|8/31/17||Perrin Schiebel||Goldman lab|
|9/7/17||Jianing Wu||Hu Lab|
|9/14/17||Yu-Hui Lin||Weitz group|
|9/21/17||David Yanni||Yunker lab|
Yasemin Ozkan Aydin
|10/5/17||Izaak Neveln||Sponberg lab|
|10/12/17||Claire Ji||Fenton Lab|
|10/19/17||Bahnisikha Dutta||Goldman lab|
|10/26/17||Sunny Hwang||Gumbart lab|
|11/2/17||Skanda Vivek||Yunker lab|
|11/9/17||Hector Velasco||Fenton lab|
|11/16/17||Olga Shishkov||Hu Lab|
|11/30/17||Hemaa Selvakumar||Curtis Lab|
Fall 2017 Abstracts
Collisional diffraction emerges from simple control in a sand-specialist snake
Elongate, limbless organisms such as snakes move through terrestrial terrains by propagating bends backward along the body. Previous research described how these bends are pressed against obstacles to propel the snake forward. However, we lack an understanding of the control mechanism which mediates the interaction between the snake and the surroundings. To discover principles of how and when to use obstacles, we studied a desert-dwelling snake, C. occipitalis, which uses a highly-stereotyped waveform to slither across homogeneous granular matter We tested the snake in a model terrestrial terrain—a single row of force-sensitive vertical posts embedded in a homogeneous substrate—and compared its performance with a robophysical model—a 12-link robotic snake using open-loop control to achieve a waveform similar to that used by C. occipitalis. We found the snake was more likely to apply force to the posts perpendicular to the direction of motion, meaning the snake was not utilizing the rigid posts to push itself forward. A similar pattern arose from the robot trials, suggesting that this may be an feature of open-loop control interacting with the obstacles. Furthermore, distributions of the snakes’ post-peg travel angles displayed preferred directions in a diffraction-like pattern with a central peak at zero and symmetric peaks at approximately plus and minus 20 and 40 degrees. This collisional diffraction pattern appeared in both the living and robot snake and persisted even when compliance was introduced to the robot’s control. This suggests that this sand-specialist snake adheres to its preferred waveform as opposed to changing the shape in response to the terrain. We posit that open-loop control of a stereotyped gait may be a simple strategy for movement in terrains with sparse heterogeneity, but if adherence to a heading is desired more sophisticated control is needed.
The elephant’s toolkit in the trunk: mechanical perfection and bio-inspired robotics
Elephant trunk is a muscular hydrostat which is comprised of 150,000 muscles, helping feed on 150 kg food every day. We found that, the elephant can grab items in a variety of sizes. For bran dust and smaller cubes, the elephant forms joint on the trunk to regulate jamming force when it grabs. For larger items, the elephant can grab aided by suction. Moreover, the elephant is able to grab heaviest items by wrapping the trunk and lifting with the elephant’s head, using the trunk as a lever. We fabricated a series of robots that not only demonstrate the strategies used for elephants’ grabbing, but open up new ways of designing universal grippers.
The effects of spatial interactions on an oscillatory tragedy of the commons
Evolution game theory and replicator dynamics has been used as a theoretical frame work to study the temporal change of composition of a population. However, there is little consideration on the mutual feedback between individual behaviors and the abundance of common resources. Weitz et. al. (2016) proposed an ODE system coupling the dynamics of population composition and abundance of common resources, which demonstrates a tragedy of the commons. Following their work, we derived an individual-based model and extended it to include spatial dimensions and allow diffusion of common resources. When spatial dimension is in included, we found a tragedy of the commons will be averted in a wider range of parameter space if the spatial component is considered.
Emergent multicellular traits are emergent physical phenomena in snowflake yeast
Multicellularity has developed multiple times in several lineages, but the profound transition our ancestors made from unicellularity happened over 600 million years ago, making it impossible to study in the lab. Snowflake yeast represents a model organism for the study of nascent multicellular life. Nascent multicellular organisms must develop heritable adaptions to group level selection in the absence of sophisticated developmental regulatory mechanisms. Here, we suggest that certain aspects of early multicellular regulation, such as the life cycle, may have emerged “for free” from physics, and propose an approach to describe such a process for snowflake yeast.
The Physics of DNA Strand Displacement
DNA strand displacement is a swapping reaction whereby a single DNA strand invades a partial duplex and dislodges a nearly identical strand. Bioengineers have embraced this reaction as a tool in nanotechnology to create complex structures, logic circuits, and even robots. In a more fundamental sense, strand exchange of nucleic acids occurs at the heart of central systems such as homologous recombination and the CRIPSR/Cas system. Despite its wide-ranging importance, the sequence dependent effects of strand displacement are largely unknown. In this week’s PoLS meeting, I will explain how we used Förster Resonance Energy Transfer (FRET) to investigate the role of sequence in the branch migration step of strand displacement. Further, I will show how branch migration depends on the direction of invasion as well as sequence. Finally, I will present a simple a free energy landscape model of branch migration.
Yasemin Ozkan Aydin
Geometric Mechanics Applied to Tetrapod Locomotion on Granular Media
Sprawled-postured tetrapods use different cyclic gait patterns during terrestrial locomotion and usually prefer stable gaits (more legs on ground at the same time) on challenging environments such as inclines. We hypothesize that properly coordinated leg and body movements could have provided a substantial benefit toward locomotion on complex media. Here, we observe crawling salamanders as a biological model for studying tetrapod locomotion on granular substrates. Further, geometric mechanics tools are used to provide a theoretical framework predicting efficacious body motions on yielding terrain. Finally, we employ these coordination strategies on a robophysical salamander model traversing a sandy ground. This analysis of salamander-like robotic motion in granular media can be seen as a first application of how tools from geometric mechanics can provide insight into the character and principles of legged locomotion.
Just how centralized is cockroach locomotor control? Comparisons to robotic and computational models
High level tasks in biology, e.g. locomotion, are often achieved with distributed control of coupled subcomponents, e.g. muscles and limbs. The coupling of these subcomponents could range from weak and local, i.e. decentralized, to strong and global, i.e centralized. We developed a measure of centralization that compares information shared between control signals and both global and local outputs. We previously found that running cockroaches lie on the centralized side of this centralized/decentralized axis. To both validate the information measure of centralization and to contextualize the cockroach result with an intuitive system, we analyzed a computational model of coupled oscillators. Our centralization measure successfully reconstructs the shift from low to high coupling strengths. Intermediate values of coupling strengths which result in positive centralization correspond well to previous fits of this model to cockroach data indicating that this model can capture the centralization of the cockroach. Since mechanical coupling in a physical system might always result in a centralized system according to our measure, we analyzed a robotic model to contrast a decentralized architecture from the centralized cockroach. The robot control was designed to be reactive to local feedback, where coordination arises through mechanical coupling that can be altered by changing the robot’s inertia. The robot is decentralized compared to the cockroach according to our measure and is maximally decentralized when mechanical coupling is decreased even though leg coordination persists. These results affirm that the cockroach does use a comparatively centralized control architecture and shows that our measure successfully assesses centralization using empirical observations.
Claire (Yanyan Ji)
Mechanism for low-energy anti-fibrillation pacing (LEAP)
Low-energy anti-fibrillation pacing (LEAP) has been suggested as an alternative treatment to symptomatic fibrillation patients. It significantly lowers the energy required compared with standard one-shock defibrillation. In our previous studies we have found the mechanism of LEAP is through the synchronization of tissue by virtual electrodes generated at the surface of conductivity discontinuity. To further lower the LEAP energy while keep the defibrillation success rate high, we need to explore a large parameter space, adjusting the number of shocks, waveform, electrode shapes and positions etc. Using numerical simulations we can reduce the number of animals needed for experiments and vary parameters easily. This requires realistic modeling in both geometry and physiology. This talk will be focused on the first step of this study, which is verifying the cardiac models against important characteristics in defibrillation experiments.
Prey and mound disassembly, manipulation and transport by fire ant swarms
Social insects work collectively to complete tasks; in many situations individuals can approach a task using different behaviors. For example, fire ants (S. invicta) which inhabit subterranean nests covered by a hemispherical mound of reconfigurable soil permeated by narrow (~1 body length wide tunnels) can engulf soft-bodied prey via manipulation of the prey, the mound, or both. Given that each ant can perform such manipulations and transport, how does the collective decide which approach to take? Laboratory housed fire ant colonies were offered diverse prey embedded with lead markers, including mealworms, crickets and shrimp. Ant-prey-soil interactions on the nest surface were recorded using overhead video and subsurface using x-ray imaging. Mealworms were collectively carried intact into the mound through a tunnel, and then disassembled within the mound; shrimp was dismantled into small pieces above the surface and carried to mound tunnels; crickets were buried after limb removal and then disassembled and moved into tunnels. Soil reconfiguration occurred in all cases. To systematically understand the varying emergent behaviors, we devised a controllable food item from Semolina flour (a “suji”). The shape, size and brittleness of the suji was controlled via the cooking process. These experiments revealed that a brittle suji was more likely to be deconstructed into small pieces before transport into tunnels; less breakable suji was typically buried or transported intact to a tunnel(if the item was small enough). Individual ants involved in feeding exhibited heterogeneity in tasks which included food maneuvering, dissection and mound reconfiguration. We hypothesize that food characteristics (like hardness and shape) select for appropriate individual behavior which gives rise to the different engulfment scenarios.
Theoretical and computational investigations into lipid bilayer permeation of drugs
Transport phenomena across biomembranes are crucial processes in cellular biology, and they are also becoming increasingly important in many medical, pharmaceutical, and environmental technologies. Therefore, determination of drug absorption is an important component of the drug discovery and development process in that it plays a key role in the decision to promote drug candidates to clinical trials. The path of a drug from the site of administration to its target cells or compartments implies the crossing of several semipermeable cell membranes; therefore it is relevant to be able to predict whether and to what extent a molecule can pass through the cell membranes. Lipid bilayers are an effective barrier to passive diffusion of ions and hydrophilic small molecules, but many others can permeate bilayers through passive diffusion at rates that depend on bilayer composition and properties of the permeating solute. In this study, we consider the membrane deformation energy as the dominant factor in drug absorption, rates of barrier crossing, and simply entering cells, as an in vitro cell-based experiments. We have investigated a new approach using the deformation free energy of a lipid bilayer based on the principle of a continuum theory. To gain atomistic insight into the passive permeability process, we have used physics-based methods and MD simulation, combined with the inhomogeneous solubility-diffusion model. The estimated permeability from our method were compared with other popular methods such as Quantitative Structure-Property Relationship (QSAR) analysis.
Autonomous collective behavior and emergent statistical properties in vehicular traffic
We explore emergent collective properties in vehicular traffic using an active matter framework.
Hector Augusto Velasco Perez
Spiral Wave Stability with Chirality
Heart disease remains the leading cause of death in the USA with an estimated 600,000 people dying from heart disease in 2010. Given the situation, it is necessary to understand the inner-workings of this diseases. Studies have shown that many cardiac diseases, such as ventricular fibrillation are caused by the mutual influence of the tissue physiology and anatomy, and the dynamics of the electrical waves that propagate and recirculate through the media. Using high performance computer simulations we studied the stability of the electrical waves with respect of the domain size and its chirality. In addition, we discuss and quantify the efficiency of the numerical methods and computer algorithms.
Biomechanics of Black Soldier Fly larvae
Black soldier fly larvae are edible maggots that transform tons of food waste into sustainable protein per day. Although they are known to have a collective motion around and inside food sources, a physical understanding of their high eating rates is missing. We investigate the eating behavior of larvae and their collective motion with and without food. We show that quorum sensing is more likely to be responsible than chemotaxis for larvae detecting food. Using constant strain compression experiments, we demonstrate that these larvae exert an active pressure in addition to the elastic pressure of their bodies. We treat larvae as an active matter system and model their pressure with a mechanical theory. Additionally, we present work on improved raising techniques for these larvae.
Dynamics of phage-biofilm-neutrophil interactions
Bacteriophage (`phage’) – viruses that infect and lyse bacteria – can be deployed therapeutically to treat infections caused by bacterial pathogens. However most reported studies of the therapeutic potential of phage neglect the spatial heterogeneity in bacterial communities, e.g., in microcolonies and biofilms. Here, we investigate the spatiotemporal dynamics arising from interactions between Pseudomonas aeruginosa, phage and neutrophils. Time-dependent high resolution confocal imaging is used to examine phage and neutrophil activity in bacterial domains/biofilms.