Calendar of MRSEC Events

End of Semester Gathering
8:30-9:30am EST | 24 Oxford Street, Room 375 - Classroom 375, Cambridge, MA

TBD abstract

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10am & 1pm EST | Harvard University Science Center, Lecture Hall B, 1 Oxford Street, Cambridge, MA

What is symmetry?
How are crystals formed?
Where can we see patterns in our daily lives?

Beauty and wonder surround us everyday. Our world is full of amazing patterns: from the smallest scale of molecules arranging into crystal structures such as snowflakes, to the stripes on a tiger, to large geological wonders like Devils Postpile. Join us at the 2023 Holiday Science Lecture for Families as we take a close look at some of the amazing patterns observed in nature and the science of their structure and formation. We will use experiments and interactive demonstrations to illustrate ideas of shape, symmetry, packing, and pattern formation!
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End of Semester Gathering
9am-6pm EST | 24 Oxford Street, Geological Lecture Hall, Cambridge, MA

Join us for the 10th Anniversary meeting of the Boston Area Antimicrobial Resistance Network! The program include sessions on Advances in Antibiotics, Advances in Diagnostics, and Alternative Approaches, alongside ample opportunities for networking among colleagues from academia and industry.

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Louison Thorens, Tufts University
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: TBD

More about the Squishy Physics Seminar

Carolyn Elya, MCB
8:30-9:30am EST | 24 Oxford Street, Room 375 - Classroom 375, Cambridge, MA

Many parasites are known to manipulate the behavior of their animal hosts, but how this occurs remains poorly understood. Recently, I discovered a strain of the mind-controlling pathogen Entomophthora muscae in wild fruit flies and developed robust methods to culture the fungus in the model organism Drosophila melanogaster. Before sunset on their final day of life, infected flies perform the “zombie” behaviors characteristic of E. muscae infection: they climb to a high location (a behavior known as “summiting”), extend their proboscises, and raise their wings in a pose that facilitates spore dispersal. Using a combination of approaches that range from behavioral neuroscience to molecular biology, I have established a mechanistic model of summiting behavior in zombie flies. Work in my lab will span multiple disciplines as we identify the fungal inputs to the fly summiting pathway as well as reveal the genetic and circuit underpinnings of additional zombie behaviors driven by E. muscae.

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Adel Djellouli, J.A. Paulson School of Engineering and Applied Sciences, Harvard University
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: The pursuit of materials with enhanced functionality has led to the emergence of metamaterials - artificially engineered materials whose properties are determined by their structure rather than composition. Through careful design of their building blocks, metamaterials with unprecedented electromagnetic, acoustic, thermal and mechanical properties have been realized, with the potential to revolutionize fields ranging from energy harvesting and conversion to sensing and imaging. Although these materials are typically based on a periodic array of solid building blocks, recent studies have demonstrated that the mixing of carefully designed units into a fluid medium can also yield remarkable properties. Such “metafluids” have enabled reconfigurable and adaptable photonic fluids, negative-acoustic-index materials and unconventional thermodynamic properties. Unlike solid metamaterials, metafluids can take the shape of their container, flow, and do not require a precise arrangement of their building blocks. These characteristics make metafluids a promising platform to enhance the functionality of numerous systems that interact with fluids during operation.

Inspired by these recent advances, here we show that by mixing highly deformable shells into an incompressible fluid we can realize a metafluid with programmable elastic response, optical behavior and viscosity. We show that the reversible buckling of the shells radically changes the characteristics of the fluid and provides exciting opportunities for expanding its functionality. First, we experimentally demonstrate both at centimeter and micrometer scale that the buckling of the shells endows the fluid a highly nonlinear behavior. Then, we numerically study how the shells geometry affects such nonlinear response. Finally, we harness the nonlinear fluid behavior to develop smart robotic systems, highly tunable logic gates and optical elements with switchable response. Further, we demonstrate that shell buckling also affects the fluid viscosity, making the flow in the laminar regime dependent not only on the pressure difference between two points but also on the absolute value of pressure at these points. As such, the proposed metafluid provides a promising platform to enhance the functionality of existing fluidic devices by expanding the capabilities of the fluid itself.

More about the Squishy Physics Seminar

7 pm EST | 1 Oxford Street, Cambridge, MA, Science Center Hall C

Presenter: Mauro Colagreco (@maurocolagreco), Chef and Owner of Mirazur (France)

Dr. Amir Mitchell, UMass Medical School
6 - 7:00pm EST | 24 Oxford Street, Haller Hall, Geo Room 375, Cambridge, MA

Abstract: Numerous non-antibiotic drugs have potent antimicrobial activity at physiological concentrations and can adversely impact the human microbiome. Despite broad recognition of this phenomenon, its mechanistic underpinning remains largely unknown. We investigated the toxicity mechanisms of two hundred antibiotic and non-antibiotic drugs using pooled genetic screens with a collection of thousands of Escherichia coli knockout strains. Analysis of two million gene-drug interactions uncovered the genes and pathways underlying drug-specific toxicity and revealed antibiotics and non-antibiotics leverage on different mechanisms of lethality. This observation suggests non-antibiotics can reveal unexploited targets for novel antimicrobials. Analysis of efflux systems and membrane proteins revealed that they widely impact antibiotics and non-antibiotics alike, implying that many non-antibiotics can inadvertently select for broad antibiotic resistance. Our systematic study suggests overall orthogonality in mechanisms of action and a pervasive risk of inadvertent cross-resistance.

More information about the MSI Seminar

MSI Coffee Hour Sign-Up with Dr. Amir Mitchell for November 17, 10am

Sheila Russo, Assistant Professor, Department of Mechanical Engineering, Boston University
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: Minimally invasive surgical (MIS) procedures pose significant challenges for robots, which need to safely navigate through and manipulate delicate anatomy while performing complex tasks to treat tumors in remote areas. Soft robots hold considerable potential in MIS given their compliant nature, inherent safety, and high dexterity. Yet, a significant breakthrough of soft robots in surgery is impeded by current limitations in the design, manufacturing, and integration of soft materials that combine actuation, sensing, and control. Scientific understanding of medical and surgical robotics is entering an exciting new era where early approaches relying on rigid materials, standard manufacturing, and conventional kinematics are giving way to Soft Material Robotics. Our research at the Material Robotics Lab at Boston University is focused on the design, mechanics, and manufacturing of novel multi-scale and multi-material biomedical robotic systems. This talk will illustrate our work towards achieving safe navigation, distal actuation, integrated sensing, and effective force transmission in MIS by highlighting different classes of soft surgical robots, i.e., soft continuum robots, soft-foldable robots, and soft reactive skins with applications in lung cancer, colorectal cancer, and brain cancer surgery.

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I-Ting Huang, OEB, Cavanaugh Lab
8:30-9:30am EST | 24 Oxford Street, Room 375 - Classroom 375, Cambridge, MA

Qiaobing Xu, Professor Department of Biomedical Engineering, Tufts University
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: Lipid nanoparticles (LNPs) represent the most advanced nonviral nanoparticle delivery systems that have been extensively investigated for nucleic acid delivery. Here I will discuss the design and development of combinatorial synthetic bioreducible and biodegradable LNPs with distinct chemical structures and properties for in vitro and in vivo intracellular mRNA delivery. In the first part of my talk, I will give an overview of the research effort in my group, including various chemistry for synthesis of the lipid library, library screening for organ and cell selective delivery, and application of the delivery for rare diseases, gene editing, and cancer vaccines. In the second part of my talk, I will discuss a specific case that we recently designed a novel lipid-based nanoscale molecular machine to enhance the destabilization and disruption of the endo-lysosomal membrane through nanomechanical action upon light irradiation. Cytosolic transport of biologics with higher efficiency is achieved comparing with conventional delivery systems.

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7 pm EST | 1 Oxford Street, Cambridge, MA, Science Center Hall C

Presenter: Alex Atala (@alexatala), Chef and Owner of the D.O.M. restaurant in São Paulo

Jessica Mark Welch, Forsyth Institute
8:30-9:30am EST | 24 Oxford Street, Room 375 - Classroom 375, Cambridge, MA

TBD abstract

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Brian Timko, Assistant Professor, Department of Biomedical Engineering, Tufts University
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: Hybrid bioelectronic tissues that integrate networks of synthetic devices and living cells offer exciting opportunities to monitor and modulate biological functions. Achieving his goal, however, requires new classes of devices that integrate seamlessly with the surrounding cells. In the first part of this talk, we will discuss our recent work to achieve device-level tissue integration via electrical, magnetic and optical modalities. In the second part of this talk, we will discuss network-level integration through bioelectronic support materials with tunable bioactive and nonlinear mechanical properties. Taken together, these advances could open new routes toward closed-loop tissue integration, with applications in neuroscience and cardiology for disease modeling, bioelectronic medicine, and tissue regeneration.

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Dr. Anthony Hyman, Institute Director - Max Planck Institute of Molecular Cell Biology and Genetics
4 - 5pm | Pierce Hall 209, 29 Oxford Street

Abstract: Prof. Dr. Anthony Hyman is Director and Group Leader at the Max Planck Institute of Molecular Cell Biology and Genetics. 1984 he received his BSc first class in Zoology from the University College in London, where he had also been working as research Assistant in 1981. From 1985 to 1987 he wrote his PhD about “The establishment of division axes in early C.elegans embryos” under the supervision of Dr. John White at the Laboratory of MolecularBiology, MRC in Cambridge, England. After that he moved to San Francisco where he did hispostdoctoral research in the lab of Prof. Tim Mitchison at the University of Californiainvestigating the mechanism of chromosome movement studied in vitro. 1993 he became GroupLeader at the European Molecular Biology Laboratory in Heidelberg, before he moved toDresden in 1999 as a founding director of the Max Planck Institute for Molecular Cell Biologyand Genetics. In 2002 he was named honorary Professor of Molecular Cell Biology at DresdenUniversity of Technology. He is best known for his work on the role of phase separation information of biological compartments.

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7 pm EST | 1 Oxford Street, Cambridge, MA, Science Center Hall C

Presenter: Luciana Bianchi (@lucianabianchi), Chef, Humanist, writer, social entrepreneur. Director of the Galapagos Foundation focused on gastronomy and Founder of MUYU, the first farm, forest and sea to table restaurant in the Galapagos islands

Ethan Garner, Harvard MCB, Professor of Molecular and Cellular Biology
8:30-9:30am EST | 24 Oxford Street, Room 375 - Classroom 375, Cambridge, MA

The process by which bacteria divide in half remains an outstanding biological problem. Our understanding of this system has been furthered by groups with different approaches studying this system. I will discuss the new insights gained from cell biological and biophysical studies into the mechanisms underlying bacterial cell division, as well our recent discovery that the force driving the most energetically difficult part of cell division arises from the simple crowding of filaments on the membrane.

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Nicolas Romeo, University of Chicago
1:00pm EST | 20 Garden Street, Room G10, Cambridge, MA and VIRTUAL

Abstract:
The cell nucleus is enveloped by a complex membrane, whose wrinkling has been implicated in disease and cellular aging. The biophysical dynamics and spectral evolution of nuclear wrinkling during multicellular development remain poorly understood due to a lack of direct quantitative measurements. We characterize the onset and dynamics of nuclear wrinkling during egg development in the fruit fly when nurse cell nuclei increase in size and display stereotypical wrinkling behaviour. A spectral analysis of three-dimensional high-resolution live-imaging data from several hundred nuclei reveals a robust asymptotic power-law scaling of angular fluctuations consistent with renormalization and scaling predictions from a nonlinear elastic shell model. We further demonstrate that nuclear wrinkling can be reversed through osmotic shock and suppressed by microtubule disruption, providing tunable physical and biological control parameters for probing the mechanical properties of the nuclear envelope, highlighting in passing the importance of nonlinear response to biological robustness.

More information about the Center of Mathematical Sciences and Applications Active Matter Seminar

Michael L. Smith, Associate Professor, Department of Biomedical Engineering, Boston University
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: Tensional homeostasis is a phenomenon of fundamental importance in mechanobiology. It refers to the ability of organs, tissues, and cells to respond to external disturbances by maintaining a homeostatic (set point) level of mechanical stress (tension). It is well documented that breakdown in tensional homeostasis is the hallmark of progression of some diseases such as cancer and atherosclerosis. This talk will first survey quantitative studies of tensional homeostasis with the goal of providing characterization of this phenomenon across a broad range of length scales, from the organ level to the subcellular level. Our results, as well as those of other groups, suggest that tensional homeostasis is an emergent phenomenon driven by collective rheostatic mechanisms that build in scale from micrometer focal adhesions to collective actions of cells in multicellular forms. Lastly, this talk will discuss the role of cadherin adhesion molecules and intracellular signaling and scaffolding proteins in regulation of tensional homeostasis, since these molecules specifically link basic science studies of this phenomenon to clinical manifestations of dysregulated cell tension.

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7 pm EST | 1 Oxford Street, Cambridge, MA, Science Center Hall C

Presenter: Bryan Furman (@bs_pitmaster), 2019 & 2020 James Beard Semifinalist, The first Pitmaster to win F&W Best New Chef (class of 2019), Chef in Residency @ Stone Barnes Center for Food & Agriculture

Jason Crawford
6 - 7:00pm EST | 24 Oxford Street, Haller Hall, Geo Room 375, Cambridge, MA

Abstract: Metabolism at the Human-Microbe Interface

The Crawford laboratory focuses on Metabolism at the Human-Microbe Interface. Genome sequencing of bacteria (and fungi) has revealed many highly unusual “orphan” biosynthetic gene clusters suspected of synthesizing novel, structurally diverse, and biologically active small molecules. These types of naturally produced molecules often regulate complex interactions with their animal hosts, hold a rich history of being utilized as human drugs, and serve as excellent molecular probes for identifying new drug targets for a wide variety of diseases. Additionally, there are still many novel metabolites of functional relevance in well-characterized animals, such as humans and mice. Using a blend of small molecule chemistry, protein biochemistry, cell biology, and microbiology, the lab exploits the natural interactions between bacteria and animals to discover new molecules with signaling, antimicrobial, immunomodulatory, and anticancer activities. The lab also connects these products to their underlying biosynthetic genes, characterizes the biosynthetic enzymes involved in their construction, and investigates their roles in biology and medicine. In this talk, I will provide an overview of our approaches and then dig into a few new metabolic systems that are conserved in a variety of gammaproteobacterial pathogens that regulate virulence programming. More information about the MSI Seminar

Michelle Teplensky, Boston University
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: Vaccines potently program the immune system through an adjuvant (activator) and antigen (target), and have been employed to fight various forms of cancer. However, their potential has yet to be fully realized, with many vaccine candidates failing out of clinical trials due to a lack of efficacy. Conventional approaches have focused on the composition with less consideration for the arrangement of the components on a single vaccine structure. This structural consideration becomes increasingly complex when evaluating the immune landscape necessary for potent tumor remission: to be effective against highly mutative aggressive tumors, cancer vaccines must activate multiple immune cell types and overcome immunosuppressive tumor environments. However, design considerations in these areas are underexplored. We highlight the opportunity to uniquely program immunological interactions and positively impact vaccine efficacy across multiple tumor types through rational and molecular antigen placement. This emphasizes the role of nanoscale vaccine structural development to raise complex multi-faceted immunity against future diseases.

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7 pm EST | 1 Oxford Street, Cambridge, MA, Science Center Hall C

Presenter: Betty Petrova (@petrovachocolates), Petrova Chocolates

Jared Mayers, CCB, Balskus Lab
8:30-9:30am EST | 24 Oxford Street, Room 375 - Classroom 375, Cambridge, MA

TBD abstract

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Fred MacKintosh, Rice University
1:00pm EST | 20 Garden Street, Room G10, Cambridge, MA and VIRTUAL

Abstract:
Various processes in living cells depend on contractile forces that are often generated by myosin motors in concert with polar actin filaments. A textbook example of this is the actomyosin contractile ring that forms during cell division. Recent evidence, however, has begun to suggest alternate or redundant mechanisms that do not depend on myosin. Experiments on simplified, reconstituted systems also point to contractility and structure formation in disordered, apolar arrays of filaments. We propose a motor-free mechanism that can generate contraction in biopolymer networks without the need for motors such as myosin or polar filaments such as actin. This mechanism is based on active binding and unbinding of cross-linkers that breaks the principle of detailed balance, together with the asymmetric force-extension response of semiflexible biopolymers. We discuss the resulting force-velocity relation and other implications of this, as well as possible evidence for non-motor force generation.

More information about the Center of Mathematical Sciences and Applications Active Matter Seminar

Kristen Dorsey, Northeastern University
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: Physically-soft mechanical sensors and actuators are poised to unlock exciting new applications in wearable devices, robotics, and human-machine interfaces. A challenge of these soft-material devices is defining and reconfiguring their properties to suit the target application. In this talk, I will discuss challenges and recent work related to designing and controlling origami-patterned sensors and actuators and additive manufacturing approaches for wearable devices and sensors. I will also present work in enhancing the stability and mechanical selectivity of stretchable sensors and discuss applications for such sensors in wearable healthcare applications and soft robotics.

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7 pm EST | 1 Oxford Street, Cambridge, MA, Science Center Hall C

Presenter: Rich Shih (@ourcookquest), Co-author of Koji Alchemy, is one of the key culinary explorers of mold-based fermentation in the United States (Wayne Earl Chinnock Photography)

Marco Jost, HMS, Blavatnick Institute
8:30-9:30am EST | 24 Oxford Street, Room 375 - Classroom 375, Cambridge, MA

Sandra Shefelbine, Northeastern University
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: The skeletal system adapts readily to changes in mechanical load, allowing cartilage and bone to alter shape and structure in response to the mechanical environment. In this talk Dr. Shefelbine will show a snapshot of her current work in which she uses experiments, imaging and computational modeling to probe the link between mechanics and bone growth, maintenance, and aging. From salamander limbs to elite ice hockey players, and mice to paraplegics she combines animal experiments, computational modeling, and clinical observations to examine the role of mechanics in skeletal adaptation.

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7 pm EST | 1 Oxford Street, Cambridge, MA, Science Center Hall C

Presenter: Joanne Chang '91 (@jbchang), Flour Bakery and Café, Myers + Chang, author of "Flour", "Flour Too", "Myers + Chang at Home", and "Baking with Less Sugar"

Max Lavrentovich, Worcester State University
1:00pm EST | 20 Garden Street, Room G10, Cambridge, MA and VIRTUAL

Abstract:
The more prosaic cousin of active matter, driven inactive matter, is still full of unexpected phenomena. I will discuss two projects involving two seemingly mundane systems, a phase-separating colloidal mixture and a lipid membrane, which demonstrate counterintuitive properties when driven out of equilibrium. We will see that the phase separating mixture, when driven by a uniform force, develops (in simulations) an intriguing pattern with a characteristic length scale set by the magnitude of the drive. We will look at some theoretical approaches to understanding the pattern formation and possible experimental realizations. The membrane, when driven by an oscillatory electric field, develops (in experiments) a long-lived metastable state with a decreased capacitance and increased dissipation. This state may have implications for neuronal processing and memory formation.

More information about the Center of Mathematical Sciences and Applications Active Matter Seminar

Margaret McFall-Ngai & Edward Ruby, Carnegie Science, Caltech
6 - 7:00pm EST | 24 Oxford Street, Haller Hall, Geo Room 102, Cambridge, MA

Abstract: Recent research has demonstrated that symbioses between animals and microbes are fundamental to the biology of most, if not all, animal species. The mutualistic association between the Hawaiian bobtail squid, Euprymna scolopes, and its luminous bacterium, Vibrio fischeri, is a powerful model to investigate signaling between the host and its microbial partner. In this system, symbiotic bacteria are acquired by horizontal transmission within hours of hatching and the symbiosis remains dynamically stable throughout the life of the host. We will address how the developmental trajectory of the host, from embryo to adult, fosters the initial colonization of the specific symbiont and maintains the symbiosis through a profound diel rhythm. In addition, we will consider how this partnership has contributed to what we know about the differences between benign or beneficial and pathogenic symbioses.

More information about the MSI Seminar

7 pm EST | 1 Oxford Street, Cambridge, MA, Science Center Hall C

Presenter: Jason Doo (@wusongroad), Chef and Owner of Wusong Road Tiki bar

Nicole Pecora, Brigham & Women
8:30-9:30am EST | 24 Oxford Street, Room 375 - Classroom 375, Cambridge, MA

TBD abstract

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Adnan Syed, MCB, Losick Lab
8:30-9:30am EST | 24 Oxford Street, Room 375 - Classroom 375, Cambridge, MA

TBD abstract

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Herbert Levine, Northeastern University
1:00pm EST | 20 Garden Street, Room G10, Cambridge, MA and VIRTUAL

Abstract:
Cell fate decisions are made by allowing external signals to govern the steady-state pattern adopted by networks of interacting regulatory factors governing transcription and translation. One of these decisions, of importance for both developmental processes and for cancer metastasis, is the epithelial-mesenchymal transition (EMT). In this talk, we will argue that these biological networks have highly non-generic interaction structures such that they allow for phenotypic states with very low frustration, i.e. where most interactions are satisfied. This property has important consequences for the allowed dynamics of these systems.

More information about the Center of Mathematical Sciences and Applications Active Matter Seminar

Michal Caspi Tal, Principal Scientist, Biological Engineering, MIT
12:00pm EST | 52 Oxford Street, Northwest Building, Lecture Hall B103, Cambridge, MA

Abstract:
Lyme disease is a tick-borne disease caused by bacteria of the genus Borrelia. The host factors that modulate susceptibility for Lyme disease have remained mostly unknown. Using epidemiological and genetic data as well as in vitro and in vivo infection assays we show a novel host defense protein in humans present in the skin, sweat, and other secretions which protects against Borrelia bacteria.

More information about the MSI Seminar

Rouzbeh Amini, Department of Mechanical and Industrial Engineering, Northeastern University
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: Mechanics plays a critical role in tissue development, regeneration, and remodeling, as cell–cell interactions and cell–matrix interactions are known to be heavily influenced by changes in the mechanical microenvironment at the extracellular matrix/cellular level. Nuclear shape alteration can be used as a metric for overall cell mechanical deformation. It may also lead to changes in gene expression and protein synthesis that could affect the biomechanics of the tissue extracellular matrix. We used engineering tools to examine how tissue mechanical loading affects the nuclear deformation. In addition, we showed that nuclear deformation is highly sensitive to the micro-structural properties of the extracellular matrix.

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7 pm EST | 1 Oxford Street, Cambridge, MA, Science Center Hall C

Presenters:
Dave Arnold (@CookingIssues), Booker and Dax (NYC), author of "Liquid Intelligence", host of "Cooking Issues," founder of the Museum of Food and Drink

Harold McGee (@Harold_McGee), author of "On Food and Cooking", "Curious Cook", "Nose Dive: A Field Guide to the World's Smells"

Dr. Michael Gilmore, MSI Co-Director
8:30-9:30am EST | 24 Oxford Street, Room 375 - Classroom 375, Cambridge, MA

What enduring properties do specific host-associated microbes have, that have allowed them to be passed generation to generation for eons, and not be displaced by other microbes? Why have some host-associated microbes emerged as leading causes of multidrug resistant infection and not others? Why bacterial species - discrete bins of related genotypes - have to exist. In our quest to understand why two species of enterococci, E. faecalis and E. faecium, emerged as leading causes of human infection, we have wrestled with these and other questions.

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The CMSA will host the ninth annual Conference on Big Data. The 2023 Big Data Conference features speakers from the Harvard community as well as scholars from across the globe, with talks focusing on computer science, statistics, math and physics, and economics.

Organizers: Michael Douglas, CMSA, Harvard University; Yannai Gonczarowski, Economics and Computer Science, Harvard University; Lucas Janson, Statistics and Computer Science, Harvard University; Tracy Ke, Statistics, Harvard University; Horng-Tzer Yau, Mathematics and CMSA, Harvard University; Lu Yue, Electrical Engineering and Applied Mathematics, Harvard University.

Register for Big Data 2023
Registration is required.

Wed, Aug 9–Fri, Aug 11: 8am-4pm @ Harvard
Explore a variety of NGSS-aligned topics like ionic compounds, intermolecular forces, acids and pH, and chemical reactions by making classroom-ready food labs including fresh cheese, caramel, brown butter, and popping boba.

This workshop is primarily intended for high school science chemistry teachers. Since it centers around hands-on labs and discussions, limited space is available and full participation is required. Our application form outlines the expectations for full participation in this virtual format.

Participants will earn:

• PDPs for their work
• a certificate of completion from Harvard University
• a stipend for both completion of the professional development and implementation of activity during the school year

This session is offered by Harvard's MRSEC and Bite Scized Education.

Register for RET PD Workshop, registration is required.   More about Harvard MRSEC RET Workshop

Mon, Aug 7–Tue, Aug 8: 9am-3pm @ Harvard
Explore a variety of NGSS-aligned topics like ionic compounds, intermolecular forces, acids and pH, and chemical reactions by making classroom-ready food labs including fresh cheese, caramel, brown butter, and popping boba.

This workshop is primarily intended for middle school science chemistry teachers. Since it centers around hands-on labs and discussions, limited space is available and full participation is required. Our application form outlines the expectations for full participation in this virtual format.

Participants will earn:

• PDPs for their work
• a certificate of completion from Harvard University
• a stipend for both completion of the professional development and implementation of activity during the school year

This session is offered by Harvard's MRSEC and Bite Scized Education.

Register for RET PD Workshop, registration is required.   More about Harvard MRSEC RET Workshop

Mon, July 31–Tue, Aug 1: Middle School; 9am-3pm on Zoom
Wed, Aug 2–Thur, Aug 3: High School (intended for High School Chemistry); 11am-5pm EST on Zoom

Explore a variety of NGSS-aligned topics like ionic compounds, intermolecular forces, acids and pH, and chemical reactions by making classroom-ready food labs including fresh cheese, caramel, brown butter, and popping boba.

This workshop is primarily intended for middle school science and high school chemistry teachers. Since it centers around hands-on labs and discussions, limited space is available and full participation is required. Our application form outlines the expectations for full participation in this virtual format.

Participants will earn:

• PDPs for their work
• a certificate of completion from Harvard University
• opportunities for stipends after implementation of activities

This session is offered by Harvard's MRSEC and Bite Scized Education.

Register for RET PD Workshop, registration is required.   More about Harvard MRSEC RET Workshop

Pragya Arora, Brandeis University
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: Dense assemblies of active particles are thought to undergo dynamical arrest akin to supercooled equilibrium liquids. However, how activity modifies the approach to a glassy state continues to be debated. Addressing this question is even as essential as a growing body of evidence suggests that dense assemblies of biological cells share hallmark traits of equilibrium glass physics. By designing synthetic active matter systems that capture certain key features of living ones, we systematically investigate active glassy dynamics in this model system. This allowed us to explore the interplay of nature and the degree of activity, shape and topological defects in glassy slowing down. We observed non-trivial relaxation mechanisms unique to active glasses. We anticipate that our experimental strategy will help prune theoretical predictions of active glasses.

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Boaz Yuval, Ph.D., Hebrew University
6 - 7:30pm | Biolabs 1065, 16 Divinity Street, Cambridge, MA and REMOTE

Abstract: Multicellular organisms maintain intimate relationships with diverse communities of microorganisms. These interactions have been studied in depth in many insect species, revealing significant and intricate effects of the microbiome on its host. In my talk, I will focus on the effects of gut symbionts on behavior of the tephritid fruit flies. Specifically, I will describe studies on olive, Oriental, and Mediterranean fruit flies that show how the microbiome affects oviposition choices by females, and foraging decisions by adults and larvae. These studies suggest the presence of an active gut-brain axis, that is modulated by the microbiome to affect sensory and motor pathways adaptively.

Zoom Online Seminar
More information about the Extavour Lab or about the Talk

Conan Wang, University of Queensland, Institute for Molecular Bioscience
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: Proteins are molecular machines that carry out the processes of life. Nature has evolved classes of miniature proteins that have unique complex topologies, constrained through backbone macrocyclization and cystine bonds. These miniature proteins or peptides are found across the major kingdoms of life, including bacteria, plants, and animals. Their highly cross-linked structures engender them with exceptional conformational rigidity, making them excellent scaffolds as drugs. In this talk, I will describe two major approaches used to re-engineer these natural proteins into therapeutics, the first is inspired by structural mimicry of protein surfaces and the second by evolution.

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Kaitlyn Becker, MIT
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: The compliance of soft robots makes them particularly well suited for grasping fragile, compliant, or topologically complex objects, as well as scenarios where target objects have an uncertain size or location. I will talk about three modes in which characteristics of the contact interface between soft grippers and their target objects can be strategically tuned and motivate these with challenging scenarios of deep-sea biological sampling. First, passive digit structures and materials can be tuned to specific contact pressure and varying object sizes. For fluidic soft grippers, the target object size, operating pressure, and payload are not independent but can be tuned separately for a given task. Second, active surface structures can be used to increase dexterity of soft grippers by modulating contact friction. Control over friction and grip force or contact pressure can be independently controlled or strategically coupled. Third, the size of contact area of a grasp can be modulated or broken up into a large collection of discrete and randomly distributed contacts. Application of a stochastic collective of contacts achieved with an array of actuators made of compliant materials and structures enables a highly adaptive grasp. While soft grippers are naturally well suited for gentle grasping, adding each of the three modalities of contact tuning, passive structure, active surface elements, and spatial distribution, can provide more robust, and adept performance. Furthermore, each modality of contact tuning can be applied independently or implemented simultaneously in a hierarchical soft gripper design.

Bio: Kaitlyn Becker is an assistant professor in the Mechanical Engineering Department and recipient of the Doherty Professorship in Ocean Utilization at MIT. She completed her B.S. in Mechanical Engineering at MIT in 2009, after which she worked on subcutaneous defibrillators as a manufacturing engineer for Cameron Health Inc, and then worked on the development of various nanofabrication technologies and UV water treatment as a senior engineer for Nano Terra Inc. She completed her PhD in Professor Wood’s Microrobotics Lab in 2021 and was postdoctoral researcher in Professor Mahadevan’s Soft Math lab at Harvard University. Her primary research thrust is on gentle and adaptive soft robots for grasping and manipulation from the desktop to the deep sea and focuses on novel soft robotic platforms that add functionality through innovations at the intersection of design and fabrication. Her work has been featured on the covers of the journals Soft Robotics and Advanced Functional Materials, and in the Unseen Oceans special exhibit in the American Natural History Museum. Her robotic platforms have also been successfully tested at depths down to 3.5km on research vessels including the Nautilus (Ocean Exploration Trust), Falkor (Schmidt Ocean Institute), and the Rachel Carlson (MBARI). She is a recipient of a Microsoft graduate research scholarship and a NSF Graduate Research Fellowship. Outside of her research and teaching in Mechanical Engineering, she also teaches glassblowing in the Department of Material Science and Engineering at MIT, where she fuses art and applied engineering in her classes.

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Dr. Chuanhua Duan, Boston University
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: Research on solid state nanopores has attracted great attention over the last two decades because of their great potentials in mimicking protein channels in cell membranes. Although significant progress has been made, past research has mainly utilized solid nanopores for translocation-based single bimolecule/particle sensing and ion/molecule transport control. What can we do with solid-state nanopores beyond these two directions? This question can be answered from two different perspectives. On one hand, single nanopores are the basic constitute of nanoporous membranes. It is therefore possible to use single nanopores to study and understand complicated transport phenomena in nanoporous membranes, paving the way for developing nanoporous membranes with better performance. On the other hand, it is worth noting that most of the past nanopore research is focused on molecule/particle translocating through the nanopore. The opposite scenario, i.e. molecules/particles blocking the nanopore, has not been extensively studied. In this talk, I will present my group’s recent efforts on exploring fundamentals and application of solid-state nanopore from these two new aspects.

First, I will present our work on exploring evaporation from single nanopores. We have developed a novel microscope-based optical measurement to measure evaporation rates down to 10 aL/s from single nanopores. I will show that the ultimate evaporation flux from ultrathin silicon nitride nanopores is not limited by liquid transport to the interface and vapor removal from the interface, but by the interfacial evaporation kinetics and shows a strong diameter dependence. I will also show that the kinetically-limited evaporation from graphene nanopores can be much larger than that from silicon nitride nanopores due to edge facilitated evaporation and minimum contaminant accumulation.

Secondly, I will introduce our latest work on studying nanoparticle-blocked nanopore systems. We have found that, when nanoparticles with sizes larger than the diameter of a nanopore are electrophoretically driven towards the nanopore, they can be either electrokinetically trapped near the nanopore or physically block the nanopore based on their surface charge polarity. These two types of nanoparticle blockage modes can respond to various electrical or mechanical stimuli and show stimuli-responsive transport. I will show how we utilize such nanoparticle-blockage-induced stimuli-responsive transport to develop new applications for nanoparticle characterization, nanopore gating as well as bio-sensing.

Bio: Dr. Chuanhua Duan received his B.S. and M.S. degrees in Engineering Thermophysics from Tsinghua University in 2002 and 2004, respectively. He obtained his Ph.D. in Mechanical Engineering from the University of California at Berkeley in 2009 under the guidance of Prof. Arun Majumdar. After staying in Berkeley for two more years as a postdoctoral researcher at the Lawrence Berkeley National Laboratory, Dr. Duan joined the Department of Mechanical Engineering at Boston University as an assistant professor in 2012. He is currently an associate professor at BU ME, leading the Nanoscale Energy-Fluids Transport Laboratory. Among his honors, Dr. Duan received the Defense Advanced Research Project Agency Young Faculty Award (YFA) in 2018, the National Science Foundation Early Faculty Career Development Award (CAREER) in 2017, and the American Chemistry Society Petroleum Research Fund Doctoral New Investigator Award in 2013. His research focuses on the study of micro- and nanofluidic transport phenomena and the development of new fluidic devices/approaches for applications in healthcare, energy systems, and thermal management.

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Jiliang Hu, MIT
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: From tropical forests to gut microbiomes, ecological communities host striking numbers of coexisting species. Beyond high biodiversity, communities exhibit a range of complex dynamics that are difficult to explain under a unified framework. Using bacterial microcosms, we perform the first direct test of theory predicting that simple coarse-grained features dictate emergent behaviors of communities. As either the number of species or the strength of interactions increases, we show that microbial ecosystems transition between three distinct dynamical phases, from a stable equilibrium where all species coexist, to partial coexistence, to emergence of persistent fluctuations in species abundances, in the order predicted by theory. Under fixed conditions, high biodiversity and fluctuations reinforce each other. Our results demonstrate predictable emergent patterns of diversity and dynamics in ecological communities.

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Jacques Fattaccioli, Paris Sciences et Lettres University
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: Response to pathogens and homeostasis is orchestrated by the complex interactions and activities of the large number of diverse cell types involved in the immune response. The innate immune response occurs soon after pathogen exposure and is carried out by phagocytic cells such as neutrophils or macrophages. The subsequent adaptive immune response involves antigen-presenting cells such as macrophages or dendritic cells; and antigen stimulation-dependent cell types such T cell subsets and B cells. As an alternative to polymers or hydrogels that are commonly used when model substrates are needed for uptake or migration studies from the point of view of mechanobiology, we developed ligand-functionalized lipid droplets to address these questions. In this talk, I will present how to make and characterize functional lipid droplets, how they can be used in the context of phagocytosis, cell migration and antigen extraction, and I will present the most recent ongoing results.

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Derin Sevenler, Massachusetts General Hospital, Department of Surgery
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: Intracellular delivery of biomolecules or nanomaterials is a critical step in many bioengineering processes across applications in science, technology, and medicine. In particular, emerging cell and gene therapies can require the genetic manipulation of extremely large numbers of cells (hundreds of trillions of cells, in some cases), and scale-up of conventional methods for delivering genetic material or gene editing complexes into cells (viral vectors, cationic polymers, electroporation) have faced issues with efficiency and/or cytotoxicity. In this talk, we will describe recent work developing a high-throughput method of intracellular delivery which used viscoelastic flow forces within a microfluidic chip to stretch and temporarily permeabilize the plasma membrane of cells, thereby enabling rapid and efficient delivery of large biomolecules including proteins, nucleic acids, and CRISPR-Cas ribonucleoprotein complexes to the cytosol. This method was notably fast, processing over 250 million cells per minute in a single microchannel (100x-1,000x faster than comparable methods) with up to 95% delivery efficiency. Altogether, viscoelastic mechanoporation seems to be a feasible method for high-throughput intracellular delivery for a range of different cell types that includes primary T and NK cells.

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Sahand Hormoz (Harvard Medical School, Dana-Farber Cancer Institute)
1:00pm EST | 20 Garden Street, Room G10, Cambridge, MA and VIRTUAL

Abstract:
Two recent projects from my lab that involve lineage trees of cells (the branching diagram that represents the ancestry and division history of individual cells). In the first project, we reconstructed the lineage trees of individual cancer cells from the patterns of randomly occurring mutations in these cells. We then inferred the age at which the cancer mutation first occurred and the rate of expansion of the population of cancer cells within each patient. To our surprise, we discovered that the cancer mutation occurs decades before diagnosis. For the second project, we developed microfluidic 'mother machines' that allow us to observe mammalian cells dividing across tens of generations. Using our observations, we calculated the correlation between the duration of cell cycle phases in pairs of cells, as a function of their lineage distance. These correlations revealed many surprises that we are trying to understand using hidden Markov models on trees. For both projects, I will discuss the mathematical challenges that we have faced and open problems related to inference from lineage trees.

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Neel Joshi, Northeastern University
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: The intersection between synthetic biology and materials science is an underexplored area with great potential to positively affect our daily lives, with applications ranging from manufacturing to medicine. My group is interested in harnessing the biosynthetic potential of microbes, not only as factories for the production of raw materials, but as fabrication plants that can orchestrate the assembly of complex functional materials. We call this approach “biologically fabricated materials”, a process whose goal is to genetically program microbes to assemble materials from biomolecular building blocks without the need for time consuming and expensive purification protocols or specialized equipment. Accordingly, we have developed Biofilm Integrated Nanofiber Display (BIND), which relies on the biologically directed assembly of biofilm matrix proteins of the curli system in E. coli. We demonstrate that bacterial cells can be programmed to synthesize a range of functional materials with straightforward genetic engineering techniques. The resulting materials are highly customizable and easy to fabricate, and we are investigating their use for practical uses ranging from bioremediation and biodegradable bioplastics to engineered therapeutic probiotics.

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Since its inception in 2004, the Microbial Science Initiative has sponsored and hosted an annual symposium for those in the Harvard and greater Boston communities. The spring event showcases magnificent research across a breadth of microbe-centric topics spanning environmental and biomedical sciences. The MSI Symposium is $20 for the public or $5 for students & postdocs. Welcome to the microbial world! Mid-morning and mid-afternoon breaks with refreshments will be provided, and there will be a 75 minute break for lunch mid-day.

Ticket registration required, $20 or $5 for Students & Postdocs, and is open to the public

Mehran Kardar, MIT
1:00pm EST | 20 Garden Street, Room G10, Cambridge, MA and VIRTUAL

Abstract:
When competing species grow into new territory, the population is dominated by descendants of successful ancestors at the expansion front. Successful ancestry depends on the reproductive advantage (fitness), as well as ability and opportunity to colonize new domains. (1) Based on symmetry considerations, we present a model that integrates both elements by coupling the classic description of one-dimensional competition (Fisher equation) to the minimal model of front shape (KPZ equation). Macroscopic manifestations of these equations on growth morphology are explored, providing a framework to study spatial competition, fixation, and differentiation, In particular, we find that ability to expand in space may overcome reproductive advantage in colonizing new territory. (2) Variations of fitness, as well as fixation time upon differentiation, are shown to belong to distinct universality classes depending on limits to gain of fitness.

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Meni Wanunu, Northeastern University
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: Nanopores have gained a lot of attention recently for their ability to sequence nucleic acids. Recently, however, a surge of interest in the use of nanopores for analyzing proteins has been witnessed. I will talk about two approaches that our lab has taken for characterizing proteins. First, I will describe a method for full-length single-file protein translocation and discrimination using a biological pore. Second, I will describe a method for probing conformational states of a protein and its electrical unfolding. With these tools in mind, it is exciting to think about possibilities in using nanopores for studying protein variants, post-translational modifications, and interactions of proteins with small molecule drugs.

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Sulin Zhang, Pennsylvania State University, Department of Engineering Science and Mechanics
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: In various electro/biochemical processes, mechanical stress generation and transmission pathways exist in parallel and interact in concert with chemical reaction and mass diffusion pathways. How might the mechanics-electrochemistry reciprocity be harnessed for energy storage and energy harvesting, and unharnessed in battery degradation? Similarly, how might the mechanics-biochemistry crosstalk be regulated in development and repair, and dysregulated in disease and injury? These questions have been stimulating new understanding at the interfaces between mechanics and other disciplines including materials, chemistry, biology, and medicine. In this talk, I will show a set of exciting phenomena in rechargeable batteries and living organisms to highlight the crosstalks. Emphasis will be placed on the fundamental mechanics linking to bio/electrochemistry, which underlies materials design, energy storage and harvesting, disease control, and nanomedicine innovation.

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Hemanoel Passareli, Visiting Scholar to Hanage Lab
12-1pm EST | 24 Oxford Street, Room 375 - Classroom 375, Cambridge, MA

Pangenome analysis has become a vital tool to understand bacterial diversity. In this Chalk Talk, we will discuss how we can interpret a pangenome from an ecological perspective to explore the evolution of microorganisms.

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Shane McInally, Brandeis University
1:00pm EST | 20 Garden Street, Room G10, Cambridge, MA and VIRTUAL

Abstract:
The sizes of many subcellular structures are coordinated with cell size to ensure that these structures meet the functional demands of the cell. In eukaryotic cells, these subcellular structures are often membrane-bound organelles, whose volume is the physiologically important aspect of their size. Scaling organelle volume with cell volume can be explained by limiting pool mechanisms, wherein a constant concentration of molecular building blocks enables subcellular structures to increase in size proportionally with cell volume. However, limiting pool mechanisms cannot explain how the size of linear subcellular structures, such as cytoskeletal filaments, scale with the linear dimensions of the cell. Recently, we discovered that the length of actin cables in budding yeast (used for intracellular transport) precisely matches the length of the cell in which they are assembled. Using mathematical modeling and quantitative imaging of actin cable growth dynamics, we found that as the actin cables grow longer, their extension rates slow (or decelerate), enabling cable length to match cell length. Importantly, this deceleration behavior is cell-length dependent, allowing cables in longer cells to grow faster, and therefore reach a longer length before growth stops at the back of the cell. In addition, we have unexpectedly found that cable length is specified by cable shape. Our imaging analysis reveals that cables progressively taper as they extend from the bud neck into the mother cell, and further, this tapering scales with cell length. Integrating observations made for tapering actin networks in other systems, we have developed a novel mathematical model for cable length control that recapitulates our quantitative experimental observations. Unlike other models of size control, this model does not require length-dependent rates of assembly or disassembly. Instead, feedback control over the length of the cable is an emergent property due to the cross-linked and bundled architecture of the actin filaments within the cable. This work reveals a new strategy that cells use to coordinate the size of their internal parts with their linear dimensions. Similar design principles may control the size and scaling of other subcellular structures whose physiologically important dimension is their length.

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12-1pm EST | 24 Oxford Street, classroom #375, Cambridge, MA

Is there an item that's been languishing on your to-do list? Do you have an assignment to do and just can't harness the motivation to take the first step? Register and join the Microbial Sciences Initiative for a Micro-Goal Lunch Hour! Open to all Harvard students and postdocs, especially those with an interest in the microbial world.

Neel Joshi, Northeastern University
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: TBD

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Mark Bowick, Kavli Institute for Theoretical Physics, UCSB
1:00pm EST | 20 Garden Street, Room G10, Cambridge, MA and VIRTUAL

Abstract:
Motivated by the existence of membrane-less compartments in the chemically active environment of living cells, I will discuss the dynamics of droplets in the presence of active chemical reactions. Therefore, I will first introduce the underlying interplay between phase separation and active reactions, which can alter the droplet dynamics compared to equilibrium systems. A key feature of such systems is the emergence of concentration gradients even at steady states. In the second part of this talk, I will discuss how these gradients can trigger instabilities in the core of chemically active droplets, giving rise to a new non-equilibrium steady state of liquid spherical shells. Finally, I will present experimental and theoretical results discussing the existence and energetic cost of this non-equilibrium steady state in a coacervate system.

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Brandy Toner
4 - 5pm EST | William James Hall, Room 105, 33 Kirkland Street, Cambridge, MA

TBD

Bryan Spring, Northeastern University, Dept. of Physics
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: This talk will introduce concepts of targeted photodynamic therapy with microscale fidelity using clinical antibody–photosensitizer (benzoporphyrin derivative monoacid A, verteporfin) conjugates. These initially quenched (“off”) photoimmunoconjugates target tumor cell-surface biomarkers and become activated upon cell-internalization ("on"). Present efforts to further develop these concepts for precision treatment of heterogenous human ovarian cancer will be discussed.

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Invited Speakers:
Corey O'Hern, Yale University
Leslie Shor, University of Connecticut
Ian Wong, Brown University
Evan Wujcik, University of Maine

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Jonathan Bauermann, Max Planck Institute for the Physics of Complex Systems
1:00pm EST | VIRTUAL

Abstract:
Morphogenesis, the process through which genes generate form, establishes tissue scale order as a template for constructing the complex shapes of the body plan. The extensive growth required to build these ordered substrates is fueled by cell proliferation, which, naively, should disrupt order. Understanding how active morphogenetic mechanisms couple cellular and mechanical processes to generate order remains an outstanding question in animal development. I will review the statistical mechanics of orientational order and discuss the observation of a fourfold orientationally ordered phase (tetratic) in the model organism Parhyale hawaiensis. I will also discuss theoretical mechanisms for the formation of orientational order that require both motility and cell division, with support from self-propelled vertex models of tissue. The aim is to uncover a robust, active mechanism for generating global orientational order in a non-equilibrium system that then sets the stage for the development of shape and form.

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Carla Fernandez-Rico, ETH Zurich
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: TBD

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Alexis Jaramillo Cartagema
12-1pm EST | 24 Oxford Street Room 375, Classroom 375, Cambridge, MA

12-1pm EST | 24 Oxford Street, classroom #375, Cambridge, MA

Is there an item that's been languishing on your to-do list? Do you have an assignment to do and just can't harness the motivation to take the first step? Register and join the Microbial Sciences Initiative for a Micro-Goal Lunch Hour! Open to all Harvard students and postdocs, especially those with an interest in the microbial world.

Xin Zhao, Hong Kong Polytechnic University
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: Photocrosslinkable polymers are polymers that can be solidified from liquid upon light exposure. They have been employed to fabricate tissue engineered constructs due to the mild conditions for crosslinking, highly tunable mechanical and structural modifiability, printability, biodegradability and biocompatibility. These biomaterials can maintain their structural integrity after biofabrication and provide topological, biochemical, and physical cues to guide cellular behaviors by creating a biomimetic microenvironment.

The emphasis of this talk is placed on how photocrosslinkable polymers can be used to achieve tissue regeneration, for example, their fabrication into various scaffolds (electrospun fibers, microspheres, and 3D printed scaffolds) to reconstruct bones. Specifically, assisted by microfluidics, we have developed photocrosslinkable methacrylated gelatin (GelMA) based microspheres encapsulating human mesenchymal stem cells (MSCs) for bone repair. Due to the mild crosslinking conditions, we found that the GelMA microspheres can provide a favourable micro-environment for MSC survival, spreading, migration, proliferation and osteogenesis. In another study, we prepared a periosteum mimicking bone aid (PMBA) by electrospinning photocrosslinkable GelMA with L-arginine-based unsaturated poly(ester amide) (Arg-UPEA), and methacrylated hydroxyapatite nanoparticles (nHAMA). Upon light exposure, the resultant hydrogel fibrous scaffolds can solidify within seconds. Via controlling the crosslinking density, we can control the scaffolds’ mechanical and degradation property. The optimal scaffold was found to provide long term structural and functional support and mediation of physiological activity. With the aid of 3D printing, we developed 3D bone scaffolds made of photocrosslinkable nanocomposite ink consisting of tri-block poly (lactide-co-propylene glycol-co-lactide) dimethacrylate (PmLnDMA, m and n respectively represent the unit length of propylene glycol and lactide) and nHAMA. It is discovered that nHAMA can rapidly interact with PmLnDMA upon light exposure within 140 seconds and form an inorganic-organic co-crosslinked nanocomposite network. This bone ink was found to provide good mechanical support and bioactivity (allow for encapsulation and long-term release of growth factors) for bone regeneration.

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Beau Schaeffer
12-1pm EST | 24 Oxford Street Room 375, Classroom 375, Cambridge, MA

Yu Qiu, Department of Earth, Atmospheric, and Planetary Sciences, MIT
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: The displacement of one fluid by another immiscible fluid in confined geometries occurs in many natural and industrial settings from geological CO₂ sequestration to microfluidics. The fluid-solid interactions are key to understanding the combined effects of wetting, capillarity and viscous forces, which, in turn, control the fluid-fluid displacement patterns. One fundamental aspect of fluid-fluid displacement in confined geometries is the wetting transition: the displacement rate above which films of the defending fluid are deposited on the confining surfaces. These films may later dewet, giving rise to complex “residual fluid” patterns. Earlier experiments in our group have shown that the wetting transition results in interface pinch-off that generates disconnected bubbles and drops even in uniform capillaries without external crossflow (Zhao et al., PRL 2018). Here I will present a phase-field model to simulate the two-phase flow with moving contact lines and investigate the interface dynamics in a smooth confinement over a wide range of wettability conditions and viscosity contrast. I will show that the pinch-off of a bubble only occurs when the invading fluid is less viscous. Since real surfaces are rough, we investigate the role of wall roughness on two-phase displacements in confined geometries by means of experiments on a microfluidic fracture with precisely-controlled structured surface. We show that the roughness induces two types of liquid films entrained on the solid surfaces: the classical Bretherton “thick film”, and a new type of “thin film” that is confined within the roughness. Each type is characterized by distinct stability criteria and dewetting dynamics. Our work shed light on the microscale physics and macroscopic displacement patterns in confined geometries that may control long-term biogeochemical reactions.

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Jörn Dunkel, MIT
1:00pm EST | VIRTUAL

Abstract:
Over the last two decades, major progress has been made in understanding the self-organization principles of active matter. A wide variety of experimental model systems, from self-driven colloids to active elastic materials, has been established, and an extensive theoretical framework has been developed to explain many of the experimentally observed non-equilibrium pattern formation phenomena. Two key challenges for the coming years will be to translate this foundational knowledge into functional active materials, and to identify quantitative mathematical models that can inform and guide the design and production of such materials. Here, I will describe joint efforts with our experimental collaborators to realize self-growing bacterial materials [1], and to implement computational model inference schemes for active and living systems dynamics [2,3].

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Andee Wallace
4 - 5pm EST | William James Hall, Room 105, 33 Kirkland Street, Cambridge, MA

The World Health Organization estimates that agricultural productivity will need to increase by 70% by 2050 to meet the food needs of a global population of 10B people. Facing a changing climate and increasing disease pressure, growers today spend nearly $80B on six billion pounds of pesticides each year, and yet still experience yield losses of 20-40% due to pests and disease. Broad-acting, chemically derived pesticides - currently the industry standard - are losing both efficacy and public support as resistance spreads and their negative environmental impacts become clear. At Robigo, we believe in building on nature’s foundation to engineer solutions that work for growers, consumers, and the environment. We have developed a scalable plug and play platform technology that leverages synthetic biology, CRISPR, and data science to engineer microbes that are naturally found out in the fields to protect crops, fight disease, and improve overall yields. Initially targeting three diseases that affect citrus, apples, and tomatoes, our microbes outperform commercial chemical pesticides and reduce disease by over 90% while increasing plant biomass by over 15%. Robigo is unlocking the potential of engineered microbes in agriculture to fundamentally change how the world grows food and create a more sustainable future for agriculture. Founded by MIT synthetic biologists, Robigo is a VC-backed, Seed-stage biotech startup based in Cambridge, MA.

Qiong Zhang, Department of Mechanical Engineering, MIT
6 - 7:30pm | Pierce Hall 301, 29 Oxford Street

Abstract: Sediment transport caused by particles rolling, sliding, and hopping on a river bed is called bedload transport. Semi-empirical formulas to predict bedload sediment flux from the driving factors, known as the transport relation, can be highly inaccurate. Simulations where the sediment particles are fully resolved are carried out to find if the predictions can be improved by considering more particle parameters. After being validated against flume experiments, the numerical scheme is used to simulate bedload transport under many conditions, and its results show that at a fixed relative hydrodynamic driving force, varying river slope (on gentle slopes), fluid depth, mean particle size, particle surface sliding friction coefficient, and grain-grain damping coefficient cause almost no variation of the transport rate. The simulations also shed light on the microscopic mechanisms such as how the fluid torque on particles helps initiate rolling and subsequent grain transport. We further use the numerical scheme to guide development of an alternative framework that can predict the flow profiles for the fast transport as well as the gradual transport beneath the bed surface without resolving the individual particles, which is a more tractable way to model large-scale bedload sediment transport problems.

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Nazim Bouatta, Harvard Medical School
3:30-5:00pm EST | 20 Garden Street Room G10, Cambridge, MA and VIRTUAL

Thursday, February 9, Lecture 1:
A brief intro to protein biology. AlphaFold2 impacts on experimental structural biology. Co-evolutionary approaches. Space of ‘algorithms’ for protein structure prediction. Proteins as images (CNNs for protein structure prediction). End-to-end differentiable approaches. Attention and long-range dependencies. AlphaFold2 in a nutshell.

Thursday, February 16, Lecture 2:
AlphaFold2 architecture. Turning the co-evolutionary principle into an algorithm: EvoFormer. Structure module and symmetry principles (equivariance and invariance). OpenFold: retraining AlphaFol2 and insights into its learning mechanisms and capacity for generalization. Applications of variants of AlphaFold2 beyond protein structure prediction: AlphaFold Multimer for protein complexes, RNA structure prediction.

Thursday, March 9, Lecture 3:
Limitations of AlphaFold2 and evolutionary ML pipelines. Current single sequence models. Protein language models (LM): single sequence + LM embeddings. Combining LM models with Frenet-Serret construction for protein structure prediction. Applying AlphaFold2 and OpenFold for language models.

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12-1pm EST | 24 Oxford Street, classroom #375, Cambridge, MA

Is there an item that's been languishing on your to-do list? Do you have an assignment to do and just can't harness the motivation to take the first step? Register and join the Microbial Sciences Initiative for a Micro-Goal Lunch Hour! Open to all Harvard students and postdocs, especially those with an interest in the microbial world.

Amin Doostmohammadi, Niels Bohr Institute, University of Copenhagen
1:00pm – 2:30pm (EST) | VIRTUAL or 20 Garden St, seminar room G-10

Abstract: I will focus on the interaction between different active matter systems. In particular, I will describe recent experimental and modeling results that reveal how interaction forces between adhesive cells generate activity in the cell layer and lead to a potentially new mode of phase segregation. I will then discuss mechanics of how cells use finger-like protrusions, known as filopodia, to interact with their surrounding medium. First, I will present experimental and theoretical results of active mirror-symmetry breaking in subcellular skeleton of filopodia that allows for rotation, helicity, and buckling of these cellular fingers in a wide variety of cells ranging from epithelial, mesenchymal, cancerous and stem cells. I will then describe in-vivo experiments together with theoretical modeling showing how during embryo development specialized active cells probe and modify other cell layers and integrate within an active epithelium.

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Douglas H. Bartlett, PhD, UC San Diego
4 - 5pm EST | William James Hall, Room 105, 33 Kirkland Street, Cambridge, MA

A major portion of microbial life on Earth is present in low-temperature/deep-sea environments, and yet much remains to be learned of their diversity, adaptations and activities. Studies of these microbes in situ and ex situ is providing fundamental and biotechnological insights, and will be critical to many possible ocean-based decarbonization processes. In this presentation I will first discuss what we have learned about proteomes and cell envelopes of piezophilic (high pressure-adapted) isolates. Then I will transition to investigations of deep-sea microbial activities using pressure-retaining seawater sampling to collect microbes with minimal temperature/pressure alteration, followed by the sorting and identification of cells active under in situ deep-sea conditions. One aspect of this work is the indication that certain microbial groups (e.g., members of the Thaumarchaeota) are highly sensitive to decompression/incubation effects, reducing their perceived significance when collected using standard methods.
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