Calendar of MRSEC Events

2018 Events
November 30, 2018 77th New England Complex Fluids Workshop at Harvard University
September 21, 2018 76th New England Complex Fluids Workshop at Brandeis University
August 11, 2018 2018 Research Experiences for Undergraduates (REU)
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June 15, 2018 75th New England Complex Fluids Workshop at MIT
June 4, 2018 2018 Research Experiences for Undergraduates (REU)
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May 30, 2018 Squishy Physics Seminar
Mark Skylar-Scott, Harvard University

5:30pm | Pearce Hall, Room 209
May 16, 2018 Squishy Physics Seminar
Alex Klotz, MIT

5:30pm | Pearce Hall, Room 209

Dynamics of knotted DNA and knots in DNA

Knots occur naturally in biological DNA, a phenomenon relevant for cellular genome organization as well as genetic sequencing technology. Knotted DNA molecules serve as a model experimental system for polymer entanglement, where fluorescent microscopy can be used to study polymer dynamics on the individual chain level. To study the dynamics of knots in DNA, we induce knotting in viral DNA using an electrohydrodynamic instability and stretch the molecules with a divergent electric field in a microfluidic channel, analogous to elongational flow. I will discuss some recent results from our experiments and simulations, including the effect of knots on the entropic elasticity of a stretched molecule, the motion of knots along elongated molecules, and the process by which knots untie as they reach the end of the molecule.
May 2, 2018 Squishy Physics Seminar
John Hart, MIT

5:30pm | Pearce Hall, Room 209
April 11, 2018 Squishy Physics Seminar
Martin Lenz, CNRS (Paris, France)
The Laboratory of Theoretical Physics and Statistical Models

5:30pm | Pearce Hall, Room 209

Slimming down through frustration

Controlling the self-assembly of supramolecular structures is vital for living cells, and a central challenge for engineering at the nano- and microscales. Nevertheless, even particles without optimized shapes can robustly form well-defined morphologies. This is the case in numerous medical conditions where normally soluble proteins aggregate into fibers. Beyond the diversity of molecular mechanisms involved, we propose that fibers generically arise from the aggregation of irregular particles with short-range interactions. Using minimal models of frustrated aggregating particles, we demonstrate robust fiber formation for a variety of particle shapes and aggregation conditions. Geometrical frustration plays a crucial role in this process, and accounts for the range of parameters in which fibers form as well as for their metastable, yet long-lived character.
April 4, 2018 Squishy Physics Seminar
Prof. Jia Niu, Department of Chemistry, Boston College

5:30pm | Pearce Hall, Room 209

Biocompatible Controlled Radical Polymerization: at the Interface of Polymer Science and Biology

Synthetic polymers as biomaterials have attracted significant research and development efforts in the recent years. Compared to the biological counterparts, synthetic polymers can provide improved physical, chemical, or mechanical properties as well as the capability to actively manipulate biological functions. However, traditional synthetic polymer biomaterials are still primarily used as crosslinked matrices, limited by the lack of defined polymer structures and low polymer grafting efficiency. The overall goal of our research is to expand the controlled polymerization techniques towards improved biocompatibility and the mimicry of biopolymers. In this seminar, two examples will be presented. First, a rapid controlled radical polymerization technique is described. In situ NMR monitoring confirmed the kinetics of this reaction and its spatiotemporal control over polymerization by light. Using this technique, synthetic polymers with narrow polydispersity (PDI < 1.3) were generated in aqueous solution at room temperature. The rapid reaction kinetics of this CRP enabled direct cytocompatible polymerization from chain transfer agents (CTAs) immobilized on the surfaces of live yeast and mammalian cells, as shown in the second example. High (>90%) cell viability and non-impaired cell functions, including cell propagation and signaling transduction, were observed for polymer-modified cells. Incorporation of various functional groups in the cell surface-initiated synthetic polymers was shown to enable post-polymerization functionalization of cell surface and mediate cell-cell interaction. These preliminary results serve as the initiators for our efforts towards applying synthetic polymeric system in various biotechnological applications, such as live cell-based sensing or catalytic systems, programmable cell assembly, and engineering cell surface with molecular or nano-scale structures.
March 30, 2018 74th New England Complex Fluids Workshop at Yale University
March 30, 2018 MCB Harvard Seminar
M. Lisa Manning, Ph.D., Associate Professor of Physics, Department of Physics and Soft and Living Matter Program, Syracuse University

1:0pm | Biological Labs 1080, 16 Divinity Avenue, Cambridge

Modeling Physical Forces at Large Scales to Discover Molecular Mechanisms in Cell Biology

March 28, 2018 Squishy Physics Seminar
Dr. María L. Jiménez, Department of Applied Physics, University of Granada (Spain)

5:30pm | Pearce Hall, Room 209

Biocompatible Controlled Radical Polymerization: at the Interface of Polymer Science and Biology

In the last decades, a great effort has been devoted to control the size, geometry and internal morphology of nanoparticles. In many practical situations, such systems are suspended in aqueous media. If this is the case, nanoparticles usually acquire surface charge, and this also determines their behavior. Both size and charge in aqueous media are usually characterized by scattering techniques. While these methods are well established, there are multiple situations in which they provide limited information. For instance, the size is not well measured when the particles are highly non-spherical. With respect to the electric properties, scattering methods provide a single characteristic quantity, the zeta potential. Hence, they cannot characterize the behavior of more complex systems, such as soft particles, soft coated particles, non homogeneous surface charge, etc. Finally, only dilute suspensions can be measured with these techniques, which is not always the desired situation.

In this talk I will show a different approach: the measurement of the electric permittivity and electric birefringence spectra of suspensions. These quantities are directly related to the polarization of the particles: under the action of electric fields, particles polarize by different mechanisms that manifest in separated frequency regimes, depending on the particle size, geometry and the electric properties of the interface particle/solution. We will show that the electric permittivity spectra provide the particle size, aggregation state and surface charge in the case of concentrated suspensions. On the other hand, the electric birefringence is very sensitive to the particle geometry and charge distribution as compared to standard techniques based on the light scattered by the particles. In particular, we will show that it is an excellent tool to obtain the size distribution in the case of non spherical particles.
March 21, 2018 Squishy Physics Seminar
Dr. Lukas Zeininger, Department of Chemistry, MIT

5:30pm | Pearce Hall, Room 209

Rapid Detection of Foodborne Pathogens using Directional Emission from Dynamic Complex Emulsions

Multiphase complex emulsions formed from two or more immiscible solvents offer a unique platform as new materials for chemical sensor applications. The temperature controlled miscibility of fluorocarbons (F) and hydrocarbons (H) enables a temperature induced phase-separation, leading to structured emulsion droplets of H and F in water (W), which can be alternated between encapsulated (F in H, and H in F), and Janus configurations by varying the interfacial tensions using surfactants. These complex emulsion droplets can selectively invert morphology in response to external stimuli such as the presence of specific analytes, small pH changes, light or high energy irradiation, and the presence of an electric or magnetic field. This, in combination with the unique optical properties of our emulsion droplets enables the application of our complex emulsions as a new transduction material for chemo- and bio-sensing applications. Here, we will show how the addition of stimuli-responsive surfactants to the complex emulsions provides a method to induce a morphology change or droplet reconfiguration as a response to the presence of specific chemical or biological analytes. In order to create a ratiometric optical read-out of small changes in the droplet morphology, emissive dyes were added to one of the two immiscible phases of the complex emulsions. The potential of these micro-colloids to manipulate light in form of waveguides led to the development of several optical transduction methods, where an adjustment of the refractive indices of the solvents results in a new unprecedented control of light propagation inside the emulsion droplets. We will demonstrate that having control over the total internal reflection of light from outside and inside the emulsion droplets results in new sensory schemes for the rapid and sensitive detection of various chemical and biological analytes, including common foodborne pathogens such as Salmonella and E.coli bacteria.
March 14, 2018 Squishy Physics Seminar
Craig Maloney, Department of Mechanical and Industrial Engineering, Northeastern University

5:30pm | Pearce Hall, Room 209

Models for sheared amorphous solids: from the particle scale to the meso-scale

Many solid-like materials lack any underlying crystalline order. Examples include soft glasses (emulsions, foams, pastes, colloidal glasses), granular packings, amorphous alloys, and glassy polymers. Over the past few decades, local shear transformations have been identified as the particle-scale processes which accommodate imposed shear and allow for yielding and flow. In this talk we will discuss coarse-grained, meso-scale models based on this notion of local shear transformations, and will quantitatively reconcile the coarse-grained approaches with particle-scale simulations and experimental data. In particular, we will discuss how the diffusion and rheology are governed by cascades of shear transformations and will show how the yield point can be thought of as a dynamical critical point with associated scaling relations with some exponents being universal, and other depending on microscopic details of the model.
March 7, 2018 Squishy Physics Seminar
Prof. Arturo Moncho Jorda, Departamento de Física Aplicada, Universidad de Granada

5:30pm | Pearce Hall, Room 209

Cosolute Partitioning in Hydrogel Particles

Hydrogels are formed by cross-linked polymer chains dispersed in water, with the ability to reversibly swell and in response to various stimuli, such as temperature, salt concentration, and pH. They can be designed to be biocompatible, biodegradable, and allow the incorporation of biomacromolecules with relatively small changes in its biological activity. Because of these features, hydrogels have been proposed as excellent candidates for transport and delivery systems of different types of cosolutes, such as biomacromolecules, drugs and chemical reactants in controlled catalysis. However, the interactions involved in the cosolute absortion and the swelling response of the hydrogel in the presence of the cosolutes are not totally understood under a theoretical point of view.

This talk will address these two problems. In the first part of the talk, the absorption of charged globular inside charged hydrogels is studied by calculating the effective interaction between the hydrogel network and the protein. Different sorption states are identified, from complete exclusion of the protein to its full absorption, passing through metastable and stable surface adsorption. The results indicate that proteins with a large dipole moment tend to be adsorbed at the external surface of the hydrogel, even if like-charged, whereas uniformly charged biomolecules tend to partition toward the internal core of an oppositely charged hydrogel. In the part of the talk, the effect that neutral hydrophobic cosolutes has on the hydrogel swelling/deswelling is studied using coarse-grained simulations and mean-field theory. The results show the existence of "cosolute-induced" collapsed states, where strongly attractive cosolutes bridge network monomers albeit the latter interact mutually repulsive.
February 28, 2018 Squishy Physics Seminar
Prof. Carlos Hidrovo, Mechanical and Industrial Engineering Department, Northeastern University

5:30pm | Pearce Hall, Room 209

Gas-Liquid Droplet Microfluidics: Fundamentals and Applications

Over the past two decades microfluidics has quickly morphed from an emerging field to a mature technology that is widely used in biotechnology and healthcare. One specific field that has thrived extensively in its adoption and development has been droplet microfluidics. The ability to compartmentalize reactions and processes into multiple individual droplets has made these systems extremely attractive in multiple and varied applications. However, most of the focus has centered on liquid-liquid systems, where dispersed droplets of a liquid are formed on another continuous, immiscible one.

This talk will focus on the relatively untapped field of gas-liquid droplet microfluidics, where liquid droplets are formed in a continuous, gaseous flow. The fundamentals of droplet formation and transport will be explored. Due to the lower viscosity of the carrier fluid, these systems tend to operate at much higher Re than those encountered in typical microfluidic systems. As such, the role of inertial forces on the dynamics of these systems will be addressed. Applications geared towards the creation of monodisperse aerosols and the sampling of gaseous targets will be discussed. A specific example on the sampling and detection of gaseous ammonia will be presented. The talk will finish with an outlook on the future of these systems.
February 21, 2018 Squishy Physics Seminar
Lisa Tran, Department of Physics, University of Pennsylvania

5:20pm | Pearce Hall, Room 209

A change in stripes for liquid crystal shells — controlling elasticity to order nanomaterials

Liquid crystals are ubiquitous in modern society. Whenever we text, use a calculator, or check our emails, we are interacting with LCDs — liquid crystal displays. These materials are the basis of the modern display industry because of their unique properties. They can be manipulated with electric fields and can alter light. They are also deformable because they are elastic: their rod-like molecules tend to align with one another. These properties allow for liquid crystals to be engineered into a pixel. Despite these advances in their technological applications so far, the structures that liquid crystals can form are yet to be completely understood. Current research aims to elucidate these structures to develop liquid crystals as biological sensors and as blue prints for assembling nanomaterials in energy applications.

Since liquid crystal molecules tend to order with one another, they can respond to geometrical confinement. Geometrical constraints can create patterned molecular structures and defects — localized, "melted" areas of disorder that can lower the distortion in the system and that can drive the assembly of objects. I will present recent work in which defects are controlled by using microfluidics to create liquid crystal double emulsion droplets — confining the liquid crystal into spherical shells. Molecular configurations are controlled by the topology and geometry of the system and by varying the concentration of surfactants. Defect structures are examined through experiments and simulations, and the surfactant concentration is altered to transition between different defect types. I will then present ongoing experiments where nanoparticles are used in place of traditional surfactants to pattern them at the liquid crystal-water interface. This work has the potential to dynamically template nanomaterials for the enhancement of liquid crystal-based optical devices and sensors.
February 14, 2018 Squishy Physics Seminar
Prof. Thomas C. Pochapsky, Department of Chemistry, Brandeis University

5:20pm | Pearce Hall, Room 209

Some surprising implications of NMR-directed simulations of substrate recognition and binding by cytochromes P450

Cytochromes P450 are a superfamily of heme-containing monooxygenases that typically catalyze the oxidation of unactivated C-H and C=C bonds by molecular oxygen, often with high regio- and stereospecificity. Over 450,000 members of the superfamily have been tentatively identified, from all genera of life, suggesting a vast range of possible substrates and even larger one of potential products. However, little is yet known about the relationship between sequence, structure and substrate/product specificity in P450s. Residual dipolar couplings (RDCs) measured for backbone amide 1H-15N correlations in substrate-free and bound forms of two P450s, the camphor 5-exo hydroxylase CYP101A1 and macrolide antibiotic biosynthetic MycG were used as restraints in soft annealing molecular dynamics (MD) simulations in order to identify average conformations of these enzymes with and without substrate bound. Multiple substrate-dependent conformational changes remote from the enzyme active site were identified in both enzymes. Perturbation response scanning (PRS) and umbrella sampling MD of the RDC-derived CYP101A1 structures are used to probe the roles of remote structural features in enforcing the regio- and stereospecific nature of the hydroxylation reaction catalyzed by CYP101A1. An improper dihedral angle Ψ was used to maintain substrate orientation in the CYP101A1 active site, and it different values of Ψ result in different PRS response maps. Umbrella sampling methods show that the free energy of the system is sensitive to Ψ, and bound substrate forms an important mechanical link in the transmission of mechanical coupling through the enzyme structure. Finally, a qualitative approach to interpreting PRS maps in terms of the roles of secondary structural features is proposed.
February 7, 2018 Squishy Physics Seminar
Prof. Yujun Song, Department of Physics, University of Science and Technology Beijing

5:20pm | Pearce Hall, Room 301

Microfluidic Synthesis of Nanomaterials and their Application for Tumor Diagnosis and Therapy

Great progresses in the coupling of nanomaterials and biomedicines have been achieved in the disease diagnosis and therapy, leading to the brand-new field in nanomedicines by conjugating nanoparticles with bio-molecules in the past decades. However, the controlled synthesis of varieties of nanoparticles and their surface modification and conjugation with desired medicines (particularly small organics with inorganic nanoparticles) are still much challenging. Here we developed a programmed microfluidic process in the controlled synthesis of varieties of hybrid nanoparticles and versatile surface modification and functionalization processes based on comprehensive coupling reactions, fulfilling these issues. Thus, surfaces of noble metal, metal@metal-oxide or ceramic nanoparticles can be conveniently modified and conjugated with biomolecules with –NHx, -COOH or –OH ligands. Using breast cancer and hepatocellular carcinoma as disease model, and noble metal and magnetic-metal@metal-oxide as nanoparticle model, several nanomedicines have been successfully synthesized based on the invented conjugation process. Their applications as molecule imaging enhancers (MRI or CT), targeting nanoprobes and anti-tumor nanomedicines were evaluated, showing excellent clinical potentials.
February 1, 2018 2018 Research Experiences for Undergraduates (REU)
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2017 Events
December 13, 2017 Squishy Physics Seminar
Prof. Jeff Gelles, Department of Biochemistry, Brandeis University

5:20pm | Pearce Hall, Room 209

Non-equilibrium control of DNA transcription

Cells in all forms of life regulate the actions of their genes by controlling the production of messenger RNAs. The regulatory molecular machinery is complex, often involving a dozen or more different proteins that may interact with each other, with RNA polymerase, with template DNA and with nascent RNA. I'll discuss projects in which we used in vitro multi-wavelength single-molecule fluorescence approaches to elucidate dynamic mechanisms by which bacterial transcript elongation is regulated. The studies show that quasi-equilibrium models are not adequate to explain these regulatory processes — they are kinetically controlled — and they reveal unexpected features of regulation, including a new transcription cycle for bacterial RNA polymerase.
December 10, 2017 Holiday Lecture Series

Hold Your Temper: Celebrating the Science of Chocolate

11:00am - 12:00pm, and 2:00pm - 3:00pm sessions | Science Center Lecture Hall B
Where does chocolate come from? Why does some chocolate melt in your mouth but not in your hand? What makes a chocolate bar smooth and creamy?
December 1, 2017 73rd New England Complex Fluids Workshop at Harvard University
September 22, 2017 72nd New England Complex Fluids Workshop at Brandeis University
June 16, 2017 71st New England Complex Fluids Workshop at Tufts University
March 24, 2017 70th New England Complex Fluids Workshop at Brandeis University

Prior Events