Anindita Basu

Microfluidic Rheology of Soft Colloids above and below Jamming

The rheology near jamming of a suspension of soft colloidal spheres is studied using a custom microfluidic rheometer that provides the stress versus strain rate over many decades. We find non-Newtonian behavior below the jamming concentration and yield-stress behavior above it. The data may be collapsed onto two branches with critical scaling exponents that agree with expectations based on Hertzian contacts and viscous drag. These results support the conclusion that jamming is similar to a critical phase transition, but with interaction-dependent exponents.

Massively parallel single-nucleus RNA-seq with DroNc-seq

Single-nucleus RNA sequencing (sNuc-seq) profiles RNA from tissues that are preserved or cannot be dissociated, but it does not provide high throughput. Here, we develop DroNc-seq: massively parallel sNuc-seq with droplet technology. We profile 39,111 nuclei from mouse and human archived brain samples to demonstrate sensitive, efficient, and unbiased classification of cell types, paving the way for systematic charting of cell atlases.

Local and global deformations in a strain-stiffening fibrin gel

Extracellular matrices composed of filamentous biopolymers like collagen and fibrin have viscoelastic properties that differ from those of rubberlike elastomers or hydrogels formed by flexible polymers. Compared to flexible polymer gels, filamentous biopolymer networks generally have larger elastic moduli, a striking increase in elastic modulus with increasing strain, and a pronounced negative normal stress when deformed in simple shear. All three of these unusual features can be accounted for by a theory that extends concepts of entropic elasticity to a regime where the polymer chains are already significantly extended in the absence of external forces because of their finite bending stiffness. An essential assumption of the theories that relate microscopic structural parameters such as persistence length and mesh size of biopolymer gels to their macroscopic rheology is that the deformation of these materials is affine: that is, the macroscopic strain of the bulk material is equal to the local strain within the material at each point. The validity of this assumption for the dilute open meshworks of most biopolymer gels has been experimentally tested by embedding micron diameter fluorescent beads within the networks formed by fibrin and quantifying their displacements as the macroscopic samples are deformed in a rheometer. Measures of non-affine deformation are small at small strains and decrease as strain increases and the sample stiffens. These results are consistent with the entropic model for non-linear elasticity of semiflexible polymer networks and show that strain-stiffening does not require non-affine deformations.

High-Throughput Single-Cell Labeling (Hi- SCL) for RNA-Seq Using Drop-Based Microfluidics

The importance of single-cell level data is increasingly appreciated, and significant advances in this direction have been made in recent years. Common to these technologies is the need to physically segregate individual cells into containers, such as wells or chambers of a micro-fluidics chip. High-throughput Single-Cell Labeling (Hi-SCL) in drops is a novel method that uses drop-based libraries of oligonucleotide barcodes to index individual cells in a population. The use of drops as containers, and a microfluidics platform to manipulate them en-masse, yields a highly scalable methodological framework. Once tagged, labeled molecules from different cells may be mixed without losing the cell-of-origin information. Here we demonstrate an application of the method for generating RNA-sequencing data for multiple individual cells within a population. Barcoded oligonucleotides are used to prime cDNA synthesis within drops. Barcoded cDNAs are then combined and subjected to second generation sequencing. The data are deconvoluted based on the barcodes, yielding single-cell mRNA expression data. In a proof-of-concept set of experiments we show that this method yields data comparable to other existing methods, but with unique potential for assaying very large numbers of cells.

Nonaffine Displacements in Flexible Polymer Networks

The validity of the affine assumption in model flexible polymer networks is explored. To this end, the displacements of fluorescent tracer beads embedded in polyacrylamide gels are quantified by confocal microscopy under shear deformation, and the deviations of these displacements from affine responses are recorded. Nonaffinity within the gels is quantified as a function of polymer chain density and cross-link concentration. Observations are compared with current theories of nonaffinity in random elastic media. We note that the mean-squared nonaffine deviation is proportional to the square of the applied strain in the linear elasticity regime, as per theoretical predictions. The measured degree of nonaffinity in the polyacrylamide gels suggests the presence of structural inhomogeneities which likely result from heterogeneous reaction kinetics during gel preparation. In addition, the macroscopic elasticity of the polyacrylamide gels is confirmed to behave in accordance with standard models of flexible poly...

Rheology of soft colloids across the onset of rigidity: scaling behavior, thermal, and non-thermal responses

We study the rheological behavior of colloidal suspensions composed of soft sub-micron-size hydrogel particles across the liquid-solid transition. The measured stress and strain-rate data, when normalized by thermal stress and time scales, suggest our systems reside in a regime wherein thermal effects are important. In a different vein, critical point scaling predictions for the jamming transition, typical in athermal systems, are tested. Near dynamic arrest, the suspensions exhibit scaling exponents similar to those reported in Nordstrom et al., Phys. Rev. Lett., 2010, 105, 175701. The observation suggests that our system exhibits a glass transition near the onset of rigidity, but it also exhibits a jamming-like scaling further from the transition point. These observations are thought-provoking in light of recent theoretical and simulation findings, which show that suspension rheology across the full range of microgel particle experiments can exhibit both thermal and athermal mechanisms.

Rapid, targeted and culture-free viral infectivity assay in drop-based microfluidics

A key viral property is infectivity, and its accurate measurement is crucial for the understanding of viral evolution, disease and treatment. Currently viral infectivity is measured using plaque assays, which involve prolonged culturing of host cells, and whose measurement is unable to differentiate between specific strains and is prone to low number fluctuation. We developed a rapid, targeted and culture-free infectivity assay using high-throughput drop-based microfluidics. Single infectious viruses are incubated in a large number of picoliter drops with host cells for one viral replication cycle followed by in-drop gene-specific amplification to detect infection events. Using murine noroviruses (MNV) as a model system, we measure their infectivity and determine the efficacy of a neutralizing antibody for different variants of MNV. Our results are comparable to traditional plaque-based assays and plaque reduction neutralization tests. However, the fast, low-cost, highly accurate genomic-based assay promises to be a superior method for drug screening and isolation of resistant viral strains. Moreover our technique can be adapted to measuring the infectivity of other pathogens, such as bacteria and fungi.

Structure-property relationships from universal signatures of plasticity in disordered solids

Behavioral universality across size scales Glassy materials are characterized by a lack of long-range order, whether at the atomic level or at much larger length scales. But to what extent is their commonality in the behavior retained at these different scales? Cubuk et al. used experiments and simulations to show universality across seven orders of magnitude in length. Particle rearrangements in such systems are mediated by defects that are on the order of a few particle diameters. These rearrangements correlate with the materials softness and yielding behavior. Science, this issue p. 1033 A range of particle-based and glassy systems show universal features of the onset of plasticity and a universal yield strain. When deformed beyond their elastic limits, crystalline solids flow plastically via particle rearrangements localized around structural defects. Disordered solids also flow, but without obvious structural defects. We link structure to plasticity in disordered solids via a microscopic structural quantity, “softness,” designed by machine learning to be maximally predictive of rearrangements. Experimental results and computations enabled us to measure the spatial correlations and strain response of softness, as well as two measures of plasticity: the size of rearrangements and the yield strain. All four quantities maintained remarkable commonality in their values for disordered packings of objects ranging from atoms to grains, spanning seven orders of magnitude in diameter and 13 orders of magnitude in elastic modulus. These commonalities link the spatial correlations and strain response of softness to rearrangement size and yield strain, respectively.

Role of Rare Earth Oxide Nanoparticles (CeO2 and La2O3) in Suppressing the Photobleaching of Fluorescent Organic Dyes

Aqueous solutions with Rhodamine dye, and fluorescently labeled polymer samples of fibrin and collagen were mixed with aqueous dispersions of cerium oxide, lanthanum oxide, iron (II) oxide nanoparticles, and OxyFluor, a commonly used reagent for suppressing photobleaching. From time dependent studies of the fluorescence from these samples, we observed that the dyes in samples containing rare earth oxide nanoparticles exhibited significantly slower rates of fluorescence decay compared to control samples without additives, or containing OxyFluor or iron oxide nanoparticles. We posit that this may be related to the oxygen free radical scavenging properties of rare earth oxides.