Abstract: Thin sheets assume a rich diversity of shapes in the natural world, ranging from folds on the earth’s crust, to the wavy shapes of leaves and flowers, down to more microscopic biomembranes and synthetic thin films. The patterns include smooth architectural motifs such as wrinkles, as well as focused localized objects such as folds and ridges. Our experiments study the emergence of complex shapes in thin, fluid-supported polymer films starting from simple featureless initial conditions via successive elastic instabilities. Understanding these patterns required new notions of ‘thinness’ or bendability, which define regimes in which textbook theories of buckling fail. I will end by describing new opportunities for wrapping and encapsulation with highly-bendable materials.
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My focus at RIT has been on radically non-spherical (asymmetric or anisometric) granular materials including long, thin cylinders, U-shaped staples and C-shaped annular-sector particles (ASPs). In this talk I’ll discuss three different experiments and simulations: 1) extensional rheology of 3d piles, 2) the influence container boundaries have on rod packings and 3) dimerization of ASPs under 2d shear. Extensional rheology is made possible by shape-dependent particle entanglement and can be explained using Weibullian weakest-link statistics.
These behaviors and models have subsequently been used to understand the rheology of ant-rafts and how elephants pick up granular foods. Granular experiments can be sensitive to pile preparation and container size. Experiments and simulations reveal the presence of both horizontal and vertical boundary layers that influence the bulk packing fraction. Finally, I’ll present preliminary experiments on annular-sector particles (ASPs) that can entangle under shear and form dimers (and trimers).
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Recent experiments and simulations have indicated that confluent epithelial layers, where there are no gaps or overlaps between the cells, can transition from a soft fluid-like state to a solid-like state, with dynamics that share many features with glass transitions. While a coherent picture has begun to form connecting the microscopic mechanisms that drive this transition with macroscopic observables, much less is known of its consequences in biological processes. Do tissues tune themselves to a fluid state in order to promote collective motion? Has evolution made use of the ability of tissues to tune themselves between fluid and solid states in programming the complex steps leading from the embryo to the organism?
In this talk I will describe our recent efforts to answer such questions using continuum and mesoscopic models. Employing the biophysical vertex model, active cells in confluent tissue are described as polygons with shape-based energies. Recent work has shown that this class of models yields a solid-liquid transition of tissue with evidence of glassy dynamics near the transition line. In our work, we extend one such model to include the influence of cell division and cell death. With careful numerical studies, we refute a recent claim that the presence of such division and death will always fluidify the tissue.
In a second effort, we develop a novel hydrodynamic model of confluent motile tissues that couples tissue rigidity to cell polarization. Using this continuum model we identify a new mechanism for pattern formation in confluent tissues via rigidity sensing that we name “morphotaxis”. We find that a single “morphotactic” parameter controls whether a tissue will remain homogeneous or will develop patterns such as asters and bands.
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Abstract
The 2018 Nobel Prize in Physics recognizes two breakthrough inventions in laser physics. The first, optical tweezers, allows scientist and engineers to use lasers like the tractor beams of Star Trek to manipulate everything from molecules to living cells. Optical tweezers have provided researchers with fingers in the microscopic world that can pull apart DNA, probe the mechanics of life, detect disease and study fundamental interactions in biology, physics, chemistry and engineering. The second breakthrough, chirped pulse amplification, enabled the construction of lasers of incredible power and precision. With the super-high power lasers came cutting-edge applications as diverse as attosecond time-resolved dynamics of atoms and molecules and laser eye surgery. In this public talk, Georgia Tech Professor Rick Trebino will give an overview of optical physics. Professors Jennifer Curtis and Chandra Raman will present a brief history of these discoveries and discuss their impacts on science and society, with an audience Q&A session afterwards.
About the Speakers
The Curtis lab, managed by Dr. Jennifer Curtis, is primarily focused on the physics of cell-cell and cell-extracellular matrix interactions, in particular within the context of glycobiology and immunobiology. Our newest projects focus on questions of collective and single cell migration in vitro and in vivo; immunophage therapy "an immunoengineering approach - that uses combined defense of immune cells plus viruses (phage) to overcome bacterial infections"; and the study of the molecular biophysics and biomaterials applications of the incredible enzyme, hyaluronan synthase.
A few common scientific themes emerge frequently in our projects: biophysics at interfaces, the use of quantitative modeling, collective interactions of cells and/or molecules, cell mechanics, cell motility and adhesion, and in many cases, the role of bulky sugars in facilitating cell integration and rearrangements in tissues.
Dr. Chandra Raman's group investigates macroscopic quantum mechanics using ultralow temperature gases—laser cooled clouds of atoms suspended inside a vacuum chamber at temperatures less than one millionth of a degree above absolute zero. We explore topics ranging from superfluidity in Bose-Einstein condensates (BECs) to quantum antiferromagnetism in a spinor condensate. Our goal is to use advanced atomic experimental techniques to illuminate contemporary phenomena in condensed matter physics, particularly in correlated quantum systems. Apart from fundamental studies, we are seeking to build cutting edge sensors that exploit the quantum properties of ultracold gases.
Rick Trebino received his B.A. from Harvard University in 1977 and his Ph.D. degree from Stanford University in 1983. His dissertation research involved the development of a technique for the measurement of ultrafast events in the frequency domain using long-pulse lasers by creating moving gratings. He continued this research during a three-year term as a physical sciences research associate at Stanford. In 1986, he moved to Sandia National Laboratories in Livermore, California, where he studied higher-order wave-mixing, nonlinear-optical perturbation theory using Feynman diagrams, and ultrashort-laser-pulse techniques with application to chemical dynamics measurements and combustion diagnostics. There he developed FrequencyResolved Optical Gating (FROG), the first technique for the measurement of the intensity and phase of ultrashort laser pulses. In 1998, he became the Georgia Research Alliance-Eminent Scholar Chair of Ultrafast Optical Physics at the Georgia Institute of Technology, where he currently studies ultrafast optics and applications. Prof. Trebino has received several prizes, including the SPIE’s Edgerton Prize, and he was an IEEE Lasers and Electro-Optics Society Distinguished Lecturer. He is a Fellow of the Optical Society of America, the American Physical Society, and the American Association for the Advancement of Science.
About The Frontiers in Science Lecture Series
Lectures in this series are intended to inform, engage, and inspire students, faculty, staff, and the public on developments, breakthroughs, and topics of general interest in the sciences and mathematics. Lecturers tailor their talks for nonexpert audiences.
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Antibiotic resistance is among the most urgent threats to public health. In this talk, I will discuss our group’s ongoing efforts to understand how E. faecalis, an opportunistic bacterial pathogen, responds to antibiotics across multiple length and time scales. First, I’ll describe recent experiments using customized, computer controlled bioreactors to demonstrate that growth inhibition depends strongly on population density for many commonly used antibiotics, potentially leading to bistable treatment outcomes in a pharmacological model of antibiotic treatment.
In the limit of high population densities, subinhibitory antibiotic concentrations can promote formation of biofilms--an effect that reflects a trade-off between antibiotic efficacy and the beneficial effects of cell lysis--while higher doses can shape the single-cell architecture of drug resistant communities. Finally, I’ll overview ongoing work combining laboratory evolution with mathematical modeling aimed at slowing resistance evolution using temporal drug sequences designed to maximize collateral drug sensitivity over different time scales.
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Beta-barrel outer membrane proteins (OMPs) are found within the outer membranes (OM) of Gram-negative bacteria and are essential for nutrient import, signaling, and adhesion. While the exact mechanism for the biogenesis of these OMPs is unknown, it is known that a 200 kDa five component complex called the beta-barrel assembly machinery (BAM) complex is responsible for this task. We have previously used X-ray crystallography and MD simulations to establish that BamA, the central and essential component, may serve as a catalyst on the membrane to reduce the energy required for insertion of new OMPs.
Further, we have shown that lateral opening of the barrel domain of BamA is required for function, suggesting a route for the insertion of new OMPs directly into the membrane. Despite these studies, it is known that the BAM complex functions most efficiently when fully assembled. To gain insight into this intriguing mechanism, recently, we reported the structure of the BAM complex from E. coli, revealing unprecedented conformational changes in the barrel domain of BamA, which may be regulated by the accessory proteins BamB, C, D, and E. The periplasmic domain of BamA was found in a closed state that prevents access to the barrel lumen from the periplasm, indicating substrate OMPs likely do not enter the barrel during biogenesis, but rather may be inserted directly at the lateral gate.
In this talk, I will review the previous studies with BamA, present the new recent structural studies of the fully assembled BAM complex, and put forth two plausible mechanisms for how the BAM complex may function in the biogenesis of new OMPs.
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Chromatin accessibility is a powerful lens to explore mechanisms of gene expression regulation, as regions of increased chromatin accessibility represent genetic elements that have the potential to regulate gene expression. To define the open chromatin landscape in primary human tissue, we collected single-cell chromatin accessibility profiles across 10 populations of immunophenotypically defined human hematopoietic cell types and constructed a chromatin accessibility landscape of human hematopoiesis to characterize differentiation trajectories. We find variation consistent with lineage bias toward different developmental branches in multipotent cell types. We observe heterogeneity within common myeloid progenitors (CMPs) and granulocyte-macrophage progenitors (GMPs) and develop a strategy to partition GMPs along their differentiation trajectory.
Furthermore, we integrated single-cell RNA sequencing (scRNA-seq) data to associate transcription factors to chromatin accessibility changes and regulatory elements to target genes through correlations of expression and regulatory element accessibility. Overall, this work provides a framework for integrative exploration of complex regulatory dynamics in a primary human tissue at single-cell resolution. We have also recently completed a survey of the chromatin accessibility landscape in primary human tumor tissue, providing a catalog of regulatory elements across human cancers.
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The dynamics and stability of ecological communities are intimately linked with the specific interactions – like cooperation or predation – between constituent species. In microbial communities, like those found in soils or the mammalian gut, physical anisotropies produced by fluid flow and chemical gradients impact community structure and ecological dynamics, even in structurally isotropic environments. Though natural communities existing in physically unstructured environments is rare, the role of environmental structure in determining community dynamics and stability remains poorly studied. We used modified Lotka-Volterra simulations of competitive microbial communities to characterize the effects of surface structure on community dynamics.
We found that environmental structure has profound effects on communities, in a manner dependent on the specific pattern of interactions between community members. For two mutually competing species, eventual extinction of one competitor is effectively guaranteed in isotropic environments. However, addition of environmental structure enables long-term coexistence of both species via local ‘pinning’ of competition interfaces, even when one species has a significant competitive advantage. In contrast, while three species competing in an intransitive loop (as in a game of rock-paper-scissors) coexist stably in isotropic environments, structural anisotropy disrupts the spatial patterns on which coexistence depends, causing chaotic population fluctuations and subsequent extinction cascades.
Thus the stability of microbial communities strongly depends on the structural environment in which they reside, and a more complete ecological understanding, including effective manipulation and interventions in natural communities of interest, must account for the physical structure of the environment.
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Georgia Institute of Technology
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