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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

79th New England Complex Fluids Meeting
UMass Boston | Friday, June 7, 2019
Registration deadline: Wednesday, June 5, 2019

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abstract list | attendees list

Abstracts for Invited Talks and Sound Bites:

Invited Talks

1. Brenner, Michael

Harvard University
"The quest to observe the turbulent cascade in real time"

2. Brown, Keith A.

Boston University
"Exploring Smart Fluids from Particles to Properties"
Smart fluids – or a fluid with suspended particles in which an applied field produces a substantial change in properties – are a fascinating class of soft materials that are widely used in applications ranging from automotive suspension to high performance speakers. However, predicting their performance from first principles remains challenging. Our underlying hypothesis is that a deeper understanding can be gained by studying highly controlled model particles and connecting these to emergent behavior of the system. Here, we explore two model systems, (1) the electric-field directed assembly of nanoparticles and (2) the mechanical properties of particle-laden interfaces. In the first section, we introduce a novel method to measure the polarizability of nanoparticles based upon modest trapping fields and fluorescence microscopy. By using this assay, we determine that nanoparticles can exhibit polarizabilities that are >30 times larger than would be expected based upon simple models, corroborating early theoretical work that includes contributions from space charge in the Debye layer. In the second section, we discuss the mechanical properties of liquid marbles, or drops of liquid coated with a layer of hydrophobic particles that render the entire structure non-wetting. By developing a novel method to study the deformation of liquid marbles, we find that while the elastic mechanics of liquid marbles are invariant of the particle coating, the failure properties of marbles depend strongly on the particle identity, suggesting that more weakly interacting particles constitute tougher marbles. These observations are further explored using a series of macroscopic experiments studying the break-up of particle rafts based on a funnel method. While there remain open questions about the behavior of smart fluids, these lessons illustrate that important insights can be gained by combining novel multi-scale characterization strategies and well-characterized particles.

Dr. Keith A. Brown is an Assistant Professor of Mechanical Engineering, Materials Science & Engineering, and Physics and the Moorman-Simon Interdisciplinary Career Development Professor at Boston University. He earned a Ph.D. in Applied Physics at Harvard University under the guidance of Robert M. Westervelt and an S.B. in physics from MIT. Following his doctoral work, he was an International Institute for Nanotechnology postdoctoral fellow with Chad A. Mirkin at Northwestern University. The Brown group studies polymers and smart fluids to determine how useful properties emerge from hierarchical structure. A considerable focus is developing approaches that increase the throughput of materials research using scanning probe lithography, machine learning, additive manufacturing, and combinatorial chemistry. Keith has co-authored 62 peer-reviewed publications, four issued patents, and his work has been recognized through the reception of awards including the Materials Science and Engineering Innovation award from Boston University, the Omar Farha Award for Research Leadership from Northwestern University, as a "Future star of the AVS," the AVS Nanometer-Scale Science and Technology Division Postdoctoral Award, and the National Defense Science and Engineering Graduate (NDSEG) Fellowship. Keith is currently serving on the Nano Letters Early Career Advisory Board and has organized symposia at the AVS International Symposium and at the MRS Fall Meeting.

3. Celli, Jon

UMass Boston
"Modeling biophysical determinants of pancreatic tumor growth, invasion and therapeutic response in 3D cell cultures"
Cancer progression is regulated not only by the molecular biology and genetics of the disease but also by the physical properties of the tumor and surrounding tissues. For pancreatic tumors in particular, the development of mechanically rigid fibrous stroma is a defining feature which has been shown to play complex roles both promoting and constraining disease progression. It remains poorly understood however, how this altered mechanical landscape, which is dynamically remodeled during tumor progression and invasion, regulates susceptibilities to cancer therapeutics. Several projects in our group examine how biophysical interactions with the tumor microenvironment impact upon phenotypic changes which determine therapeutic response. This work is enabled by the use of in vitro 3D tumor models with tunable and rheologically-characterized extracellular matrix (ECM). Combined with imaging-based analyses of phenotype and in situ microrheology measurements of dynamic matrix remodeling, this platform provides a means to co-register rigidity-dependent cell shape, mechanics, and motility with response to therapeutic intervention. We use this system to specifically contrast classical chemotherapy agents with photodynamic therapy (PDT), in which light activation of a photosensitizing agent leads to cell death by local generation of reactive oxygen species. Interestingly, our recent results show that while modulation of ECM composition to promote increased invasive motility imparts resistance to chemotherapy, the same chemoresistant populations exhibit increased sensitivity to PDT. These and other emergent findings will be discussed in the broader context of connecting cancer biophysics with cancer therapeutics.

4. Fraden, Seth

Brandeis University
"Programmable self-assembly of capsids based on the principles of virus structure"
Caspar and Klug elucidated the geometric principles that govern the structure of natural viral capsids in 1962 by providing the minimum number of distinct local symmetries that are required to form an icosahedral shell of a given size. However, understanding the symmetry rules is not sufficient to understand assembly in nature nor to determine the engineering principles to build synthetic capsids. Here, we provide a general and modular solution to de-novo creation of icosahedral virus-like shells, thereby expanding Caspar and Klug theory with engineering principles for building synthetic capsids, providing strategies for controlling the pathways, kinetics, and the yield by which subunits will arrange themselves into icosahedral symmetry. We use the methods of DNA origami to design sequence-programmable self-assembly of DNA single-strands that produces accurately-designed and rigid building blocks. We created five different increasingly large virus-like capsids with molecular masses ranging from 43 to 925 Megadaltons and with internal cavity diameters ranging from 57 nm to 280 nm. We validated the structures of the capsids and those of the underlying subunits using cryo electron microscopy and studied the capsid assembly process experimentally and with a computational model to elucidate how the kinetics and yield of target structures depends on control parameters. Our capsid building blocks represent a near-ideal manifestation of patchy particles whose geometry and interactions can be designed with sub-nanometer and kBT precision, thus achieving a long sought after goal in soft matter physics.

5. Ross, Jennifer

UMass Amherst
"Self-Organization and Self-Propulsion of Biological Building Blocks"
The cell is a complex autonomous machine taking in information, performing computations, and responding to the environment. Much of the internal structure and architecture is transient and created through active processes. Recent advances in active matter physics with biological elements are opening new insights into the physics behind how cellular organizations are generated, maintained, and destroyed. I will present two short stories with enzymes at the heart of the activity driving organization and transport. The first will discuss self-organization of microtubules in the presence of "weakly interacting" crosslinkers. The second will discuss possible mechanisms for the cell to mix itself using self-propelled single molecule enzymes. These works illustrate the importance of the fundamental physics to build structures and propel matter inside living cells while informing on new physics we can learn from biological elements and materials.

6. Veraksa, Alexey

UMass Boston
"Cellular movements during organism development"
The process of development in multicellular organisms involves complex and coordinated movements of cells. One of the critical developmental events that depends on cellular movements is gastrulation, in which new layers of tissues are generated from a simple single layer of cells in the early embryo. My laboratory uses the fruit fly Drosophila melanogaster to study developmental events in early embryogenesis. Cell movements during gastrulation are orchestrated by precisely positioned signals that cells send to one another. These signals are received and interpreted by the receptors and intracellular signaling pathways, leading to changes in cellular contractility and shape. Actin/myosin networks in cells respond to these signals by carrying out apical constrictions, which help the cells to move from the surface into the interior of the embryo during gastrulation. Signals that govern gastrulation must be correctly activated but also properly terminated, and mutations affecting these regulatory mechanisms result in aberrant development. We have shown that the Drosophila homolog of mammalian beta-arrestin proteins, Kurtz, is necessary for terminating signaling in the Fog-Mist pathway, which controls gastrulation in the embryo. Mutations in Kurtz that affect its interactions with the receptor result in excessive cellular contractions and disrupt gastrulation. This work expands our view of the regulatory systems controlling cellular movements in complex organisms, and has implications for understanding human diseases related to epithelial morphogenesis events.

Sound Bites

1. Blanc, Baptiste; Baptiste Blanc(1),Johnson Agyapong(1), Ian Hunter(1), Ning Zhou(1), Bing Xu(1), Hyunmin Yi(2), Seth Fraden(1)

(1)Brandeis University, (2)Tufts University
"Oscillating chemo-mechanical Belousov-Zhabotinsky (BZ) hydrogels"
Yoshida [JACS 1996] developed a gel that undergoes cyclic swelling and deswelling without external stimuli. This self-oscillating gel undergoes an oxidation-reduction cyclic reaction, leading to a cyclic change of solubility of the gel. We present a new synthesis technique, offering high modularity in the gel composition and shape. We present simple experimental techniques to characterize the properties of the spherical BZ gels, such as their elasticity, timescale of swelling, density and catalyst content. Moreover, we find that a single spherical BZ gel needs to be larger than a critical size to chemically oscillate, thereby limiting the amplitude of its mechanical oscillation. We finally show how the remarkably high sensitivity of the BZ gel to its chemical environment could be harvested to enhance its actuation.
Keywords: polyelectrolyte, non linear chemical oscillator, transport

2. Blouwolff, Joshua

Abcam Fireplex
"Abcam Fireplex - Hydrogels for multiplex biomarker detection"
Abcam's Fireplex multiplex assays enable biomarker discovery and verification studies directly from small volumes of biofluid, using polymer hydrogel microparticles originally developed at MIT. I'll introduce how Fireplex hydrogel microparticles are used for multiplex biomarker detection and how these hydrogel microparticles are produced.
Keywords: Hydrogel, microparticle

3. Cui, Naiwen; Yamei Cai; Huidan Zhang; Haichuan Hu; David Weitz

"Ultra High-Throughput Targeted sequencing in single cells using droplet barcoding microfluidics"
Single cell targeted sequencing is a powerful tool for genetic mutation detection, which play an important role in studying genetic heterogeneity and clonal evolution in many complex illness and diseases. Studies show that clonal evolution can contribute to treatment failure, drug resistance and metastasis in cancer. For example, Intratumoural EGFR heterogeneity in Non-Small Cell Lung Cancer (NSCLC) revealed a close relationship with tumor shrinkage under chemotherapy treatment. To provide a good representation of the whole tumor, large number of cells need to be processed due to large number of tumor cells present. Current technology could only study 96 cells at a time using plate based assays or commercially available platform, which is very difficult and expansive to scale up. We have developed a droplet-based microfluidics technology that is capable of first encapsulating single cells in droplet, amplifying multiple targeted genes in each drop and then molecularly barcode them using hydrogel barcoded beads with very high efficiency. The ability to barcode tens of thousands of cells in each experiment with such low cost makes this a great tool for many clinical applications.
Keywords: single cell; sequencing; drop-based microfluidics

4. Drybread, Erik; Mohamed Amine Gharbi

University of Massachusetts, Boston
"The Diffusion of Colloids in Simple and Complex Fluids"
In this project, we seek to understand the difference in the diffusion of colloidal particles in simple fluids versus complex fluids. The diffusion of colloids is caused by Brownian motion, which is the erratic and unpredictable movement affected by the viscosity of the liquid. However, the diffusion depends on the properties of the solvent where the colloids are immersed. We have developed a technique of image processing based on the tracking of particles using the package Trackpy in Python to understand how spherical particles diffuse in isotropic fluids: water and glycerol. Then, we have compared the results to the diffusion of particles in an anisotropic material, a nematic liquid crystal. We concluded the Brownian motion of colloidal particles is very sensitive to the viscosity of the fluid that can be controlled by changing the temperature of the system, and the order of molecules within the studied phase. For the next step of the project, we wish to investigate the effect of particle size and shape on the Brownian motion of particles.

5. Duclos, Guillaume; Daniel A. Beller, Ray Adkins, Debarghya Banerjee, Minu Varghese, Matthew Peterson, Arvind Baskaran, Federico Toschi, Vincenzo Vitelli, Sebastian Streichan, Aparna Baskaran, Michael Hagan, Robert Pelcovits, Thomas Powers, Zvonimir Dogic

Brandeis Univiersity, Physics department
"Topological defects in three dimension active nematics"
Active nematics describes a phase of matter where active particles that consume energy to produce mechanical work assemble at high density in a state with orientational order but no positional order. In 2D active nematics, the creation, self-propulsion and annihilation of charged point-like topological defects control the dynamical steady-state of the material. Here, using multi-view light sheet microscopy we investigate the nature and the dynamics of topological defects in a 3D active nematics.
Keywords: active matter, liquid crystals

6. Ellis, Perry; Giridhar Anand, David A. Weitz, Sharad Ramanathan

Harvard University
"Identifying pathogenic bacteria by phenotyping individual cells"
Identifying pathogenic bacteria in natural samples has important consequences for human health. For example, 80% of foodborne illness comes from "unknown origin" --- there are either too few pathogenic bacteria in the sample to detect, or there doesn't exist a specific test for the pathogen at fault. To address these concerns we focus on high-throughput methods that require no prior knowledge of the bacteria to assess its pathogenicity. Our current approach relies on droplet microfluidics: we co-encapsulate human tissue with the bacteria of interest, forming a functional assay capable of screening 10^6 bacteria per day.

7. Eshel, Ran; Evgeniy Boyko, Amir D Gat, Moran Bercovici

"Non-uniform electro-osmotic flow drives elastic deformation instability "
In this theoretical and experimental work, we report for the first time the deformation instability of an elastic substrate separated from a rigid surface by a viscous liquid film subjected to a non-uniform electro-osmotic flow (EOF). We first provide insight into the physical mechanisms underlying the instability by considering a simplified 1D model, inspired by electrostatic MEMS actuators, in which the elastic substrate is modeled as a rigid plate connected to a linear spring. Our linear stability analysis, supported by experimental observations, reveals an instability that is controlled by a non-dimensional parameter representing the ratio of electro-osmotic to elastic forces, and also indicates the existence of a threshold value of the electric field for the onset of instability. To experimentally demonstrate the deformation instability, we fabricated a microfluidic device consisting of a fluidic chamber with an elastic upper sheet and a rigid bottom surface which is partially coated with a cationic polyelectrolyte to create a non-uniform surface charge. We placed a rigid plate on top of the elastic sheet and measured the gap between the two surfaces, resulting from negative pressures created by the non-uniform EOF. We determine the temporal evolution of the gap by measuring the three-dimensional point spread function (PSF) of micro-beads patterned on top of the rigid plate. We demonstrate that above a certain threshold of the electric field, the system exhibits instability, which collapses the upper plate onto the bottom surface. Furthermore, using both theoretical predictions and experimental observations, we identify three distinct dynamic behaviors, which we refer to as (i) a stable steady state case, (ii) a bottleneck case, and (iii) an immediate collapse case. We believe that the mechanism illustrated in this work, together with the provided analysis and experimental demonstration, may prove valuable for the implementation of instability-based actuators.
Keywords: Non-uniform electro-driven flow, Fluid structure interactions, Instability

8. George, Elizabeth; Ryan Preusse, Dr. Mohamed Amine Gharbi

University of Massachusetts Boston
"Engineered Topological Defects in Smectic Liquid Crystal at Curved Interfaces"
In this project we explore the effect of curvature on the organization of defects in a smectic liquid crystal. The experimental system is comprised of 4 n-Octyl-4-Cyano-Biphenyl (8CB) liquid crystal on an undulated interface with hybrid anchoring. We create surfaces with controlled morphologies and curvature to investigate the role of geometry in controlling defects in smectic liquid crystal. The goal of our work is to explore the way in which the curvature of the undulated surface affects the order and geometric confinement of the liquid crystal. Our preliminary results indicate that curved interfaces play an import role in controlling the formation of defects in both the nematic and the smectic mesophases. The structure formed by these defects can be used to direct the assembly of functional nanomaterials and biomaterials to create a new generation of smart materials. A fuller understanding of the mechanisms that govern the relationship between defects in the nematic and defects in the smectic are underway.  
Keywords: liquid crystal, focal conic domains, smectic, nematic

9. Greenfield, Michael; Suvrajyoti Kar

University of Rhode Island
"Surprise in the Temperature Dependence of Characteristic Ratio"
The physical space spanned by a single polymer chain in solution or in a melt depends on the molecular weight and the temperature-dependent balance between attractions and repulsions for polymer-solvent and polymer-polymer interactions. At the theta condition that balances these interactions, the characteristic ratio C_\infty relates the size, quantified by radius of gyration or end-to-end distance, to the number of bonds along the chain backbone. We calculated characteristic ratio by applying the rotational isomeric state model, which enables a large number of independent conformations to be sampled, and found a surprising feature of the temperature dependence. For monodisperse chains, the probability densities of chains that occupy small or medium sizes are relatively large and show relatively small changes with temperature. Only the lower probability densities of the most extended chains show a relatively large change with temperature. The contribution of this small number of chains is enough to account for the entirety of characteristic ratio temperature dependence within an ensemble average. This suggests that changes in characteristic ratio with temperature reflect changes for a small number of chains, not an overall shift in chain swelling across an ensemble of chains.
Keywords: polymer, characteristic ratio, scaling

10. Harris, Daniel; Roberto Camassa, Robert Hunt, Zeliha Kilic, and Richard M. McLaughlin

Brown University / UNC Chapel Hill
"Diffusion-Induced Aggregation"
An extremely broad and important class of phenomena in nature involves the settling and aggregation of matter under gravitation in fluid systems. In this work, we observe and rationalize a new fundamental effective attractive mechanism by which particles suspended within stratification may self-assemble and form large aggregates without need for short-range binding effects such as adhesion. This phenomenon arises through a complex interplay involving solute diffusion, impermeable boundaries, and geometry.
Keywords: self-assembly, aggregation, diffusion, stratification

11. Hauck, Nicolas; Carola Graf, Max J. Männel, Julian Thiele

Leibniz-Institute of Polymer Research Dresden, Germany
"Microscopic polymer hydrogels loaded in microreactors to perform enzymatic cascades towards polyketide synthesis"
To support the cell-free synthesis of non-natural polyketides, which may serve as novel approach in drug development, we utilize droplet microfluidics to prepare microscopic polymer hydrogels with tailored size and porosity. These are composed of furan-functionalized hyaluronic acid and poly(ethylene glycol) dimaleimide which are cross-linked inside monodisperse aqueous droplets via Diels-Alder cycloaddition. The integration of nitrilotriacetic acid moieties loaded with nickel ions into the gel particles allows for immobilizing His-tagged enzymes via metal-chelate complex formation. Utilized enzymes are expressed as fluorescent fusion proteins. That way, the immobilization efficiency and distribution within the microscopic polymer hydrogels are studied via fluorescence intensity. Furthermore, microreactors are used to study the enzymatic cascade in a defined environment under continuous flow. Hence, reaction conditions (e.g., temperature) as well as perfect mixing ratio of the immobilized enzymes and an optimal flow of the substrates through the microreactor are investigated.
Keywords: hydrogel, enzymatic cascade, microreactor

12. Hristov, Delyan R.; Cristina Rodriguez-Quijada, Kimberly Hamad-Schifferli

University of Massachusetts Boston
"Optimising the synthesis and properties of immunoprobes used in paper based assays for detection of infectious diseases"
The ASSURED criteria (affordable, sensitive, specific, user-friendly, rapid and robust, equipment-free and deliverable to end users) outlined by the WHO in 2012 aimed to provide a framework for the development of point of care (POC) devices to be used for same day diagnostics in a wide variety of diseases. Paper based assays, such as lateral flow assays (LFAs) and microfluidic paper-based analytical devices (μPADs) have garnered a lot of attention in the diagnostics community in the past decade as they may fulfill the WHO requirements. Though different versions exist, the most basic form of paper based assays do not require electricity or external equipment, cost ~$5 per unit, can detect target molecules in the or below nM concentration range and give users a straight forward yes/no answer within minutes. However, such systems have seen limited commercial release due to challenges related to development and optimization generally observed as lack of reliability, specificity and/or sensitivity. Among the biggest challenges of such devices is the design and development of nanoparticle probes used to capture the target and as labeling agent. Less than optimal design can result in undesirable non-specific interactions leading to probe aggregation or loss of specificity and/or function. Research focuses on identifying and resolving key aspects of the nanoparticle probe surface which could reduce non-specific interactions and improve test reliability.
Keywords: LFA, Paper-based assay, immunoprobe, biosensors, rapid diagnostics

13. Huang, Tina; Ran Ran, Simon Matoori, Anqi Chen, Laura Arriaga, David 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

14. Ionkin, Nikolay P.; Jeong-Hyun Kim, Daniel Harris

Brown University
"Bouncing Dynamics of Liquid Marbles"
Liquid marbles are millimetric droplets of fluid coated in a hydrophobic powder, which behave like soft solids that can readily roll and bounce. In this talk, we demonstrate that a liquid marble bouncing on a vertically vibrated surface demonstrates a period-doubling cascade to chaos as the vibration amplitude is increased. The resulting sequence of bifurcations is highly reminiscent to that of the extensively studied 1D model of a bouncing ball on a vibrating platform. Unlike the classical model however, our bouncer is relatively soft, and thus the time duration of contact with the surface is significant relative to the vibration period. Direct comparison to theoretical predictions are currently in progress, and may help further elucidate the subtle mechanical behavior of these complex fluid objects.
Keywords: liquid marbles, chaos

15. Joodaki, Faramarz; Lenore M. Martin, Michael L. Greenfield

University of Rhode Island
"Vibrational Study of Helical and Helix-Hinge-Helix Structures of an Anti-Microbial Peptide by Molecular Dynamics and Instantaneous Normal Mode Analysis"
Several experimental studies have been done on anti-microbial peptides (AMPs) as a strong potential to be a new class of antibiotics. These studies demonstrated that AMPs interact with a lipid bilayer of bacteria and destroy them that results in bacteria death. Current studies have stated that helical formation of AMPs on a bacterial membrane is a leading cause of a membrane disruption. Some studies also demonstrated that the presence of a hinge region in a helical structure increased the activity of AMPs bacteria. LM7-2 is a novel AMP that were designed by combining two natural AMPs (Ryder and Martin, URI Cell and Molecular Biology). During 100ns NPT molecular dynamics (MD) simulation of a helical LM7-2 in solution, LM7-2 reached to a helix-hinge-helix structure 6 times, and then returned to its helical structure. The large-scale motions of peptides result from small-amplitude fluctuations of atoms. Among those fluctuations, amide bands I, II, and III are sensitive to the secondary structure of peptides. Hence, we studied the instantaneous vibrational analysis of LM7-2 in helical and helix-hing-helix structures by two different methods. In the first method, C-N and C-O distances and NCO angle of all amide groups were calculated (each fs) for 200 ps MD time period of a helical and a helix-hinge-helix LM7-2. Then, Fourier Transfer have been applied on these results to convert data from the time domain to the frequency domain that provides amide band frequencies for each amide groups through the peptide. In the second method, all-atom normal mode analysis (NMA) were applied instantaneously (each 0.1 ps) on the results of 0.1ns MD simulation of both helical and helix-hinge-helix LM7-2. Amide bands were monitored and averaged during MD simulation for each residue and for both a helical and a helix-hinge-helix LM7-2. The results show that amide band III of residues in the hinge area were more sensitive and have shifted to lower or higher frequencies between a helical and a helix-hinge-helix LM7-2. Studying both helical and hinged structures over MD simulations show that number and kinds of inter-peptide and intra-peptide hydrogen bond of amide groups are relative to amide band shifts.
Keywords: anti-microbial peptide, helical, hinge, normal mode analysis, amide band

16. Julien, Elisa; G. Gerber, T. Cochard, Y. Hue, W. Steinhardt, D. A. Weitz

Harvard University
"Particles motion during hydraulic fracture collapse"
Proppants are particles (sand like materials) injected within fracking fluid during the hydraulic fracturing process. They keep the newly fractures open to hold high permeability paths to recover the oil trapped in common shales reservoirs. We developed an experimental approach where we use a transparent model (polymeric gels) to observe the particles deposition during fracture collapse. By measuring the evolution of the fracture volume and imaging both fracture and particles we provide a general understanding of proppants transport and deposition during the hydraulic fracking process.
Keywords: Hydraulic fracture, proppants transport

17. Kumar, Ajay Harishankar; Thomas Powers, Daniel Harris

Brown University
" Taylor-Aris Dispersion of Elongated Rods"
Particles transported in fluid flows, such as cells or nanorods, are rarely spherical in nature. In this study, we simulate the dispersion of an initial concentration of elongated rods with high aspect ratio in 2D pressure-driven shear flow using a Monte Carlo Brownian Dynamics method. The rods translate due to diffusion and advection, and rotate due to rotational diffusion as well as their classical Jeffery’s orbit in shear flow. When rotational diffusion dominates, we recover the classical Taylor Dispersion result for the longitudinal spreading rate by using an orientationally averaged translational diffusivity for the rods. However, in the high shear limit, the rods tend to align with the flow and ultimately spread faster as a direct consequence of their anisotropic diffusivities. The relative importance of the shear-induced orbit and rotational diffusivity can be defined as a rotational Peclet number, and allows us to bridge these two regimes.
Keywords:  Taylor-Aris Dispersion, Anisotropy, Jeffery’s orbit

18. La, Jeffrey; Chandra Yelleswarapu

UMass Boston
"Quantitative phase contrast imaging using photothermally induced phase transitions in liquid crystals"
Fourier phase contrast imaging improves image contrast of live biological species using photothermally induced birefringence in dye-doped liquid crystals. When the liquid crystal cell is at the focal plane, un-scattered light (background information) is intense enough to induce isotropy in the liquid crystals (LC), while light scattered by the sample is introduced to a phase change by the LC. This can be used to qualitatively increase contrast in an image. By incorporating phase shifting interferometry, this method can yield quantitative measurements of sample thickness.
Keywords: quantitative phase imaging, fourier phase contrast, liquid crystals

19. Liao, Wentian; Maira Constantino, Rama Bansil, Manuel Amieva

Boston University
"The effects of protein ChePep on reorientations and run speeds of Helicobacter pylori"
By utilizing chemotaxis, bacteria can escape from harsh environment and redirect to a suitable environment. Helicobacter pylori, for instance, can distinguish external acidic signal, redirect, penetrate mucus layer and finally colonize at gastric epithelial surface. The redirection of H. Pylori is controlled by the rotation of flagella whose direction is modulated by phosphorylation and dephosphorylation of CheY. In order to be continuously responsive to external environment, phosphorylated CheY needs returning to unphosphorylated CheY through the localization of CheZ at the flagellar pole of H. Pylori. CheZ localization is governed by the binding between CheZ and protein ChePep. Thus, ChePep is thought to be important at chemotaxis of H. Pylori. To specifically analyze the functionality of ChePep, phase contrast microscopy was used to record the motion of both WT and ΔChePep at 40 X magnification and 33 fps. Trajectories were segmented into reorientations and runs for further comparison on runs speeds, reorientation angle changes etc. At high magnification (100x), the body size parameters, body rotation rate, velocity of both WT and ΔChePep H. pylori was also analyzed by using Celltool. We found that ΔChePep shows a higher average speed and more reorientation events compared with WT while body rotation rate was almost the same. The results are consistent with previous hypothesis of ChePep regulation of the chemotaxis system and that ΔChePep mutants possess overactive flagellar motor.
Keywords: chemotaxis, ChePep, H. pylori

20. Liu, Ruoshi ; Pengyu Hong, Michael M. Norton, Seth Fraden

Brandeis University
"Topological Defect Detection & Experimental Video Synthesis in 2D Confined Active Nematics with Deep Neural Networks"
The motion of topological defects in active nematics has been modeled by a number of hydrodynamic theories that remain to be fully tested, which we will do by measuring defect dynamics using video microscopy and comparing with theory. However, classical image processing techniques are cumbersome, as variations in image quality and defect morphology require fine tuning for each data set and impede high-throughput processing of experimental data. Here, we use a Convolutional Neural Network (CNN) to efficiently and precisely measure the locations of active defects. We compare results obtained wtih CNN with results generated by traditional image processing algorithms. Beside topological defect detection, we use Deep Neural Networks (DNN) to study the spatiotemporal behavior of active nematics. We developed a tool based on Convolutional LSTM (ConvLSTM) to forecast the behavior of active nematics based on a few frames of experimental data. We compare these synthesized video with real experimental data.
Keywords: Topological Defect Detection, Deep Neural Networks, Experimental Video Synthesis, Spatiotemporal Pattern Modeling

21. Nawar, Saraf ; David Weitz

Harvard John A. Paulson School of Engineering and Applied Sciences
"Scalable Microfluidic Production of Double Emulsions and Microcapsules"
Double emulsions are multiphase core-shell droplets which find applications in a wide range of applications for encapsulation of functional actives. While microfluidics enables production of complex emulsions with excellent precision, throughput is generally low, thus typically limiting the application of emulsion droplets for bench-scale or niche applications. In this talk, I present a scalable microfluidic system using thermoplastic chip material for the production of monodisperse double emulsions. Not only do we achieve a high degree of control over double emulsion structure, but the droplet system is easily parallelizable, thus enabling us to significantly increase the production throughput of core-shell emulsion droplets while maintaining structural uniformity. Such scalable microfluidic systems are expected to be highly applicable for the industrial-scale production of microcapsules.
Keywords: microfluidics; emulsions

22. Nicholson, Schuyler; Rebecca A. Bone and Jason R. Green

University of Massachusetts Boston
"Typical Stochastic Paths in the Transient Assembly of Fibrous Materials"
When fueled by external energy sources, molecular self-assembly can form a myriad of morphological structures which are dynamic. For finite fuel supplies, assembled structures are transient, as reactions compete and molecular subunits transition between different chemical states. Here we model the experimentally-realized chemically-fueled self-assembly of a supramolecular material. Our model reproduces fiber lifetimes, as well as stochastic fiber growth and collapse. The vast space of assembly pathways, combined with the inherent nonequilibrium nature of the system, makes a theoretic prediction of material properties a challenge. Using a stochastic thermodynamic-information theoretic framework we show how observables, such as molecular concentration and fiber length, can be accurately estimated from the dynamics of the underlying kinetics, only using a tiny percentage of all assembly pathways. This typical set contains <0.23% of all sequences yet they hold >99% of the probability.
Keywords: self-assembly, information theory, stochastic thermodynamics

23. Norton, Michael; Christopher Simonetti, Maria Eleni Moustaka, Seth Fraden

Brandeis University
"Optimal Control of a 3-ring Oscillator Network"
The Belousov-Zhabotinsky reaction is a limit cycle oscillator with dynamical attributes comparable to neurons. By fabricating microfluidic wells filled with the BZ chemistry, we create reaction-diffusion networks with rich dynamical patterns that can yield fundamental insights into the dynamics of neural networks. A simple network of three inhibitor-coupled wells connected in a ring possesses two stable, dynamical steady states: clockwise and counterclockwise traveling waves. By photochemically perturbing the wells, we can change the intrinsic frequencies of each well. Using a simple model, we find a spatiotemporal light sequence using optimal control theory that irreversibly drives the system between attractors. This work lays the groundwork for the switching of locomotive gaits in soft robots and the storage of information in dynamical states.
Keywords: Oscillators, Nonlinear dynamics, Networks, Control

24. Pimentel, Alyssa; Kimberly Hamad Schifferli, Jason Evans

University of Massachusetts, Boston
"Studying the effects of a preformed protein corona on immunoprobes on lateral flow assay results"
Lateral flow assay (LFA) is a paper-based assay designed to detect an immunoprobe when it binds to a specific antigen in addition to an antibody preprinted on the strip, resulting in visible signal. LFAs are of interest to the nanomedicine community due to its low cost production and ease of use. However, immunoprobe target interaction can be hindered due to non-specific binding of other molecules in the sample, for example, protein corona formation. This could result in false positives, false negatives or the absence of signal on both the test and control lines. The protein corona is a layer of proteins adsorbed onto the surface of the immunoprobe, which could cover the antibody on the surface of the nanoparticle, preventing it from being recognized by the antigen. Designing a corona using a specific protein may alter the composition of the naturally occurring protein corona, and thereby improve immunoprobe target binding. Here we evaluate the applicability of this strategy to LFAs.
Keywords: nanoparticle, lateral flow assay, antibody

25. Preusse, Ryan; Mohamed Amine Gharbi, Elizabeth George

University of Massachusetts, Boston
"Role of Curvature in Controlling the Arrangement of Defects in Smectic Liquid Crystals"
Defects are highly sought after in liquid crystals and have various technological applications. They can be used to act as a microlens as well as direct the assembly of nanomaterials and biomaterials, alongside various other energy applications. A uniform smectic liquid crystal exhibits no defects under matching boundary conditions, and uniform defects under hybrid boundary conditions. The goal of this work is to control defects through geometric confinement on different types of undulated surfaces under hybrid boundary conditions. It was found that defect size has a direct correlation to the depth of the sample. It was also found that line defects remain after the phase transition from the nematic. With two different types of defects forming in the sample, a more complex method of directed assembly can be implemented.
Keywords: Defects, Smectic, Curvature

26. Qi, Maggie; Qin Maggie Qi, Samir Mitragotri

Harvard University
"Mechanism of transdermal delivery of macromolecules assisted by ionic liquids"
Skin is a strong diffusive barrier especially to the permeation of large hydrophilic molecules owing to its anatomy, posing a great challenge to utilizing the transdermal route for various drug delivery applications. Using ionic liquids (IL) to chemically enhance the transport of macromolecules is a novel technique attracting immense research interests recently. A fundamental understanding of the role of IL underlying this process is still lacking and is essential to broadening its applications for pharmaceutically-relevant macromolecules. We will present both our experimental and theoretical work trying to understand the complex interactions among skin (barrier), IL (solvent) and drugs (macromolecules) and unravel this transport enhancement mechanism. We will discuss the scaling of molecular weight versus permeability, which shows a slower decay in the presence of IL. This striking change of scaling relationship sheds light on the advantage of IL over other enhancement techniques for large molecules in particular.
Keywords: ionic liquids, drug delivery, biological transport

27. Quijada, Cristina Rodriguez; K. Hamad-Schifferli

UMass Boston
"Leveraging crossreactive antibodies and multicolored nanoparticles for detection of emerging outbreaks"
Rapid diagnostic tests (RDT) can be used as the first barrier to tackle emerging infectious disease outbreaks in endemic areas because they are cheap, portable and can be used by non-experts. A biological fluid is added to the paper strip giving rise to a colored line readable by eye. However, RDTs rely on antibodies specific for the disease. Only the mass production of Abs can take up to a year, which is too slow to tackle an emerging outbreak jeopardizing the patient management and disease containment. Here, we take stockpiled cross reactive antibodies from a closely related virus and repurpose them so the biomarker from a similar disease can be detected. This approach uses gold nanoparticles of different colors and image analysis to classify the different biomarkers from closely related viruses. This technique allows to exploit stockpiled antibodies to come up with a rapid test on the ground during the critical phase of the emerging outbreak.
Keywords: rapid diagnostics, infectious diseases, antibody cross reactivity, multicolor gold nanoparticles, machine learning

28. Senbil, Nesrin; Seth Fraden

Brandeis University
"Spatiotemporal control of 2-D active matter by light"
Active nematics are class of liquid crystals that powers up from internally generated energy. Precise spatiotemporal control in active matter systems is still missing. Our experimental system consists of stabilized microtubules, light sensitive kinesin motors and polymer polyethylene glycol (PEG) at planar fluid/fluid interfaces. Light sensitive kinesin motors will pull on the microtubule bundles and induce various defects when activated by light (460nm, blue). Our goal is to control the defect direction and activity of this experimental system by using Digital Light Processing (DLP) by projecting various light patterns.

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

Harvard John A. Paulson School of Engineering and Applied Sciences
"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

30. Wadhwa, Navish; Rob Phillips, Howard C. Berg

Harvard University/California Institute of Technology
"Tunable self-assembly of the bacterial flagellar motor"
Multisubunit protein complexes are ubiquitous in biology and perform many of life’s essential functions. Scientific literature often treats such assemblies as static: their function is assumed to be independent of their manner of assembly, and they are assumed to remain intact until damaged or degraded. Recent observations of the bacterial flagellar motor bring these notions into question. The torque-generating stator units of the motor assemble and disassemble in response to changes in viscous load. We used electrorotation to drive tethered cells forward, which decreases motor load, and measured the resulting stator dynamics. No disassembly occurred while the torque remained high, but all of the stator units were released when the motor was spun near the zero-torque speed. When the electrorotation was turned off, so that the load was again high, stator units were recruited, increasing motor speed in a stepwise fashion. A model in which speed affects the binding rate and torque affects the free energy of bound stator units captures the observed torque-dependent stator assembly dynamics, providing a quantitative framework for the environmentally regulated self-assembly of a major macromolecular machine.
Keywords: Self-assembly, bacterial flagellar motor, multisubunit complex, molecular motor

31. Zhang, Kaixuan; Zhen Li, Martin Maxey, Shuo Chen, George Karniadakis

Brown university/Tongji University
"Self-cleaning of textured hydrophobic surfaces by coalescence-induced wetting transition"
The superhydrophobic leaves of a lotus plant and other natural surfaces with self-cleaning function have been studied intensively for the development of artificial biomimetic surfaces. The surface roughness generated by hierarchical structures is a crucial property required for superhydrophobicity and self-cleaning. Here, we demonstrate a novel self-cleaning mechanism of textured surfaces attributed to a spontaneous coalescence-induced wetting transition. We focus on the wetting transition as it represents a new mechanism, which can explain why droplets on rough surfaces are able to change from the highly adhesive Wenzel state to the low adhesion Cassie−Baxter state and achieve selfcleaning. In particular, we perform many-body dissipative particle dynamics simulations of liquid droplets (with a diameter of 89 μm) sitting on mechanically textured substrates. We quantitatively investigate the wetting behavior of an isolated droplet as well as coalescence of droplets for both Cassie−Baxter and Wenzel states. Our simulation results reveal that droplets in the Cassie−Baxter state have much lower contact angle hysteresis and smaller hydrodynamic resistance than droplets in the Wenzel state. When small neighboring droplets coalesce into bigger ones on textured hydrophobic substrates, we observe a spontaneous wetting transition from the Wenzel state to the Cassie−Baxter state, which is powered by the surface energy released upon coalescence of the droplets. For superhydrophobic surfaces, the released surface energy may be sufficient to cause a jumping motion of droplets off the surface, in which case adding one more droplet to the coalescence may increase the jumping velocity by one order of magnitude. When multiple droplets are involved, we found that the spatial distribution of liquid components in the coalesced droplet can be controlled by properly designing the overall arrangement of droplets and the distance between them. These findings offer new insights for designing effective biomimetic self-cleaning surfaces by enhancing spontaneous Wenzel-to-Cassie wetting transitions, and additionally, for developing new noncontact methods to manipulate liquids inside the small droplets via multiple-droplet coalescence.
Keywords: Self cleaning, Droplet coalescence, Wetting transition

32. Zhang, Weixia; Liangliang Qu, Hao Pei, Zhengwei Wu, David A. Weitz

Harvard University
"Controllable Fabrication of Inhomogeneous Microcapsules for Osmotic Pressure Triggered Release"
The inhomogeneous microcapsules are fabricated using a microfluidic approach and the inhomogeneity of shell thickness in the microcapsules can be controlled by tuning the flow rate ratio of the middle phase to the inner phase. We demonstrate the swelling of these inhomogeneous microcapsules begins at the thinnest part of shell and eventually leads to rupture at the weak spot with a low osmotic pressure. Systematic studies indicate the rupture fraction of these microcapsules increases with the increasing inhomogeneity. The inhomogeneous microcapsules are demonstrated to be impermeable to small probe molecules, which enables long-term storage. Thus, these microcapsules can be used for long-term storage of enzymes, which can be controllably released through osmotic shock without impairing their biological activity. Our study provides a new approach to design effective carriers to encapsulate biomolecules and release them on-demand upon applying osmotic shock.
Keywords: Microfluidics, inhomogeneous Microcapsules, Osmotic Pressure, Triggered Release

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