Computations in Science Seminars

Previous Talks: 2022

Jan 2022
5
Wed 12:15
Seminar postponed in response to COVID-19
Jan 2022
12
Wed 12:15
Seminar postponed in response to COVID-19
Jan 2022
19
Wed 12:15
Seminar postponed in response to COVID-19
Jan 2022
26
Wed 12:15
Seminar postponed in response to COVID-19
Feb 2022
2
Wed 12:15
Seminar postponed in response to COVID-19
Feb 2022
9
Wed 12:15
Seminar postponed in response to COVID-19
Feb 2022
16
Wed 12:15
Seminar postponed in response to COVID-19
Feb 2022
23
Wed 12:15
Seminar postponed in response to COVID-19
Mar 2022
2
Wed 12:15
Seminar postponed in response to COVID-19
Mar 2022
9
Wed 12:15
Seminar postponed in response to COVID-19
Mar 2022
23
Wed 12:15
OPEN
Mar 2022
30
Wed 12:15
Alison Sweeney, Yale University
Host: William Irvine ()
Organizer: Kabir Husain ()
Photonic Self-Assembly in Squids and Octopuses: New Insights toward a Physical Mechanism

Squids and octopuses occupy every optical niche of the ocean, from mud flats to the midwater abyss. In each of these disparate environmental radiances, camouflage is generated by a layer of skin cells containing sub-visible-wavelength-scale arrays of a high-refractive-index protein called reflectin. In shallow contexts, the reflectance of this layer matches the albedo of a given species' background, while in open ocean contexts, animal-generated light scattering through this layer matches the radiance of the surrounding water. These feats of photonic engineering are achieved via self-assembly of the enigmatic reflectin protein.

After about two decades of work, we still do not have a clear physical picture of reflectin protein-protein interactions to know how or why some mixtures of these proteins make mirrors in vivo, while other mixtures of similar proteins make light guides. This talk explores and weighs the evidence for several novel hypotheses of reflectin assembly mechanisms generated by my group, including the free energy of the proteins' association with lipid bilayers and the bilayers' corresponding physical phases; the evidence for true patchy-colloid physics in reflectins; the possibility of a surface-induced phase transition; and the possible role of a novel, flexible metal coordination. None of these mechanistic possibilities are mutually exclusive. While we do not yet have a complete experimental picture of this system, it is increasingly clear that squid are leveraging assembly constructs at the cutting edge of current theoretical understanding in the fields of soft matter and self-assembly.

Apr 2022
6
Wed 12:15
Rama Ranganathan, University of Chicago
Organizer: Kabir Husain ()
Evolutionary principles of protein structure and function

Proteins can fold spontaneously into well-defined three-dimensional structures and can carry out complex biochemical reactions such as binding, catalysis, and long-range information transfer. The precision required for these properties is achieved while also preserving evolvability – the capacity to adapt in response to fluctuating selection pressures in the environment. What is the basic design of proteins that supports all of these properties? Going beyond direct physical analysis, statistical analysis of genome sequences have, in recent years, provided a powerful and general approach to this problem. Using different methodologies, this approach has revealed both direct structural contacts as well as collective functional modes within protein structures. In this talk, I will present approaches for probing the physical mechanisms implied by the evolution-based models and present ideas for how such mechanisms may be constrained by and originate from the dynamics of the evolutionary process. This work represents a step towards a theory for the physics of proteins that is consistent with evolution.

Apr 2022
13
Wed 12:15
Alexander Petroff, Clark University
Host: William Irvine ()
Organizer: Yuqing Qiu ()
A fast-swimming bacterium collides with a hard surface

The sediment-dwelling bacterium \textit{Thiovulum majus}, which swims at a speed of $600\,\mu$m/s, is one of the fastest known bacteria. When such a cell collides with a hard surface it either escapes rapidly into the bulk fluid or else becomes hydrodynamically bound to the wall. We first show that these dynamics preserve a memory of the cell's trajectory before the collision, which is gradually erased by contact with the surface. This erasure of information is consistent with a first-passage problem. Next, we investigate the two-dimensional motion of cells that are hydrodynamically bound to the surface. These cells diffuse laterally over the surface. When two cells diffuse within a critical distance of one another, they form a stable dimer of co-rotating cells. These dimers grow into two-dimensional active crystals composed of hundreds of cells. We analyze the large-scale motion of these crystals and their stability.

Apr 2022
20
Wed 12:15
OPEN
Apr 2022
27
Wed 12:15
Ann Kennedy, Northwestern University
Host: Stephanie Palmer ()
Organizer: Yuqing Qiu ()
Rotational and attractor dynamics for hypothalamic regulation of motivated behavior

As we interact with the world around us, we experience a constant stream of sensory inputs, and generate a constant stream of behavioral actions. What makes brains more than simple input-output machines is their capacity to integrate sensory inputs with an animal’s own internal motivational state—alertness, hunger, level of stress—to produce behavior in a manner that is flexible and adaptive. While some experimental work has examined the effect of motivational states such as alertness on neuronal population dynamics, a key theoretical question is how motivational states might be maintained by the brain, and how they might interact with each other to collectively shape behavior in an adaptive manner. Here, we contrast neural population dynamics in two hypothalamic nuclei involved in control of social behavior—the ventrolateral part of ventromedial hypothalamus (VMHvl) and medial preoptic area (MPOA)—and find pronounced differences in how actions and motivational states are encoded among these cells. We hypothesize that this reflects a more general distributed framework by which the interacting nuclei of the hypothalamus shape animal behavior.

May 2022
4
Wed 12:15
OPEN
May 2022
11
Wed 12:15
OPEN
May 2022
18
Wed 12:15
Thierry Emonet, Yale University
Host: Arvind Murugan ()
Organizer: Kabir Husain ()
Odor motion detection by an olfactory system aids navigation of turbulent odor plumes.

For many animals, survival depends on the ability to navigate odor plumes to their sources. This task is complicated by turbulent air motions, which break continuous odor streams emanating from sources into disconnected odor patches swept by the wind. Animal studies have revealed a general strategy to navigate odor plumes: reorient upwind when the odor is present, but go crosswind or downwind when signals become sparse to regain contact with the plume. In this strategy, the olfactory system is used to detect the identity, intensity and arrival time of odor packets, while the main directional cue is wind direction. This is because gradients of odors, which can be detected by comparing odor intensity between the two antennae, tend to fluctuate in many directions.

We have discovered that besides detecting the identity and intensity of odor packets, the Drosophila olfactory system also detects the direction of motion of odor packets. Fluid simulations and theory shows that odor motion provides a secondary directional cue, which points towards the center of the odor plume and therefore is complementary to the wind direction. Using a virtual reality setup to decouple wind from odor signal, we find that flies detect odor motion from the temporal correlations of the odor signal between its two antennae, in a computation similar to motion detection in vision. Manipulating spatio-temporal correlations in the virtual odor signal demonstrates that flies indeed exploit odor motion when navigating odor plumes. In sum, our results show that Drosophila can compute the direction of motion of odors independent of the wind, and that they use this capability in natural plume navigation. This work suggests a novel role for previously observed bilateral signal processing in the olfactory circuit.

May 2022
25
Wed 12:15
OPEN