NECF Meeting Abstracts
58th New England Complex Fluids Meeting
MIT | Friday, February 28, 2014
Registration deadline: Monday, February 24, 2014
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Abstracts for Invited Talks and Sound Bites:Invited Talks
Brenner; Michael Brenner
"Ideas in Self-Assembly"
Broedersz; Dr. Chase Broedersz
"Organizing the Bacterial Chromosome for Division"
The organization of the bacterial chromosome is complicated by the requirement for replication and segregation. Chromosome segregation is mediated by partitioning proteins of the ParABS system in a variety of bacteria. At its heart, this segregation machinery includes a large protein-DNA complex consisting of roughly 1000 ParB proteins. The nature of interactions between DNA-bound ParB proteins, and how these determine the structural properties of the partitioning module remain unclear. To uncover the biophysical principles that determine the organization of the partitioning complex, we developed a simple model for interacting proteins on DNA. We found that a combination of 1D spreading bonds and a 3D bridging bond between ParB proteins constitutes a minimal model for condensation of a 3D ParB-DNA complex. These combined interactions provide an effective surface tension that prevents fragmentation of the ParB-DNA complex. The central predictions of this model directly address recent experiments on ParB-induced gene-silencing and the effect of a DNA "roadblock" on ParB localization. Furthermore, our model provides a simple mechanism to explain how a single centromeric parS site on the DNA is both necessary and sufficient for the formation and localization of the ParB-DNA complex.
Invited; Koby Nahmias
Hebrew U. of Jerusalem
"From Streamline Velocimetry to Non-dimensional Analysis of Flow in Retinal Microaneurysms"
"Mechanistic Analysis of Pathogen Interactions with the Mucus Barrier"
The goal of our research is to elucidate the mechanisms that govern selective filtering by mucus, an important biological hydrogel which coats wet surfaces in the body of all animals. Mucus has critical, but poorly understood, biological functions in protecting tissues from attack by pathogens, and facilitating transport of particulate material. I will present our work on basic mechanisms by which mucus barriers exclude, or allow passage of different molecules and pathogens, and the mechanisms pathogens have evolved to penetrate mucus barriers. We hope to provide the foundation for a theoretical framework that captures general principles governing selectivity in mucus, and likely other biological hydrogels such as the extracellular matrix, and bacterial biofilms. Our work may also be the basis for the reconstitution of synthetic gels that mimic the basic selective properties of biological gel-based barriers.
"Circulating tumor cells (CTCs) detection using drop-base microfluidics toward early prostate cancer diagnosis"
Prostate cancer is the second leading cause of cancer death in men. One man in 7 will get prostate cancer during his lifetime. And one man in 36 will die of this disease. The enumeration and characterization of circulating tumor cells (CTCs),which are found in the peripheral blood of prostate cancer patients, provide a potentially accessible source for cancer diagnosis and prognosis. By using a microfluidic device we were capable of isolating rare circulating tumor cells (CTCs) by making droplets using whole blood of patients with metastatic disease. We start with single cell encapsulation of our sample; follow by lysed cell encapsulation which releases mRNA that later on got encapsulated into drops and digital PCR. These droplets were detected to distinguish between healthy cells and cancer cells. For the purpose of this presentation, our goal is to demonstrate few techniques that we used to make our droplets using PDMS devise and some of our results to show the beauty of Microfluidic device that can eventually lead us to early Prostate cancer diagnoses.
Keywords: CTC detection, using microfluidics
Arpag; Goker Arpag*, Shankar Shastry**, William O. Hancock**, Erkan Tuzel*
*Department of Physics, Worcester Polytechnic Institute; **Department of Bioengineering, Penn State University
"Experimental and computational investigations into cooperative cargo transport by mixtures of kinesins from different families"
Intracellular cargo transport often involves multiple motor types, either having opposite directionality or having the same directionality but different speeds. Although a significant progress has been made in characterizing them at the single-molecule level, predicting ensemble behavior of motors is challenging. To understand how diverse kinesins attached to the same cargo coordinate their movement and uncover the force-dependent properties of them, we carried out microtubule gliding assays using pairwise motor mixtures from the kinesin-1, 2, 3, 5 and 7 families. To match their processivities and ensure identical binding to the glass substrate, the motors were fused to the dimerization domain and coil-1 of kinesin-1, and the neck-linkers were adjusted to have a uniform length of 14 amino acids. Uniform motor densities were used and microtubule-gliding speeds were measured as the fast motor ratio varied from 0 to 1. Coarse-grained computational model of gliding assays recapitulated these experimental findings for the ensemble behavior. The simulations incorporate force-dependent velocities from the literature along with mechanical interactions between motors bound to the same microtubule. The force dependence of unbinding appears to be the key parameter that determines behavior in the multi-motor assays and motor compliance plays a minimal role in the observed gliding speed. Simulations also make predictions for the force dependent dissociation rates for single molecule experiments. The gliding assays combined with the modeling allows us to test hypotheses regarding the characteristics of diverse kinesins under predominantly axial load, avoiding the large normal forces inherent in optical tweezer experiments.
Keywords: Cargo transport, microtubule and kinesin motors
Ban; Catalin R. Picu
Rensselaer Polytechnic Institute
"Sample Size Effects in Calculating the Stiffness of Random Fiber Network Models"
Elastic fibers sitting on the edges of a Voronoi diagram can make an elastic network. We're using such networks to simulate mechanics of various materials such as the extra cellular matrix. It's known that the stiffness of such model networks varies more for smaller sample sizes as compared to fiber segment lengths. We observe that the stiffness of the tested networks converges to an asymptotic value as the sample size grows larger. I'll be presenting related elastic stiffness calculations for the different kinds of networks tested. These calculations show the confidence range for further studies on the Voronoi network models.
Keywords: Random Fiber Networks, Voronoi Networks, Elasticity, Size Effects
Basu; Chris Ford†, Biyu Li†, Dawn Thompson†, Dave Weitz*, Aviv Regev†
†Broad Institute of MIT and Harvard; *School of Engineering and Applied Science, Harvard University
"Host-pathogen interaction at controlled MOI"
Very recent studies using FACS and microfluidics have revealed considerable heterogeneity in the transcription of critical immune genes within seemingly homogenous cell populations. We are developing a novel platform for studying host-pathogen interactions using a combination of live-cell imaging and droplet-based microfluidics. This will allow us to (1) infect cells with pathogens at a defined multiplicity of infection (MOI) in stable micro-emulsion droplets; (2) incubate and image ‘live’ cells in droplets, where each droplet represents an isolated, stable and reproducible micro-environment; (3) use fluorescent reporters of cell-states to track and sort individual cells, in a “live sorting” assay that can be done repeatedly during infection without disturbing the cell micro-environment; and (4) perform (a) population-level and (b) single-cell RNA-Seq on both host and pathogen cells. Notably, the cells can be easily removed from droplets and re-encapsulated at later time points, thus allowing for long-term studies that allow population interactions like paracrine signaling, but still provide single-cell resolution when needed. The modular compendium of tools developed here will be applicable to diverse host-pathogen systems.
Keywords: host-pathogen, MOI, microfluidics, RNA-Seq
Bourouiba; Barry Scharfman
"Fluid fragmentation in violent expirations "
Violent expirations such as coughs and sneezes feature turbulent multiphase flows that may contain pathogen-bearing droplets. As such, they play a key role in the spread of many respiratory infectious diseases. Here, we report direct observations of the physical mechanisms involved in droplet formation at the exit of the mouth during violent expirations. In particular, we identify a rich variety of fragmentation processes and track and measure the dynamic properties of the small droplets that form. Our findings are used to improve the prediction of the range of respiratory pathogen transport and the resulting contamination.
Keywords: fragmentation, sneezing, coughing, viscoelasticity, ligaments, bags, beads on string
Bruss; Gregory M. Grason
UMass - Polymer Science and Engineering
"Defect-induced shape transitions in filament bundles"
From extracellular proteins to artificially fabricated materials, cohesive filament bundles are found across many systems. Employing continuum elasticity theory and numerical simulations, we study the interdependence between the organization of cohesive filaments arranged into a bundle, and their global structure, focusing on the effects of topological defects on equilibrium bundle shape. We analyze the structural stability of parallel filament bundles possessing 5- and 7-fold disclinations in their cross section, whose presence gives rise to inhomogeneous patterns of compressive and tensile stress. We argue that a generic coupling between filament tilt and inter-filament strains leads to a class of defect-induced shape instabilities, which are the filamentary analogue of defect-induced buckling transitions of 2D membranes, and can be understood as a consequence of the generic Helfrich-Hurault instability of layered materials under tension. We show that bundles containing 5-fold disclinations prefer twisted motifs, and 7-fold disclinations give rise to radial undulations. Furthermore, the pitch and wavelength of these deformations are conditional on the relative cost of filament bending and cohesive interactions.
Keywords: Filament Bundles, Defects, Instabilities
Chen; Dong Chen, Maria. M. Santore
University of Massachusetts Amherst
"Tension alters phase transitions of vesicle membranes"
Model phospholipid vesicle membranes have long provided insight into the nature of bio-membranes and also promoted development of bio-materials - drug delivery liposome. The rich thermodynamic behavior and domain morphology in these membranes have been mapped to investigate the phase boundaries as well as membrane organization. In two-component phosphatidylcholine unilamellar vesicles, we report a dramatic influence of tension on the fluid–solid transition and resulting phases: At fixed composition, systematic variations in tension produce differently shaped solid domains (stripes or hexagons), shift fluid–solid transition temperatures, and produce a triple-point intersection of coexistence curves at elevated tensions, about 3 mN/m for 30% DOPC/70% DPPC. Tension therefore represents a potential switch of microstructure in responsive engineered materials; it is an important morphology-determining variable in confined systems, and, in biological membranes, it may provide a means to regulate dynamic structure.
Keywords: membrane tension, domain morphology, phase transition
MIT - Department of Physics
"Dissipation and Organization in Active Matter Far from Equiilibrium"
It has long been known that dissipation (entropy production) is associated with structure formation in driven many-particle systems, but a practically useful quantitative statement of this relationship in physics terms has proved challenging to describe. Here we will propose a new theoretical approach to this problem and briefly speculate about its implications for our understanding of how patterns form in complex fluids.
Eral; William E. Uspal, Patrick S. Doyle
MIT chemical Engineering
"Engineering particle trajectories in microfluidic flows using particle shape"
Recent advances in microfluidic technologies have created a demand for techniques to control the motion of flowing microparticles. Here we consider how the shape and geometric confinement of a rigid microparticle can be tailored for ‘self-steering’ under external flow. We find that an asymmetric particle, weakly confined in one direction and strongly confined in another, will align with the flow and focus to the channel centreline. Experimentally and theoretically, we isolate three viscous hydrodynamic mechanisms that contribute to particle dynamics. Through their combined effects, a particle is stably attracted to the channel centreline, effectively behaving as a damped oscillator. We demonstrate the use of self-steering particles for microfluidic device applications, eliminating the need for external forces or sheath flows.
Keywords: microfluidics, hydrodynamics
Juarez; Paulo E. Arratia
"Symmetry-breaking instability of DNA suspensions in planar extensional flow"
It is not well understood how polymer molecules that are driven far-from-equilibrium affect bulk flow behavior in simple extensional flows and give rise to unique rheological properties such as viscoelasticity. We present experimental results of dilute DNA suspensions undergoing planar extensional flow in cross-slot microfluidic devices. Bulk flow behavior and fluorescently labeled DNA molecules are simultaneously observed near the stagnation point. At low strain-rates, DNA suspensions maintain a symmetric flow profile similar to a Newtonian fluid. At high strain-rates, however, DNA suspensions display a symmetry-breaking flow instability similar to a viscoelastic fluid. Direct visualization of DNA molecules shows that they (1) undergo a stretch-coil transition when approaching the stagnation point followed by a (2) coil-stretch transition when exiting the stagnation point producing large amounts of stretching and molecular scission.
"Worst packing shapes"
Which convex shapes leave the most empty space in their densest packing? Ulam conjectured that spheres are the answer in 3D. In 2D other shapes, such as the regular octagon, are worse at packing than circles, and we show that in dimensions above three a slightly dented sphere is also worse than the perfect sphere. However, in 3D, we show that any shape close enough to the sphere is necessarily better than the sphere at packing. So, what makes 3 dimensions special? We also show that the regular heptagon might be worst at packing in 2D: any shape close enough to it packs better than it.
Keywords: hard spheres, packing
Maloney; Krystyn J. Van Vliet
"Mechanical fluidity of single biological cells"
Mechanical characteristics of single cells are used to identify and possibly leverage interesting differences among cells or cell populations. Fluidity---hysteresivity normalized to the extremes of an elastic solid or a viscous liquid---can be extracted from multiple rheological measurements of cells, including creep compliance and oscillatory phase lag. With multiple strategies available for acquisition of this nondimensional property, fluidity may serve as a useful and robust parameter for distinguishing cell populations, and for understanding the physical origins of deformability in soft matter.
Keywords: fluidity, rheology, viscoelasticity, cells, hysteresivity, damping, power law
Massenburg; Esther Amstad, PhD, David Weitz, PhD
"Understanding Different Methods of Clogging in Microchannels"
Nearly every application involving solid transport, from arteries to filters, is subject to clogging. The length scales and geometries that characterize these applications are well defined, but the clogging mechanism is poorly understood. Previous models assume that clogging in uniform microchannels is well described by a slow, predictable buildup of individual particles at the constriction which is the narrowest point in the microchannel. We use a microchannel to study the mechanism by which filters clog using suspensions containing latex microspheres. Our microchannels clog if particles gradually build up at the walls. Interestingly, particles also cluster upstream and clog the microchannels once they detach. These clusters-induce clogging does not follow the established clogging models.
Keywords: Microfluidics, Clogging
McDermott; Ian Morrison, Dave Weitz
"Electrocratic Dispersions in Low-Dielectric Liquids"
Dispersions in low dielectric constant media were once thought to be purely sterically stabilized because ionization is small. Stabilization came from soluble polymers so the dispersions were called lyophilic. In the middle of the last century, petroleum engineers discovered that even low concentrations of ions created significant electric fields during petroleum processing; sometimes leading to fires. These low concentrations of ions were attributed to low concentrations of high molecular polymers or surfactant structures such as micelles. Fowkes et al discovered that some polymeric dispersants added to lubrication oils to disperse engine soot created significant electric potentials on the soot. He suggested that the efficacy of these dispersants was due to a combination of electric repulsion and steric barriers formed by polymer adsorption. This is electrosteric stabilization.
This work introduces a method to differentiate the magnitudes of these two mechanisms. That is, salt titrations of stable, dilute dispersions in low dielectric liquids. Further, this work shows that some common oil dispersants stabilize dispersions by electrostatic forces alone, at least in dilute solutions and so the dispersions are electrocratic.
Keywords: nonpolar dispersions
Parsa; David Weitz
"Effect of medium wettability on dynamics of multiphase flow in porous media "
We study the dynamics of flow of multiple immiscible fluids in a 3D model porous medium. Using confocal microscopy we are able to visualize multiphase flow within the porous media . We study the effects of wettability of the medium on the displacement of each phase. The distribution of shapes and size of each phase fluid at small Capillary number is greatly affected by wettability.
Keywords: porous media, multiphase flow, wettability
"Phase Separation of Rotationally Driven Particles"
One interesting example of active matter is a system in which particles are driven purely rotationally, and any translational motion or ordering is the result of interactions between particles. Nguyen et al. presented an example of such a system, and demonstrated phase separation of particles driven in opposite directions. I present computations on a similar system, but treating the interactions by smoothing out particles rather than accounting for discrete collisions. This smoother system makes for faster computations and extends the parameter space that can be considered. Initial results show a non-monotonic dependence of phase separation on both driving torque and particle density.
Keywords: active matter, computation
Saint Anselm College
"A model for autonomous Brownian motors: the Brownian diode "
We consider a motor which is essentially a Brownian particle permeable to molecules of the surrounding thermal bath, which can flow in and out the particle (as a physical realization of permeable Brownian objects, one can mention for instance micro-gels and lipid vesicles like liposomes). When a molecule is inside the particle, it experiences a potential similar to that in the transition-state theory, i.e. characterized by two stationary states with a finite energy difference (potential drop) dU separated by a potential barrier. The internal potential drop dU maintains the diode-like asymmetry of molecular fluxes through the particle, which results in the particle's stationary drift. The complexity of chemical processes involved is hidden in a single parameter dU, not dissimilar to how an electric battery is characterized by its voltage.
Keywords: Brownian motors, active matter systems
Seeman; Paul L. Dubin
UMass-Amherst, Dept of Chemistry
"Protein charge anisotropy and phase separation: Role of Electrostatics"
A wide range of classical soft-matter characterization methods are applied to the study of complex phase behavior in protein-based systems. Such interactions stem from protein self-association, heteroprotein interactions, and protein/polyelectrolyte interactions. The common feature in all of these is attractive interactions due to protein charge anisotropy, as visualized via electrostatic modeling. Recent work involves development of phase separation based methods for purification of biotherapeutics.
Keywords: phase separation, proteins, polyelectrolytes, electrostatics, soft matter
Sengupta; Christian Bahr, Stephan Herminghaus
Environmental Microfluidics Group MIT/ Dynamics of Complex Fluids, Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
State-of-the-art microfluidic techniques rely usually on an isotropic carrier fluid, the flow of which is modulated using morphological patterns on the microchannels, or application of external fields. Replacing the isotropic fluid by an anisotropic liquid crystal introduces a flexible but versatile approach to guided transport of microscopic cargo in microfluidic devices. We have deomonstrated that topological line defects can be threaded at will through the microfluidic channels and used as a ‘soft rail’ whose position is controlled through easily accessible experimental parameters. Colloid particles and small water droplets, the ‘working horses’ of microfluidics, are trapped and consequently guided by the defect line through the microfluidic device. Furthermore, the microfluidic pathway provides a unique tool for engineering defects, and to hierarchically tune the effective topological strength of the system. Topological microfluidics introduces a unique platform which paves the way to flexible micro-cargo and opto-fluidic concepts in microfluidic settings.
Keywords: liquid crystals, topological defects, microfluidics
"Thermodynamics of self-assembly of mesoporous silica particles"
Self-packaging, or self-assembly of nanoscopic building blocks is attractive way of assembly of mesoscopic material because of intrinsic simplicity and low-cost of self-assembly. Examples of the assembly of quantum dots, gold nanoparticles into “crystalline” lattices, fibers, supramolecular films, etc. were reported. An ultimate example of such hierarchical self-assembly gives us the world of biological objects. Exciting 3D silica structures assembled by nature (diatoms, microsponges) are studied by several groups. However, the general mechanisms that control the self-assembly of nanoscopic building blocks are far from being well understood. Investigation of these mechanisms and development of new higher-level complexity “meso” synthetic approaches is our strategic goal.
Meso(nano)porous silica particles, which are self-assembled in a sol gel template synthesis, demonstrate an example of shapes of high complexity, similar to the one observed in biological world. Despite such complexity, here we present the evidence that at least a part of formation of these shapes is an (quasi)equilibrium thermodynamic process. We demonstrate it for an example of mesoporous fibres, one of the abundant shapes. We present a quantitative proof that the fiber free energy is described by the Boltzmann distribution, which is predicted by the equilibrium thermodynamics. This finding may put a new ground for quantitative description of morphogenesis of complex self-assembled shapes, including biological hierarchy.
Keywords: self-assembly; complex shapes; thermodynamics
Stolovicki; Lloyd W. Ung , David A. Weitz
"Droplet Chemostats on a chip"
The chemostat is a continuous-culture apparatus developed by Novick and Szilard that enables growth of cells in a well-controlled environment, in which all external parameters remain constant throughout the experiment. The culture volume is held constant by continuously adding fresh medium at a constant rate and removing used medium and cells at the same rate. In steady state the population growth rate is equal to the chemostat dilution rate. The controlled conditions of the chemostat enable the measurement of population response to specific factor by varying only one environmental factor at a time.
Laboratory chemostat sizes vary between 0.1-10 liters, involving several pumps and independent hardware, making experiments involving multiple chemostats experimentally difficult to engineer. Constant dilution of such large volumes is also resource intensive, requiring preparation of very large volumes of nutrient medium. In addition, analysis of the contents of each chemostat becomes increasingly complex to manage as the number increases.
To overcome these limetations, we are developing a robast and relaiable drop-based microfluidic devices with ~1000 of chemostats on a single chip. The basic idia is to use each droplet (~1µL) as a chemostat vessel. Every population in every drop is treated as an independent chemostat population.each chemostat droplet is constantly diluted by using drop-based techniques of on-chip volume addition and removal. Analyzing the populations is possible as bulk or single-cell resolution measurements using exisiting drop-based methods. Because the contents of the drops never touch the walls of the device, and because the device can be constantly mixed, fouling of the walls is reduced.
Keywords: Microfluidics, Chemostat, Population’s Dynamics
Ziblat; Shaorong Chong, Xuling Zhu, Priscilla Yang and Dave Weitz
New England Biolabs Inc Ipswich, Department of Microbiology and Immunobiology at Harvard Med-school, School of Engineering and Applied Sciences, Harvard.
"Elucidating lipid domains function by combinatorial screening of protein-lipids interactions"
Cell membranes composed of thousands of lipid species, differing in their alkyl chains, headgroups and degree of saturation. Changes in lipid composition or even the absence of a single lipid have shown to lead to severe pathologies and death. The leading hypothesis which explains the role of lipids in membrane functionality is that the lipids segregate into distinct domains. These lipid domains can with high specificity incorporate or exclude proteins, hence inhibit or accelerate biological processes at the membrane surface. Knowledge of protein-domain interactions is essential to understand cell functionality.
This research provides a new methodology, which determines the lipid composition a protein has a high affinity to. The method utilizes a liposome library composed of hundreds of liposomes, each made of a different lipid composition. It is made of ~70 different lipid species and is the largest and most diverse composition of lipid liposomes ever made. Measurements are performed by microfluidics and confocal microscopy. Our study demonstrates that proteins transmembrane domains have high specificity to lipid compositions.
Keywords: Lipid domains, Membrane proteins, Liposomes, Vesicles
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