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2017 Discussion Meetings

Center for Soft Matter and Biological Physics Friday Discussion Meetings

Fall 2017

Organizer: Vinh Nguyen

These meetings occur on Fridays from 4:00pm to 5:00pm in Robeson 304 (unless otherwise indicated)

September 2017
September 1

Friday 4:00pm
304 Robeson Hall

Physics Department Faculty Meeting. No talk scheduled.

September 8

Friday 4:00pm
304 Robeson Hall

CSB Center Meeting. No talk scheduled.

September 15

Friday 4:00pm
304 Robeson Hall

Discussion with Prof. Nigel Goldenfeld (J. Mark Sowers Distinguished Speaker)

Organizer: Uwe Täuber

September 22

Friday 4:00pm
304 Robeson Hall

Physics Department Faculty Meeting. No talk scheduled.

September 29

Friday 4:00pm
304 Robeson Hall

No talk scheduled.

Organizer: Vinh Nguyen

October 2017
October 6

Friday 4:00pm
304 Robeson Hall

No talk scheduled

October 13

Friday 4:00pm
304 Robeson Hall

Fall Break. No talk scheduled.

October 20

Friday 4:00pm
304 Robeson Hall

Physics Department Faculty Meeting. No talk scheduled

Organizer: Vinh Nguyen

October 27

Friday 4:00pm
304 Robeson Hall

(poster)

Jacob Carroll  (Department of Physics, Virginia Tech)

Topic: Sparsely Encoding Convolutional Neural Networks I

Neural networks are a family of models that range from the biologically inspired recurrent networks that serve as models of the brain, to the feed-forward, deep-learning networks that have been at the forefront of machine learning in recent years. This talk will introduce a specific type of neural network, that while biologically inspired, has been developed for the purpose of machine learning and computer science: the sparsely encoding convolutional neural network. This talk will explain this model in detail, and will serve as the basis for a second talk in January that will explore observed finite-size scaling in these sparsely encoding convolutional neural networks.

Organizer: Vinh Nguyen

November 2017
November 3

Friday 4:00pm
304 Robeson Hall

(poster)

Yanfei Tang   (Department of Physics, Virginia Tech)

Topic: Young-Laplace Equation

Organizer: Vinh Nguyen

November 10

Friday 4:00pm
304 Robeson Hall

(poster)

Prof. Hildegard Meyer-Ortmanns (Jacob University Bremen, Germany)

Topic: ABOUT INTERESTING CYCLES IN OSCILLATORY SYSTEMS AND IN GAMES OF WINNERLESS COMPETITION

Upon identifying physical aging in oscillatory systems we discovered two interesting phenomena in a system of repulsively coupled Kuramoto oscillators, which have a rather rich attractor space. One is the emergence of long-period orbits, whose periods are orders of magnitude longer than the period of individual oscillators. The cycles here consist of repeating temporary patterns of phase-locked motion. The other phenomenon refers to the self-similarity of these cycles, when the strength of deviations from a uniform natural frequency distribution is appropriately tuned. In connection with winnerless games of competition we search for heteroclinic cycles that are supposed to be responsible for spiral pattern formation and even hierarchies of spirals, when these games are placed on a spatial grid. Here we indicate ongoing work.

Organizer: Vinh Nguyen

November 17

Friday 4:00pm
304 Robeson Hall

Physics Department Faculty Meeting. No talk scheduled

Organizer: Vinh Nguyen

November 24

Friday 4:00pm
304 Robeson Hall

Thanksgiving Holiday. No talk scheduled.

December 2017
December 1

Friday 4:00pm
304 Robeson Hall

Chengyuan Wen (Department of Physics, Virginia Tech)

Topic: Evaporation of Liquids

Organizer: Vinh Nguyen

December 8

Friday 4:00pm
304 Robeson Hall

(Department of Physics, Virginia Tech)

Talked Canceled and Rescheduled for Future

Organizer: Vinh Nguyen

   

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

   
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Center for Soft Matter and Biological Physics Friday Discussion Meetings

Spring 2017

Organizer: Vinh Nguyen

These meetings occur on Fridays from 4:00pm to 5:00pm in Robeson 304 (unless otherwise indicated)

January 2017
January 20

Friday 4:00pm
304 Robeson Hall

Faculty search event. No talk scheduled.

January 27

Friday 4:00pm
304 Robeson Hall

Faculty search event. No talk scheduled.

February 2017
February 3

Friday 4:00pm
304 Robeson Hall

Faculty search event. No talk scheduled.

February 10

Friday 4:00pm
304 Robeson Hall

Faculty search event. No talk scheduled.

February 17

Friday 4:00pm
304 Robeson Hall

Faculty search event. No talk scheduled.

February 24

Friday 4:00pm
304 Robeson Hall

Faculty search event. No talk scheduled.

March 2017
March 3

Friday 4:00pm
304 Robeson Hall

Faculty meeting. No talk scheduled.

March 10

Friday 4:00pm
304 Robeson Hall

Spring Break. No talk scheduled.

March 17

Friday 4:00pm
304 Robeson Hall

APS March Meeting. No talk scheduled.

March 24

Friday 4:00pm
304 Robeson Hall
Sheng Chen (Dept. of Physics, Virginia Tech)

Topic: Computational study of biodiversity with evolution and natural selection

Organizers: Vinh Nguyen and Will Mather

March 31

Friday 4:00pm
304 Robeson Hall
Heather Deter (Dept. of Physics, Virginia Tech)

Topic: Big data analysis of differential production within toxi-antitoxin systems

Organizers: Vinh Nguyen and Will Mather

April 2017
April 7

Friday 4:00pm
304 Robeson Hall

Special talk in engineering. No CSB talk scheduled.

April 14

Friday 4:00pm
304 Robeson Hall
William Ducker (Dept. of Chemical Engineering, Virginia Tech)

Topic: Micrometer-sized spheres driven into crystalline array by simple simple rubbing

Organizers: Vinh Nguyen and Will Mather

April 21

Friday 4:00pm
304 Robeson Hall

No talk scheduled.

Organizers: Vinh Nguyen and Will Mather

April 28

Friday 4:00pm
304 Robeson Hall

Faculty Meeting, No CSB Talk Scheduled

May 2017
May 5

Friday 4:00pm
304 Robeson Hall

Exam week. No CSB talk scheduled.