Center for Soft Matter and Biological Physics Friday Discussion Meetings

Spring 2019

Organizer: Vinh Nguyen

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

January 2019
January 4

Friday 4:00pm
304 Robeson Hall

"No CSB Discussion Meeting Scheduled"

Organizer: Vinh Nguyen

January 11

Friday 4:00pm
304 Robeson Hall

"No CSB Discussion Meeting Scheduled"

Organizer: Vinh Nguyen

January 18

Friday 4:00pm
304 Robeson Hall

"No CSB Discussion Meeting Scheduled"

Organizer: Vinh Nguyen

January 25

Friday 4:00pm
304 Robeson Hall
(Flyer)

Center for Soft Matter and Biological Physics Workshop (Location Blacksburg Community Center)

"No Discussion Meeting"

Organizers: William Ducker & Katrina Loan

January 28

"Special Date and Time" Monday 5:30pm
304 Robeson Hall

Student discussion with Dr. Rui Zhang (University of Chicago)

Host: Shengfeng Cheng

February 2019
February 1

Friday 4:00pm
304 Robeson Hall

Student discussion with Dr. Ting Ge (Duke University)

Organizer: Shunsaku Horiuchi

February 8

Friday 4:00pm
304 Robeson Hall

Student discussion with Dr. Daniel Sussman (Syracuse University)

Organizer: Michel Pleimling

February 15

Friday 4:00pm
304 Robeson Hall

Student discussion with Dr. Antonia Statt (Princeton University)

Organizer: Uwe Tauber

February 18

"Special Date and Time" Monday 5:30pm
304 Robeson Hall


Student discussion with Dr. Cihan Nadir Kaplan (Harvard University)

Host: Rana Ashkar

February 22

Friday 4:00pm
304 Robeson Hall

"APS March Meeting Practice"

Organizer: Vinh Nguyen

February 25

"Special Date and Time" Monday 5:30pm
304 Robeson Hall


Student discussion with Dr. Trung Dac Nguyen (Northwestern University)

Host: Daniel Capelluto

March 2019
March 1

Friday 4:00pm
304 Robeson Hall

"Faculty Meeting"

Organizer: Vinh Nguyen

March 8

Friday 4:00pm
304 Robeson Hall

"APS March Meeting" (Boston)

"No discussion meeting scheduled"

Organizer: Vinh Nguyen

March 15

Friday 4:00pm
304 Robeson Hall

"Spring Break continuing ends March 17"

"No CSB Discussion Meeting Scheduled"

Organizer: Vinh Nguyen

March 22

Friday 4:00pm
304 Robeson Hall
(poster)


Organizer: Vinh Nguyen

March 29

Friday 4:00pm
304 Robeson Hall
(poster)

"Faculty Meeting"

"No Discussion Meeting"

Organizer: Vinh Nguyen

April 2019
April 5

Friday 4:00pm
304 Robeson Hall
(poster)

"Faculty Meeting"

:No Discussion Meeting"

Organizer: Vinh Nguyen

April 12

Friday 4:00pm
304 Robeson Hall
(poster)

Nicole Abaid (Biomedical Engineering and Mechanics, Virginia Tech)

"Passive and active sensing in the Vicsek model

While many social animals move in groups using passive senses like vision, bats form very large colonies while using on sonar for navigation. Sonar is a so-called active sense, which relies on a self-generated signal (sound) rather than one already present in the environment (e.g., light for vision). From an engineering perspective, using active sensing in large groups poses many challenges centered around interference between signals produced by peers. However, experimental work with bats suggests that these animals may be capable of using their peers' signals for passive sonar, which may ameliorate some of these complications.  Taking this system as inspiration, we explore the possibility of combining passive and active sensing in a well-studied model which shows collective behavior, the Vicsek model. The Vicsek model enforces a local alignment rule in groups of self-propelled particles perturbed by noise. Phase transition is observed in both the presence and absence of passive sensing, yet the range of parameters for which ordered and disordered group states exist dramatically changes when passive sensing is used. Notably, we find numerous cases of the model for which the implementation of passive sensing increases the robustness of the collective behavior to noise.

Organizer: Vinh Nguyen

April 19

Friday 4:00pm
304 Robeson Hall
(poster)

"Faculty Meeting"

"No Discussion Meeting"

Organizer: Vinh Nguyen

April 26

Friday 4:00pm
304 Robeson Hall
(poster)

Dr. Saptarshi Chakraborty (Physics, Virginia Tech)

"Polymer-Stabilized Colloidal Catalysts: Role of Polymers and Strategies for Recovery and Reuse"

Gold nanoparticles (AuNPs) have attracted enormous attention due to their unique catalytic activities. Colloidal AuNPs provides the benefit of selectivity, greater surface area per mass of catalyst compared to supported catalysts, catalyzes reactions under mild conditions and are very effective for chiral catalysis. On a per metal basis colloidal AuNPs demonstrate higher catalytic activity than their supported counterparts. Colloidal AuNPs however requires surface functionalization with ligands to prevent aggregation which causes surface passivation and significant reduction in catalytic activity. Colloidal AuNP catalytic activity is strongly dependent on ligand packing and conformation on the AuNP surface. Large polymeric ligands demonstrate increase in available surface area leading to increased catalytic activity, while small molecule ligands lead to complete AuNP surface passivation. A major drawback of colloidal AuNPs as catalysts is the catalyst recovery from the product stream. We have employed small pH sensitive ligands as AuNP stabilizers to show that AuNPs can be recovered from the product stream by altering the pH to selectively precipitate or phase transfer catalyst into organic solvents. However, due to the high small molecule packing density on AuNP surface, complete surface passivation was observed. Catalytic activity could be recovered by partially functionalizing the AuNP surface, however at the cost of recoverability. To maintain catalytic activity in recoverable catalysts, we have developed pH sensitive polymer ligands by synthesizing thiolated polymer ligands. AuNPs functionalized with thiolated polymer, demonstrate similar recoverability while retaining high catalytic activity. Application of colloidal AuNP as catalysts, thus entails fine tuning ligand MW, structure, catalytic activity and recoverability.

Organizer: Vinh Nguyen

May 2019
May 3

Friday 4:00pm
304 Robeson Hall
(poster)

Prof. Jonathan Boreyko (Mechanical Engineering, Virginia Tech)

"Fun with Water: Catching Fog, Building Trees, and Freezing Bubbles"

Nature displays incredible feats of fluid mechanics that have much to teach us. Here, we study and exploit four different kinds of nature-inspired fluid phenomena: two involving liquid-phase behavior and two involving freezing water. First, we’ll explain how coastal redwoods have inspired a “fog harp” that harvests several times more water than existing fog harvesters. Second, we demonstrate that synthetic trees are capable of passively pumping water against gravity on the same scale as natural trees. The beauty of freezing bubbles is explained by novel physical models. Finally, we show that simple scaling laws can rationalize the development of passive anti-frosting surfaces

Organizer: Vinh Nguyen

May 8

Wednesday 4:00pm
304 Robeson Hall
(poster)

Classes end


(No CSB Discussion Meeting)

Organizer: Vinh Nguyen

May 10

Friday 4:00pm
304 Robeson Hall
(poster)

Exams Begin


(No CSB Discussion Meeting)

Organizer: Vinh Nguyen

May 17

Friday 4:00pm
304 Robeson Hall
(poster)

University Commencement and College and Department Ceremonies


(No CSB Discussion Meeting)

Organizer: Vinh Nguyen

Center for Soft Matter and Biological Physics Friday Discussion Meetings

Summer 2019

Organizer: Vinh Nguyen

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

May 2019
May 24

Friday 1:30pm
304 Robeson Hall
(poster)

"CSB Symposium Week"

"No Discussion Meeting"

May 31

Special Time: Friday 4:00pm
304 Robeson Hall
(poster)


Ruslan Mukhamadiarov and Shengfeng Deng (Physics, Virginia Tech)

"Central Concepts of Nonlinear Dynamics and Chaos"

In a series of Center summer meetings, Shengfeng Deng and I will explore the central concepts of nonlinear dynamics and chaos. We will demonstrate how these abstract ideas can be applied in physics and biology. The list of topics that we plan to cover includes one- and two-dimensional flows, bifurcations, Lorenz equations, one-dimensional maps, and fractals. This talk series is intended mainly for graduate students and will be held in the form of informal discussion meetings.

Host: Uwe Tauber

June 2019
June 7

Friday 1:30pm
304 Robeson Hall
(poster)

Tuo-Xian Tang (Biological Sciences, Virginia Tech)

"The Functional Basis of Phafin2 in Autophagy"

Autophagy is a highly conserved cellular pathway in the eukaryotic cells. A portion of the cytosol, which contains invading pathogens and long-lived proteins, is taken up by an autophagosome. This double-membrane organelle fuses with lysosomes, where the contents were digested by the lysosomal enzymes. Previous data showed that Phafin2 was involved in autophagy. After the induction of autophagy, Phafin2 and Akt accumulate on the lysosomal membranes through the interactions between Phafin2 and phosphatidylinositol 3-phosphate (PtdIns(3)P). Phafin2 has two domains, one N-terminal PH (Pleckstrin Homology) domain and one C-terminal FYVE (Fab 1, YOTB, Vac 1, and EEA 1) domain. In this study, the binding affinity between PtdIns(3)P and Phafin2 was studied by surface plasmon resonance. Results showed that Phafin2 binds PtdIns(3)P with high affinity, triggering minor conformational changes in the protein. We also demonstrated that Phafin2 FYVE domain is responsible for the binding of PtdIns(3)P. Another interesting finding is that Phafin2 can cause membrane curvature, which may be required for tethering of lysosomes to autophagosomes, and consequently initiating autophagy.

Host: Vinh Nguyen

June 14

Friday 1:30pm
304 Robeson Hall
(poster)

Shengfeng Deng (Physics, Virginia Tech)

"Phase Portraits of Two-Dimensional Flows"

Higher-dimensional phase spaces can display more intricate and interesting dynamics. Two dimensional phase space already shows fixed points with different kinds of stabilities, and winding trajectories etc. We first discuss linear systems in two dimensions and the classification of fixed points, which will play an important role in the classification for fixed points of nonlinear systems. The phase portraits then allows us to predict the long-term behaviors of many physical systems.

Host: Uwe Tauber

June 21

Friday 1:30pm
304 Robeson Hall
(poster)

James Stidham (Physics, Virginia Tech)

"Ordering in Magnetic Skyrmion Lattices"

Ordering in magnetic skyrmion lattices is an active area of research for skyrmion systems. In this talk, I will present recent results obtained using Langevin molecular dynamic simulations, based on a previously derived particle model of skyrmion. Using a Vornoi cell algorithm, we examined the effect of the Magnus force present in skyrmion systems and how it affects ordering when noise is both present and absent in the system. We observed power law behavior during late time ordering in these skyrmion systems.  We also found power law behavior when looking at the difference in time of consecutive events as the system orders.

Host: Michel Pleimling

June 28

Friday 1:30pm
304 Robeson Hall
(poster)

Ruslan Mukhamadiarov (Physics, Virginia Tech)

"Nonlinear Dynamics and Chaos: Limit Cycles and 2-D Bifurcations"

Ubiquitous in nature, limit cycles are inherently nonlinear phenomena that can model systems with self-sustained oscillations. I am going to outline the existence conditions for the limit cycles, and I will show how the concept of limit cycles can be applied to study nonlinear oscillation problems. In the second part of the talk we will revisit the bifurcations and extend the concepts that we covered in the first meeting to the phase plane. I am also going to consider the other possible scenarios that arise in two dimensions, namely Hopf bifurcations and global bifurcations of cycles.

Host: Uwe Tauber

July 2019
July 5

Friday 1:30pm
304 Robeson Hall
(poster)

"Last day of Classes of Summer Session I"

No Discussion Meeting

July 12

Friday 1:30pm
210 Robeson Hall
(poster)

Prof. David Minh (Chemistry, Illinois Institute of Technology)

"New Computational Tools for Designing Compounds Active Against Biological Macromolecules"

Most pharmaceuticals are small organic molecules that work via noncovalent interactions with biological macromolecules. Although drugs have saved or improved countless lives, drug discovery remains an inexact science that involves much trial and error. The main focus of my research group is the development of computer modeling tools to quickly characterize noncovalent protein-ligand interactions. Most of our tools are based on implicit ligand theory, a theoretical framework that I derived to predict how tightly molecules bind and how they influence the population of conformations accessed by their targets. At this point, we have established that our methods are able to reproduce results of more computationally expensive approaches. We are working on making them more efficient and feasible to use with large libraries of chemical compounds. We have also advanced the theory of end-point binding free energy methods, in which binding affinity is predicted based on molecular simulations of the bound complex.

Host: Igor Tolokh

July 19

Friday 1:30pm
304 Robeson Hall
(poster)

Austin Warren
(Physics, Virginia Tech)

"Nonlinear Dynamics and Chaos: Lorenz System and 1-D Maps"

Despite being entirely predictable in principle, many deterministic systems display extremely complicated, apparently random long term behavior. This chaotic behavior appears in many practical everyday problems, from understanding how populations grow to predicting tomorrow's weather. In this talk, I'll be discussing what we mean when we talk about chaos and what it looks like in practice. In particular, we'll be looking at how chaos emerges from order in two well-known systems: the continuous Lorenz system and the discrete logistic map.

Host: Uwe Tauber

July 26

Friday 1:30pm
304 Robeson Hall
(poster)

Connor Mackert
(Physics, Virginia Tech)

"Gray Scott Model Parameter Adjustment Effects"

The Gray Scott Model has been subject of numerous investigations. Due to the nonlinear nature of the reaction-diffusion system many studies have used overly broad strokes. Through systematic parameter adjustment we are able to find novel system pattern formations that were previously overlooked.

Host: Michel Pleimling

August 2019
August 2

Friday 1:30pm
304 Robeson Hall
(poster)

Vinh Ho
(Physics, Virginia Tech)

“Broadband and High Responsivity Graphene-based Photodetectors at Room-temperature”

Ability to covert light of graphene occurs in an ultra-broadband spectral range from violet to mid-infrared region, making graphene as desirable photodetectors for various technology applications in imaging, sensing, spectroscopy and telecommunication. However, the low responsivity of graphene photodetectors about 10 mA/W, due to the ultra-fast recombination of photocarriers, limits their potential applications. Here, we have engineered the interface between graphene and dielectric films to introduce trapping centers. The interface layer efficiently convert the photon energy into a large electrical signal. Thus, our graphene-based photodetectors have showed a high sensitivity up to 2 × 10^5 A/W together with a fast response time in a broadband spectral at room temperature.

Host: Vinh Nguyen

August 9

Friday 1:30pm
304 Robeson Hall
(poster)

"TBD"

Host:

August 16

Friday 1:30pm
304 Robeson Hall
(poster)

"Exams Begins for Summer Session II

August 23

Friday 1:30pm
304 Robeson Hall
(poster)

Anri Karanovich (Physics, Virginia Tech)

“Nonlinear Dynamics and Chaos: Fractals and Strange Attractors”

The emergence of deterministic chaos in many nonlinear systems, including the Lorentz map and the logistic map, is closely related to the existence of strange attractors - nontrivial closed subsets of the phase space, fractal in nature, to which nearby trajectories are converging. In order to gain a deeper insight into the patterns of the system evolution and its chaotic behavior, we need to study the main properties and geometric characteristics of the strange attractors.  In the first part of the talk, I will define and provide basic examples of fractals, and then discuss the notion of fractional dimensionality and the various ways to measure it.  In the second part, we will consider the simple examples of strange attractors, their characteristic features, methods of analysis, and relation to the chaotic properties of the system.

Host: Vinh Nguyen