Spring 2016 Colloquium Series
Active Matter: from Colloids to Living Cells
Date: Thursday, June 2nd, 2016
Speaker: Cristina Marchetti, Syracuse
Systems ranging from bird flocks to bacterial suspensions to colloids propelled by self-catalytic reactions are examples of active matter – individually driven, dissipative units that self-organize in collectives with coordinated motion at large scales. In this talk I will highlight common properties of these diverse systems and describe recent progress in understanding and classifying their complex behavior using modeling and simulations.
Hosts: Eric Corwin/Marina Guenza
Temperature-Like Variables in Granular Materials
Date: Thursday, May 26th, 2016
Speaker: Karen Daniels, North Carolina State University
Statistical mechanics has provided a powerful tool for understanding the thermodynamics of materials. Because granular materials exhibit reproducible statistical distributions which depend in simple ways on macroscopic parameters such as volume and pressure, it is tempting to create a statistical mechanics of athermal materials. I will describe a suite of experiments on two-dimensional granular materials which investigate to what extent these ideas are meaningful. For example, under agitated conditions, we measure both bulk and particle-scale dynamics, and find a number of thermal-like behaviors including diffusive dynamics, a granular Boyle’s Law with a van der Waals-like equation of state, and energy equipartition for rotational and translational degrees of freedom. However, the scarcity of free volume within a granular material provides a crucial control on the dynamics, and each of the above thermal-like behaviors is accompanied by interesting caveats. In an apparatus designed to generate a large number of static configurations, we test whether or not various temperature-like variables are able to equilibrate between a subsystem and a bath. We find that while a volume-based temperature known as “compactivity” fails to equilibrate, a stress-based temperature succeeds (with some unfortunate side-effects). This points to the importance of interparticle forces in controlling the mechanics of granular materials.
Host: Eric Corwin
Collective Dynamics, Deadly Competition, and Shape Switching in Bacterial Colonies
Date: Thursday, May 19th, 2016
Speaker: Harry Swinney, University of Texas at Austin
Bacillus subtilis bacteria growing in a colony are found to exhibit large (non-thermal) number fluctuations. Also, the swimming bacteria are observed to form dynamic clusters where the orientational correlations of bacteria within a cluster are scale invariant. Studies of another rod-shaped swimming bacterium found commonly in soil, Paenibacillus dendritiformis, reveal that neighboring colonies secrete a previously unknown toxic protein, Slf, which is not secreted by the bacteria in isolated colonies. A mathematical model gives insight in to this deadly competition. Some bacteria within a colony survive by switching their shape from a long motile rod to an immobile Slf-resistant spherical shape. If these spherical bacteria later encounter sustained favorable conditions, they secrete a signaling molecule that induces a switch back to the motile rod-shaped form. The genes that encode the switching pathway are widespread among bacterial species, suggesting that this survival mechanism is not unique to P. dentritiformis.
Host: Tristan Ursell
Vibration Propagation in Spider Webs
Date: Thursday, May 12th, 2016
Speaker: Ross Hatton, Oregon State University
Due to their poor eyesight, spiders rely on web vibrations for situational awareness. Web-borne vibrations are used to determine the location of prey, predators, and potential mates. The influence of web geometry and composition on web vibrations is important for understanding spider’s behavior and ecology. Past studies on web vibrations have experimentally measured the frequency response of web geometries by removing threads from existing webs. The full influence of web structure and tension distribution on vibration transmission; however, has not been addressed in prior work. We have constructed physical artificial webs and computer models to better understand the effect of web structure on vibration transmission. These models provide insight into the propagation of vibrations through the webs, the frequency response of the bare web, and the influence of the spider’s mass and stiffness on the vibration transmission patterns.
Host: Jim Remington
Structure and Stability in Canonical Cortical Computations
Date: Thursday, May 5th, 2016
Speaker: Yashar Ahmadian,UO, Institute of Neuroscience, Departments of Biology and Mathematics
The cerebral cortex, or the gray matter, is evolutionarily the newest part of the brain, and underlies most of our intelligent behavior. After an introduction to biological neural networks and theoretical approaches to studying their dynamics, I will present my work on the dynamics of local neural circuits in the cortex. The vast majority of cortical neurons are of the excitatory type and they are highly interconnected: a typical neuron receives thousands of excitatory inputs and in turn excites other neurons. How does such a network prevent runaway activity despite this strong positive feedback? Single-neuronal biology provides one stabilizing mechanism: neurons cannot activate at indefinitely high rates for biophysical reasons. But this still leaves open the following question: can cortical networks self-organize into a stable state with moderate activity, without relying on single-neuronal saturation? I will show that fast feedback from the minority of inhibitory neurons is generically sufficient to dynamically stabilize cortical networks even when single-neuronal nonlinearities are of the expansive, non-saturating type.
I will then explore the computational consequences of this collective inhibitory stabilization, and show that it accounts for a wide range of “contextual modulation” effects (modulations of responses of neurons to their preferred stimuli by contextual stimuli). Contextual modulation is a ubiquitous and canonical brain computation, and is an early manifestation of the global integration of sensory information that underlies higher level perception and object recognition.
I will also discuss some of the transient and time-dependent properties of such networks, and how our theory accounts for modulations of cortical oscillations and correlated ‘noise’ in the visual cortex. Time allowing, I will briefly mention my work using random matrix theory and large-N expansions to study the interplay of disordered and structured network connectivity in the dynamics of neural networks.
Host: Raghu Parthasarathy
Tools for Ultrafast Spectroscopy
Date: Thursday, April 28th, 2016
Speaker: Dr. Matthew Kelley, Senior Scientist Newport Corporation
In this talk I will introduce Newport’s Technology and Application Center and touch briefly on most of our products and activities. I will spend most of the time discussing two products that I am responsible for: Transient Absorption Spectroscopy (TAS) and Time-Resolved Fluorescence Spectroscopy (TRFLS). I will introduce each spectroscopy and give background on the operation and instruments that go into each product. Then I will discuss the advantage of each type of spectroscopy and cover some representative applications.
Host: Bryan Boggs
Impact Response of Granular Materials: From the Origin of the Universe to Catastrophic Asteroid Strikes
Date: Thursday, April 21st, 2016
Speaker: Xiang Cheng, University of Minnesota
Granular materials are large conglomerations of discrete macroscopic particles. Examples include seeds, sand, coals, powder of pharmacy, etc. Though simple, they show unique properties different from other familiar forms of matter. The unusual behaviors of granular materials are clearly illustrated in various impact processes, where the impact-induced fast deformation of granular materials leads to emergent flow patterns revealing distinctive granular physics. Here, we explored the impact response of granular materials in two specific experiments:
First, we investigated impact cratering in granular media induced by the strike of liquid drops—a ubiquitous phenomenon relevant to many important environmental, agricultural and industrial processes. Surprisingly, we found that granular impact cratering by liquid drops follows the same energy scaling and reproduces the same crater morphology as that of asteroid impact craters. Inspired by this similarity, we develop a simple model that quantitatively describes various features of liquid-drop imprints in granular media. Our study sheds light on the mechanisms governing raindrop impacts on granular surfaces and reveals an interesting analogy between familiar phenomena of raining and catastrophic asteroid strikes.
Second, we performed the granular analog to “water bell” experiments. When a wide jet of granular material impacts on a fixed cylindrical target, it deforms into a sharply-defined sheet or cone with a shape mimicking a liquid of zero surface tension. The jets’ particulate nature appears when the number of particles in the beam cross-section is decreased: the emerging structures broaden, gradually disintegrating into diffuse sprays. The experiment reveals a universal fluid structure arising from the collision of discrete particles, which has a counterpart in the behavior of quark-gluon plasmas created by colliding heavy ions at the Relativistic Heavy Ion Colliders.
Host: Eric Corwin
Observation of Gravitational Waves from a Binary Black Hole Merger
Date: Thursday, April 14th, 2016
Speaker: Raymond Frey, University of Oregon
On September 14, 2015 at 09:50:45 UTC the two detectors of the Laser Interferometer Gravitational-Wave Observatory (LIGO) simultaneously observed a transient gravitational-wave signal due to the inspiral and merger of a binary black hole system at a distance of more than one billion light-years. The signal was very clearly detected, allowing the LIGO collaboration to claim the first direct detection of gravitational waves, the ripples in spacetime predicted 100 years ago by Einstein.
This was also the first indication that black holes in this range of mass — about 30 times the mass of the sun – exist in nature. In this talk, I will discuss how the detection was made, the tests of Einstein’s theory of general relativity, the implications for astrophysics, and the future of gravitational-wave astronomy.
Communication Shapes Collective Information Encoding of Chemosensing
Date: Thursday, April 7th, 2016
Speaker: Bo Sun, Oregon State University
Chemosensing is a major task assigned to a cell and is critical to its survival, differentiation, and other functions such as motility. Since the seminal work of Howard Berg and Edward Purcell, physicists have been trying to crack the code of cell chemosensing. While most of studies have been focusing on single cell level chemosensing and response, we have initiated projects to understand how a group of communicating cells encode information differently. In particular, we study the calcium dynamics of fibroblast cells in response to extracellular ATP, a scenario resembles the processes during inflammation and wound healing. We find there are two collective coding mechanisms of a monolayer of fibroblast cells: correlations and inter-spike-interval. We have further characterized the robustness of each coding mechanism with respect to attack by cancer cells.
Host: Eric Corwin
Biologically Inspired Soft Matter Devices in Robotics
Date: Thursday, March 31st, 2016
Speaker: Yigit Menguc, Oregon State University
Incredible biological mechanisms have emerged through evolution, and can provide a wellspring of inspiration for engineers. One promising area emerging from biological inspiration is the design of devices and robots made of compliant materials, as part of a larger field of research in “soft robotics.” In this talk, the topics of designing soft, biologically inspired mechanisms will be presented in two case studies: controllable adhesives and soft wearable sensors. Additionally, the talk will cover the methods of fabricating soft devices through 3D printing, soft lithography, and laser micromachining. Surfaces covered in arrays of micro-fibers, inspired by the toes of a gecko, rely on compliance to repeatedly and controllably adhere to almost any surface while simultaneously shedding dirt. Sensors made of liquid metal encapsulated in rubber as soft as skin can track motion of the human body while naturally moving with its kinematics. However, these exciting soft mechanisms have certain challenges. The biological mechanisms that serve as a source of inspirations are made of materials that are vastly more compliant than the metal and plastic that engineers and roboticists normally use. To imitate and improve on nature’s design, we must create mechanisms with materials like fabric and rubber. It is difficult to characterize these hyperelastic, viscoelastic, and generally nonlinear materials, and it is difficult to integrate them into traditional fabrication techniques, but the development of such soft robotic devices promises to bring robots more and more into our daily lives.
Host: Eric Corwin