|02/01/2018||Jeff Gau||Sponberg Lab|
|02/08/2018||Yu-Hui Lin||Weitz Group|
|02/15/2018||Ben Kalziqi||Yunker Lab|
|02/22/2018||Jessica Faubel||Curtis Lab|
|03/01/2018||Ashley Coenen||Weitz Group|
|03/08/2018||APS March Meeting|
|03/15/2018||Bo Lee||Hu Lab|
|03/29/2018||Joy Putney||Sponberg Lab|
|04/05/2018||Jonathan Michel||Yunker Lab|
|04/12/2018||Derek Hart||Kim Lab|
|04/26/2018||Karl Lundquist||Gumbart Lab|
Spring 2018 Abstracts
Christian Hubicki and Erin McCaskey
Biological and Robophysical Investigation of Root Circumnutation through Heterogeneous Substrates
Circumnutation, the circular motion exhibited by the tip of a growing plant root, is exhibited by a variety of plant species, but its function is not well-understood. We hypothesize that the circumnutation characteristics of these plant species result in greater success in growing around substrate heterogeneties (e.g. obstacles embedded in soil). In a recent discovery by the Benfey Lab at Duke University, mutated rice species’s roots were grown showing different circumnutation characteristics, even greatly reducing circumnutation. This manipulation allowed us to experimentally test the performance of root growth strategies in both a circumnutating species and its non-circumnutating mutant counterpart. We grew both rice variants in a gel substrate laden with rigid obstacles. To monitor multiple simultaneous root growth trials, an automated picture acquisition system was built to obtain videos of different rice species growing in the gel substrate. Preliminary experiments conducted show promising support of our hypothesis, but current work is being done to increase the data set and quantitatively measure circumnutation characteristics. To more-systematically investigate the mechanics of circumnutation in heterogeneous substrates, we constructed a simple robophysical model of a growing root. Preliminary experiments show that circumnutation in the “robo-root” reduces the probability of obstacles physically halting growth progress.
Mechanics of insect flight
Flapping flight at the centimeter scale is one of the most energetically demanding modes of locomotion. Flying insects have been thought to have evolved a resonant flight system to improve energy economy. However, the actuators (muscles) in insects have strong strain dependencies. We hypothesize that this coupling between forcing and kinematics gives rise to an unexplored class of dynamical systems. We began by characterizing the dynamic mechanical properties of the thoracic exoskeleton (transmission between muscle and wings) in the hawkmoth Manduca sexta. We isolated the exoskeleton and drove sinusoidal length sweeps from 0.1 to 90 Hz with physiological amplitudes. We find that a linear model captures the bulk mechanical properties of the heterogeneous thorax. The thorax was 75% elastically efficient across a wide range of frequencies and amplitudes. This lead to a total body-mass specific power return of 6 W kg-1, which reduces inertial power demands by 20%. With this mechanical representation of the flight apparatus, we can begin to understand how the coupling between strain-dependent actuators and deformable structures affects flapping flight dynamics.
The effects of spatial interactions on an oscillatory tragedy of the commons
Game theory has long been an essential tool for the study of evolutionary dynamics of biological systems. However, the study of evolutionary game theory rarely considers the joint dynamics of how individual strategies shape the environment as well as how payoff of strategies differ in response to changing environments. To address this joint dynamics, Weitz et. al. recently proposed a nonlinear model of coevolution between individual strategies and environment . The model exhibits a range of dynamical behaviors in the joint strategy-environment state space. Of particular interest is the emergence of an “oscillatory tragedy of the commons”, in which the system oscillates between extremal states due to the feedback of individual strategies.
Nonetheless, the mean-field ODE treatment does not account for the effect of population noise and local interactions, which are present in real ecological systems. To include such effects, we derived individual-based game rules based on the ODE model  and implemented them in spatially explicit simulations, where individuals can only interact with others and the environment locally. In doing so, we found that including explicit spatial interactions in the model averts a tragedy of commons in a wider range of parameter regimes compared to the ODE model . In addition to stabilizing the system, local interactions also lead to novel spatiotemporal dynamics. The individual-based, spatially explicit model displays coherent patterns, including dynamic clusters and wave-like invasions, that emerge from an initially well-mixed population. Studying this model may provide insights into possible mechanisms leading to the tragedy of the commons and conditions for which the tragedy can be averted.
 Weitz, Joshua S., et. al. “An oscillating tragedy of the commons in replicator dynamics with game-environment feedback.” Proceedings of the National Academy of Sciences 113.47 (2016): E7518-E7525.
Killing to Fluctuate
Unlike equilibrium atomic solids, biofilms—soft solids composed of bacterial cells—do not experience significant thermal fluctuations at the constituent level. However, living cells stochastically reproduce and die, provoking a mechanical response. We investigate the mechanical consequences of cellular death and reproduction by measuring surface-height fluctuations of biofilms containing two mutually antagonistic strains of Vibrio cholerae that kill one another on contact via the type VI secretion system. While studies of active matter typically focus on activity via constituent mobility, here, activity is mediated by reproduction and death events in otherwise immobilized cells. Biofilm surface topography is measured in the nearly homeostatic limit via white light interferometry. Although biofilms are far from equilibrium systems, measured surface-height fluctuation spectra resemble the spectra of thermal permeable membranes but with an activity-mediated effective temperature, as predicted by Risler, Peilloux, and Prost [Phys. Rev. Lett. 115, 258104 (2015)]. By comparing the activity of killer strains of V. cholerae with that of genetically modified strains that cannot kill each other and validating with individual-based simulations, we demonstrate that extracted effective temperatures increase with the amount of death and reproduction and that death and reproduction can fluidize biofilms. Together, these observations demonstrate the unique physical consequences of activity mediated by death and reproduction events.
Biomimetic Hyaluronan Polymer Brush Grown from Enzymes
Polymer brushes are a versatile platform for performing fundamental studies of polymer physics, while also having the potential to design functional surfaces with industrial and biomedical applications in mind. I will present a novel platform to fabricate, characterize, and pattern hyaluronan-based polymer brushes at interfaces using the enzyme hyaluronan (HA) synthase. The brushes are microns thick, regenerative, and easily tuned. Their extreme thickness makes them amenable to unusual characterization techniques like direct visualization of the brush’s thickness and penetration by nanoparticles or proteins. Methods to pattern the HA polymer brushes using a UV laser on a confocal microscope, as well as altering the grafting density by UV-deactivation of the HA synthase will be presented. I will share data regarding the range of grafting densities available with this approach and provide examples of polymer brush gradients generated in this fashion. This new experimental platform represents a unique approach to fabricating polymer brushes, distinct from the ubiquitous grafting to or from approaches, and will allow for a wide range of characterization studies.
Inferring interactions from time-series in microbe-phage communities
Viruses of microbes, or phages, are found in high abundances in the environment and in human-associated microbiomes. In marine environments, phages are estimated to turn over 10 to 40 percent of microbes daily through lysis, contributing to microbial mortality and redirecting nutrient flow between trophic levels. Understanding the ecological dynamics of microbial communities requires knowledge “who infects whom”, that is, which phages can infect which microbes. However elucidating phage-microbe interactions in situ remains a difficult and open question. In this work, we review a model-based approach to inferring phage-microbe interactions from measured abundance time-series (Jover et al, 2016). We extend this model-based approach to simultaneously infer heterogeneous microbe-microbe competition in the presence of phages and present promising in silico results. In addition, we apply this model-based approach to an in situ microbial community time-series (without phages) and compare inferred microbe-microbe competition to previous results (Stein et al, 2013).
Alexander Bo Lee
Sniffing to improve machine olfaction
For mammals, sniffing plays an important role in transporting odors to receptor proteins in the nose. We look at how sniffing can be used to improve machine olfaction applications. With our own custom e-nose, we demonstrate that sniffing can enhance the performance of a gas sensor, and that useful features can be extracted from the data to distinguish between different odors. We also look into using sniffing as a way to expand machine olfaction to underwater applications, taking inspiration from the star-nosed mole. By imitating the unique star-nose with laser-cut plastic stars, we show how the external geometry of the nose plays a role in stabilizing bubbles used to pick up odors. The application of sniffing in underwater chemical sensing could lower the costs of environmental monitoring in the future.
Encoding in a Comprehensive, Spike-Resolved Motor Program
Organisms from flies to humans must execute motor control on a variety of time scales. To execute movements, an animal’s nervous system must transmit motor commands through action potentials, or “spikes”, to muscles. Spike trains carry encoded information that allow an animal to actively respond to its environment and change its locomotor behaviors as part of a closed neuromechanical loop; this information is often called a motor program. To better understand the significance of these spike trains for motor control, it is important to characterize how information is encoded and whether the encoding strategy depends on the dynamics of the locomoting animal. A growing body of evidence shows that temporal encoding is used to precisely time muscle activity in a variety of motor tasks in a diversity of animals. While temporal encoding strategies have been examined in single motor units, little is known about whether information content is tuned to muscle function or how information is encoded across muscles. We recorded spike-resolved EMGs from 10 flight muscles that represent a nearly complete motor program in the hawk moth (Manduca sexta) as it tracked a robotic flower with a simple 1 Hz sinusoidal trajectory in tethered flight, while simultaneously measuring the yaw torque output. We demonstrate that the magnitude of temporally encoded mutual information is higher than the magnitude of rate encoded mutual information for all muscles. We find no evidence for differences in encoding strategy between putative flight power and steering muscles, indicating a consistency of information content and encoding strategy across muscles varying greatly in morphology and function. We also demonstrate that pairwise combinations of muscles encode net redundant information, and that most of this net redundant information is encoded temporally. Temporal encoding enables coordination across muscles, and provides a large part of the bandwidth of encoded information in the hawk moth flight motor program.
Why is Structural Hierarchy So Prevalent in Biological Materials?
Structural hierarchy, in which materials possess distinct features on multiple length scales, is ubiquitous in nature. Many biological materials, such as bone, cellulose, and muscle, have as many as ten hierarchical levels. While structural hierarchy confers many mechanical advantages, including improved toughness and economy of material, it also presents a problem as each hierarchical level substantially increases the amount of information necessary for proper assembly. This seems to conflict with the broad prevalence of naturally occurring hierarchical structures. At the present, there is no general framework for understanding the interplay between structures on disparate length scales; such a framework is a critical tool for accounting for the robustness of hierarchical materials to defects. Here, we use simulations and experiments to validate a generalized model for the tensile stiffness of hierarchical, stretching-stabilized networks with a nested, dilute hexagonal lattice structure, and demonstrate that the stiffness of such networks becomes less sensitive to errors in assembly with additional levels of hierarchy. Following seminal work by Maxwell and others on criteria for stiff frames, we extend the concept of connectivity in network mechanics, and find a similar dependence of material stiffness upon each hierarchical level. More broadly, this work helps account for the success of hierarchical, filamentous materials in biology and materials design, and offers a heuristic for ensuring that desired material properties are achieved within the required tolerance.
Searching for Polymer Tangles
Topology plays a crucial role in polymer dynamics. Previous experiments have shown that ring-shaped polymers in dense polymer solutions have different diffusion and relaxation mechanisms than do linear polymers. Theoretical work attributes these differences to a ring polymer’s closed shape; such polymers lack free ends and therefore cannot reptate past their neighbors. These results suggest that topology can fundamentally change the dynamic properties of polymer solutions. However, despite their importance, very few experiments have specifically studied the dynamics of topological interactions at the level of individual polymer pairs. We aim to detect such interactions by observing a dilute, mono-disperse sample of DNA molecules with fluorescence microscopy, for both open and closed polymer shapes. Our preliminary results are suggestive, but still inconclusive: polymer interactions are very short-lived, making it difficult to scrutinize their dynamics with our current experimental setup. By improving our temporal resolution, we will be able to better investigate how topology affects polymer pair interactions. With these new results, we could gain new fundamental insight into how topology affects the material properties of soft matter.