Center for Soft Matter and Biological Physics Summer Discussion Meetings

Summer 2017

These meetings occur on Fridays from 1:30pm to 2:30pm in Robeson 304 (unless otherwise indicated)

< 2016 | May | June | July | August | 2018 >

May 2017
May 26

Friday 1:30pm
304 Robeson Hall
 

No talk scheduled.

June 2017
June 2

Friday 1:30pm
304 Robeson Hall

CSB Seminar
Prof. P. S. Krishnaprasad   (University of Maryland)

Topic: Subriemannian geometry and finite time thermodynamics

Subriemannian geometry has its roots in optimal control problems. The Caratheodory-Chow-Rashevskii theorem on accessibility also places the subject in contact with an axiomatic approach to macroscopic thermodynamics. Explicit integrability of optimal control problems in this context is of interest. As in the case for integrability questions in mechanics, here too symmetries and conservation laws have a key role. In this talk we discuss model problems and results pertaining to such questions in isolated systems and ensembles of interacting systems. Of special interest is the problem of determining thermodynamic cycles that draw useful work from fluctuations. This work is in collaboration with PhD student Yunlong Huang, and Dr. Eric Justh of the Naval Research Laboratory.

Organizers: Vinh Nguyen

June 9

Friday 1:30pm
304 Robeson Hall
Wen Xiong   (Dept. of Biological Sciences, Virginia Tech)

Topic: Structural and functional basis of alternative endosomal ESCRT-0 protein complexes

Early endosomes represent the first sorting station for vesicular ubiquitylated cargo. Cargo transport is mediated by the endosomal sorting complex required for transport (ESCRT) machinery. Similar to the structural organization of ESCRT-0 proteins, alternative ESCRT-0 (alt-ESCRT- 0) proteins, such as Tollip and Tom1, also present multiple ubiquitin-binding domains, including the C2 and CUE (Tollip) and VHS and GAT (Tom1) domains. Tollip localizes the Tollip-Tom1 complex at endosomal compartments by association with phosphatidylinositol 3-phosphate (PtdIns(3)P) through its central C2 domain. Tom1, through its GAT domain, is recruited to endosomes by binding to Tollip's Tom1-binding domain (TBD) through an unknown mechanism. Our NMR data revealed that Tollip TBD is a natively unfolded domain that partially folds at its N-terminus when bound to the first two helices of the Tom1 GAT domain through high affinity hydrophobic contacts. Furthermore, this association abrogates binding of Tollip to PtdIns(3)P by additionally targeting its C2 domain. Binding of the Tollip C2 domain is mediated by the third helix of the Tom1 GAT domain. We propose that association with Tom1 favors Tollip's release from endosomal membranes, allowing Tollip to commit to cargo trafficking. To directly test the ability of Tom1-Tollip complexes to bind ubiquitinated cargo within a lipid bilayer, a system was developed to measure the distribution of an ubiquitin-conjugated substrate at nanometer-scale resolution using AFM so as to clarify the formation mechanism of Tom1-Tollip complex in the absence and presence of monoubiquitin and polyubiquitin chains, and the modulatory role of PtdIns(3)P. Also, we identified a conserved central hydrophobic patch at the ubiquitin surface to be the binding site for the Tom1 VHS domain. The ubiquitin hydrophobic patch is also involved in Tom1 GAT domain binding, suggesting that Tom1 can bind ubiquitin molecules through two independent sites.

Organizers: Vinh Nguyen

June 16

Friday 1:30pm
1028 Pamplin Hall
Udaya Sree Datla and Sheng Chen   (Dept. of Physics, Virginia Tech)

Topic: The spatiotemporal network dynamics of acquired resistance in engineered microecological systems

Organizers: Vinh Nguyen

June 23

Friday 1:30pm
304 Robeson Hall
Chuanhui Chen   (Dept. of Physics, Virginia Tech)

Topic: Scanning probe Microscopy Study of Molecular Nanostructures on 2D Materials

Nanostructures self-assembled from molecules adsorbed on emerging two-dimensional (2D) materials confer physical and chemical properties desirable for potential applications in photovoltaics, electronics and quantum information. In this talk, I will present our scanning tunneling microscopy (STM) study of temperature evolution of quasi-one dimensional (1D) C60 nanostructures on rippled graphene. We demonstrated that C60 molecules can be arranged into a quasi-1D chain structure through careful control of the subtle balance between the linear periodic potential of rippled graphene and the C60 surface mobility, which can transition to a more compact hexagonal close packed stripe structure by annealing at a higher temperature. I will also present the formation of sub-monolayer C60 and perylenetetracarboxylic dianhydride (PTCDA) on graphene wrinkles. Beyond graphene, I will briefly discuss our STM investigation on few-layer molybdenum disulfide (MoS2) and liquid-cell atomic force microscopy (AFM) study of Toll interacting protein (Tollip) on a lipid membrane.

Organizers: Vinh Nguyen

June 30

Friday 1:30pm
304 Robeson Hall
Wei Song   (Dept. of Biological Sciences, Virginia Tech)

Topic: Design of a Disabled-2-derived peptide to impair platelet-mediated cancer cell extravasation

Disabled-2 (Dab2) targets membranes and triggers a wide range of biological events, including endocytosis and platelet aggregation. Dab2, through its phosphotyrosine-binding (PTB) domain, inhibits platelet aggregation by competing with fibrinogen for ?IIb?3 integrin receptor binding. We have shown that the N-terminal region, including the PTB domain (N-PTB), drives Dab2 to the platelet membrane surface by binding to sulfatides through two sulfatide-binding motifs (SBM), modulating the extent of platelet aggregation. SBM peptide contains two helices when embedded in dodecylphosphocholine micelles, reversibly binds to sulfatides with moderate affinity, lies parallel to the micelle surface, and when added to a platelet mixture, reduces the number and size of sulfatide-induced aggregates. Moreover, tumor cells are reported to have the ability of aggregating platelets, which occurs following tumor cell intravasation into the vasculature, thereby facilitating tumor cell migration, invasion and arrest within the vasculature. Contributions of platelets aggregation to tumor cell survival and spread suggest platelets as a new avenue for therapy. Overall, our findings identify and structurally characterize a minimal region in Dab2 that modulates platelet homotypic interactions, all of which provide the foundation for rational design of a new generation of anti-aggregatory peptide for therapeutic purposes of cancer.

Organizers: Vinh Nguyen

July 2017
July 7

Friday 1:30pm
304 Robeson Hall
Prof. Shengfeng Cheng   (Dept. of Physics, Virginia Tech)

Topic: Evaporation as a Phenomenon and a Tool

Organizers: Vinh Nguyen

July 14

Friday 1:30pm
304 Robeson Hall
Shadi Sadat Esmaeili   (Dept. of Physics, Virginia Tech)

Topic: Breaking of Time Translation Invariance in Kuramoto Dynamics

We identify the breaking of time-translation invariance in a deterministic system of repulsively coupled Kuramoto oscillators, which are exposed to a distribution of natural frequencies. We consider grid sizes with different characteristics of the attractor space, which is by construction quite rich. This may cause long transients until the deterministic trajectories find their stationary orbits. The stationary orbits are limit cycles with periods that extend over orders of magnitude. It is the long transient times that cause the breaking of time-translation invariance in autocorrelation functions of oscillator phases. This feature disappears close to the transition to the monostable phase, where the phase trajectories are just irregular and no stationary behavior can be identified.

Organizers: Vinh Nguyen

July 21

Friday 1:30pm
304 Robeson Hall
Harmeet Singh  (Dept. Engineering Mechanics, Virginia Tedh)

Geometric singularities in the mechanics of strings and rods

We will discuss propagating geometric discontinuities in one-dimensional bodies, particularly those mediated by partial contact with obstacles that may serve as singular sources of momentum and energy. Invariance arguments and basic assumptions about contact interactions reveal counterintuitive behavior during pick-up, lay-down, impact, peeling, and other processes. Related phenomena can be found in string instruments, mooring lines, and many other systems.

Organizers: Vinh Nguyen

July 28

Friday 1:30pm
304 Robeson Hall
 

No talk scheduled.

August 2017
August 4

Friday 1:30pm
304 Robeson Hall
 

No talk scheduled.

August 11

Friday 1:30pm
304 Robeson Hall
Laura Hanzly   (Dept. of Biological Systems Engineering, Virginia Tech)

Topic: Protein Nanoscale Self-Assembly and Nanofiller Applications

Proteins can easily be manipulated to suite a variety of applications. Proteins have the capability of forming macroscopic structures as well as the ability to assemble on the nanoscale. Here, the modification and nanoscale self-assembly of the protein wheat gluten will be discussed. Interesting effects on the kinetics of self-assembly are observed when wheat gluten is assembled in mediums other than pure water. Practical applications for wheat gluten as a nanofiller in materials such as synthetic rubber are currently being investigated.

Organizers: Vinh Nguyen

August 18

Friday 1:30pm
1028 Pamplin Hall

CSB Steering Committee Meeting. No talk scheduled.

August 25

Friday 1:30pm
304 Robeson Hall
Parviz Seifpanahi Shabane   (Dept. of Physics, Virginia Tech)

Topic: Intrinsically Disordered Proteins -- What do they look like?

Organizers: Vinh Nguyen

   
Virginia Polytechnic Institute & State University 
Center for Soft Matter and Biological Physics MC 0435, 850 West Campus Drive, Blacksburg, VA 24061 
Phone: (540) 231-6544; Fax: (540) 231-7511