Calendar of MRSEC Events

2018 Events

February 1, 2019 REU Application Deadline

Research Experiences for Undergraduates program details

Through the REU program, we provide a coordinated, educational and dynamic research community to inspire and encourage young scientists to continue on to graduate school. We emphasize professional development workshops and seminars for a career in science and engineering. Weekly faculty seminars highlight research and community activities are integrated into the program. Undergraduate students research in world-class laboratories, and focusing on an in-depth research project while exploring multidisciplinary research topics to hone your science communication skills. We are seeking undergraduates from chemistry, physics, biology, computer science, mathematics (applied and pure), statistics, and engineering. Students without prior research experience, including freshman and sophomore students, are especially encouraged to apply.
December 12, 2018 Squishy Physics Seminar
Prof. Amir Taghavy, UMass Dartmouth

6 - 7:30pm | Pearce Hall, Room 209
December 5, 2018 Squishy Physics Seminar
Prof. John Hart, MIT

6 - 7:30pm | Pearce Hall, Room 209

Additive Manufacturing Across Scale

Abstract: Throughout history, innovations in manufacturing processes—such as movable type printing, and low-cost conversion of iron to steel—have catalyzed industrial growth and improved our standard of living. Now, additive manufacturing (AM) technologies, ranging from printing of low-cost electronics to automated assembly of large structures, promise to accelerate the scale-up of new products and reshape the constraints of supply chains. Motivated by this vision, I will first describe our research on high-resolution flexographic printing of electronic materials. Using nanoporous stamps comprising polymer-coated carbon nanotubes (CNTs) we achieve ultrathin micrometer-scale printing of colloidal inks, surpassing the resolution of industrial flexographic printing. We study the mechanism of ink transfer between liquid-filled CNT stamps and solid substrates, and develop guidelines for high-speed printing with controlled thickness. Second, I will highlight our work in extrusion AM—including a high-speed desktop 3D printer for rapid prototyping with polymers and composites, and a new technique for direct-write evaporative assembly of macroscopic colloidal crystals.

Bio: John Hart is Associate Professor of Mechanical Engineering, Director of the Laboratory for Manufacturing and Productivity, and Director of the Center for Additive and Digital Advanced Production Technologies (ADAPT) at MIT. John’s research group, the Mechanosynthesis Group, aims to accelerate the science and technology of advanced manufacturing in areas including additive manufacturing, nanostructured materials, and the integration of computation and automation in process discovery. He has also co-founded three advanced manufacturing startup companies and launched the world’s first massive open online course on manufacturing processes (MIT 2.008x on edX). John has been recognized by prestigious awards from the United States NSF, ONR, AFOSR, DARPA, ASME, and SME, by two R&D 100 awards, and most recently by the MIT Ruth and Joel Spira Award for Distinguished Teaching in Mechanical Engineering and the MIT Keenan Award for Innovation in Undergraduate Education.
December 3, 2018 Holiday Lecture Series
Cooking is a Call to Act

7 - 8pm | Science Center Lecture Hall C

Presenter: Massimo Bottura

Massimo Bottura (@MassimoBottura), Osteria Francescana in Modena, Italy, voted best restaurant in the world in 2018, founder of @foodforsoul_it
November 30, 2018 77th New England Complex Fluids Workshop at Harvard University
November 29, 2018 Materials Seminar
Liqiang Mai, Wuhan University of Technology, China

3 - 4:00pm | Maxwell Dworkin Room 119

New materials, New energy, New opportunities.

Ever-growing energy needs and depleting fossil fuel resources demand the pursuit of sustainable energy alternatives. Accompanied by the development and utilization of renewable energy sources, efficient energy storage has become a key topic. Electrochemical energy storage devices are considered to be one of the most practical energy storage devices capable of converting and storing electrical energy generated by renewable resources, which are also used as the power source of electric vehicles and portable electronic devices. The ultimate goals of electrochemical energy storage devices are long lifespan, high safety, high power, and high energy density. This talk will focus on high-voltage cathodes, high-capacity anodes and solid electrolyte for next-generation rechargeable batteries. Meanwhile the issues and challenges for the key materials in rechargeable batteries will be summarized and addressed.

Liqiang Mai, Changjiang Scholar Chair Professor of Materials Physics and Chemistry, Distinguished Young Scholar of the National Science Fund of China, Dean for International Affairs of International School of Materials Science and Engineering at Wuhan University of Technology. He received Ph.D. degree from WUT in 2004 and carried out postdoctoral research in Prof. Zhonglin Wang's group at Georgia Institute of Technology (2006-2007). He worked as an advanced research scholar in Prof. Charles M. Lieber's group at Harvard University (2008-2011) and Prof. Peidong Yang’s group at University of California, Berkeley (2017).

Prof. Liqiang Mai is mainly engaged in research field of nano energy materials and micro/nano devices. He has published over 290 papers tagged by SCI in leading journals such as Nature, Nat. Nanotechnol., Nat. Commun., Joule, Adv. Mater., J. Am. Chem. Soc./em>, Angew. Chem. Int. Ed., Chem., Acc. Chem. Res., Energy Environ. Sci., etc. He has conducted more than 30 research projects as project principal such as National Basic Research Program of China, National Natural Science Foundation of China, etc. He is the winner of China Youth Science and Technology Award, and Guanghua Engineering Award, Nanoscience Research Leader award, etc. He is the guest editor of Adv. Mater., and serves on the Editorial and Advisory Boards of Joule (Cell press), Acc. Chem. Res., ACS Energy Lett., Adv. Electron. Mater., Nano Res., and Sci. China Mater.
November 28, 2018 Squishy Physics Seminar
Yoav Green, T. H. Chan School of Public Health, Harvard University

6 - 7:30pm | Pearce Hall, Room 209

The Fluid Dynamics of Nanochannels and Biological Systems

Abstract: Nanochannels and nanopores are ubiquitous to nature and technology. They can be found in macroscopically large permselective membranes such as those used for desalination in electrodialysis systems, or small system such as cell membranes. The sub-micron scale in such systems allows them not only to desalinate water, harvest energy, and serve as highly sensitive bio-molecular detectors, but it also allows these nanochannels to behave as diode-like current rectifiers.

In nanofluidics systems, a nanochannel is typically connected to much larger microchannels/reservoirs. Until recently, in the nanofluidics community it was assumed that the effects of the microchannels is negligible. In this talk, I will present contradicting evidence to this assumption. I will then present a new modified paradigm which emphasizes the importance of the microchannels themselves as well as the microchannel-nanochannel interfaces. These new insights are extremely useful for designing new nanofluidic based systems.

To conclude, I will present my recent research in biomechanics that focuses on relating the kinematics of an epithelial monolayer of cells to its kinetics. As the epithelial monolayer migrates collectively, each constituent cell exerts intercellular stresses on neighboring cells and exerts traction forces on its substrate. The relationship between the velocities, stresses and tractions is fundamental to collective cell migration but it remains unknown. It will be shown that the observed dynamics does not conform to the simple and commonly assumed laws of a linear Hookean solid or Newtonian fluid. Rather the mechanics are much more complicated and likely because of the active nature of the cells. These findings are crucial for developing a deeper understanding of collective cellular behavior.

Bio: Yoav Green is currently a post-doctoral researcher in the Harvard T. H. Chan School of Public Health where he is working in the field of biomechanics. Before that Yoav received his PhD in mechanical engineering from the Technion - Israel Institute of Technology where his research fields were nanofluidics and electrokinetics. Yoav also holds a MSc in physics (astrophysics and astronomy) from the Weizmann Institute of Science, and BSc in aerospace engineering from the Technion.
November 27, 2018 Materials Today Publishing Seminar
Materials Today Publishers and Editors

4:30 - 5:30pm | Pierce Hall 209

Materials Today Publishing Seminar

In this session we will discuss the publishing landscape, including the varied roles of Authors, Editors, Referees, and Publishers in connecting communities. We'll take a look at research trends from a publishing perspective, and together will explore new and existing publishing issues; including ethics, article sharing, journal and article metrics, open access, article transfer, novel article formats, data sharing, and other essentials. In addition we will be joined my current Editors who can share best practices for publication in high impact journals such as Materials Today, including journal selection, article style & structure and article submission. The seminar will be presented by a collection of Publishers and Editors from Elsevier’s Materials Today team and will conclude with a Q & A section. ( Dr. Xingcai Zhang who serves as a Materials Today writer will lead the workshop/panel discussion.

Materials Today is a monthly peer-reviewed scientific journal, website, and journal family established in 1998 by Elsevier. Materials Today Journal covers all aspects of materials science and has an Impact Factor of 24.537. Besides Materials Today, Materials Today website covers more than 100 materials related journals published by Elsevier. It is a great opportunity to interact with Materials Today Publishers and Editors.
November 14, 2018 Squishy Physics Seminar
Fikile Brushett, MIT

6 - 7:30pm | Pearce Hall, Room 209

Developing materials design criteria for next-generation redox flow batteries

Electrochemical energy storage has emerged as a critical technology to enable sustainable electricity generation by alleviating intermittency from renewable sources, reducing transmission congestion, enhancing grid resiliency, and decoupling generation from demand. Redox flow batteries (RFBs) are rechargeable electrochemical devices that store energy via the reduction and oxidation of soluble active species, which are housed in external tanks and pumped to a power-generating reactor. As compared to enclosed batteries, RFBs offer an attractive alternative due to decoupled power and energy, long service life, and simple manufacturing, but further cost reductions are needed for ubiquitous adoption.

Recent research has focused on the discovery and development of new redox chemistries. Of particular interest are low cost organic molecules and / or nonaqueous electrolytes with wide electrochemical windows, since decreasing materials cost and increasing cell potential offer credible pathways to lowering battery price. Though exciting, most of these emerging concepts only consider new materials in isolation rather than as part of a battery system. Understanding the critical relationships between material properties and overall battery price is key to enabling systematic improvements in RFBs. In this talk, I will discuss the use of techno-economic modeling as a guide for application-informed fundamental science to identify key technical hurdles, to highlight new research avenues, and, ultimately, to decrease time to commercialization.
November 12, 2018 Holiday Lecture Series
From Low and Slow Smoking to High Heat Wok Cooking: Explore the Transfer of Heat and Application of Fire and Smoke. No Mirrors.

7 - 8pm | Science Center Lecture Hall C

Presenter: Tiffani Faison

Tiffani Faison (@TiffaniFaison), Sweet Cheeks BBQ, Tiger Mama, Fool's Errand
November 7, 2018 Squishy Physics Seminar
Georgios "Yorgos" Katsikis, MIT

6 - 7:30pm | Pearce Hall, Room 209

Deadly parasites, whirligig toys and droplet computers: do the math!

Abstract: I will present three problems on biophysics, low-cost diagnostic devices, and microfluidics. First, I will talk about a mathematical “T-swimmer” model, based on slender-body theory, that we developed to study how submillimeter-scale parasites swim in freshwaters to infect humans causing schistosomiasis, a disease comparable to malaria in global socio-economic impact. Juxtaposing this model with biological experiments and robotic prototypes, I will show how these parasites break time-reversal symmetry and propagate at an optimal regime for efficient swimming. Second, I will describe an ultralow-cost (20 cents), lightweight (2 g), human-powered paper centrifuge designed on the basis of a mathematical model of a nonlinear, non-conservative oscillator inspired by the ancient whirligig toy. Our centrifuge achieves speeds of 125,000 r.p.m., separates pure plasma from whole blood in less than 1.5 min and isolates malaria parasites in 15 min. Finally, I will talk about a microfluidic platform that performs universal logic operations with droplets. Through a reduced-order model and scaling laws for understanding the underlying physics, I will demonstrate droplet-based AND, OR, XOR, NOT, and NAND logic gates, fanouts, a full adder, a flip-flop and a finite-state machine.
November 5, 2018 Holiday Lecture Series
Gastronomic Sciences: The Interdisciplinary Approach of the Basque Culinary Center to Research and Innovation

7 - 8pm | Science Center Lecture Hall C

Presenters: Joxe Mari Aizega, Diego Prado, and Juan Carlos Arboleya

Joxe Mari Aizega (@JMAizega), Basque Culinary Center
Diego Prado (@diegopradovs), BCCinnovation
Juan Carlos Arboleya (@JuanArboleya), Basque Culinary Center
October 31, 2018 Squishy Physics Seminar
Edvin Memet, Harvard University

6 - 7:30pm | Pearce Hall, Room 209

Microtubule softening and fraying

In this two-part talk, I will start by quickly introducing recently published results ( suggesting that above a critical strain microtubules become softer due to the flattening and eventual buckling of their cross-section (Brazier buckling). This result may be particularly relevant in light of ongoing debate in the literature regarding the mechanical properties of microtubules, with estimates ranging over several orders of magnitude. In the second part of my talk, I will discuss work that involves the same optical trapping setup, except we are now buckling a two-microtubule bundle (the second MT being depleted onto the first one and having one end free and the other trapped). We find that the second microtubule deadheres ('frays') with increasing buckling amplitude and eventually readheres ('heals') when the buckling amplitude is decreased again. This process is hysteretic, in that healing does not happen at the same strain as fraying. I will show that energy loss due to stress rearrangement at bonding/debonding events is responsible for hysteresis and examine how hysteresis size and onset depend on adhesion and elasticity parameters in both the discrete and continuum limits.
October 29, 2018 Holiday Lecture Series
Let It Flow: Exploring Viscosity in Tate Dining Room & Bar

7 - 8pm | Science Center Lecture Hall C

Presenter: Vicky Lau

Vicky Lau Asia's Best Female Chef 2015, Tate Dining Room & Bar, Hong Kong
October 24, 2018 Holiday Lecture Series
Going Down the Donut Hole...

7 - 8pm | Science Center Lecture Hall C

Presenters: Wylie Dufresne and Ted Russin

Wylie Dufresne (@WylieDufresne), Du's Donuts & Coffee, BK, formerly WD~50
Ted Russin (@CIACulinarySci) School of Culinary Science and Nutrition, Culinary Institute of America
October 24, 2018 Squishy Physics Seminar
Prof. Luyi Sun, University of Connecticut

6 - 7:30pm | Pearce Hall, Room 209

Multifunctional Biomimetic Nanocoatings: from an Intact Thin Film to Microcracks to Wrinkles and the Corresponding Property Tuning

Abstract: In this presentation, nanocoatings with three distinct microstructures inspired by nature will be discussed. In the first part, organic/inorganic hybrid nanocoatings with a nacre-like microstructure generated via a facile co-assembly process will be presented. Thanks to the high concentration (up to 70 wt%) of well-aligned inorganic nanosheets and a well-integrated structure after crosslinking, such thin coatings exhibit exceptional mechanical, barrier, and flame retardant properties, while maintaining a high transparency. In the second part, inspired by marine organisms that can use muscle-controlled surface structures to achieve rapid and reversible changes in transparency, color, and patterns, a series of strain dependent mechanochromic devices will be presented. Utilizing microcracks generated via deformation-controlled surface-engineering, rigid nanocoatings affixed atop a soft substrate exhibit a broad range of mechanochromic behaviors with high sensitivity and reversibility. In the third part, a series of moisture responsive wrinkle dynamics inspired by human skin on a similar bilayer structure featuring different reversibility and stability will be discussed. These unique responsive dynamics result in the invention of a series of optical devices triggered by moisture, including anti-counterfeit tabs, encryption devices, water indicators, light diffusors, and anti-glare films. The above three biomimetic nanocoatings are promising for widespread applications.
<em>Nature Communications</em> <strong>2016</strong>, doi: 10.1038/ncomms11802
October 22, 2018 Squishy Physics Seminar
Uri Sivan, Technion-Israel Institute of Technology

3 - 4pm | MD, Room 119

The Last Nanometer - Hydration Structure of DNA and Solid Surfaces in X10,000,000 magnification

Recent advancements in atomic force microscopy facilitate atomic-resolution three-dimensional mapping of hydration layers next to macromolecules and solid surfaces. These maps provide unprecedented information on the way water molecules organize and bind these objects. Since the hydration structure governs the energetics of solvation and interactions between objects immersed in solution, the new data are invaluable when trying to resolve fundamental questions such as identification of molecular binding sites and interaction mechanisms. After a short presentation of our home-built microscope, characterized by sub 0.1 Å noise level, the talk will focus on three representative studies. The first one will disclose that water molecules grow epitaxially on certain crystalline substrates, forming 3d ordered structures extending to about 1 nm from the surface. The second study will present our recent success in obtaining ultra-high resolution images of DNA and 3d maps of its hydration structure (e.g., Fig. 1 below). This study shows that labile water molecules concentrate along the DNA grooves, in agreement with known position of DNA binding sites. The third case will disclose our recent discovery that in solutions in contact with atmosphere, hydrophobic surfaces are generically coated with a dense layer of condensed gas molecules with density close to that of liquid nitrogen. This layer not only renders the hydrophobic interaction a certain universality, but also identifies the source of hydrophobic attraction—one of the oldest puzzles of physical chemistry.

October 17, 2018 Squishy Physics Seminar
Scott Manalis, Professor of Biological Engineering, Koch Institute for Integrative Cancer Research, MIT

6 - 7:30pm | Pearce Hall, Room 209

New tools for monitoring phenotypic properties of single cells

I will present two projects where novel approaches are used to monitor phenotypic properties of single cells. The first focuses on single-cell mechanics, which are critical in processes such as tissue development and cancer invasion. However, monitoring mechanical changes of the same cell with high-temporal resolution remains challenging primarily due to invasiveness of the measurement. I will show that scattered acoustic fields from a living cell measured inside a fluid-filled vibrating microchannel is dependent on the cortex thickness and elastic modulus. By monitoring acoustic scattering with a temporal resolution of <1 min continuously throughout multiple generations in mammalian cells, we observe mechanical dynamics during mitosis on timescales that have previously been difficult to access. The second project focuses on circulating tumor cells (CTCs), which play a fundamental role in cancer progression. However, in mice, limited blood volume and the rarity of CTCs preclude longitudinal, in-depth studies of these cells using existing liquid biopsy techniques. To address this, we have devised a method for collecting CTCs from an un-anesthetized mouse longitudinally—spanning multiple days or weeks—to study acute perturbations (e.g. drug treatment) or potentially long-term phenotypes (e.g. tumor progression) within the same mouse. I will show that our microfluidic-based approach eliminates confounding biases driven by inter-mouse heterogeneity that can occur when CTCs are collected across different mice for single-cell RNA-Seq measurements.

October 15, 2018 Holiday Lecture Series
Liquid Fire: the Science of Philippine Kinilaw

7 - 8pm | Science Center Lecture Hall C

Presenter: Margarita Forés

Margarita Forés (@MargaritaFores), Asia's Best Female Chef 2016, Cibo Restaurants, Manila, Philippines
October 10, 2018 Squishy Physics Seminar
Perry Ellis, School of Physics, Georgia Tech

6 - 7:30pm | Pearce Hall, Room 209

Active nematics on the surface of a toroid

Active materials are driven far from the ground state by the motion of their constituent particles, thereby making them inherently non-equilibrium materials. For an active nematic, this results in a continuous creation and annihilation of +/- 1/2 topological defect pairs. Here, we confine an active nematic to the surface of a toroid and focus on how the curvature of the underlying surface couples to not only the topological charge but also to the topological defect density and creation and annihilation rates.

October 1, 2018 Holiday Lecture Series
Gluten vs. Fiber: Innovative Approaches to Baking More Flavorful Bread

7 - 8pm | Science Center Lecture Hall C

Presenter: Ayr Muir

Ayr Muir (@CloverFoodLab), founder & CEO of Clover Food Lab
September 26, 2018 Squishy Physics Seminar
Hyunsik Yoon, Department of Chemical and Biomolecular Engineering, Seoul National University of Science & Technology

6 - 7:30pm | Pearce Hall, Room 209

Physical Properties of Bio-Inspired Asymmetric Features

In Mother Nature, we can find lots of asymmetric features in insects, plants, and animals. The asymmetric structures show directional characteristics due to the difference of physical or chemical properties in directions. In this talk, directional wetting properties on asymmetric surfaces and clustering-and-recovering events of high-aspect-ratio asymmetric pillar arrays will be discussed.

September 24, 2018 Holiday Lecture Series
The Science of Sugar

7 - 8pm | Science Center Lecture Hall C


Joanne Chang '91 (@jbchang), Flour Bakery and Café, Myers + Chang, author of "Flour," "Flour Too," "Myers + Chang at Home," and "Baking With Less Sugar"
September 21, 2018 76th New England Complex Fluids Workshop at Brandeis University
September 19, 2018 Squishy Physics Seminar
Wei Zhang, University of Massachusetts Boston

6 - 7:30pm | Pearce Hall, Room 209

Development of small molecule inhibitors & probes for druggable targets

This presentation highlights our recent effort on the development of green and highly efficient methods for drug-like molecule synthesis and asymmetric catalysis. A series of technologies including fluorous technologies, multicomponent reactions, and organocatalysis are integrated to maximize reaction and separation efficiency in the synthesis of diverse heterocyclic scaffolds with substitution, skeleton, and stereochemistry variations. Through the collaboration with Harvard and other medical schools in US and Europe, our compounds have been integrated to a number of drug discovery programs. Several lead compounds have been developed for druggable targets such bromodomains (BET, CBP), kinases (PLK1), MDM2, PARP1&2, HIV-1, and RORgt targets which are related cancer, immune, inflammation, and other diseases.

September 17, 2018 Holiday Lecture Series
ACID TRIP: Brightening Your Life, through Food, with Vinegar

7 - 8pm | Science Center Lecture Hall C


Gabriel Bremer La Bodega (Watertown) and former Salts Restaurant (Cambridge)
Michael Harlan Turkellarlanturk), author of "Acid Trip: Travels in the World of Vinegar," "The Beer Pantry," and "Offal Good;" host on The Food Seen, HeritageRadioNetwork and's BURNT TOAST podcast
September 12, 2018 Squishy Physics Seminar
Jiawei Yang, Harvard University

6 - 7:30pm | Pearce Hall, Room 209

Hydrogel Adhesion

Hydrogel adhesion, integrating hydrogels with a variety of materials—from soft, living tissues to hard, rigid metals—has sparked unprecedented capabilities and advanced many emerging technologies in designing functional materials, biomedical applications, soft ionotronics and electronics, and robots. However, achieving strong hydrogel adhesion is fundamentally challenging. This talk presents the chemistry, mechanics and topology for strong hydrogel adhesion. I will highlight several our recently developed bonding methods, including molecular stitching, bridging and bonding, to strongly bond any type of hydrogel with other materials, and retain a soft and stretchable interface. Unlike traditional adhesion, our adhesion is programmable, and can be designed as permanent adhesion, transient adhesion, and triggerable de-adhesion. This method further inspires many diverse applications, ranging from strong tissue adhesives, wearable devices, to underwater adhesion.

September 10, 2018 Holiday Lecture Series
Current Trends in Science and Cooking

7 - 8pm | Science Center Lecture Hall C
September 5, 2018 Squishy Physics Seminar
Gilad Yossifon, Israel Institute of Technology

6 - 7:30pm | Pearce Hall, Room 209

Active Particles as Mobile Microelectrodes for Unified Label-Free Selective Cargo Transport

Utilization of active particles to transport both biological and inorganic cargo has been widely examined in the context of applications ranging from targeted drug delivery to sample analysis. Generally, carriers are customized to load one specific target via a mechanism distinct from that driving the transport. Here, we unify these tasks and extend loading capabilities to include on-demand selection of multiple nano/micro sized targets without the need for pre-labelling or surface functionalization. An externally applied electric field is singularly used to drive the active cargo carrier and transform it into a mobile floating electrode that can attract or repel specific targets from its surface by dielectrophoresis; enabling dynamic control of target selection, loading and rate of transport via the electric field parameters. Adding directed motion via magnetic stirring enables to develop these active particles into in-vitro assays with single cell precision and building blocks for bottom-up fabrication.

August 22, 2018 Squishy Physics Seminar
Nadir Kaplan, Harvard University

5:30 - 7pm | Pearce Hall, Room 209

Theoretical design of hard and soft biomimetic materials

Realizing next-generation materials with intricate shapes or complex signal processing abilities to perform adaptive functions greatly benefits inspiration from biological systems. In the first part of this talk, I will present a geometrical theory that explains the growth and form of carbonate-silica precipitates, which exemplify biomineralization-inspired formation of inorganic brittle microarchitectures. The theory predicts new assembly pathways of arbitrarily complex morphologies and thereby guides the synthesis of light-guiding optical structures. The second part will concern a soft matter analog of information storage and differentiation in living organisms, which constantly process dynamic environmental signals. Specifically, I will introduce a continuum framework of a hydrogel system that utilizes unique cascades of mechanical responses, transport and complexation of chemical stimuli to expand the sensing repertoire beyond standard hydrogels that rapidly equilibrate to their surroundings. Altogether, the confluence of theory and experiment enables the design of optimized hard or soft biomimetic materials for applications ranging from bottom-up manufacturing to soft robotics to data encoding.

August 15, 2018 Squishy Physics Seminar
Andrew Wong, Harvard University

5:30 - 7pm | Pearce Hall, Room 209

Advances in Aqueous Organic Redox Flow Batteries

Rising demand for utility-grid and micro-grid energy storage has spurred rapid advancements in electrochemical energy storage systems. Aqueous organic redox flow batteries (AORFB) are among the technologies poised to catch this wave of innovation and discovery. This talk will include the historical progression of AORFB chemistries from acid, to alkaline, to neutral pH conditions. Advancements of these novel chemistries through enhancements in polymer ion exchange membranes, porous carbon electrodes, and fluid flow distribution will also be discussed. Finally, unique insights into AORFB enabled by optical techniques will shed light on future improvements waiting to be designed.

August 11, 2018 2018 Research Experiences for Undergraduates (REU)
move out
August 8, 2018 Squishy Physics Seminar
Luhan Ye, Harvard University

5:30 - 7pm | Pearce Hall, Room 209

Thick and flexible electrode design for advanced lithium-ion batteries

The power and energy density of a battery cell is quickly diminished by the inclusion of excess inactive materials. Given that the amount of inactive materials is directly determined by the number of battery layers, as each layer requires a separator and current collector, minimizing the number of layers is critical in optimizing the performance of a battery. It is shown here that ionic polymers can be utilized to drastically improve the thickness of each battery layer and, by extension, reduce the number of layers needed for a given total capacity. This is achieved by the ionic polymer enabling both improved ion conductivity and flexibility, the key limitations faced when maximizing electrode thickness.

August 1, 2018 Squishy Physics Seminar
Apoorva Sarode, Harvard University

5:30 - 7pm | Pearce Hall, Room 209

Biologically Inspired Approaches for Effective Drug Delivery

Over eons of evolution, biological systems have reached an unparalleled sophistication in their performance. The wide array of nano- and microscale entities in nature, from spiral-shaped bacteria to biconcave red blood cells, hints at the importance of shape in biology. Furthermore, the distinct features like size and rigidity of these cells are very crucial to carry out their native functions. Inspired by these cues, we are developing various polymer-based biomimetic carriers for targeted drug delivery. This talk will shed light on our lab’s contribution in understanding the effect of physico-mechanical parameters of polymeric particles in drug delivery (uptake, circulation, targeting, etc.). The discussion will also focus on application of these fundamental findings for the treatment of cancer and cardiovascular disorders.

July 25, 2018 Squishy Physics Seminar
Frans Spaepen, Harvard University

5:30 - 7pm | Pearce Hall, Room 209

Live 3D modeling with colloids: a retrospective

Colloidal particles, being large and slow and hence trackable in the confocal microscope, can be used to gain insight into complex problems in materials science on the particle (i.e., atomic) level. This talk will be an informal survey of the many projects in our long-standing collaboration with the Weitz group to exploit this technique: the deformation of amorphous materials, the motion of dislocations, the kinetics of solidification, the observation of crystal nucleation, the dynamics and stiffness of the solid-liquid interface, the structure and dynamics of grain boundaries,... With lots of pictures and movies.

July 18, 2018 Squishy Physics Seminar
Felix Wong, Harvard University

5:30 - 7pm | Pearce Hall, Room 209

Mechanics and dynamics of translocating filaments on curved membranes

Protein filaments that bind to curved membranes and translocate in directions determined by principal membrane curvatures exhibit rich behavior, as suggested by prior studies on bacterial filament systems. Here we model the direct binding of protein filaments to membranes and show that it is energetically favorable for filaments to orient in a manner compatible with their intrinsic curvatures. We then model the curvature-based translocation of an ensemble of filaments and show that their macroscopic properties, such as localization, can vary significantly depending on membrane geometry. Finally, we discuss the implications of our study to bacterial morphogenesis and regulation of rod shape by the bacterial actin homolog MreB. Our work introduces general methods likely to be of interest to both biologists and physicists.

This work is carried out in collaboration with Ethan Garner (MCB).

July 11, 2018 Squishy Physics Seminar
Rees Garmann, Harvard University

5:30 - 7pm | Pearce Hall, Room 209

Watching viral capsids self-assemble

The formation of a viral capsid—the highly-ordered protein shell that surrounds the genome of a virus—is the classic example of self-assembly in biology. As far back as the 1950s and 1960s, researchers have been reconstituting viral capsids in the laboratory simply by mixing together the viral coat proteins and genome molecules. The high yields of proper capsids that assemble in such experiments is remarkable, given the complexity of the structures.In this talk, I will describe our ongoing efforts to understand the kinetics of viral capsid assembly by monitoring the formation individual capsids. In our experiments, we inject a solution of viral coat proteins over a glass coverslip on which viral RNA strands are tethered to the surface. Using an optical technique called interferometric scattering microscopy, we measure how many proteins bind to each RNA as a function of time. Our measurements reveal some new features of the assembly process—such as an initial nucleation step, and the possibility of subsequent nucleation steps—that may help us understand how viruses regulate the assembly of correct capsids, and also how assembly can go awry.

June 27, 2018 Squishy Physics Seminar
David Nelson, Harvard University

5:30 - 7pm | Pearce Hall, Room 209

On Growth and Form of Microorganisms on Liquid Substrates

The interplay between fluid flows and living organisms plays a major role in the competition and organization of microbial populations in liquid environments. Hydrodynamic transport leads to the dispersion, segregation or clustering of biological organisms in a wide variety of settings. To explore such questions, we have created microbial range expansions in the laboratory by inoculating two identical strains of S. cerevisiae (Baker’s yeast) with different fluorescent labels on a nutrient-rich fluid 10^4 to10^5 times more viscous than water. The yeast metabolism generates intense flow in the underlying fluid substrate several times larger than the unperturbed colony expansion speed. These flows dramatically impact colony morphology and genetic demixing, triggering in some circumstances a fingering instability that allows these organism to spread across an entire Petri dish within two days. We argue that yeast colonies create fluid flow by consuming nutrients from the surrounding fluid, decreasing the density of the substrate fluid, and ultimately triggering a baroclinic instability when the fluid’s pressure and density contours are no longer parallel. Our results suggest that microbial range expansions on viscous fluids will provide rich opportunities to study the interplay between advection and spatial population genetics.

Work carried out in collaboration with Severine Atis, Bryan Weinstein and Andrew Murray
June 20, 2018 Squishy Physics Seminar
Berna Özkale Edelmann, Harvard University

5:30 - 7pm | Pearce Hall, Room 209

Dynamic single cell mechanotransduction with optically responsive extracellular matrices

The interactions between cells and the surrounding extracellular matrix (ECM) help guide key processes such as cell spreading, proliferation, and differentiation. The mechanochemical communication between cells and their microenvironment is highly dynamic and complex. For organs such as the lung and the heart, strain and its frequency are crucial parameters for tissue function. Understanding the dynamic relationship between a single cell and its microenvironment is key to deciphering tissue level complexity. Our understanding of mechanotransduction so far has mainly relied on static models which are insufficient in fully recreating the dynamic microenvironment. Recent studies involving dynamic models have shown that externally applied forces can actively guide cellular processes. However, the influence of frequency and magnitude of applied forces on cellular mechanoresponses and their downstream effects are not well understood. In this talk, I will present a dynamic approach to studying mechanotransduction at the single cell level. I will first introduce an optically responsive artificial ECM which contracts under near-infrared (NIR) light and relaxes rapidly when the light is turned off. This approach allows for precisely confined actuation of the optically responsive ECM around a single cell. I will then discuss how locally applied cyclic stretching affects two cellular mechanoresponses, namely the nuclear translocation of a mechanoresponsive transcriptional regulator and the triggering of stretch activated ion channels.

June 15, 2018 75th New England Complex Fluids Workshop at MIT
June 13, 2018 Squishy Physics Seminar
Katia Bertoldi, Harvard University

5:30 - 7pm | Pearce Hall, Room 209

Soft robots: where robotics meets mechanics

Soft robots comprising several inflatable actuators made of compliant materials have drawn significant attention over the past few years because of their ability to produce complex motions through nonlinear deformation. Their design simplicity, ease of fabrication and low cost sparked the emergence of soft robots capable of performing many tasks, including walking, crawling, camouflaging and assisting humans in grasping, suggesting new paths for space exploration, biomimimetics, medical surgery and rehabilitation. However, to achieve a particular function existing fluidic soft robots typically require multiple input lines, since each actuator must be inflated and deflated independently according to a specific preprogrammed sequence.

An interesting avenue to reduce the number of required input signals is the direct exploitation of the highly nonlinear behavior of the system without the introduction of additional stiff elements. In this talk I will present three different strategies that we have recently explored to achieve this. First, I will show that a segmented soft actuator reinforced locally with optimally oriented fibers can achieve complex configurations upon inflation with a single input source. Then, I will demonstrate that the non-linear properties of flexible two-dimensional metamaterials are also effective in reducing the complexity of the required input signal. Finally, through a combination of evolutionary optimization and experiments I will show that fluid viscosity in the tubes can be harnessed to design fluidic soft robots capable of achieving a wide variety of target responses through a single input.

June 6, 2018 Squishy Physics Seminar
Shima Parsa, Harvard University

5:30 - 7pm | Pearce Hall, Room 209

Origin of polymer enhanced oil recovery

Polymer flooding is one of the most economically viable methods for enhanced oil recovery. By flowing a small volume of polymer solution into the reservoir, after an initial recovery by water, a considerable additional amount of oil is recovered. However, the commonly accepted mechanisms for the enhanced recovery based on viscoelastic properties of the polymer solution are inadequate to explain the enhanced recovery observed in all different conditions. We use confocal microscopy to investigate the origin of polymer enhanced oil recovery by measuring the velocities of the displacing fluid around trapped oil in a 3D micromodel of porous media. A completely different mechanism for improved recovery is observed. Polymer retention in the pore space results in highly heterogeneous changes in the velocities of the displacing fluid and in some pores provides large enough viscous pressure to mobilize the trapped oil ganglia. Our pore level measurements provide new insights into the origin of polymer enhanced recovery.

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

Multimaterial Multinozzle Arrays for Rapid 3D Printing

Knots occur naturally in biological DNA, a phenomenon relevant for cellular genome organization Direct ink writing (DIW) can be used to deposit viscoelastic inks into three-dimensional multimaterial architectures. Using inks that range from ceramics to biological tissues, DIW is uniquely capable of driving technological development in 3D printing from ‘printed form’, towards ‘printed function’. However, the exploration of potential architectures is critically limited by the low throughput of DIW; for a constant filament diameter and print speed, the print time increases with the cube of the size of the printed part. Here, we use stereolithography to manufacture multimaterial multinozzle 3D (MM3D) printheads that enable the rapid construction of multimaterial architectures. We demonstrate 1D and 2D arrays of multimaterial nozzles, each capable of generating continuous filaments that switch materials at up to 50 Hz. We derive and experimentally validate an analytical model to predict the print parameter space in which MM3D nozzles can operate. Using these MM3D printheads, we generate a Miura origami fold using patterns of stiff and soft epoxy inks which vary in stiffness by almost four orders of magnitude. This MM3D system promises to enhance the scalability of multimaterial DIW, particularly for inks with limited pot-lives.

May 17, 2018 Squishy Physics Seminar
Matan Yah Ben Zion, NYU - Center for Soft Matter Research

2:00pm | Cruft Hall, Room 309

Colloidal Self Assembly - from Synthesis to Function

Although stereochemistry has been a central focus of the molecular sciences since Pasteur, its province has previously been restricted to the nanometric scale. I will present our approach of combining DNA nanotechnology with colloidal science to program the self-assembly of micron-sized clusters with structural information stemming from a nanometric arrangement. We bridged the functional flexibility of DNA origami on the molecular scale, with the structural rigidity of colloidal particles on the micron scale, by tuning the mechanical properties of a DNA origami complex. We demonstrate the parallel self-assembly of three-dimensional micro-constructs, evincing highly specific geometry that includes control over position, dihedral angles, and cluster chirality. I will end my talk describing two recent projects where we used these techniques to synthesize and study active systems: light driven fluid micro-particles, and sedimenting irregular clusters.

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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