Graduate Student Seminar Scheduled for October 31, 2012

The Fall 2012 Beckman Institute Graduate Student Seminar Series continues on Wednesday, October 31. The seminar will feature three short talks from students Soheil Soghrati, Ru Wang, Hang Yu. The seminar will be held in Beckman Institute Room 1005 and a pizza lunch will be served to those attending the talks.

The Beckman Institute Graduate Student Seminar Series presents the work of outstanding graduate students working in Beckman research groups. The seminars begin at Noon in Beckman Institute Room 1005 and are open to the public. Lunch will be served.

Computational Modeling and Design of Actively-Cooled 3D Woven Microvascular Composites
Soheil Soghrati

A novel approach to introduce bio-inspired three-dimensional microvascular networks in actively-cooled structural 3D woven composites for high-temperature applications has been introduced. We also develop a new computational technique to design the configuration of the embedded microchannels. To manufacture the microvascular composite, sacrificial fibers of catalyst-impregnated polylactide (PLA) are first woven with structural reinforcement fibers, such as glass and carbon fibers, in 3D architectures and composites are manufactured using the resin transfer molding process. Fabrication of hollow micro-vascular channels is achieved through thermally triggered de-polymerization of the sacrificial fibers and removal of the resulting monomer in vapor form. The resulting microvascular composites achieve thermal management in composites through two primary mechanisms: (a) by absorbing and removing heat from the system via the continuous circulation of a coolant, and (b) by redistributing heat inside the composite via an optimized network design for enhanced convective cooling. A novel Interface-enriched Generalized Finite Element Method (IGFEM) is employed to model the embedded microchannels in the microstructure of the woven composite and to evaluate the thermal response of the actively-cooled composite. Numerical simulations are validated with experimental measurments, obtained through infrared imaging of the temperature field in an actively-cooled microvascular composite specimen. The computational tools are then used to determine optimal microchannels configuration that yields the lowest temperature in the domain, while maintains the flow efficiency and mechanical properties of the material.

Dispersion-relation Spectroscopy of Intracellular Transport
Ru Wang

The interior of a living cell is a busy place. Molecular motors move materials along prescribed biopolymer tracks. This sort of active transport is required to rapidly move products over large distances within the cell, where passive diffusion is too slow. Just as understanding the flow of traffic is essential for probing the economy of a major city, exploring the intracellular traffic patterns of cells is fundamental to elucidating their activity. We examine intracellular traffic patterns using a new application of spatial light interference microscopy (SLIM). We used this quantitative phase imaging method to measure the dispersion relation, i.e. decay rate vs. spatial mode, associated with mass transport in live cells. This approach applies equally well to both discrete and continuous mass distributions without the need for particle tracking. From the quadratic experimental curve specific to diffusion, we extracted the diffusion coefficient as the only fitting parameter. The linear portion of the dispersion relation reveals the deterministic component of the intracellular transport. Our data show a universal behavior where the intracellular transport is diffusive at small scales and deterministic at large scales. Measurements by our method and particle tracking show that, on average, the mass transport in the nucleus is slower than in the cytoplasm. We further applied this method to studying transport in neurons. By modifying a traditional phase contrast microscope, we are able to use SLIM to map the changes in index of refraction across the neuron and its extended processes. What we found was that in dendrites and axons, the transport is mostly active, i.e., diffusion is subdominant.

Membrane Sculpting by F-BAR Domains Studied by Molecular Dynamics Simulations
Hang Yu

Membrane folding

Interplay between cellular membranes and their peripheral proteins drives many processes in eukaryotic cells. Proteins of the Bin/Amphiphysin/Rvs (BAR) domain family, in particular, play a role in cellular morphogenesis, for example curving planar membranes into tubular membranes. However, it is still unclear how F-BAR domain proteins act on membranes. Electron microscopy revealed that, in vitro, F-BAR proteins form regular lattices on cylindrically deformed membrane surfaces. Using all-atom and coarse-grained (CG) molecular dynamics simulations, we show that such lattices, indeed, induce tubes of observed radii. A 250 ns all-atom simulation reveals that F-BAR domain curves membranes via the so-called "scaffolding" mechanism. Plasticity of the F-BAR domain permits conformational change in response to membrane interaction, via partial unwinding of the domain's 3-helix bundle structure. A CG simulation covering more than 350 us provides a dynamic picture of membrane tubulation by lattices of F-BAR domains. A series of CG simulations identified the optimal lattice type for membrane sculpting, which matches closely the lattices seen through cryo-electron microscopy.