NECF Workshop

Abstracts for Invited Talks and Soundbites

80th New England Complex Fluids Meeting
Brandeis University | Friday, September 20, 2019
Registration deadline: Wednesday, September 18, 2019

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Invited Talks

1. Cohen, Tal

MIT
"Growth, instability, and failure: bringing order into the chaos of natural phenomena"
Natural phenomena such as growth, instability, and failure, can be highly dependent upon stochastic mechanisms at the microscale, which may be activated, for example, by the existence of initial imperfections, the action of molecular motors, or the diffusion of constituents. Yet, at the macroscale, astonishing order is often observed. In this talk, I will discuss our recent attempts to bring a deterministic understanding to explain such processes by focusing on some examples. We will consider the growth of cavities in soft materials and their transition into cracks, and the growth of bodies by chemical reactions of association or dissociation on their boundaries.
Keywords: 

2. Harris, Daniel

Brown University
"Hydrodynamic mechanisms for particle aggregation at fluid interfaces"
Understanding the forces on small bodies at fluid interfaces has significant relevance to a range of natural and artificial systems. In this talk, I will discuss two recent investigations of fluid-induced attraction mechanisms of non-Brownian particles, at free surfaces and within density stratified fluids.

In the first part, I will present direct measurements of the attractive force between centimetric disks floating at an air-water interface. It is well known that objects at a fluid interface may interact due to the mutual deformation they induce on the free surface, however very few direct measurements of such forces have been reported. In the present work, we characterize how the attraction force depends on the disk radius, mass, and relative spacing. The magnitudes of the measured forces are rationalized with scaling arguments and compared directly to numerical predictions.

In the second part, we observe and rationalize a new fundamental effective attractive mechanism by which particles at isopycnals within a density stratified fluid may self-assemble and form large aggregates without need for short-range binding effects (adhesion). This phenomenon arises through a subtle interplay of effects involving solute diffusion, impermeable boundaries, and the geometry of the aggregate. Control experiments with two particles isolate the individual dynamics, which are quantitatively predicted through numerical integration of the underlying equations of motion.

Ongoing and future work in these areas will also be discussed.
Keywords: 

3. Sgro, Allyson

Boston University
"Coordinating multicellular biological behaviors through intracellular signaling"
Coordinating biological behaviors across groups of cells is critical for a wide range of biological processes ranging from development to wound healing. How these basic group phenomena are regulated, potentially by modulating factors like the frequency of synchronized signaling or the speed of group migration at the level of single cells is still an open question. Identifying what single cells tune in their own signaling programs to produce these phenotypic changes in group-wide behaviors would yield parameters we can control when reprogramming these systems for our benefit. To address this challenge, we are pursuing complimentary efforts in two model systems where single-cell level and collective signaling can be simultaneously visualized with group behaviors: the social amoeba, Dictyostelium discoideum, and synthetic stromal tissues. We are interrogating signaling behaviors in these systems using a combination of techniques to visualize and control cellular signaling. Through directly controlling signaling, we can causally link our observations of single-cell signaling dynamics to the population-wide behaviors they control. Together, these efforts will allow us to identify how population-wide multicellular behaviors are regulated at the level of single-cell signaling.
Keywords: 

4. van Rees, Wim

MIT
"Simulation and inverse-design of thin shape-shifting structures"
Recent progress in additive manufacturing and materials engineering has led to a surge of interest in shape-­changing plate and shell-like structures. Such structures are typically manufactured in a planar configuration and, when exposed to an ambient stimulus such as heat or humidity, morph into their desired three­-dimensional geometry. Viewed through the lens of differential geometry and elasticity, the application of the physical stimulus can be understood as local changes in the metric tensor of the sheet. In this talk we present our numerical approach for simulating the elastic response to such a metric change for thin structures. In addition, we discuss our theoretical contributions on the inverse-design of shape­ shifting bilayers. Finally, we will show how these developments have led to the design and experimental realization of a multi-material 4D printed lattice that can undergo complex, predictable 3D shape changes.
Keywords: 


Sound Bites

1. Aghvami, Ali

"In situ TEM monitoring of DNA origami virus like capsid assembly"
Monitoring kinetics of virus assembly at the nanoscale remains a major challenge in virus studies. While virus capsid assembly simulations have identified different kinetic pathways of the assembly, current visualization methods have not been able to validate proposed mechanisms experimentally due to low temporal resolution. TEM images are often taken when capsomers and capsids are fixed for negative staining or Cryo-TEM imaging. We develop a monitoring system based on in-situ TEM of DNA-origami virus like particles to capture the time-lapse movie of the assembly. We recently demonstrated a robust method for self-assembly of virus like capsids DNA nanostructure of various sizes by designing specific capsomers. In this work, we tag each capsomer with a functionalized gold nano particle to make them visible in the cell. This platform is suitable for In-Situ TEM and lets us capture images of the capsomers during the self-assembly procedure. Our real-time high-resolution picture of self-assembly will provide details of kinetics elucidating several aspects of assembly such as nucleation and growth rates, and dependence of assembly rates on binding affinities. These results will help developing novel antiviral agents that intervene assembly at the right time during the capsid formation.
Keywords: DNA origami - Self assembly

2. Agyapong, Johnson; Ian Hunter, Baptiste Blanc, S. Ali Aghvami, Seth Fraden

Department of Physics, Brandeis University, Waltham, Massachusetts
"The Chemical Stability of Belousov Zhabotinsky (BZ) Microgels in Response to Changes in Reactant Flow Rate"
In 1995, Yoshida developed a gel capable of swelling and deswelling without external stimuli. This behavior is due to an autonomous oscillating reaction rhythmically changing the solubility of the gel network in the solvent. The chemical and mechanical oscillation of BZ gels are interconnected so by understanding one, we can make inferences about the other. We focus on the dependence of chemical activity on the physical size, and environment of spherical non-swelling polyacrylamide hydrogels. The gel’s oscillating chemical concentration was measured using brightfield microscopy. We observed three cyclic patterns in gels of the same chemical concentrations. The observed patterns were dependent on the ratio of surface area to volume of gel and the flow rate of reactants. The ratio of surface area to volume of a gel determines a gel’s chemical sensitivity to its environment. Gels with small surface area to volume ratio were less sensitive to changes in flow rate and vice versa. Our work describes the chemical behavior of a microreactor in response to changes in the flow rate of reactants in a microfluidic device. This information is useful toward microfluidic fabrications and soft robotic designs that utilize reaction diffusion-driven swelling and deswelling.
Keywords: Microreactors, Microfluidics, Soft Robotics, BZ reaction

3. Clark, Andrew; Andrew G Clark, Miriam Montero Salcedo, Nelaka Govinna, Samuel Lounder, Ayse Asatekin, Peggy Cebe

Tufts University
"Probing structure and conductivity in blends of PVDF with a zwitterionic copolymer using dielectric relaxation spectroscopy"
Blends of poly(vinylidene fluoride) (PVDF) blended with a random copolymer of methyl methacrylate and sulfobetaine-2-vinylpyridine (PMMA-r-SB2VP) were investigated using dielectric relaxation spectroscopy. PMMA-r-SB2VP is a random copolymer containing zwitterionic moieties (RZCP) that enhance the antifouling properties of PVDF. Dielectric spectra collected in the temperature range from 25 oC to 140 oC showed large effects from conductivity, obscuring dipolar relaxations at high temperatures. The neat RZCP spectra showed 2 relaxation peaks that are attributed to the α and β relaxations of PMMA, with no additional relaxations present from the zwitterionic groups. Blends of PVDF and the RZCP show none of the relaxations seen in the neat RZCP, while the αc relaxation associated with the crystalline phase of PVDF is seen in the blends. The relaxation times of the αc peak show an Arrhenius temperature dependence, with the activation energy decreasing as the content of copolymer increases. Analysis of the conductivity relaxation shows a larger DC conductivity in the blends than in the RZCP and PVDF homopolymer. Conductivity also followed the Arrhenius law and the activation energy of the conductivity relaxation follows the same trend as seen for the αc relaxation. The higher DC conductivity of the blends indicates that the combination of zwitterionic side groups as well as unique microstructure greatly affect the charge transport characteristics.
Keywords: dielectric relaxation, zwitterion, copolymer, PVDF

4. Dahl, Joanna

UMass Boston
"Non-contact Mechanical Characterization of Extracellular Vesicles"
Cells exchange information by secreting micro­ and nanosized extracellular vesicles (EVs) ranging in size from 30nm to 5um. While it was once thought these cell-derived membranous vesicles were simply cell debris, recent efforts have determined that EVs have profound biological significance and therefore potential for clinical therapies and disease diagnostics. There is still much to understand about fundamental EV biological, physical, and chemical properties before clinical applications can be developed. The mechanical behavior of EVs---the physical implications of the lipid, protein, and nucleic acid constituents and their arrangements, all of which are linked to EV biological signature, cell of origin, and mode of biogenesis---has hardly been explored. To date, EV mechanical properties have been measured with atomic force microscopy with its problematic adhesion and hard substrate effects for small, soft EVs. We present preliminary measurements of single microscale EVs derived from human blood plasma using a non-contact microfluidic technique.
Keywords: extracellular vesicle, microfluidics

5. Deveney, Brendan; Joerg Werner

Harvard
"Thermoresponsive polymer shells"
Upper critical solution temperature (UCST) polymers are stimuli-responsive materials that undergo an insoluble to soluble transition at a specific temperature. Gels formed by cross-linking these polymers undergo a similar transition from a non-swollen to swollen state with changes in temperature. Swelling is associated with an increase in the gel network's permeability that may have potential for the controlled capture and release of small molecules. Here we report first steps in synthesizing UCST polymer microgels and briefly discuss applications.
Keywords: Thermoresponsive polymer

6. Fang, Huang; Alexander Hensley,Stefan Paquay, John Edison, Michael Hagan, W.Benjamin Rogers

Brandeis University
"Exploring nucleation pathways and solid-solid transitions in two-dimensional binary colloidal crystallization"
Crystals are prevalent in many natural and manmade systems, including metals, minerals, proteins, and colloids. Although the crystal structures themselves are often well understood, the microscopic pathways by which crystals form are difficult to observe or predict. We use a combination of computer simulations and microscopy experiments to investigate the crystallization pathways of DNA-coated colloids. We observe a rich diversity of phase behavior, including both one-step and two-step nucleation pathways, as well as a spontaneous solid-solid phase transition during the crystallization of two-dimensional binary mixtures. I will show how a competition between the free-energy landscapes of two different structures could cause the two-step nucleation by calculating free energy landscapes with respect to crystal size and symmetry using biased sampling techniques. These results may help shed light on fundamental aspects of nucleation, as well as provide new methods for controlling the self-assembly of materials made from colloids.
Keywords: colloids, crystallization, kinetic pathway

7. Gault, Zach; Zsolt Terdik, Peter Lu, Joerg Werner, David Weitz

Harvard University
"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.
Keywords: 

8. Giso, Mathew; Haoda Zhao, Patrick T Spicer, Timothy J Atherton

Tufts University, University of New South Wales
"Sculpting high aspect ratio crystals from an oil in water emulsion"
We present a process to sculpt elongated particles from an oil in water emulsion. The oil droplets can be crystallized by reducing the temperature. With the addition of surfactants, it is possible to induce dewetting of the crystals by their own liquid phase. By tuning the relative rates of dewetting and crystallization, a rich variety of crystal shapes can be grown in an easily scalable process. We explain these experimental findings using a non-equilibrium Monte Carlo model that captures both the crystallization and dewetting processes. Our results reproduce the wide range of shapes seen in experiment and provide insights to control their final morphology.
Keywords: Emulsion crystallization, High Aspect Ratio Particles

9. Hayakawa, Daichi; Douglas Hall, Gregory Grason, W. Benjamin Rogers

Brandeis University, University of Massachusetts Amherst
"DNA origami particles self-assemble into nano-tubes"
Proteins in nature serve as building blocks to assemble complex structures with a variety of functions. For example, α- and β- tubulins self-assemble to form chiral tubes called microtubules, which offer structural support and transportation in cells. We explored the capability of using DNA origami, a method for creating precise nanostructures in large quantities, to assemble triangular subunit particles which assemble into nano-tubes, similar to microtubules. The lock-and-key interaction placed on each side of the triangle specifies the interaction matrix, as well as the angle of binding which affects the curvature of the nano-tube. The TEM images of the assembled structure show not only curved surfaces, but also signs of loop structures. In the future, our methods can be used to create more complex surface geometries with applications such as size-limiting assembly and periodic surface structures.
Keywords: DNA origami, self-assembly

10. Hensley, Alexander; W. Benjamin Rogers

Brandeis University
"Measuring crystal nucleation and growth of DNA-grafted colloidal particles"
Crystallization is a phase transition in which a fluid of particles forms a solid lattice. In nature it produces diamonds and snowflakes, while in industry it leads to the crystalline silicon used in electronic circuits. Micrometer scale particles can also form crystals. For example particles coated in DNA can form a variety of crystals whose structures and properties can be prescribed by the choice of DNA sequences. We study nucleation and growth of colloidal crystals due to this DNA hybridization. We use a microfluidics-based approach in which we produce hundreds of monodisperse, isolated droplets filled with colloidal particles and then track the formation of crystals within each droplet as a function of time. We find that the initial nucleation of crystals from a supersaturated solution involves overcoming a free-energy barrier whose height decreases drastically with increasing temperature. We also find that once nucleated, the crystals grow at a rate that is limited by the diffusive flux of colloidal particles to the growing crystal surface. These findings may help us to devise strategies to tune the nucleation rates and crystal growth kinetics independently, which will be helpful as we try to engineer higher quality or more complex self-assembled structures.
Keywords: DNA, colloids, self-assembly, crystallization, microfluidics, nucleation

11. Huang, Tina; Anqi Chen, Ran Ran, David A.Weitz

Harvard University
"Microfluidic Fabrication of Asymmetric Polymer and Lipid Vesicles"
Lipid vesicles are aqueous volumes surrounded by a bilayer of lipid molecules, which are amphiphilic molecules with their head groups facing water and tail groups facing oil. These vesicles are simple models that mimic cell membranes and can be used for drug delivery. Similarly, block copolymers are amphiphilic molecules that form vesicles by themselves or with lipids. Like lipid vesicles, polymer vesicles can also be used for drug delivery and cell membrane mimicry. One interesting type of lipid/polymer vesicle is the asymmetric vesicle, in which its bilayer is composed of two dissimilar lipid monolayers or a lipid monolayer and a polymer monolayer. Importantly, all eukaryotic cell membranes exhibit this type of asymmetry and asymmetry is also proposed to enhance mechanical properties of the membrane. Here, we use microfluidics to fabricate mono disperse and highly controllable asymmetric vesicles, which unlike the conventional methods that often end up with highly poly disperse samples. To achieve this, asymmetric vesicles are produced using water/oil1/oil2/water emulsions in a glass capillary device, with different lipids/polymers immersed in two different volatile oil phases. Using the asymmetric vesicles, we are trying to measure how mechanical properties are affected by this asymmetry and also how to improve the degree of asymmetry in our vesicles even more. In future, we envision asymmetric lipid/polymer vesicles could open a new door in the field of drug delivery.
Keywords: Microfluidic, Lipid, Polymer, Asymmetry, Vesicle

12. Hunter, Ian; Ian Hunter, Mike Norton, Seth Fraden

Brandeis University Fraden lab
"Generating gaits with near identical microfluidic oscillators"
Experimental observation that synthetic coupled oscillators can form the same phase locked pattern as between legs of moving quadrupedal animals has revealed a method to customize dynamical nonlinear networks to possess such spatiotemporal steady states. The synthetic oscillators are composed of the BZ reaction, which autonomously, periodically changes chemical concentration in time, confined in PDMS reactors. The reactors are placed 10s of microns away from one another, allowing diffusive transport of select chemical intermediates through the PDMS. When 4 such reactors are placed in a ring, the reactors oscillate at phase shifts relative one another with the same phase shifts as between legs of quadrupeds. A novel method, combining constraints due to the dihedral symmetry of the system and robust, rhythmic nature of the reactors chemical oscillation, clarifies how this behavior emerges.
Keywords:  Microfluidic reactors, Nonlinear oscillations, Complex networks, Neural dynamics

13. Ionkin, Nikolay P.; Fernando Vereda, Daniel M. Harris

Brown University
" Shear-induced migration of a suspension under planar confinement"
The oscillatory flow of a suspension of neutrally buoyant, non-Brownian spherical particles in a rectangular channel at low Reynolds number is experimentally studied. Particles, which are practically confined to a plane, migrate towards regions of lower shear rate. Prior experimental and numerical work in oscillating Poiseuille flow has demonstrated the importance of strain amplitude on shear-induced migration. In this talk, we present the early results for the dynamics of shear-induced migration, and the dependence on particle concentration and strain amplitude in this new channel geometry.
Keywords: 

14. Joshi, Chaitanya; Zahra Zarei, Michael M. Norton, Aparna Baskaran, Michael F. Hagan, Seth Fraden

Brandeis University
"Dynamics of 2D Active Nematics under Annular Confinement"
Active nematics (ANs) are a class of non-equilibrium system with constituents that consume energy at the molecular level to generate motion. While the dynamics of a bulk 2D AN are turbulent, confinement can provide a systematic way of achieving control over the flow. Motivated by recent experiments, we investigate the behavior of 2D ANs confined to an annulus. Studying the effects of geometry and activity, we find a phase behavior exhibiting coherent circulation, dancing defects and chaotic flows. This work also helps towards understanding how curvature affects the flows in a channel geometry.
Keywords: active matter, confined, nematics, computations, theory

15. Katsikis, Georgios

MIT
"A Microfludic Sonar for measuring the stiffness of biological matter"
I will present a microfluidic approach that is a radical shift from how we measure mechanical properties of biological matter ranging from cells to viruses. I am using acoustic fields in a microfluidic device operating as a sonar, and enabling high-precision measurements of mass and stiffness in a flow-through format (1,000 particles per hour). Moreover, my approach is contactless and non-invasive for cells. Combining experimental microfluidics and analytical acoustic theory, I will give a sneak peak into proof-of-principle experiments and scaling laws demonstrating the potential of a new metrology for characterizing biological entities and soft matter in a broader sense.
Keywords: cell stiffness, acoustics, microfluidics

16. Liao, Wentian; Clover Su, Kasia Bieniek and Rama Bansil

Boston University
"Torque estimations of Helicobacter pylori in different pHs using Resistive Force Theory"
Helicobacter pylori which can survive at the harsh environment of human stomach can penetrate protective mucus layer of human stomach and colonize at the gastric epithelium surface. Due to the viscoelastic properties of mucus layer varies with pH, translational and rotational motility of H. pylori are influenced by both H+ concentration and adjacent mucus properties. In order to quantitively characterize the contribution of the two factors to H. pylori motility, we use phase contrast microscopy to image the motility of H. pylori in both BB10 and PGM in different pH. H. pylori are stuck in PGM below pH4 due to gelation of mucin in low pH and rotate faster than neutral pH. Furthermore, with the body parameters, translational and rotational rate obtained from 100X magnification and 100 fps videos, we use resistive fore theory to estimate the body torque and motor torque of H. pylori in different pH when considering both cell body and flagellar bundle as helix. The results show that the torque in BB10 remain relatively constant along all pH, while torque in PGM shows an obvious peak around pH4.
Keywords: mucus, body rotation, torque, resistive force theory

17. Lowensohn, Janna; Alexander Hensley, Michael Perlow-Zelman, W. Benjamin Rogers

Brandeis University
"Establishing design rules for linker-mediated assembly and crystallization of colloids"
NA is a promising tool for programming the self-assembly of new materials: its interactions are chemically specific, tunable, and predictable. In principle, DNA can be grafted to colloids to favor the formation of a predetermined aperiodic structure. Linker-mediated binding of DNA-coated colloids is an experimental system that could create these hundreds of specific interactions in practice. In this system, DNA-coated particles interact through DNA linker strands dissolved in solution. Using optical microscopy, we study the melting transition of a linker system as a function of linker concentration, grafting density, and DNA sequences. We find a phase diagram different from that of directly hybridizing DNA-coated colloids, featuring a re-entrant melting transition at high linker concentrations and a region of stable coexistence between solid and fluid. These results show the tunability and capacity of our linker-mediated system, and demonstrate how it might expand the design space for aperiodic and adaptive structures.
Keywords: DNA, colloids, self-assembly, linkers

18. Mahavadi, Sharath C.

Schlumberger - Doll Research
"Crude Oil Chemistry @ Interfaces"
Crude oil is a mixture of complex chemistries. Traditionally, these chemistries are classified as Saturates, Aromatics, Resins and Asphaltenes (SARA) based on solubility and simple chromatographic separation. This coarse classification is reasonable to understand and appreciate differences among crude oils from different sources. However, it proved to be insufficient to understand and address production challenges such as emulsions, wettability, organic scales are a few to mention. Here we present a closer look at chemistry of crude oil especially at the oil-water interface. This will provide better understanding on the role of these different chemistries in production challenges and potentially, more efficient solutions to address these challenges.
Keywords: Interfacial Chemistry, Naphthenic Acids, Asphaltenes,emulsions

19. Manafirad, Arash; Manafirad, Arash, Menendez Cintia; de Pablo, Juan; Thayumanavan, Sankaran; Dinsmore, Anthony

University of Massachusetts Amherst
"Micro-manipulation of an active lipid bilayer system"
Cells control their lipid membrane property such as permeability of selected solutes in an active manner. Here, we report on a synthetic system that switches permeability in response to light. We use experiments and simulations to study giant unilamellar lipid vesicles that contain a photoisomerizing unit (azobenzene) that channels photochemical excitation into mechanical energy within the membrane. We use micropipette aspiration and hold the vesicles at a constant tension (1mN/m) and expose them to UV light with controlled dosage. The membrane water permeability, surface area, interior volume, and stretching modulus are all measured in situ. The results will allow us to mimic cell function and to design smart, responsive artificial systems.
Keywords: lipid-azoebenzene, active bilayer-active membrane- giant vesicles

20. Merminod, Simon; John R. Edison, Huang Fang, W. Benjamin Rogers

Brandeis University
"Characterizing DNA-mediated colloid-membrane interactions"
In some butterfly wing scales, a cellular membrane is folded into a periodic nanostructure which generates color and iridescence by constructive interference of visible light. Inspired by this biological achievement, where protein binding is thought to mediate the energetics and dynamics of membrane folding, we aim to build photonic-crystal materials from self-assembly of small particles on artificial membranes. We start by characterizing the interactions between colloidal particles and a supported phospholipid membrane. We graft single-stranded DNA onto them, so that hybridization of complementary strands generates a specific, attractive force between the particles and the membrane. Using a total internal reflection microscope, we measure interactions with femtonewton resolution and kilohertz dynamics. We find that ligand-receptor affinity dramatically affects the energetics and dynamics of particle-membrane interactions: over a temperature range of a few degrees Celsius, adhesion strength varies by about 10 kT, while bound lifetimes and particle mobility change by orders of magnitude. These results may lead to better understanding of self-assembly of particles on fluid membranes, and ultimately enable self-assembling, membrane-based materials with remarkable optical properties.
Keywords: colloids, membranes, DNA, TIRM, ligand-receptor-mediated interactions

21. Milani, Matteo; Stefano Aime

Harvard University
"Droplet Sorter"
Mechanical properties of cells represent an important phenotypical marker providing insights into cellular differentiation and adaptation, as well as pathological changes of cells such as cancer. Indeed, change in cell stiffness is a key feature of cancer cells having a key role in the way they spread and create metastasis. The characterization of biological cells requires, by its very nature, a hard statistic, consequently, sample-to-sample experiments like macroscopic rheology, microrheology, AFM, nanoindentation, optical and magnetic stretching require high throughput in order to get a consistent description of a given system. In order to face such a challenge, an increasingly adopted strategy is represented by microfluidics, allowing testing and sorting hundreds or thousands of cells per second. The basic idea is the following: a well-defined elongational stress will be applied on the cell (droplet) by forcing it through a constriction, and its deformation will be measured using a light scattering apparatus. The advantage of this approach relies on the fact that the information on size and shape is encoded in the scattering signal in a much more informationally-efficient way with respect to normal images.
Keywords: droplet, microfluidics

22. Moustaka, Maria Eleni; Mike Norton,Viktor Horvath,Baptiste Blanc,Seth Fraden

Brandeis University, Fraden Lab
"Control of a microfluidic three-ring chemical oscillator network "
We study synchronization patterns in microfluidic networks containing Belousov-Zhabotinsky (BZ) chemical oscillators. In our experiments, the auto-catalytic, light-sensitive, BZ reaction is confined to micro-fabricated wells constructed from the elastomer PDMS. Using soft lithography, PDMS networks are arranged into wells with controlled topology. Each well can be regarded as a single network node that sends and receives inhibitory signals. Here we present the dynamics of a 3-node ring network. This network has two equivalent circular traveling waves of excitation. Control over the chirality of the wave can be achieved by exploiting the light sensitivity of the BZ catalyst, which can modulate the frequency of an individual node. In experiment, we perturb the network by changing the light intensity and duration of each of the three BZ wells. This network provides a model of gait switching in central pattern generators and a dynamic method of information storage.
Keywords: Microfluidic reactors, Nonlinear oscillations, Complex networks, Neural dynamics

23. Nazemifard, Neda; Saeed Mozaffari; Plamen Tchoukov; Jan Czarnecki

University of Alberta
"Nanofluidics for Thin Film Rheology"
Rheology (the relation between stress and deformation in fluid systems) at the interface of fluid-fluid or fluid-solid layer dominates the behavior of many complex fluid systems. Interfacial rheology has been primarily linked to the long-term stability of dispersions, emulsions, and foams. Exact measurement of viscosity of interfaces is extremely challenging and is usually done by indirect methods such as addition of tracing particles that could affect the chemistry of the complex fluid system. We designed and developed a nanofluidic system containing channels as small as 50nm to measure the viscosity of thin liquid films. The setup has been used to analyze the viscosity of thin oil film in water-in-crude oil emulsion system at the onset of asphaltene aggregation.
Keywords: nanofluidics, emulsion stability, Bingham fluids

24. OttinoLoffler, Bertrand; Mehran Kardar

MIT
"A Richards-Like Stochastic Population Growth Model"
A quick soundbite describing a model for range-expanding bacteria that incorporates spatiotemporal noise in fitness levels. We briefly discuss the macroscopic importance of microscopic noise and roughness in population fronts, including some results from KPZ universality, and give motivation for our specific SPDE model of bacterial growth. We then discuss how positive and negative linear growth rates drive two holistically distinct behaviors, and then discuss some of the mysteries and difficulties surrounding the marginal case of zero linear growth.
Keywords: Population Growth, Surface Dynamics, KPZ Universality

25. Patino, Nicholas; Emily Padston, Hyerim Hwang, Zsolt Terdik, Katharine Jensen, Frans Spaepen

Harvard University, Williams College
"Bogers-Burgers f.c.c.-b.c.c. Transition Mechanism in Colloidal Crystals"
Colloidal crystals are good models for atomic crystalline systems due to their resolvable sizes and trackable speeds which can be observed under confocal microscopy. Using an electric bottle to tune the volume fraction in a colloidal crystal, a phase transition can be induced between the body centered cubic and face centered cubic phases. Given the similitude between the phase behavior of the colloid and corresponding atomic systems, we conducted an investigation of the microscopic mechanisms governing the phase transition to compare it with atomic systems. The colloid was found to have similarities with the Bogers-Burgers mechanism proposed in 1964 for hard sphere systems, along with the one-step model proposed by Cyril Cayron in 2012. Consistencies with the mechanism include: 70℉-Plane angle shifts, 5.4% interplanar growth between close packed planes, the Kurdjumov-Sachs Orientation Relation, stacking faults averaging 1 every 3 slip plane, and a slight rotation of the (111) f.c.c. plane. An interesting note is the principle strain being roughly half that which was anticipated by the Bogers-Burgers mechanism. This different strain provides more evidence against the Bain Strain being the smallest principle strain for the transition, as Cayron has also suggested.
Keywords: colloid, phase transition

26. Poe, Beatrice Lunsford; Francesca Serra

Johns Hopkins University
"Lenses in Topological Defects in Cholesteric Liquid Crystals Confined to Microchannels"
Smectic liquid crystals with hybrid alignment form topological defects called Focal Conic Domains that focus light like lenses. When adding a chiral dopant to the liquid crystal material inducing a helical director, the nematic phase will become a chiral-nematic or cholesteric phase which behaves differently. The introduction of chirality should not affect the smectic phase as any twist must be expelled in order for the parallel layers to properly align, however, similar lenses arise in the cholesteric phase despite its very different topological defects. We examine the properties of these lenses in the two phases and try to find a correlation between the objects forming the lenses in each phase.
Keywords: Liquid Crystals

27. Rosenthal, Raoul

Harvard University
"Continuous directed evolution "
Currently great amounts of man-years and monetary resources are invested into directed evolution because this technique allows to adapt biomolecules to the specific needs of a process. Directed evolution allows to bridge the gap between what nature offers and the specific needs of an application, be it academic or industrial. Microfluidics is an upcoming field that can promises to greatly speed up the selection of enzyme and antibody variants. Whereas this miniaturization promises to bring significant cost reductions for directed evolution, genetic library generation has not undergone a similar revolution. By combining a novel in vivo mutagenesis method with microfluidics we work towards fully automating and reducing the duration of a typical directed evolution scheme from months to days.
Keywords: Microfluidics, directed evolution, high throughput screen

28. Saad, Ahmed

Harvard University
"Viscoelasticity of Crude Oil-Water Interfaces"
In this work we investigate the mechanism behind the formation of viscoelastic films at the crude oil/water interfaces and how brine composition affects both the mechanical and chemical properties of these films. We are using a novel technique for performing accurate interfacial shear rheology using a setup that, for the first time, allows measurement of interfacial properties while changing the chemical composition of the fluids without damaging or affecting the interfacial films. We plan to incorporate Fourier Transform-Infrared Spectroscopy (FTIR) to determine the chemical species present at the interface under different conditions. In addition, we will use fluorescent confocal microscopy to image the interfacial films using microfluidic devices designed to pin the oil/water interface.
Keywords: interfacial rheology, Asphaltenes; crude oil, viscoelasticity

29. Sabato, Matteo; Stefano Aime

Harvard SEAS - WeitzLab
"Microscopic aspects of crack dynamics in model soft solids"
Failure and crack formation are extremely widespread phenomenons that occur in both natural and artificial materials. Whether it is due to the action of an external force or just by aging, any object, at some point, breaks. However, despite its ubiquitous nature, our understanding of the microscopic features of crack propagation is still lacking. As a part of a larger project, aiming to begin unraveling some of the driving forces of this phenomenon, we developed an innovative technique to measure the deformation produced by the crack with resolution down to the sub-micrometric scale. The technique relies on an advanced and innovative analysis of the light dynamically scattered by a colloidal gel as it cracks under stress caused by water injected at a constant rate. Data processing allows us to reconstruct the two-dimensional deformation field in the propagation plane and the plastic activity associated with the crack opening. Exploiting this technique, we aim to shine a light on the relationship between the microscopic features of the sample and the macroscopic dynamics of the crack.
Keywords: failure, cracks, light scattering

30. Saha, Sarthak; Shuo Sui & Sarah L. Perry

University of Massachusetts Amherst
"Polymer based microfluidic devices for protein crystallography"
X-ray crystallography is the main technique for determining the 3D structure of proteins, and allows for understanding how protein structure affects function. Traditional methods of mounting individual crystals for X-ray diffraction analysis are tedious and can damage fragile protein crystals. Furthermore, manual mounting is very difficult for micron-scale crystals, and represents an opportunity for array-style microfluidics devices. Microfluidics has a long history using soft lithography or photolithography for device manufacture. Our lab has developed epoxy-based devices with excellent X-ray compatibility; unfortunately, the manufacturing techniques used have traditionally been associated in batch processes on wafers. We are looking to develop Roll-to-Roll fabrication strategies for such X-ray compatible microfluidic chips, allowing for a transition toward continuous manufacturing.
Keywords: Crystallography, Microfluidics, Roll-to-Roll

31. Senbil, Nesrin; Seth Fraden

Brandeis University
"Spatio-temporal control of 2-D active matter by light"
Active matter systems convert chemical energy into mechnaical energy and their dynamics is interesting due to being out of equilibrium. In our experiments, we work with microtubules(MT) and Kinesin 401 motor proteins at oil/water interface, where the motor proteins are only activated by blue lights(lambda~ 460nm). Sample is brought to 2D by gentrification, and exposure to blue light induces bundle formation. In 2D active nematic system, two types of topological defects exist; +1/2(motile) and -1/2 (non-motile). Our goal is to confine the sample in various light patterns and control the motion of +1/2 defects by projecting different light patterns.
Keywords: 

32. Tang, Jay X.; George Araujo, Joy Zheng

Brown University
"Assessment of transient bacterial attachment to a solid surface by applying an electric field"
Microbial attachment to surfaces is ubiquitous in nature. We report an experiment on pilus-less mutants of Caulobacter crescentus weakly attached to a plastic surface and subjected to an electric field parallel to the surface in a stick-slip fashion. These individual cells transiently but repeatedly attach to the surface in the presence of an electric field. Even while transiently detached, these bacteria move significantly slower than the unattached bacteria in the same field of view. We refer this behavior of repeated and transient attachment as "quasi-attachment". The speed of the quasi-attached bacteria exhibits large variations, frequently dropping close to zero for short intervals of time. This study sheds light on the process of bacterial interaction with surfaces and suggests applying electric field as a useful method to investigate bacteria-surface interaction.
Keywords: bacterial motility, bacterial adhesion, transient attachment, reversible binding, electrophoresis, galvanotaxis

33. Tsuda, Victor Massatoshi Kawakami; Stephen J. DeCamp, Nicolas Chiu Ogassavara, Stephan Koehler, Jeffrey J. Fredberg

Harvard School of Public Health
"Collective cell migration and energy metabolism"
From embryo development to cancer metastasis, epithelial cell layers dynamically rearrange and move as a single unit by undergoing collective cell migration. During collective migration, cells modulate their physical properties; migration speeds increase, traction stresses rise, and cell shapes elongate. These dynamical, mechanical and morphological changes require additional energy consumption and, therefore, must ultimately result from alterations in cell metabolism. However, the metabolic processes that energetically support collective cell migration remain unclear. Here we explore the collective migration of expanding epithelial cell layers while simultaneously extracting single-cell resolved metabolic data and characterizing canonical energy-producing pathways. Our findings indicate that collective cell migration requires significant alterations to the basal bioenergetic state of the cell. Therefore, when cell migration occurs, cells must undergo a metabolic switch.
Keywords: collective cell migration, bioenergetics, biomechanics, metabolism, biophysics

34. Xie, Zhaoyu; Timothy J. Atherton

Tufts University
"Percolation governs order to disorder transition for two-dimensional dense particle packing"
Dense particle packing helps to understand the properties of diverse systems such as granular media, colloids and amorphous solids. These packings tend to maximize the local density.There is a lot of work focusing on mono dispersed sphere packing in 2D flat space, where the system crystallizes and forms hexagonal structure. For packings in finite-size space or on curved surface, both theory and experiments confirm the existence of defects, i.e. particles with other than six neighbors, under bulk crystalline structure. In this work we study packings deviating from mono dispersed sphere packings. By varying the size or shape of particles, we find out that more defects would appear and disrupt the crystalline structure. We discover a generic principle about the growth of these defects that it follows the percolation theory no matter how the particles are changed or what surface the packings are on.
Keywords: packing, percolation

35. Zarei, Zahra; Zahra Zarei, Seth Freden

Brandeis University
"defect analysis in 2D active nematic"
Defects play an important role in active-matter systems. They are nucleated because of the bend instability and in steady state are continuously created and annihilated. In this study we investigate a 2D active nematic confined in an annulus, which exhibits a rich dynamical behavior of the plus half defects. We measure the positional-orientational distribution of defects in different confinements. We define three different states for the defects based on their positions and orientations, and calculate their transition rates.
Keywords: Defect, active nematic , Annulus

36. Zhu, Yilin; Clover Su, Rama Bansil

Boston University
"Creation of pH gradients for bacteria chemotaxis"
H. pylori colonizes the gastric mucosa where a pH gradient is established across the mucus layer. In order to investigate the chemotaxis of H. pylori away from low pH we are trying to generate a pH gradient in a microfluidic cell. However, it is not easy to build a steady pH profile because acid has a high diffusivity in the liquid. Previously Clover Su demonstrated a way to build a steady pH profile using colloid dye, Coomassie Bright Blue (CBB) to dye the hydrochloric acid which slows acid diffusion and using pH-sensitive fluorescent dye as indicator of pH profile. We are planning to use a universal dye to do the pH gradient experiment because it can indicate a wide range of pH, making it easier to quantitatively analyze the pH profile without adding an additional fluorescent dye. Our goal is to calibrate the pH vs color changes using universal dye, generate pH gradients, and compare the experimental data with theoretical predictions using a diffusion model.
Keywords: pH gradient, universal dye, diffusion model

37. Zuraw, Sarah; Anthony D. Dinsmore , Mahsa Siavashpouri , Zvonimir Dogic

University of Massachusetts Amherst
"Deformation and disruption of lipid membranes via particle binding: Experiments with tunable particle shape and adhesion"
We seek to understand the effects of DNA origami nano-rods on membrane structure and morphology. We combine giant unilamellar lipid vesicles (GUVs) with a sufficiently high concentration of oppositely charged nano-rods and observe the interactions. The adhesion of the nano-rods to the membrane is a tunable parameter controlled by the lipid composition, and results in three primary behaviors. At weak adhesion strengths, vesicles adhere to one another and form a stable gel, with the nano-rods acting as a glue that holds the gel together. At intermediate adhesion strengths, gel forms but is subsequently destroyed by avid binding of the nano-rods. At higher adhesion strengths, the vesicles are ruptured by the nano-rods without ever forming a gel. These behaviors can be explained respectively by shallow, deep, or complete wrapping of the nano-rods onto the lipid membrane. These results are a robust example of tuning response in a synthetic membrane system and provide a physical understanding of the design principles toward controlled membrane morphologies. These results will lead to a bio-inspired membrane material that is stimuli-responsive, has high surface area and is reconfigurable.
Keywords: Membrane, Vesicles, Materials, Nano particles, DNA Origami

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