New England Complex Fluids Workgroup

Abstracts for Invited Talks and Sound Bites:

Invited Talks

1. Invited; Shekhar Garde

Rensselaer Polytechnic Institute

"Hydration Phenomena at the Interface of Physics and Biology: A New Fluctuations-based Perspective"
Water-mediated interactions (e.g., hydrophobic interactions) govern a host of biological and colloidal self-assembly phenomena from protein folding, micelle and membrane formation, to molecular recognition. Macroscopically, hydrophobicity is often characterized by measuring a droplet contact angle on a surface. At the nanoscale, such measurements are not feasible, e.g., for surfaces of proteins or nanoparticles. Using theory and molecular simulations, we present a new perspective that connects the behavior of water (esp. density fluctuations) near nanoscale interfaces to their hydrophobicity/philicity. This new perspective provides a computational tool for characterizing the hydrophobicity patterns on protein surfaces, which are relevant for binding, recognition, and aggregation. Simulations also show how the properties of water at interfaces influence binding, folding, and dynamics of flexible molecules in interfacial environments. Our current understanding of the hydration of ions, osmolytes, and solution additives, when combined with this new perspective, provides insights into the role of water in multicomponent biological interactions.
Keywords:

2. Invited; Michael Aizenberg

Wyss Institute for Biologically Inspired Engineering, Harvard University

"Responsive Gel-Based Dynamic Materials: from Chemo-mechano-chemical Transduction to Artificial Homeostasis"
Living organisms exhibit unique homeostatic abilities, maintaining tight control of their local environment through inter-conversions of chemical and mechanical energy and self-regulating feedback loops organized hierarchically across the length scales. In contrast, most synthetic materials are incapable of undergoing continuous self-monitoring and self-regulating behavior, based on the limited single-directional chemo-mechanical or mechano-chemical modes. In this talk we will present our progress in designing hybrid dynamic materials that convert chemical inputs into mechanical motion that, in turn, triggers a different, secondary chemical response. Our strategy utilizes a liquid bilayer system with hydrogel-supported, catalyst- bearing microstructures, which are separated from a reactant-containing ‘nutrient’ layer. Reconfiguration of the pH-responsive gel in response to a pH change induces the reversible actuation of the microstructures in and out of the nutrient layer and serves as a highly precise ‘on-off’ switch for the secondary chemical transformations. We apply this design to trigger a variety of processes-fluorescence quenching, catalytic decomposition of hydrogen peroxide, or a complex enzymatic reaction-that undergo reversible, repeatable cycles synchronized with the motion of the microstructures and the driving external chemical stimulus, pH. Ultimately, we create an exemplary internally-regulated, self-sustained homeostatic system that maintains a user-defined parameter – temperature – by exploiting a continuous feedback loop between exothermic catalytic chemical reactions in the nutrient layer and the mechanical action of the temperature-responsive gel.
Keywords:

3. Invited; Darren Link, Richard Jacubinas, Ian Morrison, Christopher Harrison, Patrick Spicer

BASF, Raindance, Harvard, Schlumberger, Proctor & Gamble (respectively)

"Panel on Industry - Academic relations"
A 90 minute panel session composed of researchers from industry will explore the academic / industrial relationship. In addition to taking questions from the floor, the panel will address questions such as what kind of training and education do industrial labs seek in job applicants? What (scientific) knowledge should applicants possess? experience? skills? creativity? business knowledge? What should the universities do to better prepare students for a career in industry? What is the opinion of the industrial scientists and managers of the research being done at universities? And how does research done in industry compare to that done in universities? How common are collaborations between industry and academic researchers? What makes a successful collaboration? When does industry use academic consultants?
Keywords:

Sound Bites

1. akella; Prof. Seth Fraden

Brandeis University

"Enhancing Nucleation Rates using Porous Silica"
The role of nucleants in promoting protein crystal nucleation is an on-going field of research. Porous silica acts as heterogeneous nucleation centers and enhances nucleation rates. For the protein lysozyme there are multiple polymorphs and we demonstrate that porous silica preferentially increases one of the polymorphs. Preliminary studies are presented in which good nucleation statistics are obtained through optical microscopy studies of thousands of crystallization trials in identical water-in-oil emulsion drops produced using microfluidics.
Keywords: Enhancement, Nucleation, Lysozyme

2. Bruss; Gregory M. Grason

University of Massachusetts

"Filament Bundles: Twist Without Chirality"
There are many are examples of structures in biology that are composed of filaments that self-assemble into twisted bundles. In such assemblies, twist hinders the perfect crystalline order of the fibers, necessitating energetically unfavorable defects into the packing. Therefore, it is reasonably expected that to overcome this consequence, intrinsic chirality accounts for why bundles are twisted rather than straight. However, we find that twist also has the effect of reducing the surface energy of the assembly. This suggests that perhaps filaments may readily self-assemble into twisted bundles, regardless of any intrinsic chirality or chiral-based interactions.
Keywords: Self-Assembly, Twisted Bundles

3. Cabanas; Rafael A. Cabanas, Camille Girabawe, Seth Fraden

Brandeis University

"Stories of fish and love"
We will present a new microfluidic device that allows production and control over one single drop, concept known as drop on demand. The way the chip is operated is critical for the success of the drop production and manipulation. We will also sketch some basic applications for it.
Keywords: Microfluidics, drop on demand.

4. Cajamarca; Gregory Grason

University of Massachusetts Amherst

"Twisting of tubular self-assemblies driven by adhesive interactions. "
We study the self-assembly of tubular filaments using a model consisting of two helices with opposite torsion wrapping around one another as the global twist of the bundle increases. The separation between the filaments also changes depending on the strength of the adhesive forces. We analyze two different types of potentials driving the adhesion between the helices: the first potential consists of two opposite interactions, a (repulsive) Debye-Huckel electrostatic force and a (attractive) depletion force (DHD); the second one is a Lennard-Jones interaction. We are able to show similarities between the two types of interactions in limiting cases dominated by geometry: very thin tubes (thread regime) and very thick tubes (contact regime). We also characterize the profiles of the interaction energies as a function of the angle between the helices and analyze the stability of these types of bundles to a global twist.
Keywords: Self-assembly, helices, twist, depletion.

5. Chen; Michael Heymann, Daniela Nicastro, Zvonimir Dogic

Department of Physics, Brandeis University

"Energy Consumption of Actively Beating Eukaryotic Flagella"
Motile cilia and flagella are important for propelling cells or driving fluid over tissues. The microtubule-based core in these organelles, the axoneme, has a nearly universal ``9+2'' arrangement of 9 outer doublet microtubules assembled around two singlet microtubules in the center. Thousands of molecular motor proteins are attached to the doublets and walk on neighboring outer doublets. The motors convert the chemical energy of ATP hydrolysis into sliding motion between adjacent doublet microtubules, resulting in precisely regulated oscillatory beating. Using demembranated sea urchin sperm flagella as an experimental platform, we simultaneously monitor the axoneme's consumption of ATP and its beating dynamics while key parameters, such as solution viscosity and ATP concentration, are varied. By isolating swimming cells in emulsion droplets we can directly measure energy consumption at the single-cell level.
Keywords:

6. DeCamp; Tim Sanchez, Dan T.N. Chen, Michael Heymann, Zvonimir Dogic

Brandeis University

"Motile Droplets from Active 2D Nematics"
We study a diversity of self-organized, collective phenomena that arise within a far-from-equilibrium system comprised of microtubules, kinesin motor clusters, and a depletion agent that induces MT bundling. We focus on how MTs can self-assemble at a surfactant-stabilized oil-water interface to form an active 2D nematic that exhibits fast streaming flows as well as collective buckling and fracturing. Additionally, we observe the spontaneous unbinding and annihilation of charge +1/2 and -1/2 defects. When confined to a spherical geometry inside an emulsion droplet, the streaming defects and associated internal stresses lead to an entirely new form of droplet self-motility. We are currently studying both the defect dynamics, as well as the droplet motility. Finally, active nematics can be assembled at completely flat 2D interfaces as well as interfaces of variable curvature.
Keywords: Microtubule, Liquid Crystal, Nematic, Kinesin, active matter, self organization, assembly

7. Deng; Daosheng Deng

Prof. Martin Bazant group, MIT

"Overlimiting Current and Shock Electrodialysis in Porous Media"
Deionization is the most challenging step in water purification for human use or safe disposal. Standard methods, such as reverse osmosis and electrodialysis, are limited by bulk diffusion and convection, but in porous media, surface conduction and electro-osmotic flow also contribute to ionic fluxes. Recently, it has been predicted that these surface phenomena can support over-limiting current (exceeding diffusion limitation) and propagating deionization shocks without any hydrodynamic or chemical instability. In this paper, we present the first experimental demonstrations of overlimiting current in a porous material and water deionization by the method of “shock electrodialysis" (ED). The apparatus consists of a silica glass frit (1 mm thick with 500 nm mean pore size) in an aqueous electrolyte (CuSO4 or AgNO3)passing ionic current from a reservoir to a cation-selective membrane (Nafion). The current-voltage response is consistent with the new theory based on electro-osmotic flow over a broad range of reservoir salt concentrations (0.1mM-1.0M), after accounting for (copper) electrode polarization and pH-regulated silica charge. Above the limiting current, brackish water (0.1M) can be desalinated (< 10 mM) and then deionized (< 10mM) with reasonable efficiency by extracting water from a 0.5 mm outlet, which is spanned by a steady deionization shock in the pressure-driven flow. The deionization factor depends on the ionic charges and diffusivities.Since the sub-micron pores also filter particles by size, shock ED effectively combines ultrafiltration and deionization in one step and opens new possibilities for “membraneless" electrokinetic separations within porous media.
Keywords: electrokinetics, overlimiting current, porous media, deionization, water purification

8. Dressler; n/a

University of Massachusetts Amherst

"Inertial Theories for Dilute Viscoelastic Polymer Blends with a Volume Preserving Microstructure"
The rheology, microstructure, and non-Newtonian fluid mechanics of dilute immiscible polymer blends are investigated. To derive thermodynamically consistent flow equations for these materials, the Hamiltonian framework of non-equilibrium Thermodynamics is adopted. For a given set of non- equilibrium variables, this formalism allows to derive a set of local rate equations from a Poisson bracket, a dissipation bracket, and a Hamiltonian functional. Flow equations for polymer blends with inertia are developed and the theory is reduced to a set of flow equations without inertia. Furthermore, the viscosity coefficients of the non-inertial theory are expressed in terms of the viscosity coefficients of the inertial theory. It is shown that non-equilibrium Thermodynamics allows to derive local rate equations for materials as complex as polymer blends and that non-equilibrium Thermodynamics allows to coarse or fine grain between several levels of description. Reference: M. Dressler, “Inertial theories for dilute viscoelastic polymer blends with a volume preserving microstructure” J Non-Newton Fluid Mech, 173-174, pp. 40–48, 2012.
Keywords: droplet deformation, viscoelasticity, inertial flow theories

9. Heymann; Seth Fraden and Dongshin Kim

Brandeis University

"Multi-height precession alignment with pre-developed alignment marks"
Alignment is a critical and time-consuming process when fabricating multi-height photoresist masters. We increase visual contrast by pre-developing alignment marks to ease fabrication of masters with thick resist layers deposited on much thinner ones. We use a vernier calliper based alignment mark to achieve high precision alignment.
Keywords: SU8 master

10. Hilitski; Andy Ward, David Welch

Brandeis University

"Sliding and Friction of Microtubule Bundle"
Building artificial cilia is an overarching theme in biophysics research conducted at Dogic lab. In nature, cilia is a complex construct made of cross-linked microtubule (MT) bundles and driven by molecular motors. We intend to utilize same building blocks to construct simple and easily tunable biological oscillator. Making MT bundle and examination of its properties is the first step on the way to this long-term goal. In a bundle, two spatially aligned polymers are held together by excluded volume interaction. We achieve bundling by introducing depletion agent (polyethylene glycol, PEG) to the dilution of microtubules. Electrostatic repulsion due to intrinsic surface charge is screened by addition of salt (potassium chloride, KCl). Resulting microtubule interaction potential is attractive, and tends to maximize bundle overlap length. We use laser tweezers and umbrella sampling technique to measure interaction potential characteristics over range of PEG and salt concentrations. We also investigate bundle friction and sliding by moving one microtubule along the other.
Keywords: Microtubule, bundle, depletion, optical tweezers

11. Jensen; Daniel Pennachio, Emily Redston, Maria Persson Gulda, David Weitz, Frans Spaepen

Harvard University

"Building complex structures using simple spheres"
Hard spheres undergo phase transitions as a function of volume fraction, but that's hardly the whole story. Starting from initially-dilute colloidal liquids, we use sedimentation onto a patterned substrate to form densely-packed colloidal crystals and glasses. We examine the complementary roles of deposition flux and substrate boundary condition on the resulting structures, and apply these results to design and create more complex hard-sphere structures.
Keywords: colloid, crystal, glass, structure formation

12. Morse; Jay X. Tang

Brown University

"Effects of molecular adsorption and surface chemistry on bacterial swimming"
The effects of solid surfaces on hydrodynamic flows and the resulting swimming patterns of microswimmers are well studied phenomena. Recently, more studies have began examining these same systems near the interface of two fluids. Of particular interest to our group is how the presence of an air/water interface affects the behavior of self-propelled flagellated bacteria. We find that the chemical composition of the growth medium in which the swimmers are suspended greatly impacts swimming trajectories. This is due to the adsorption of certain molecules at the interface, altering the physical properties of the surface.
Keywords: Bacterial Swimming, Surface Chemistry, Hydrodynamics near Surfaces

13. Opathalage

Brandeis University

"Probing sub-resolution particle dynamics with Differential Dynamic Microscopy"
Differential Dynamic Microscopy is a technique which combines scattering and microscopy, which usually are considered as two complimentary techniques. This technique can be used to characterize the dynamics of sub-resolution particles in an optical microscope. Simulated and experimental time series images of a colloidal dispersion are analyzed in Fourier space to extract the diffusion constant. The results are verified in simulation and with experiment for Brownian motion of colloids in a viscous medium.
Keywords: DDM, characteristic time, sub-resolution particles

14. Radhakrishnan; Patrick T. Underhill

Rensselaer Polytechnic Institute

"Influence of shear on globule formation in dilute solutions of flexible polymers and particles"
Dilute solutions of flexible polymers interacting with proteins or particles often show formation of globules under certain conditions. All atom simulations of such systems are computationally expensive due to the separation of length and time scales between polymers and particles. So, we examined globule formation using a coarse-grained Brownian Dynamics model. We have analyzed the influence of shear on the formation and breakup of the polymer-particle globules. Neglecting hydrodynamic interactions between beads, we find that shear enhances globule formation by calculating the mean first passage times. Second, we examine the unraveling of globules on increasing the shear rate.
Keywords: shear, globule formation, polymer-particle mixtures

15. Sanchez; Zvonimir Dogic, Stephen DeCamp, Dan Chen, Daniela Nicastro, David Welch

Brandeis University, Zvonimir Dogic Lab

"All-in-one model system: from self-organized beating bundles to active nematics"
We have developed a highly tunable and robust model system for studying active matter and self-organized phenomena. Consisting of only simple components - microtubules, kinesin motor clusters, and a depletion agent that bundles the MTs - we see a striking diversity of distinct behaviors. Rather than focus on one example, this sound bite will provide a broad overview (and movies) of the richest and most relevant behaviors we've observed. So far, these include the spontaneous cilia-like beating of internally driven microtubule bundles, the emergence of metachronal waves in bundle arrays, extensile bundles and active flowing 3D gels, the self-assembly of active streaming 2D nematics, and finally self-propelled emulsion droplets. Taken together, these observations exemplify how assemblages of animate microscopic objects exhibit highly sought-after collective and biomimetic properties, challenging us to develop a theoretical framework that would allow for a systematic engineering of their far-from-equilibrium material properties.
Keywords: self-organization, active matter, cilia, gel, active nematic, cytoskeleton, microtubule, kinesin

16. Sarkar

Bulbul Chakraborty Group, Brandeis University

"Force Tilings and Rigidity of Dry Granular Solids"
There is a fundamental question about how dry grains without any cohesive interaction becomes solid. It has long been thought that structures in dry granular systems form in response to external stresses [Cates 1998]. Recent work in our group [Bi et.al.2011] has suggested that rigidity of granular solids is related to persistent structures in Force or Maxwell-Cremona tilings. In my talk, I shall (a) describe an algorithm to generate force tiles from arbitrary disordered networks, and (b) analyze the evolution of structures in these tiling as the system is sheared. References: 1. [Cates 1998] Cates, M.E.; et al. (August 1998). "Jamming, Force Chains, and Fragile Matter". Physical Review Letters 81 (9): 1841{1844. 2. [Bi et.al.2011] Dapeng Bi; et.al. "Jamming by Shear". Nature 480, 355{358 (15 December 2011)
Keywords: Algorithm, Granular Network, Force Tile

17. shao; Chinedum Osuji

Yale University

"Suspension rheology of polymer particles with thermosensitive deformability"
The rheology of particulate suspensions has been observed to be a strong function of particle deformability. For example, the shear thinning of red blood cell suspensions is shown to increase with an increase in the deformability of the cell membrane, with important implications for circulatory behavior [Magnus I. Gregersen, Science (1967)]. Likewise, shear thickening is nearly ubiquitous in concentrated suspensions of rigid particles but almost absent in suspensions of softer, more deformable objects [Howard A. Barnes, Colloids and Surfaces (1994)]. However, we still lack a comprehensive description of the role of particle deformability in suspension rheology. This is due in large part to the difficulty of systematically and independently varying particle rigidity, volume fraction, interaction strength and size. We report here on the preparation and characterization of a colloidal system that permits such variation. The polymeric particles of poly n-butyl methacrylate were synthesized with suspension polymerization in the presence of a polymerizable surfactant in water and exceeded amount of initiator and chain transfer agent. The use of a reactive species allows the surfactant to be covalently attached to the particle, with the degree of stabilization tunable by the molecular weight, concentration and species of the surfactant. The large amount of initiator and chain transfer agent result in a low molecular weight of polymer, which ensures a low glass transition and flow temperature of polymer. The elasticity of the particles can be changed over several decades simply by manipulating temperature in an experimentally convenient regime. For a fixed time-scale, below Tg, particles behave as near-rigid spheres, while, above Tg, they are soft yet viscous droplets with structural flexibility. We present results of dilute and concentrated suspension rheology and tentatively interpret our data based on the relative magnitude of the polymer relaxation time and the rheologically defined timescale.
Keywords: deformability, rheology

18. Sharma; Rafael A. Cabanas , Seth Fraden, Zvonimir Dogic

Brandeis University

"Equation of state of colloidal membranes using microfluidics"
We present a new experimental technique based on microfluidics to obtain pressure-area isotherm of colloidal membranes assembled by mixing rod-like fd virus and a non-adsorbing polymer. The internal composition of membranes transform from fluid like state to an amorphous solid like state as the osmotic pressure is increased.
Keywords: colloidal membranes, microfluidics

19. Tompkins; Seth Fraden

Brandeis University

"1D from 2: optical boundary conditions for reduced dimensionality"
We have developed a method for creating one dimensional rings of coupled non-linear chemical oscillators out of a two dimensional array. Our methodology involves using the Belousov-Zhabotinksy (BZ) chemical reaction with a photo-inhibitable catalyst and a custom Programmable Illumination Microscope (PIM) to selectively quell individual micrometer scale droplets of BZ within a two dimensional emulsion environment. By carefully selecting which drops are oscillatory versus stationary we can create customized geometries of oscillators of equal or reduced dimensionality with constant chemical boundary conditions. As a test for our system we've produced the first direct analog of the rings of oscillators theorized by Turing in his seminal paper on morphogenesis and experimentally demonstrated all six of his predicted states.
Keywords:

20. Uspal; H. Burak Eral, Patrick S. Doyle

MIT

"Shape asymmetric particles assemble under flow in quasi-two-dimensional microchannels"
Emerging applications in microfluidics increasingly require the imposition of spatial and temporal order on flowing suspensions of particles. Via combined theoretical and experimental approaches, we consider how particle shape can be tailored for flow induced assembly in a shallow, "quasi-two-dimensional" microchannel. Our main finding is that when fore-aft symmetry is broken, a single rigid particle will spontaneously align with the external flow field and migrate laterally to the channel centerline. Via a simple theoretical model, quantitatively borne out by experiments, we show how assembly arises from the interplay of lateral confinement by side walls and a particle’s hydrodynamic self-interaction. Contrary to common supposition, assembly does not require time reversal symmetry breaking. Building on this understanding of a single particle, we show that clusters of multiple asymmetric particles likewise assemble into spatially ordered, “crystalline” states.
Keywords: hydrodynamics, flow-induced assembly

21. Xu; Prof. Jianshu Cao

Department of Chemistry, MIT

"Modeling DNA deformation relaxation"
We report a study of DNA deformations by a coarse grained mechanical model. The DNA molecule at study is deformed by external forces induced by its binding to a protein. The way this deformation relaxes along the DNA chain is examined. We discovered that this deformation decays exponentially away from the binding site at a newly discovered lengthscale, which is in very good agreement with recent experimental observations. This new lengthscale is proposed to be results of competition between inter and intra DNA strand energy optimization. The knowledge of the local deformation relaxation will help us better understand how the repair mechanism inside cells finds the defected site out of millions of normal sites and in that direction help us design drugs (proteins) to do the searching even more efficiently.
Keywords: DNA, allostery, deformation, defects

22. Zakhary; Thomas Gibaud, Zi Jing Teoh, Ed Barry, Zvonimir Dogic

Brandeis University

"Quantifying the membrane-to-ribbon transition in 2D colloidal membranes"
Frustration is an important phenomenon in self-assembly which results in the formation of complex phases. We investigate a system of two-dimensional colloidal monolayer membranes composed of rod-like fd viruses, and demonstrate that the competition between inter-rod attraction and chirality results in a reversible transition to an array of twisted ribbons. Using optical microscopy, we elucidate the fluctuation spectrum of the membrane edge, and find that a peak develops at a characteristic wavelength close to the transition. We also present preliminary results in determining the free energy landscape associated with the transition by taking force extension data using optical tweezers.
Keywords: Self Assembly, Frustration, Chirality, Twisted Ribbons,

23. Zimoch; Gareth H. McKinley, A.E. Hosoi

MIT

"Tuning Capillary Breakup in Discontinuously Rate Thickening Suspensions"
Using Discontinuously Rate Thickening Suspensions (DRTS) as a model system, we show how formation of Beads-on-a-String morphologies can be controlled through viscous drag in capillary breakup of liquids. To minimize the effect of gravity, we developed a new experimental method where the filament is supported in a horizontal position at the surface of an immiscible oil bath by the interfacial tension of the oil-air interface. We show that the evolution of thin DRTS filaments in capillary breakup experiments and the process of formation of complex high aspect ratio structures are well represented with a set of 1-dimensional equations solved numerically.
Keywords:

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