) bind to the surface of the NPs through their thiol group, which means that the hydrophilic amino group and two hydrophobic ethyl groups are exposed to the medium. Previous studies have shown that the amphiphilic nature of the ends exposed to the medium endows the NPs with a unique temperature-dependent dispersion behavior in water: they precipitate at 0 8C while they dissolve at higher temperatures (70 8C). These observations prompted us to study the phase-transfer behavior of DEAET-stabilized CdTe NPs in a two-phase system of immiscible liquids. As shown in Figures 1 A and 1D, the orange-emitting DEAET-stabilized CdTe NPs are present in the toluene phase at 0 8C. Upon increasing the temperature to 27 8C, however,

Mesh sensitivity in peridynamic simulations

Abstract In this work, we investigate the suitability of several meshing strategies for use with a common peridynamics solution scheme. First, we use a manufactured solution to quantify the influence of different meshes on the accuracy and conditioning of a nonlocal boundary value problem in one and two dimensions. We explore convergence behavior, the effects of model parameters, and sensitivity to perturbations. We then apply the same meshing strategies to a three-dimensional impact simulation that employs the full peridynamic mechanical theory. We present a qualitative comparison of the fracture patterns that result, and suggest best practices for generating meshes that lead to efficient, high-quality numerical simulations of peridynamic models.

Complex effects of molecular topology on diffusion in entangled biopolymer blends

By combining single-molecule tracking with bond-fluctuation model simulations, we show that diffusion is intricately linked to molecular topology in blends of entangled linear and ring biopolymers, namely DNA. Most notably, we find a previously unreported non-monotonic dependence of the self-diffusion coefficient for linear DNA on the fraction of linear DNA comprising the ring-linear blend, which we argue arises from a second-order effect of ring DNA molecules being threaded by varying numbers of linear DNA molecules. Results address several debated issues regarding molecular dynamics in biopolymer blends, which can be used to develop novel tunable biomaterials.

Self-organization of Te nanorods into V-shaped assemblies: a Brownian dynamics study and experimental insights.

Computer modeling of nanoscale processes provides critical quantitative insights into nanoscale self-organization, which is hard to achieve by other means. Starting from a suspension of Te nanorods, it was recently found that short nanorods (50 nm) self-organized into checkmark-like V-shaped assemblies over a period of a few days, whereas long nanorods (2200 nm) did not. This experimental fact was difficult to explain, and so here we use Brownian dynamics simulations of a dilute suspension of hard spherocylinders to better understand the process of self-organization. With the assumption that close encounters between nanorod tips result in their merger into V-particles, it was found that the ratio of the initial rate of nanorod formation for the short and long rods was 3760. By systematically varying the length and the concentration, we found that the concentration of the nanorods, rather their length, was primarily instrumental in setting the initial rate of checkmark formation. Using a simple kinetic model in conjunction with experimental data, we find that approximately 30,000 close encounters are required on average for a single successful merger. This study gives an important reference point for understanding the mechanism of the formation of complex nanostructured system by oriented attachment; it also can be extended to and provides conceptual leads for other self-organized systems.

On the relationship between two popular lattice models for polymer melts.

A mapping between two well known lattice bond-fluctuation models for polymers [I. Carmesin and K. Kremer, Macromolecules 21, 2819 (1988); J. S. Shaffer, J. Chem. Phys. 101, 4205 (1994)] is investigated by performing primitive path analysis to identify the average number of monomers per entanglement. Simulations conducted using both models, and previously published data are compared in an attempt to establish relationships between molecular weight, lengthscale, and timescale. Using these relationships, an examination of the self-diffusion coefficient yields excellent agreement not only between the two models, but also with experimental data on polystyrene, polybutadiene, and polydimethylsiloxane. However, it is shown that even with the limited set of criteria examined in this paper, a true mapping between these two models is elusive. Nevertheless, a practical guide to convert between models is provided.

Analytical rheology of branched polymer melts: Identifying and resolving degenerate structures

Recently, a computational algorithm based on Bayesian data analysis was presented to invert the linear rheology of branched polymers [Shanbhag, S., Rheol. Acta 49, 411–422 (2010)]. When rheological data of an unknown polymer mixture are supplied, the algorithm produces an exhaustive distribution of structures and compositions, consistent with the rheology. Frequently, it identifies multiple or degenerate structures. In this proof-of-concept paper, a resolution of the degeneracy is sought by appealing to the concept of combinatorial rheology [Larson, R. G., Macromolecules 34, 4556–4571 (2001)], where the unknown sample is strategically blended with a well-characterized fraction. Experimental load is alleviated by identifying the optimal type, molecular weight, and composition of the polymer fraction to blend with the unknown sample, to discriminate between the degenerate structures, most conclusively. Two methods are proposed and tested on a particular mixture that is characterized by severe degeneracy. Bo...

Implications of microscopic simulations of polymer melts for mean-field tube theories

Despite the success of the mean-field tube theory in predicting the stress relaxation of linear and branched polymers, several important issues remain unresolved. Recent simulation methods that address some of these issues are shedding light on the dynamics of entangled polymer molecules. In this survey, we consider a class of coarse-grained models for polymer melts called slip-link models, which have been used to study the phenomena of constraint release, branch-point diffusion, and the relationship between the plateau modulus and entanglement spacing. We also consider the bond-fluctuation lattice model, and the pearl-necklace molecular dynamics model in conjunction with recently developed algorithms to identify primitive paths. The ability of these latter models to identify the primitive path network enables molecular simulations to be used to test and improve mean-field tube models. The implications of these simulations for the mean-field tube potential in the absence of constraint release, and for the dilution exponent which controls the strength of constraint release, are examined.

Analytical Rheology of Polymer Melts: State of the Art

The extreme sensitivity of rheology to the microstructure of polymer melts has prompted the development of “analytical rheology,” which seeks inferring the structure and composition of an unknown sample based on rheological measurements. Typically, this involves the inversion of a model, which may be mathematical, computational, or completely empirical. Despite the imperfect state of existing models, analytical rheology remains a practically useful enterprise. I review its successes and failures in inferring the molecular weight distribution of linear polymers and the branching content in branched polymers.

Estimating self-diffusion in polymer melts: how long is a long enough molecular simulation?

We performed molecular simulations of polymer melts of three different molecular weights, with 1000 polymers for simulation run time , where is the relaxation time, using the bond-fluctuation model. We computed the mean-squared displacement, and applied weighted least squares with statistical bootstrap to infer the self-diffusivity and the associated uncertainty from these long simulations. We investigated the effect of limited simulations by using only a subset of these long simulations. We found that using and was a safe choice that led to relatively stable estimates of the mean self-diffusivity. We considered simulations of much poorer quality, and , and found that the proposed method accurately reflected the uncertainty even in the shortest simulations. This is in contrast with the standard practice of using 2–3 independent simulation runs to characterise uncertainty, which not only underestimates the true uncertainty in poor data-sets, but is also computationally more demanding.