Computations in Science Seminars
Jan 2020
22
Wed 12:15
Rebecca Schulman, Johns Hopkins University
e-mail:
Host: Arvind Murugan ()
Organizer: Elizabeth Lee ()
Programming the dynamic behavior of biomolecular materials and nanostructures using DNA circuits and reaction networks

Biological materials operate far from equilibrium and their dynamic behavior adapts to the surrounding environment as a result of coupling to chemical, mechanical and transport processes and networks of interacting signals that interpret environmental signals and control downstream kinetics. I will describe two model systems we have developed to explore the design principles for these types of responsive materials. Engineered semiflexible filaments, DNA nanotubes, can be used understand how reaction kinetics, diffusion, and chemical reaction networks can regulate growth. Nanotubes can be assembled into structures such as bridges between molecular endpoints or hierarchical networks. DNA polymerization-induced hydrogel shape change can be directed by chemical circuits that interpret upstream signals and produce outputs that initiate a shape change response. These circuits, by amplifying chemical signals, can induce high-energy changes in material shape in response to small amounts of chemical inputs. In these hydrogels the dynamics of shape change are governed by the interplay of DNA polymerization, signal transduction, transport of oligonucleotides and water, and polymer network remodeling, many of which operate on similar time scales. I will conclude by discussing how coupling hydrogel shape change with force sensors could be used for mechanical feedback.

Jan 2020
29
Wed 12:15
Alex Levine, UCLA
e-mail:
Host: Vincenzo Vitelli ()
Organizer: Steven Strong ()
Exploring soft low-dimensional structures in the cell: Fluctuations, mechanics, and geometry

Biology provides us with a number of effectively one- and two-dimensional elastic structures. The cytoskeleton of cells abounds with long, stiff protein filaments organized into bundles and networks. Cells are bound by and contain a wide variety of membranes, some of which have complex geometries. These lower dimensional structures are sufficiently soft to be strongly fluctuating at ambient temperature. In addition, evolution has engineered a plethora of cross-linking proteins and molecular motors that interact with these structures.

In this talk, I discuss a few examples of the role of fluctuations in soft low-dimensional biological structures, introducing the fluctuation-induced (Casimir) interaction between linkers in filament bundles. The Casimir interaction drives a new type of first-order filament bundling transition, leading to a disordered “line glass” network. I report on the collective mechanics of such filament networks. Finally, within a single bundle, I show that quenched-in braids introduce kinks (localized bends) in the time-averaged contour of the bundle, and explore how such kinks anneal over time.

Feb 2020
5
Wed 12:15
Justin Burton, Emory University
e-mail:
Host: Sid Nagel ()
Organizer: Yuqing Qiu ()
Intermittent Dynamics and "Turbulence" in a Many-Body System

Complex systems are known to exhibit emergent properties that are missing on the constituent level. An example is the appearance of intermittent transitions between distinct dynamical states. Using a levitated, quasi-2D layer of charged microparticles, our recent experiments (Gogia et al., PRL, 2017) showed that a nonequilibrium, many-body system can display intermittent dynamics by switching between an ordered, crystalline state and a gas-like, excited state. The emergent dynamics are a direct consequence of coupling between the inertial dynamics, structural disorder induced by particle size variation, and external noisy forcing. The behavior can be reproduced is a simulation with as little as 50 particles. The key lies in a separation of energy scales. Energy pumped into one degree of freedom will eventually couple non-linearly to other excitable modes and thermalize the system. The behavior bears a striking resemblance to the transition to turbulence in pipe flow, where increasing the flow velocity leads to intermittent "puffs" of turbulence. This transition also depends sensitively on disorder through the roughness of the pipe walls. In analogy to the Reynolds number, we are able to describe our system through a simplified set of equations and a single dimensionless number characterizing the ratio of external forcing to dissipation. This analogy may help identify the minimal ingredients for observing such intermittent, turbulent dynamics in other discrete systems.

Feb 2020
12
Wed 12:15
Jeremy England, GSK AI
e-mail:
Host: Arvind Murugan ()
Organizer: Elizabeth Lee ()
Feb 2020
19
Wed 12:15
OPEN
Feb 2020
26
Wed 12:15
Denis Bartolo, ENS Lyon
e-mail:
Host: William Irvine ()
Organizer: Grayson Jackson ()
Mar 2020
11
Wed 12:15
Cary Forest, UW Madison
e-mail:
Host: William Irvine ()
Organizer: Yuqing Qiu ()
Mar 2020
18
Wed 12:15
OPEN
Mar 2020
25
Wed 12:15
Zvonimir Dogic, UC Santa Barbara
e-mail:
Host: William Irvine ()
Organizer: Peter Chung ()
Apr 2020
1
Wed 12:15
Madhusudhan Venkadesan, Yale University
e-mail:
Host: Heinrich Jaeger ()
Apr 2020
8
Wed 12:15
Alexandra Zidovska, NYU
e-mail:
Host: Margaret Gardel ()
Organizer: Peter Chung ()
Apr 2020
15
Wed 12:15
OPEN
Apr 2020
22
Wed 12:15
OPEN
Apr 2020
29
Wed 12:15
OPEN
May 2020
6
Wed 12:15
Sabetta Matsumoto, Georgia Tech
e-mail:
Host: Arvind Murugan ()
May 2020
13
Wed 12:15
OPEN
May 2020
20
Wed 12:15
OPEN
May 2020
27
Wed 12:15
OPEN
Jun 2020
3
Wed 12:15
OPEN