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An atom is cooled by a standing-wave light field between two high-quality mirrors. Cavity cooling avoids the usual light scatter into the surroundings. Instead, the light leaking out of the mirrors is blue-shifted to a higher frequency (image credit: Pepijn Pinkse Max Planck Institute of Quantum Optics)
Artist's impression of an atom cooling device
NECF Meeting Abstracts

72nd New England Complex Fluids Meeting
Brandeis University | Friday, September 22, 2017
Registration deadline: Wednesday, September 20, 2017
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Abstracts for Invited Talks and Sound Bites:

Invited Talks

1. Bathe

" Programming Functional DNA Nanoparticles"

Scaffolded DNA origami offers the ability to program nearly arbitrary structured DNA nanoparticle geometries on the 10 to 100 nanometer scale. Applications of these assemblies include programmed therapeutic delivery, metallic nanoparticle fabrication, designer excitonic circuits, and self-assembly of higher-order 2D and 3D crystalline materials. To facilitate the autonomous design of complex nanoparticle geometries for these preceding applications, we have developed fully automated, top-down sequence design algorithms for the synthesis of nearly arbitrary target geometric shapes based on scaffolded DNA origami. Anti-parallel (DX) or parallel (PX) crossover motifs may be used to program nanoparticles with either synthetic staple strands or single-stranded DNA scaffold alone. Nanoparticle edges may be composed of either two, six, or arbitrary alternative numbers of parallel helices, depending on the target size and mechanical properties desired. Asymmetric PCR is implemented to synthesize fully synthetic scaffold sequences on the 2 to 12kb scale without relying on viral genomes that contain protein-coding sequences. Folding assays are used together with 3D cryo-electron microscopic reconstructions to validate nanoparticle designs. Ongoing and future applications of these designer nanoparticles to gene-based therapies and functional materials will be presented.


Pan, K., Bricker, W., Ratanalert, S., Bathe, M. Structure and conformational dynamics of scaffolded DNA origami nanoparticles. Nucleic Acids Research, 45: 6284 (2017).

Designer nanoscale DNA assemblies programmed from the top down. Veneziano, R., Ratanalert, S., Zhang, K., Pan, K., Zhang, F., Yan, H., Chiu, W., Bathe, M. Science, 352: 1534 (2016).

Casting inorganic structures with DNA molds. Sun, W., Boulais, E., Hakobyan, Y., Wang, W., Guan, A., Bathe, M., Yin, P. Science, 346: 717 (2014).


2. Bradley

UMass Amherst
"Seeded Emulsion Polymerization for Non-Spherical Particles and Clickable Janus Colloids"
Versatile synthesis schemes for diverse colloidal building blocks are essential to the continued development of self-assembled structures for fundamental studies in condensed matter and practical applications in advanced materials. While there are many techniques for colloidal synthesis, emulsion-based methods are ideal for large scale synthesis, but are often limited in chemistry and morphology. In our work, we design new emulsion-based syntheses that exploit polymerization-induced phase separation to control the structure and composition of anisotropic colloids. We will first demonstrate the synthesis of non-spherical polystyrene particles through the formation of pure-sided Janus particles and subsequent removal of a sacrificial phase. The particle shape is dictated by the intermediate Janus structure which we show can be controlled by choosing the appropriate sacrificial polymer, surfactant, and monomer ratio. In addition to controlling the shape of colloids, we can also tailor the chemical functionality through the use of click chemistry. We will show that we can synthesize clickable Janus particles containing a click-active acetylene moiety that can be functionalized through thiol-yne click reactions with commercially available thiols. Janus particles are modified to be amphiphilic by introducing either carboxyl, hydroxyl, or amine moieties. We also demonstrate that regulating the extent of the modification can be used to control the particle morphology, and thus the type of emulsion stabilized, as well as to fabricate composite Janus particles through sequential click reactions. Thiol-yne click chemistry offers a fast-reacting and modular synthesis method to transform clickable seed Janus particles. Our ability to design the structure and composition of diverse colloids will provide versatile new building blocks for self-assembly.

3. Fardin

Universite Paris Didero
"Rheology with 3 time scales"
Are cats liquid? Drawing on this seemingly absurd question, I will discuss the use of three important time scales in rheology: the relaxation time, the inverse shear-rate, and the experimental time. To illustrate the regimes found by comparing these time scales, I will compare the Newtonian flow of water, and the non-Newtonian flow of wormlike micelles.

4. Zhao

"Soft Living Materials and Machines"

Nature designs a vast library of soft materials to constitute most machineries of living bodies. Soft living materials possess a set of attributes — such as high compliance, resilience, robustness, and capabilities of sensing, responding and self–healing — unattainable in conventional engineering materials. For example, articular cartilage, a natural hydrogel that contains 70% water, can maintain impressively high fracture toughness under millions of cycles of loads. Skeletal muscles can achieve high actuation stress, strain and energy efficiency, yet operating over years. Mussel secrets soft glues to form extremely robust adhesions to rocks and metals in flowing water with high salinity. What are nature's strategies in designing various soft living materials? How to fabricate soft materials that possess properties and functions as living organisms? Can we integrate soft living and engineered machines to create new forms of machines or life?

These questions have fostered a nascent field that not only advances fundamental knowledge in mechanics and materials but also impacts on our society's grand challenges in health, food, water and joy of living. In this talk, I will show that unconventional polymer network architectures represent a general strategy to design soft living materials with extraordinary properties. Guided by our theory, I will demonstrate the design of synthetic cartilages, artificial muscles, and mussel-inspired glues with world-record performances. I will then introduce a general method based on our 3D bio-printing system to integrate soft materials, living cells with sensors, actuators and computer chips for systematic design of various soft living machines. The interplays between theory, experiments and design will be emphasized throughout the talk.


Sound Bites

1. Abdi; Craig Maloney

"Thermally activated transitions in an essentially athermal system"
We present Brownian simulations on dilute suspensions of superparamagnetic particles subject to rotating magnetic fields. At sufficiently high rates, above the second bifurcation, the typical behavior of a small set of particles, initially aligned in a chain along the axis of the field is to go through an episode of chaotic motion and, after some time to decay into one of a number of possible periodic orbits with a compact spatial structure. Transitions out of the periodic orbits back to chaos is also possible at non-zero temperatures. Dynamics above the second bifurcation could be described as a Markov process with no memory. We report on associated rate constants for the transitions which depend on Mason number and temperature. The entry into the periodic orbits is governed by the underlying chaotic dynamics, however, the exit out of them is a thermal process.
Keywords: paramagnetic colloids, rotating field, chaos, periodic orbit, Markov process, Arrhenius process

2. Aghvami; Seth Fraden

"Studying laser induced protein crystallization with Second Harmonic Generation & Fluorescence Lifetime Microscopy"
It has been shown, when high energy laser pulses are shot to a supersaturated protein solution, it improves the crystallization rate. However, the mechanism of this higher rate of crystallization is still not clear. We found that by shooting the laser to the protein solution we can denature the protein and nucleation can be started from denatured protein. We used FLIM and SHG microscopy techniques to detect denatured protein and protein crystals in supersaturated protein solution which is shot by the laser.

3. Beller; David Nelson, Sherry Chu, Mehran Kardar

Brown University
"Ancestral lineages as coalescing (super)diffusive random walkers in biological range expansions"
Range expansions, the spread of a population into new territory, occur in many biological scenarios such as invasive species and tumor growth. For populations of non-motile individuals, ancestral lineages traced backward in time follow coalescing diffusive or superdiffusive random walks, in both experimental and theoretical model systems. We study a key quantity called T_2, the expected time since common ancestry for two individuals at the advancing front, which is proportional to the number of genetic differences accumulated by successive mutations. Using continuum theory and the lattice-based "stepping-stone" numerical model, we examine how T_2 depends on parameters such as the time since the range expansion began, the size of the habitat and its boundary conditions, and diffusive vs superdiffusive behavior.
Keywords: Coalescent theory, population genetics, superdiffusion

4. Beuken; Irmgard Bischofberger

"Interplay between fingering and jamming in fluid instabilities"
The displacement of a material by a fluid can induce the spontaneous formation of complex patterns. For example the displacement of a Newtonian fluid by air leads to the well-established viscous fingering instability. But what happens when one of the fluids is a non-Newtonian fluid that exhibits shear-thickening and shear-jamming behavior (such as cornstarch-water mixtures) as a response to an applied stress? Our preliminary results on cornstarch-water mixtures displaced by air in a Hele-Shaw cell suggest an extraordinarily rich behavior: the system can exhibit three distinct modes of pattern formation as a result of the transition of the system from liquid to solid: smooth fingering in the fluid regime and two distinct modes of fractures, branched fractures developing in all directions radially from the injection point and single fast cracks, both characteristic of solid materials. We will discuss the parameters that set the transitions between these types of growth and their relation to the rheology of the suspension.
Keywords: Fingering, fracture, stress, packing fraction

5. Bruss; Sharon C. Glotzer

University of Michigan
"Congestion model of active particle phase separation"
Self-propelled particles phase separate into coexisting dense and dilute regions above a critical density that depends on the particles’ rotational noise. The statistical nature of their stochastic motion lends itself to various theories that predict the onset of phase separation. However, these theories are ill equipped to describe such behavior when noise become negligible. We present a predictive model that does not require any stochastic ingredient. Rather, it relies on two density-dependent timescales: the mean time particles spend between collisions; and the mean lifetime of a collision. We show that only when the former is less than the later, do collisions last long enough to acquire additional collisions, thus developing a growing cluster and initiating phase separation. Using both analytical calculations and active Brownian particle simulations, we measure these timescales and determine the critical density for phase separation in both 2D and 3D.
Keywords: Active matter, phase separation

6. Cho; Irmgard Bischofberger

"Multiscale probing of colloidal gel dynamics"
Understanding mechanical properties of colloidal gels in the context of their microstructure and internal dynamics remains a challenge, because of the richness of different length and time scales involved. We apply Differential Dynamic Microscopy (DDM) to the non-ergodic system to explore multiple scales simultaneously by mapping, and consequently extracting dynamic information from, a time correlation function that exhibits stretched exponential decay. Our initial results suggest that, as a gel evolves, its network retains diffusive behavior at small length scales, but displays more pronounced stretched exponential decay in the correlation function, which conforms to our qualitative evaluation of its real space images. A complete validation of DDM applied to a simple colloidal gel can pave the way for an analysis of more complex systems, such as a binary mixture of colloidal particles that bear different interparticle strengths.
Keywords: colloidal gel, Differential Dynamic Microscopy

7. Collins; Alison O'Neil, Xu Zhang, Julie Brouchon, John Heyman, Lee Rubin, Dave Weitz

Harvard SEAS
"Collagen Drops For Neocortical Spheroid Differentiation"
Neocortical organoids, cultured from induced pluripotent stem cells (iPSCS), reproduce aspects of human brain biology and their study may lead to medical applications. We are trying to simplify and speed up one aspect of the neocortical organoid growth protocol: encapsulating stem cell spheroids in a liquid that gels. The mechanical property of the gel helps the stem cells change into neurons. We flow collagen containing spheroids, NaOH with growth media, and oil into a Polydimethylsiloxane (PDMS) chip. The NaOH initiates the gelation of the collagen. The basified collagen pinches off into drops in the oil and is then heated to complete gelation. We will show a movie of successful encapsulation of the spheroids into collagen drops that gel.
Keywords: collagen, stem cells, drop

8. DeBenedictis; Timothy J Atherton

Tufts University
"Simulating smectic oily streaks "
A smectic liquid crystal film on a flat surface with frustrated boundary conditions will form an “oily streak” pattern characterized by the smectic layers arranging into hemicylinders that lie parallel on the surface. Experiments have shown that the topography of the free surface of an oily streak pattern reflects this hemicylindrical structure. Using a finite element continuum theory model with adaptive mesh refinement and a moving mesh, we simulate the oily streak pattern and examine the topographical features that result from different relative strengths of the anchoring potentials and surface tension.
Keywords: smectic liquid crystal, finite elements, moving mesh, oily streaks

9. Dellatolas; Thibaut Divoux, Ming Guo, Irmgard Bischofberger

"Hydrogel reinforcement by filler nanoparticles"
We investigate the effect of free, non-interacting polystyrene nanoparticles dispersed in agarose hydrogels on the mechanical properties of the gels. Above a critical particle volume fraction, the gel stiffness drastically increases. Remarkably, this increase is independent of the particle size, the surface properties of the particles and even the type of polymer network. Moreover, the same increase has been observed in gels where particles act as cross-linkers and very similar characteristics govern the reinforcement of rubbers. This suggests a common mechanism for the strengthening associated with a local reinforcement of the network induced by the particles.
Keywords: hydrogel, colloidal particles, network reinforcement

10. Ding; Kuo-chan Hung, John Heyman, David Weitz

"Droplet microfluidic platform for rapid isolation of rare antigen-specific primary B-cells"
The conventional method to isolate monoclonal antibody against a given antigen is lengthy and inefficient. We developed a droplet-microfluidic platform to isolate cells based on binding of their secreted antibody. Our platform is capable of isolating desired cells even if they consists of only 0.1% of the total population. We are able to isolate primary B-cells and retrieve antibody sequences from isolated cells.
Keywords: Microfluidics, antibody

11. Duclos; Sebastian Streichan, Zvonimir Dogic

Brandeis university
"3D active nematics composed of microtubules and fd virus"
We doped a passive 3D nematic liquid crystal composed of elongated fd virus with Microtubules (MTs) and clusters of Molecular motors that can slide the MTs passed one another. This composite material assembles into a three dimensional active liquid crystal. We are currently looking at the structure and the dynamics resulting from the active sliding of the MTs.
Keywords: active matter, liquid crystals

12. Fang

"Study 2D DNA-grafted colloids’ phase behavior using molecular dynamics"
Coating colloidal particles in DNA strands is a robust way to observe self-assembly phase behavior in a microscopic environment. Specific interactions can be constructed between colloidal particles via engineering DNA strand length, base pair sequence, as well as via applying environmental controls such as temperature. In this project, molecular dynamics simulations were utilized to study how interactions between two species of DNA-coated colloidal particles affected self-assembly and phase behavior. These simulations confined the system to a 2D surface allowing the particles less freedom to minimize free energy than that of a 3D space. Simulation results predict the existence of metastable phases and diffusionless transformation across phase boundaries.
Keywords: self-assembly, DNA-grafted colloids

13. Fang; Ben Rogers

"Study 2D DNA-grafted colloids’ phase behavior using molecular dynamics"
Coating colloidal particles in DNA strands is a robust way to observe self-assembly phase behavior in a microscopic environment. Specific interactions can be constructed between colloidal particles via engineering DNA strand length, base pair sequence, as well as via applying environmental controls such as temperature. In this project, molecular dynamics simulations were utilized to study how interactions between two species of DNA-coated colloidal particles affected self-assembly and phase behavior. These simulations confined the system to a 2D surface allowing the particles less freedom to minimize free energy than that of a 3D space. Simulation results predict the existence of metastable phases and diffusionless transformation across phase boundaries.
Keywords: self-assembly, DNA-grafted colloids

14. Gault; Zsolt Terdik, Joerg Werner, Dave Weitz

Harvard University
"In situ visualization and mechanical study of a transparent filled rubber"
Filled rubbers are composite materials containing two interpenetrating phases: crosslinked elastomers, and a ‘filler’ consisting of colloidal particle aggregates. Above a critical volume fraction, the colloidal aggregates form a system-spanning subnetwork that reinforces the elastomer network and introduces a new energy loss mechanism at low strains of only 1-5%. This low-strain energy loss mechanism, known as the Payne Effect, is one of the mechanical hallmarks of filled rubbers and is a major contributor to rolling friction in tires. The goal of this project is to probe these microstructural dynamics in a model filled rubber, in combination with bulk rheological tests, to gain new insight into physics of the Payne effect.

15. Gharbi; Zvonimir Dogic and Seth Fraden

Brandeis University
"Curvature driven controlled dynamics in active nematic liquid crystals"
We explore the effect of curvature on the dynamic of defects in an active nematic liquid crystal. We create surfaces with controlled morphologies and opposite Gaussian curvature to investigate the role of geometry in controlling the non-equilibrium dynamics of defects in active nematics. The goal of our work is to illustrate how the interplay between order, activity, and geometric confinement can lead to stabilized flows in active matter. Our preliminary results indicate that curved interfaces play an import role in controlling the trajectories of defects in non-equilibrium systems. A fuller understanding of the mechanisms that govern ordered dynamics in active nematic liquid crystals is under development.
Keywords: Active nematic, topological defects, curvature

16. Giso; Andrew M. Mascioli, Timothy J. Atherton

Tufts University
"Simulated Annealing of Particles Constrained to a Sphere"
Packings on curved surfaces necessitates the presence of defects. Previous work demonstrated that jammed packings on curved surfaces need fewer contacts than linear analogues. We investigate how defects emerge when a surface is not completely covered. Hard spheres are constrained to a sphere under the force of gravity and a stochastic force. The simulation proceeds till the particles are in a jammed state. We then use various metrics to understand the underlying properties of the system.
Keywords: Simulated Annealing, Jamming, Packing

17. Hensley; Ben Rogers

Brandeis University
"Measuring DNA Grafted Colloid Crystal Nucleation Rates"
Grafting DNA onto colloidal particles can `program' them with information that tells them how to self-assemble. The hybridization of complementary DNA strands grafted on to the particles leads to an interaction that is tunable via temperature. We begin to explore the roles of interaction strength of the DNA strands grafted to particles on the nucleation rates and barriers to nucleation as they form crystals. We do this by using a microfluidic dropmaker to make an emulsion of monodisperse aqueous droplets in oil with the droplets containing two species of DNA grafted particles with complementary strands. We plan to perform a counting experiment where the number of droplets that have not yet formed crystals is counted over time at various temperatures. By gathering statistics for a large number of droplets, nucleation rates and barriers can be estimated at a variety of interaction strengths (temperatures).
Keywords: DNA, self-assembly, nucleation

18. Hunter; Mike Norton, Amanda Chisholm, Youssef Fahmy, Seth Fraden

Brandeis University
"Preparing homogeneous photosensitive oscillatory chemical reactors"
Preparation of networks of homogeneous, photosensitive, oscillatory, micronscale BZ chemical reactors will be discussed. Photosensitive mixtures of the BZ reaction within microfabricated lattices are of great interest as they have proven to be a platform for testing quantitative theories related to pattern formation and control of active, non-equilibrium networks. The chief sources of heterogeneity in the dynamics of the microreactors will be detailed. A novel method of measuring the heterogeneity of light projected onto a microscopic sample, necessary to quantify the extent to which the photosensitive oscillators are made heterogeneous by light, using common lab supplies will be presented. An algorithm to correct light heterogeneity measured with this method will be shown. Progress in creating a routine which will track actively oscillating BZ wells, and iteratively adjust light until they oscillate with the same period will outlined.
Keywords: Complex networks, Non-linear control, Lambertian optics, microfluidics

19. Joshi; Elias Putzig, Aparna Baskaran and Mike Hagan

Brandeis University
"Microscopic simulations of active nematics: Effect of inherent flexibility of microtubule bundles on defects shape"
Active nematics are liquid crystals that are driven out of equilibrium by energy-dissipating active stresses. In such systems the ordered nematic state is unstable to the proliferation of topological defects, which undergo birth, streaming dynamics, and annihilation to yield a seemingly chaotic dynamical steady state. In this work, we describe large-scale simulations of a particle-based computational model for active nematics, motivated by an experimental active nematic system containing extensile bundled microtubules and molecular motor proteins. Extending upon previous theoretical and computational work, our model explicitly describes degrees of freedom internal to bundles, allowing us to study the connection between the microscale material properties of active units and emergent behaviors such as defect shapes and inter-defect correlations. We identify a scaling relation between these behaviors and a combination of activity and bending rigidity, which demonstrates that increased activity renormalizes the bending rigidity to smaller values. We also present a systematic way to estimate macroscale material constants such as the bending modulus from observations of defect shapes in experimental or simulation data.
Keywords: Active matter, Polymers, Liquid Crystals, Nematics

20. Kang; John Lisman, Michael Hagan

Brandeis University
"Structural principles for stable synapses and long-term memory"
There is increasing evidence suggesting that memory storage involves graded enlargement of synapses. Thus synapses must be able to change size in response to external stimuli, yet once changed, must be structurally stable to insure the persistence of long-term memory. In this work, we explore physical principles that enable self-assembled structure to be stable at a fixed size despite continual turnover of its individual constituents. First, we present three equilibrium size regulation mechanisms to achieve finite stable size, all of which satisfy detailed balance. We then discuss two general classes of non-equilibrium mechanisms for size control, which differ in the direction of probability flow among steady states. We present one biologically relevant example for each class. To compare all models on an equal footing, our analysis focuses on how the size distribution depends on the free subunit concentration. We find that different mechanisms are characterized by distinct concentration-dependent stable sizes and size fluctuations, which provides testable predictions for experimentally differentiating among these mechanisms.
Keywords: synapses, structural stability, non-equilibrium steady state, self-assembly

21. Lowensohn; Guillermo Narvaez Paliza, W. Benjamin Rogers

Brandeis University
"Quantitative study of linker-mediated binding between DNA-grafted colloids"
DNA is a potentially useful tool for self-assembling novel materials from colloidal particles: its interactions are chemically specific, tunable, and can be predicted from the base sequence. Examples of exotic materials could be aperiodic, prescribed assemblies of many particle species or reconfigurable photonic materials (like glasses or crystals) that can change their structure, and thus their stop band, on demand. However, existing approaches, which rely on direct hybridization of DNA strands grafted to colloidal particles, are too limited in their design space to build such materials. This project explores an alternative paradigm, in which particles interact through DNA strands dissolved in solution instead of through direct binding of grafted strands. The project is divided into three parts: (1) exploring the phase behavior of a suspension containing two different species of DNA-grafted colloidal particles, which interact through a single complementary linker sequence dissolved in the solution; (2) developing a statistical mechanical model relating DNA sequence, linker concentration, and grafting density to the observed phase behavior; and (3) using what we learn in part (2) to design mixtures of competitive linkers to produce new kinds of interactions, like ones whose specificity depends on temperature. Developing new kinds of interactions is the first step toward creating reconfigurable particle-based materials with tunable optical properties.
Keywords: Programmable Self Assembly

22. Merminod; W. Benjamin Rogers

Brandeis University
"Characterizing DNA-mediated interactions between colloidal particles and fluid membranes"
Membrane-mediated interactions between proteins lead to fascinating self-assembled structures, such as the 'purple membrane' in Halobacteria. Here, we present a model system for exploring the physical mechanisms leading to self-assembly of colloidal particles on solid surfaces. Specifically, we graft single-stranded DNA onto colloidal particles and a glass coverslip, so that hybridization of complementary DNA molecules generates an attractive, specific force between them. Using total internal reflection microscopy, we measure particle-surface attractions with kT-scale accuracy and the associated binding kinetics with high temporal resolution. We aim at exploring how the strength, specificity, and dynamics of the interactions that emerge depend on the molecular attributes of the ligands and receptors. These experiments may help shed light on self-assembly of small particles bound to membranes.
Keywords: DNA, particles at interfaces

23. Metcalf; S.J. Decamp and Z. Dogic

"Dynamics of 2D Active Nematics"
We study the diverse phenomena that emerge from extensile bundles composed of microtubules (MTs), motor proteins, and a depletion agent which are confined to a 2D oil-water interface. Here, we characterize and quantify the dynamics of this system on many length scales. By tracking individual filaments, we are able to probe the system on the microscopic scale. We find that the microtubules exhibit dipolar extensile dynamics. The speed of these dynamics scales with ATP concentration until the system is saturated. These results quantitatively agree with measurements made on the mesoscale using fluorescence recovery after photobleaching (FRAP). From these experiments, we extract a time scale for the system. We also characterize the active length scale of the system by looking at the vortex area distribution of the MT flows. We find that the distribution is exponential in agreement with numerical results. These measurements allow for direct comparison of this tunable experimental system to the theoretical models of active nematics.
Keywords: active nematics

24. Nawar; Feng Xin, Max Zieringer, Lu Mi, Dave Weitz

Harvard SEAS
"Thermoplastic microfluidic chips for the scalable production of double emulsions"
Thermoplastic microfluidic dropmakers offer a wide range of advantages for the high throughput production of micron to millimeter-scale drops, especially in industrial settings, particularly in applications where large volumes of monodisperse drops are needed. While thermoplastics can be functionalized in a wide range of ways to produce water-in-oil or oil-in-water drops, that is, single emulsions, it is much more challenging to produce complex emulsions (such as double emulsions) in parallelized thermoplastic chips, as it requires segregated wettability. Here we describe PMMA-based microfluidic double emulsion devices where channels have been fabricated using laser engraving. This method allows for the production of water-in-oil-in-water double emulsions, which we have done using two different device designs. We also discuss parallelization of dropmakers using these approaches.

25. Norton; Ian Hunter, Marilena Moustaka, Amanda Crisholm, Youssef Fahmy, Seth Fraden

Brandeis University
"Multistable Dynamical Network of Chemical Oscillators"
Coupled-oscillators networks are an important class of dynamical systems found in both the natural and engineered worlds. The spatio-temporal patterns exhibited by such networks depend heavily on inter-nodal interactions and topology. Using the Belousov-Zhabotinksy chemical reaction as our oscillator and a microfluidic chip to control topology, we examine the dynamics of a 4-ring network of inhibitor-coupled wells. While the network is small, it possesses multiple stable attractor states each possessing distinct dynamics. As such, it is a model system for understanding how to design controllers for complex systems with multiple fixed points. In this talk, preliminary experimental results will be compared to numerical models. Our goal is to create minimal models that predict the possible attractor states of the system and their basins of attraction.
Keywords: Nonlinear Dynamics, Networks, Oscillators

26. Opathalage; Michael Norton, Michael Juniper, Blake Langeslay, Seth Fraden, Zvonimir Dogic

Brandeis University
"Defect dynamics of the 2D confined active nematic liquid crystals"
We study the role of boundary conditions on a simplified experimental model of biological active matter system composed of extensile filamentous bundles of microtubules driven by clusters of kinesin motors, to elucidate the structure and dynamics of active nematic liquid crystals. These bundles form a dense quasi-2D active nematic liquid crystals when sediment onto a surfactant-stabilized oil-water interface. We further confine this system onto different boundary conditions, imposing total topological charge and obstructing the natural length scales of the bundles. We observe unique dynamical behavior under high confinement in the order of hundred micrometers. The system produces two circulating +1/2 defects, drive the material toward the edge of the circle. The circulating behavior is eventually destroyed by buckling of the nematic at the container wall which nucleates a +/- 1/2 defect pair. This behavior is remarkably periodic until the energy supply of the system; ATP is drained.
Keywords: Active Nematic, Confinement, Microtubule-Kinesin

27. Paquay; Chris Sigl, Hendrik Dietz, Seth Fraden, Mike Hagan

Brandeis University
"Self-assembly of coarse-grained DNA origami subunits"
DNA origami is an fruitful method to create a wide range of simple and complex objects on the nanometer scale. By folding DNA into truncated tetrahedra ("triangles") with protrusions and recessions on their outer edges, one can add attractive interaction between these triangles. This way, the triangles can self-assemble into icosahedra much the way virus coat proteins do, but on larger, more accessible length- and timescales. These icosahedra could in turn be an ideal candidate for producing functional materials because of the unprecedented control over the subunit structure and functionality. To guide the design of these building blocks we perform molecular dynamics simulations of coarse-grained, rigid triangles with reactive patches. By probing the self-assembly kinetics and assembly products as a function of the reactive patch properties we attempt to determine the optimal design strategy for the DNA origami building blocks in order to build octahedra and icosahedra. In particular, I will focus on the influence of the interaction strength on the assembly yield.
Keywords: self-assembly, DNA origami, simulations

28. Sheehy; W. Ben Rogers, Seth Fraden

Brandeis University
"Using DNA Origami to Study the Dynamics of Self-Assembly"
DNA origami is a useful tool for studying pathways of self-assembly. With the ability to create unique shapes and interactions with nanometer accuracy, DNA origami allows for the construction of a novel set of self-assembling systems. One such shape is a triangular origami tile that assembles into lattices in two dimensions. By probing the system with atomic force microscopy and and total internal reflection fluorescence microscopy, we will study the dynamics of the self-assembling system in order to better understand the underlying pathways to assembly. Additionally, we aim to extend the benefits of specific interactions by creating DNA origami particles on the colloidal length scale, allowing for the use of optical measurement techniques to further study the dynamics of self-assembly.
Keywords: Self-assembly, DNA origami,

29. Stolovicki; Elad Stolovicki, Lloyd Ung, Roy Ziblat and David A. Weitz

"Drop chemostats: White biotechnology on a chip"
White biotechnology, the production of chemicals using cells or enzymes, is increasingly employed as it results in higher, overall greener chemical processes. Bio-production is also ideally suited in cases where the selectivity of enzymes for a specific molecule enantiomer (chirality) is critical. By using an emulsion of small drops of growth medium in oil as a micro-reactor, we can optimize the production yield of a desired bio-product, preforming toxicity tests or response-resistance assays. Another key feature of our system is that each, individual droplet emulates a larger-scale bioreactor that can be grown using batch, fed-batch or continuous culture methods. Thus, drop micro-reactors have the advantages of reducing R&D production time and cost by having thousands of parallel experiments, greatly reduced quantities of reagents, and compact space requirements.
Keywords: white biotechnology bio-production, drop micro-reactors, microfluidics, green chemistry

30. Terdik; David Weitz, Frans Spaepen

Harvard University
"Traction force rheology"
We present a new technique, traction force rheology, to directly measure the mechanical response of colloidal solids (crystals and glasses) in response to imposed shear strain, while observing the dynamics of individual colloidal particles using confocal microscopy. The technique consists of forming a composite bilayer consisting of a colloidal solid on top of a soft, polymer gel with embedded tracer particles. A precisely controlled shear strain is applied to the bilayer leading to controlled deformation of the colloidal crystal/glass. In addition to directly observing rearrangements and defects that occur within the colloidal crystal/glass during plastic deformation, we also measure the deformation of the tracer particles embedded in the polymer gel. Given the observed deformation of the polymer gel and the measured mechanical modulus, the traction forces exerted on the polymer gel by the colloidal solid can be inferred using traction force microscopy. Experimental details, challenges, and current results will be discussed
Keywords: rheology, colloids, mechanics

31. Xie; Timothy J. Atherton

Tufts University
"Dynamic packing on arrested spherical coalescence"
It’s showed in the experiment that the coalescence of two emulsion droplets could be arrested in an intermediate shape if the surface tension is offset by the interaction of particles coated on the surface. We simulate the evolution of the system with hard particles diffusing on the surface from when the two droplets just contact each other. The coalescence is halted if the particles couldn’t move without overlapping others. We tend to investigate how the relaxation speed influence the final packing from the simulation.
Keywords: coalescence, packing

32. Zhang; Irmgard Bischofberger

Massachusetts Institute of Technology
"Dendritic growth in the viscous fingering instability "
The displacement of a more viscous fluid by a less viscous one in a quasi-two dimensional geometry leads to the formation of complex fingering patterns. In isotropic systems, intricate branching morphologies arise from repeated tip-splitting of the evolving finger. When anisotropy is introduced into the system, the growth morphology changes dramatically: the fingers now exhibit dendritic growth, characterized by stable needle-like protrusions decorated with regular side-branches. We investigate these dendritic structures in anisotropic environments provided by engraving a six-fold symmetric lattice on our Hele-Shaw cell for a large range of viscosity ratios between the less-viscous inner fluid and the more-viscous outer one. Remarkably, the imposed six-fold symmetry only leads to six-fold symmetric growth at the lowest viscosity ratio. At higher values, the pattern instead adopts a twelve-fold symmetry; in addition to the six main branches evolving in the imposed direction, an additional six sub-branches emerge, at a 30° angle to the preferred growth direction. We discuss how this transition from six- to twelve-fold symmetry is related to an intrinsic length scale in the fluids that sensitively depends on the viscosity ratio.
Keywords: Instability, Dendrites, Length scale, viscosity ratio

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