Computations in Science Seminars

Previous Talks: 2019

Jan 2019
16
Wed 12:15
Margaret Gardel, University of Chicago
e-mail:
Host: Arvind Murugan ()
Organizer: Steven Strong ()
Controlling the Shape of Cells within Tissue

Mature epithelial tissues have distinct cellular architecture, which is maintained despite externally applied forces, wounding, and cell division or death. Here we investigate how a model tissue develops and maintains cellular structure by quantifying single cell dynamics and cell shape in newly formed monolayers of MDCK cells. Cells initially aggregate through a process resembling wound healing into a confluent monolayer with elongated cells that remain motile. After formation, individual monolayers evolve over time to reach a similar final state with more hexagonal cell shapes and arrested dynamics, resembling mature epithelial tissues. By quantifying cell trajectories, we observe glassy dynamics controlled by cell shape, which have been previously predicted by vertex models. On substrates of different stiffness, monolayers form and evolve with different cell number density but the same relationship between cell shape and speed suggesting that the dynamics are density independent. We find when inhibiting several regulators of the actin cytoskeleton that cell speed and shape remain correlated but the correlation is shifted toward more elongated cell shapes. The magnitude of this shift differs for each inhibitor but velocity correlation length decreases proportionately to the change in final cell shape. We show that these results can be recapitulated in vertex models which incorporate polarization coupling between neighboring cells. Our results demonstrate that multicellular coordination of cell motility plays an important role in regulation of cell shape and determination of final tissue structure.

Jan 2019
23
Wed 12:15
Shmuel Rubinstein, Harvard
e-mail:
Host: William Irvine ()
Organizer: Grayson Jackson ()
The physics of crushing and smashing: Cascades and cataclysmic change

Many of the big problems we are facing involve far from equilibrium systems that entail a cataclysmic change. Climate, turbulence and earthquakes, developmental biology, evolution and even aging and death. These phenomena are rare (sometimes occurring only once) and are entirely irreversible. While understanding the physics of such irreversible processes is of both fundamental and practical importance, these problems also pose unique challenges. These challenges, as they manifest in turbulence, were beautifully portrayed by Richardson:

“Big whirls have little whirls that feed on their velocity, and little whirls have lesser whirls and so on to viscosity” Lewis Fry Richardson (1922)

In his short verse, Richardson captures the essence of the turbulent cascade—the conveyance of kinetic energy across scales that underlies the universal dynamics of turbulent flows. Indeed, such conveyance of important physical quantities (energy, stress, frustration and even information) down and up a vast range of scales underlines the dynamics of many systems. The same applies to how a multi-contact frictional interface will form and break or how correlated defect structures determine the strength of a space-rocket, how an intricate network of creases will form when we crumple a thin sheet or when soda can is smashed. The challenge in understanding these systems is in capturing the events as they occur, keeping up with the dynamics on all scales and at all times. Here, I will review our work on several key irreversible system and introduce the new tools we developed to address their unique evolution and discuss the interesting physics we learned.

Jan 2019
30
Wed 12:15
CANCELLED: Xiang Cheng, University of Minnesota
Rescheduled for Feb. 27, 2019
Feb 2019
6
Wed 12:15 PM
Andrej Košmrlj, Princeton University
e-mail:
Host: Arvind Murugan ()
Organizer: Elizabeth Lee ()
Phase separation in multicomponent liquid mixtures

Multicomponent systems are ubiquitous in nature and industry. While the physics of binary and ternary liquid mixtures is well-understood, the thermodynamic and kinetic properties of N-component mixtures with N>3 have remained relatively unexplored. Inspired by recent examples of intracellular phase separation, we investigate equilibrium phase behavior and morphology of N-component liquid mixtures within the Flory-Huggins theory of regular solutions. In order to determine the number of coexisting phases and their compositions, we developed a new algorithm for constructing complete phase diagrams, based on numerical convexification of the discretized free energy landscape. Together with a Cahn-Hilliard approach for kinetics, we employ this method to study mixtures with N=4 and 5 components. In this talk I will discuss both the coarsening behavior of such systems, as well as the resulting morphologies in 3D. I will also mention how the number of coexisting phases and their compositions can be extracted with Principal Component Analysis (PCA) and K-Means clustering algorithms. Finally, I will discuss how one can reverse engineer the interaction parameters and volume fractions of components in order to achieve a range of desired packing structures, such as nested "Russian dolls" and encapsulated Janus droplets.

Feb 2019
13
Wed 12:15
Jörn Dunkel, MIT
e-mail:
Host: William Irvine ()
Organizer: Peter Chung ()
Wrinkles and spaghetti

Buckling and fracture are ubiquitous phenomena that, despite having been studied for centuries, still pose many interesting conceptual and practical challenges. In this talk, I will summarize recent experimental and theoretical work that aims to understand the role of curvature and torsion in wrinkling and fragmentation processes. First, we will show how changes in curvature can induce phase transitions [1] and topological defects [2] in the wrinkling patterns on curved elastic surfaces. In the second part, we will revisit an observation by Feynman who noted that spaghetti appears to fragment into at least three (but hardly ever two) pieces when placed under large bending stresses. Using a combination of experiments, simulations and analytical scaling arguments, we will demonstrate how twist can be used to control binary fracture of brittle elastic rods [3].

[1] Nature Materials 14, 337 (2015) [2] PRL 116: 104301 (2016) [3] PNAS 115: 8665 (2018)

Feb 2019
20
Wed 12:15
Greg Voth, Wesleyan University
e-mail:
Host: William Irvine ()
Organizer: Steven Strong ()
A new view of the dynamics of turbulence from measurements of rotations of particles with complex shapes

Non-spherical particles in turbulent flows are important in a wide range of problems including ice crystals in clouds, fibers in paper-making, marine plankton, and additives for turbulent drag reduction. We have developed experimental methods for precise tracking of the position and orientation of non-spherical particles in intense 3D turbulence. Using 3D printed particles, we can fabricate a wide range of shapes and explore how particle orientation and rotation are affected by particle shape. We find particles are strongly aligned by the turbulence. A simple picture in which particles are aligned by the fluid stretching they experience explains many of the key observations about how particles align and rotate. This same picture sheds new light on some old problems about how vorticity aligns with the strain rate tensor in turbulent flows. It has also allowed us to create a fascinating particle shape which we call a chiral dipole that shows a preferential rotation direction in isotropic turbulent flow.

Feb 2019
27
Wed 12:15
Xiang Cheng, University of Minnesota
e-mail:
Host: Tom Witten ()
Organizer: Grayson Jackson ()
From Flocking Birds to Swarming Bacteria: A Study of the Dynamics of Active Fluids

Active fluids are a novel class of non-equilibrium complex fluids with examples across a wide range of biological and physical systems such as flocking animals, swarming microorganisms, vibrated granular rods, and suspensions of synthetic colloidal swimmers. Different from familiar non-equilibrium systems where free energy is injected from boundaries, an active fluid is a dispersion of large numbers of self-propelled units, which convert the ambient/internal free energy and maintain non-equilibrium steady states at microscopic scales. Due to this distinct feature, active fluids exhibit fascinating and unusual behaviors unseen in conventional complex fluids. Here, combining high-speed confocal microscopy, holographic imaging, rheological measurements and biochemical engineering, we experimentally investigate the dynamics of active fluids. In particular, we use E. coli suspensions as our model system and illustrate three unique properties of active fluids, i.e., (i) abnormal rheology, (ii) enhanced diffusion of passive tracers and (iii) emergence of collective swarming. Using theoretical tools of fluid mechanics and statistical mechanics, we develop a quantitative understanding of these interesting behaviors. Our study illustrates the general organizing principles of active fluids that can be exploited for designing “smart” fluids with controllable fluid properties. Our results also shed new light on fundamental transport processes in microbiological systems.

Mar 2019
20
Wed 12:15
Hana El-Samad, University of California, San Francisco
e-mail:
Host: Arvind Murugan ()
Organizer: Elizabeth Lee ()
Biological control: The versatile ways in which cells use feedback loops

In 1939, Walter Cannon wrote in his book The Wisdom of the Body: “The living being is an agency of such sort that each disturbing influence induces by itself the calling forth of compensatory activity to neutralize or repair the disturbances”. Since this remarkable statement that postulates the use of feedback control to support life, we have come to appreciate that the use of feedback loops is ubiquitous at every level of biological organization, from the gene to the ecosystem. In this talk, we introduce a technology to study feedback operation in endogenous biological systems. We also discuss some recent progress in building feedback control systems with biological molecules that can modulate the operation of cellular pathways.

Mar 2019
27
Wed 12:15
Arvind Murugan, University of Chicago
e-mail:
Host: William Irvine ()
Organizer: Peter Chung ()
Materials that learn from examples

We usually design materials to target desired behaviors defined in a top-down manner. Learning theory offers an alternative where desired behaviors are defined by a list of examples. In learning, a material changes as it physically experiences such examples. We then test the material to see if it has the “correct” response to novel conditions never seen before (‘generalization’). Can real materials ‘learn’ from their history in this manner? We study the physical requirements for such information processing in terms of disorder, non-equilibrium driving and non-linearities using theory and experiments in disordered sheets, elastic networks, and molecular self-assembly.

Apr 2019
3
Wed 12:15
Greg Bewley, Cornell University
e-mail:
Host: William Irvine ()
Organizer: Steven Strong ()
The structure of turbulence and of granular beds

My work centers on turbulence, both its intrinsic properties and its role in various environmental settings. Over a bed of sand, it lifts and transports the grains. Left to itself, the turbulence slowly dissipates and disappears. In the first part of my talk, I will introduce experiments motivated by the question of how quickly turbulence consumes kinetic energy. Surprisingly we do not generally know how to predict the consumption rate, though the process underlies general turbulence phenomena and modeling. What we found is that the rate is invariant with respect to changes in the intensity of the turbulence, so long as the flow is slow relative to the speed of sound. I will introduce a new experiment in which we observe how the picture changes when the flow is no longer so slow. In the second part of my talk, I describe an experiment motivated by the question of how turbulence deforms granular beds. The experiments reveal a new mechanism that produces bedforms, a mechanism associated with fluctuating pressure gradients generated in a fluid-saturated particle bed by a plate oscillating in the water above it.

Apr 2019
10
Wed 12:15
Oskar Hallatschek, UC Berkeley
e-mail:
Host: Arvind Murugan ()
Organizer: Zhiyue Lu ()
The role of jackpot events in the dynamics of evolution

Luria and Delbrück discovered that mutations that occur early during a growth process lead to exceptionally large mutant clones. These mutational “jackpot” events are thought to dominate the genetic diversity of growing cellular populations, including biofilms, solid tumors and developing embryos. In my talk I show that jackpot events can be generated not only when mutations arise early but also when they occur at favourable locations, which exacerbates their role in adaptation and disease. I will also consider the impact of recurrent jackpot events, which lead to a bias favoring alleles that happen to be present in the majority of the population. I argue that this peculiar rich-get-richer phenomenon is a general feature of evolution driven by rare events.

Apr 2019
17
Wed 12:15
Nikta Fakhri, MIT
e-mail:
Host: Arvind Murugan ()
Organizer: Grayson Jackson ()
Thermodynamics of active matter

Cellular structures constantly consume and dissipate energy on a variety of spatiotemporal scales in order to function. While progress has been made in elucidating their organizing principles, much of their thermodynamics remains unknown. In this talk, I will address the question: why measure dissipation in such nonequilibrium systems? I will show that by measuring a multi-scale irreversibility (time-reversal asymmetry) one can extract model-independent estimates of the time-scales of energy dissipation based on time series data collected in an experimental biological system. I further demonstrate that the irreversibility measure maintains a monotonic relationship with the underlying biological nonequilibrium activity. The basic idea of estimating irreversibility for various levels of coarse-graining is quite general; we expect it to lead to important inferences whenever there is a well-defined notion of dissipative scale.

Apr 2019
18
Thu 2:00 PM
Detlef Lohse, University of Twente
e-mail:
Host: Heinrich Jaeger ()
Organizer: Steven Strong ()
Evaporation of multicomponent droplets
Joint JFI Theory Seminar: 2PM Thursday in GCIS E223

While the evaporation of a single component droplet meanwhile is pretty well understood, the richness of phenomena in multicomponent droplet evaporation keeps surprising us. In this talk we will show and explain several of such phenomena, namely evaporation-triggered segregation thanks to either weak solutal Marangoni flow or thanks to gravitational effects, and the evaporation of ternary liquid droplet, which can lead to spontaneous nucleation of droplets consisting of a new phase. We will also show how this new phase can be utilized to self-lubricate the droplet in order to suppress the coffee stain effects. The research work shown in this talk combines experiments, numerical simulations, and theory.