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2018 Discussion Meetings

Center for Soft Matter and Biological Physics Friday Discussion Meetings

Fall 2018

Organizer: Vinh Nguyen

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

August 2018
August 24

Friday 4:00pm
304 Robeson Hall
(poster)

Faculty Meeting (No CSB Discussion Meeting)

Organizer: Vinh Nguyen

August 31

Friday 4:00pm
304 Robeson Hall
(poster)

Organizer: Vinh Nguyen

September 2018
September 7

Friday 4:00pm
304 Robeson Hall
(poster)

Organizer: Vinh Nguyen

September 14

Friday 4:00pm
304 Robeson Hall
(poster)

Organizer: Vinh Nguyen

September 21

Friday 4:00pm
304 Robeson Hall
(poster)

Deepali Shirsekar (Mechanical Engineering)

“Bidirectional Reflectance Measurement of Black Coating Z302 for use in Optical Instrument Design ”

The bidirectional reflectance distribution function (BRDF) plays a fundamental role in the optical characterization of a surface. The BRDF is a measure of the amount of light incident from one direction that is scattered by a surface in another direction. This talk introduces the concept of BRDF and presents the thesis research of graduate student, Deepali Shirsekar, to investigate the BRDF of black coating, Aeroglaze Z302. Work includes design and fabrication of a high-accuracy bidirectional reflectometer and its use to measure the bidirectional reflectance of a black absorber Aeroglaze Z302®. A BRDF model consisting of diffuse, glossy, and specular components is fitted to the experimental results. Finally, the Monte Carlo ray-trace (MCRT) method is used to simulate the performance of any optical instrument which has Z302 material coated on its active surfaces.

Organizer: Vinh Nguyen

September 28

Friday 4:00pm
304 Robeson Hall
(poster)

Faculty Meeting (No CSB Discussion Meeting)

Organizer: Vinh Nguyen

October 2018
October 5

Friday 4:00pm
304 Robeson Hall
(poster)

Nazia Munir (Mechanical Engineering)

"Investigation of the Gold-Black Absorption Mechanism"

The material called gold-black is an absorptive material frequently used in various thermo-detector. The advantages of gold-black that make it preferable over the other absorptive material is that it has the absorptivity almost one (α=1) in the visible and infrared range which means that it absorbs all the radiation incident on it and appears black in an observer’s eye. For this unique property gold-black has been used in thermal detector such as in micro-bolometer. The micro-bolometer converts the incident radiation to an electrical signal. Gold-black is used as a coating on the micro-bolometer to ensure a 100% absorption of the radiation. Micro-bolometer with gold-black coating has several applications specially in various program of Earth Radiation Budget where the global warming is closely monitored with satellite having micro-bolometer attached on it. The purpose of this effort is to establish a model of gold-black so that it can be used more efficiently in various detector. We seek a first-principle model for predicting the spectral absorptivity of gold-black. Gold-black has been widely used in various thermal and optical applications for more than a century. In most relevant contributions to the literature, gold-black is treated as a homogeneous layer whose behavior is governed by its bulk optical properties. However, on the microscopic level gold-black more closely resembles a fuzzy layer of moss or a miniature forest. This suggests that the optical behavior of gold-black can be better characterized by taking into account its actual morphology. We propose to model a layer of vacuum-deposited gold-black as a “fractal forest” where each branch of each tree is isolated and considered as an individual building block. In this treatment each individual branch acts as a dipole antenna with the forest as a whole behaving as a random-fractal antenna array. The approach of the current effort is to develop a model for the conversion of incident electromagnetic (EM) radiation to sensible heat by an individual branch behaving as a lossy antenna. The output of such a model would be the energy conversion efficiency (absorptivity), corresponding to a given wavelength, of a single branch having a specified length, diameter, and orientation with respect to incident EM radiation. The overall absorptivity of the forest at that wavelength would then be based on the statistical description of the spatial and angular distributions of branches of various length and diameter. The required statistical rules would be derived from microscopic study of actual gold-black layers.

Organizer: Vinh Nguyen

October 12

Friday 4:00pm
304 Robeson Hall
(poster)

Faculty Meeting (No CSB Discussion Meeting)

Organizer: Vinh Nguyen

October 19

Friday 4:00pm
304 Robeson Hall
(poster)

"Fall Break" (No CSB Discussion Meeting)

Organizer: Vinh Nguyen

October 26

Friday 4:00pm
304 Robeson Hall
(poster)

Harrison Wood (Biomedical Engineering and Mechanics)

“A study on the effects of in-plane swelling gradients on orthotropic plates”

In this study, we examine the effects of in-plane swelling gradients on resulting shapes of thin, orthotropic plates. Emphasis is placed on understanding how different swelling gradients and orthotropic material properties result in different shapes. This talk focuses on introducing the topic of incompatible elasticity applied to programming swelling functions and shapes in plates, and summarizes the current research of graduate student Harrison Wood on swelling and warping of engineered wood products. Several surface parameterizations are explored to explain warped shapes of orthotropic plates. An energy expression based on mid-plane strains and curvatures is minimized with respect to surface parameters, and competition between stretching and bending energy terms is studied to determine equilibrium shapes. Using some simple toy models of plate warp as inspiration, some scaling arguments are being developed to validate certain behaviors and shapes, such as the case where a specific in-plane swelling gradient results in a cylindrical-like shape at equilibrium for an orthotropic plate.

Organizer:Vinh Nguyen

November 2018
November 2

Friday 4:00pm
304 Robeson Hall
(poster)

Prof. Michael Flatte (University of Iowa)

Meeting with Students

Organizer: Giti Khodaparast

November 9

Friday 4:00pm
304 Robeson Hall
(poster)

Prof. William Ducker (Chemical Engineering)

"Absorption at Confined Interfaces"

Thin liquid films have different properties than bulk solutions because of the effects of the fields extending from the boundaries. These altered properties are important in determining the stability of colloid and nano-particle suspensions, wetting films, adsorption in confined spaces, and in the fabrication and application of nanoscale devices. Our interest is in adsorption, which affects many of these applications: there is a multitude of applications where surfactants, polymers, ions, etc. are adsorbed to effect changes in thin films, for exam-ple, to alter the stability of colloidal particles. We describe measurements of adsorption between two flat plates when the plates are separated by 0 – 65 nm and several results for several examples: depletion of a simple ion in dilute solution and adsorption in very concentrated salt solutions. These measurements have been made possible by our development of new tech-nique. Measurement of all separations is achieved simultaneously by measuring visible-light interference in a wedge-shaped crack created between an oxidized-silicon wafer and a glass wafer. The adsorbed amount is measured from the fluorescence emission of a dye, after accounting for the optical interference. The specific measurement is of the depletion of a divalent anion, fluorescein, in aqueous solution between two anionic solids. For dilute solutions at large separations between the flat plates, the dye is depleted rela-tive to the bulk concentration. At smaller separations, the depletion of the dye decreases. The range of the depletion and the magnitude of depletion decrease with shorter Debye-length. Both of these effects are con-sistent with a simple calculation using the Poisson-Boltzmann equation. For concentrated solutions, results do not agree with Poisson-Boltzmann theory. That theory predicts that the surface potential decays exponential-ly with a decay length (Debye-length) that decreases with increasing concentration. Results are consistent with an increase in decay length with increasing concentration. We make comparisons to results in ionic liq-uids and drawn conclusions for crystal growth through particle attachment. We

Organizer: Vinh Nguyen

November 16

Friday 4:00pm
304 Robeson Hall
(poster)

Faculty Meeting (No CSB Discussion Meeting)

Organizer: Vinh Nguyen

November 23

Friday 4:00pm
304 Robeson Hall
(poster)

Thanksgiving Break (No CSB Discussion Meeting)

Organizer: Vinh Nguyen

November 30

Friday 4:00pm
304 Robeson Hall
(poster)

Michael Kane (Mechanical Engineering)

"Topography and Mechanical Properties of Nanostructured PNIPAM Films"

PNIPAM is a thermo-responsive polymer that has wide applications in biological applications, including its use as a cell growth scaffold. In this talk, we will discuss some of the recent measurements that we have done on PNIPAM films on nanostructured substrates. Using Atomic Force Microscopy, we investigate the surface topography of the films at different temperatures as well as their mechanical properties in different parts of the sample.

Organizer: Rana Ashkar

December 2018
December 7

Friday 4:00pm
304 Robeson Hall
(poster)

First Day of Exams (No CSB Discussion Meetings)

Organizer: Vinh Nguyen

Center for Soft Matter and Biological Physics Friday Discussion Meetings

Summer 2018

Organizer: Vinh Nguyen

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

May 2018
May 25

Friday 1:30pm
304 Robeson Hall
(poster)


Organizer: Vinh Nguyen

June 2018
June 1

Friday 1:30pm
304 Robeson Hall
(poster)

Organizer: Vinh Nguyen

June 8

Friday 1:30pm
304 Robeson Hall
(poster)


Organizer: Vinh Nguyen

June 15

Friday 1:30pm
304 Robeson Hall
(poster)


Organizer: Vinh Nguyen

June 22

Friday 1:30pm
304 Robeson Hall
(poster)

Ruslan Mukhamadiarov (Physics, Virginia Tech)

"Transverse Temperature Interface in Katz-Lebowitz-Spohn Model"

Driven lattice gas with attractive nearest neighbor interactions and periodic boundaries demonstrate intriguing dynamics, when parts of lattice held at different temperatures. In two dimensions, this complex system experiences a jamming transition in the high temperature zone, and forms stripes in the low temperature regions. Density profiles are strikingly similar with those for Asymmetric Exclusion Process (ASEP) with open boundary conditions when injection and ejection rates are equal. In this talk, I will discuss the dynamics of two-temperature driven lattice gas system and characterize its density profile using analytical results and Monte Carlo simulations.


Organizer: Vinh Nguyen

June 29

Friday 1:30pm
304 Robeson Hall
(poster)

Prof. Uwe Tauber (Virginia Tech, Physics)

"Interactive Discussion: Manuscript writing"


Organizer: Vinh Nguyen

July 2018
July 6

Friday 1:30pm
304 Robeson Hall
(poster)

Shadi Esmaeili

"An Exploration of Characteristics of System of Kuramoto Oscillators"

Coupled oscillators and emergent synchronized patterns can be found in many phenomena in nature. Kuramoto model is the simplest model of coupled oscillators with an exact solution that can explain many such phenomena. By choosing a proper coupling constant and topology the system shows multi-stability. Also, by choosing non-homogeneous frequencies long period orbits emerge in the system. We study the effects of the change in different parameters of the system (e.g. coupling constant and width of frequency distribution) as well as the response of the system to external noise.


Organizer: Vinh Nguyen

July 13

Friday 1:30pm
304 Robeson Hall
(poster)

Ahmadreza Azizi (Physics, Virginia Tech)

"Microscopic description of Generalized Voter Model"

The Langevin equation of critical phenomena in the presence of two symmetric absorbing states is considered as a novel macroscopic description of generalized Voter model (GVM). Numerical integration of GVM in two dimensions shows that the direct transition from a disorder phase to either of the absorbing states is described by voter critical point. Also, indirect transitions to the ordered state can happen where the Voter critical point is split into Ising and Directed percolation (DP) critical points. Although the Langevin description of GVM is successful, there is no known microscopic version of GVM in two dimensions which clearly presents all three critical points together. We will study one of the possible ways to achieve a microscopic version of GVM with Voter, Ising and DP critical points.


Organizer: Vinh Nguyen

July 20

Friday 1:30pm
304 Robeson Hall
(poster)

Prof. John B. Phillips (Biological Sciences, Virginia Tech)

"Quantum Biology meets Behavioral Biology (and a Behavioral Biologist): a new sensory system and a new class of sensory receptors in the mammalian retina"

The ability of animals to detect the Earth’s magnetic field remains the least understood of the major senses. Many vertebrates have two functionally distinct magnetoreception mechanisms: a light-dependent, photoreceptor-based mechanism that provides directional (‘compass’) information and a non-light-dependent, magnetite-based mechanism that provides positional (‘map’) information. The light-dependent magnetic compass (LDMC) is mediated by a manifestly quantum process thought to involve a light-dependent radical pair reaction that forms long-lived, spin-coordinated radical pair intermediates (“radical pair mechanism” or RPM). The most compelling evidence for the RPM is the finding that magnetic compass orientation in a variety of animals can be altered or abolished by exposure to low-level radio frequency (RF) fields (> 1nT) that can alter the electron-spin dynamics of the radial pair. Interest in the RPM spans a wide range of disciplines, and has been a primary impetus for the emerging field of Quantum Biology. Studies of murine rodents (mice, rats, etc.) have played a central role in both basic and applied (i.e., biomedical) research on mammalian spatial behavior and cognition. A number of well-characterized spatial cells (e.g., head direction cells, place cells, grid cells, boundary vector cells, and velocity cells; see 2014 Nobel Prize in Medicine) underlie a path integration system that encodes the animal’s spatial position as it moves through the environment. However, the spatial circuitry characterized to date only provides accurate navigational information over distances of a few 10s of meters, falling well short of the 100s of meters routinely moved by even small rodents like deer mice (20g) under natural conditions. A magnetic compass sense can dramatically increase both the range and accuracy of a path integration system, as well as play important roles in many other aspects of spatial behavior and cognition. Nevertheless, the consensus of the literature is that murine rodents do not rely on magnetic cues, despite evidence that a magnetic compass is virtually ubiquitous in other animals, including some mammals (bats, mole rats, dolphins). Contrary to the prevailing view in the literature, we have found that mice and rats have a well-developed magnetic compass. However, consistent behavioral and neurophysiological responses to magnetic cues can only be elicited reliably when the testing apparatus is shielded to screen out low-level RF noise. We have also identified photoreceptors in animals as different as flies, frogs, and mice that appear specialized for detection of the geomagnetic field. In this talk, I’ll briefly discuss evidence: (1) that there are a specialized photoreceptors in which the response to light is dependent on the alignment of an earth-strength magnetic field, (2) that in animals where specialized photo-magnetoreceptors are located in the compound eye (flies) or retina (birds, mice), the magnetic field may be perceived as a 3-dimensional pattern of light intensity and/or color superimposed on the animal’s surroundings, (3) that both behavioral and neurophysiological responses to magnetic cues can be altered or abolished by low-level radio frequency noise at intensities commonly found in laboratory environments, and (4) that the magnetic field plays multiple, previously unrecognized, roles in the spatial behavioral and cognition of murine rodents over a variety of spatial scales.


Organizer: Vinh Nguyen

July 27

Friday 1:30pm
304 Robeson Hall
(poster)

Professor Michel Pleimling (Physics, Virginia Tech)

"Aging processes in systems far from equilibrium I: An overview of the phenomenology of physical aging"

Physical aging scaling is encountered in numerous systems with slow dynamics. In this talk I introduce the phenomenology of physical aging and show that many of the characteristic features of physical aging can be understood through the investigation of simple coarsening systems. Dynamical scaling of two-time quantities like the autoresponse and autocorrelation functions is discussed for systems with a single time-dependent length scale.


Organizer: Vinh Nguyen

August 2018
August 3

Friday 1:30pm
304 Robeson Hall
(poster)

Professor Uwe Tauber (Physics, Virginia Tech)

“Interactive Discussion on Applications”


Organizer: Vinh Nguyen

August 10

Friday 1:30pm
304 Robeson Hall
(poster)

Professor Michel Pleimling (Physics, Virginia Tech)

"Aging processes in systems far from equilibrium II: Systems with complex ordering processes"

In this talk I first discuss aging scaling properties of a many-species system undergoing coarsening with non-trivial in-domain dynamics. The second part of the talk is devoted to physical aging in interacting skyrmion matter. Two-time correlation functions are analyzed to study the non-linear stochastic relaxation dynamics in the aging regime.


Organizer: Vinh Nguyen

Center for Soft Matter and Biological Physics Friday Discussion Meetings

Spring 2018

Organizer: Vinh Nguyen

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

January 2018
January 5

Friday 4:00pm
304 Robeson Hall
(poster)

"No CSB Discussion Meeting Scheduled"

Organizer: Vinh Nguyen

January 12

Friday 4:00pm
304 Robeson Hall
(poster)

"No CSB Discussion Meeting Scheduled"

Organizer: Vinh Nguyen

January 19

Friday 4:00pm
304 Robeson Hall
(poster)

"No CSB Discussion Meeting Scheduled"

Organizer: Vinh Nguyen

January 26

Friday 4:00pm
304 Robeson Hall
(poster)

"No CSB Discussion Meeting Scheduled"

Organizer: Vinh Nguyen

February 2018
February 2

Friday 4:00pm
304 Robeson Hall
(poster)

"No CSB Discussion Meeting Scheduled"

Organizer: Vinh Nguyen

February 9

Friday 4:00pm
304 Robeson Hall
(poster)

Jacob Carroll (Department of Physics, Virginia Tech)

"Sparsely Encoding Convolutional Neural Networks II"

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 continue to 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 how these systems are used for imaged denoising, and how finite size scaling was observed in these networks as they denoised images across many different values of sparsity. This finite size scaling implies that these systems undergo a continuous as sparsity is varied.

Organizer: Vinh Nguyen

February 16

Friday 4:00pm
304 Robeson Hall
(poster)

Priyanka (Department of Physics, Virginia Tech)

"Study of anomalous behavior in one-dimensional harmonic system"

I will start with some theoretical models which have been developed to understand the violation of Fourier's Law in the lower dimension. Anomalous transport, nonlinear temperature profile etc, are the key feature of these model. In detail, I will talk about one of these models (harmonic chain with volume exchange) and present some its analytical and numerical results. I will present exact expression of two-point function in a stationary state and also shows that the dynamics are governed by fractional Laplacian.

Organizer: Vinh Nguyen

February 23

Friday 4:00pm
304 Robeson Hall
(poster)

Weigang Liu (Department of Physics, Virginia Tech)

"A numerical study of the two-dimensional complex Ginzburg-Landau equation"

The complex Ginzburg-Landau equation with additive noise is a stochastic partial differential equation that describes a remarkably wide range of physical systems: coupled non-linear oscillators subject to external noise near a Hopf bifurcation instability; spontaneous structure formation in non-equilibrium systems, e.g., in cyclically competing populations; and driven-dissipative Bose-Einstein condensation, realized in open systems on the interface of quantum optics and many-body physics. We employ a finite-difference method to numerically solve the noisy complex Ginzburg-Landau equation on a two-dimensional domain with the goal to investigate the coarsening dynamics following a quench from a strongly fluctuating defect turbulence phase to a long-range ordered phase. We start from a simplified amplitude equation, solve it numerically, and then study the spatio-temporal behavior characterized by the spontaneous creation and annihilation of topological defects (spiral waves). We check our simulation results against the known dynamical phase diagram in this non-equilibrium system, tentatively analyze the coarsening kinetics following sudden quenches between different phases, and have begun to characterize the ensuing aging scaling behavior.

Organizer: Vinh Nguyen

March 2018
March 2

Friday 4:00pm
304 Robeson Hall
(poster)

Physics Faculty Meeting (No CSMB Discussion Meeting)

Organizer: Vinh Nguyen

March 9

Friday 4:00pm
304 Robeson Hall
(poster)

"Spring Break" (No CSB Discussion Meeting Scheduled)

Organizer: Vinh Nguyen

March 16

Friday 4:00pm
304 Robeson Hall
(poster)

CSB Faculty Meeting (No CSMB Discussion Meeting)

Organizer: Vinh Nguyen

March 23

Friday 4:00pm
304 Robeson Hall
(poster)

Ali Charkhesht (Department of Physics, Virginia Tech)

"Probing Collective Motions of Proteins and Hydration Dynamics by a Wide Range Dielectric Spectroscopy"

Studying dynamics of proteins in their biological milieu such as water is interesting because of their strong absorption in the terahertz range that contain information on their global and sub-global collective vibrational modes (conformational dynamics) and global dynamical correlations among solvent water molecules and proteins. In addition, water molecules dynamics within protein solvation layers play a major role in enzyme activity. However, due to the strong absorption of water in the gigahertz-to-terahertz frequencies, it is challenging to study properties of the solvent dynamics as well as conformational changes protein in water. In response, we have developed a highly sensitive megahertz-to-terahertz dielectric spectroscopy system to probe the hydration shells as well as large-scale dynamics of these biomolecules. . Thereby, we have deduced the conformation flexibility of proteins and compare the hydration dynamics around proteins to understand the effects of surface-mediated solvent dynamics, relationships among different measures of interfacial solvent dynamics, and protein-mediated solvent dynamics based on the complex dielectric response from 50 MHz up to 2 THz by using the system we developed. Comparing these assets of various proteins in different classes helps us shed light on the macromolecular dynamics in a biologically relevant water environment.

Organizer: Vinh Nguyen

March 30

Friday 4:00pm
304 Robeson Hall
(poster)

Physics Faculty Meeting (No CSMB Discussion Meeting)

Organizer: Vinh Nguyen

April 2018
April 6

Friday 4:00pm
304 Robeson Hall
(poster)

Physics Faculty Meeting (No CSMB Discussion Meeting)

Organizer: Vinh Nguyen

April 13

Friday 4:00pm
304 Robeson Hall
(poster)

Riya Nandi (Department of Physics, Virginia Tech)

"Short-Time Dynamics of Three-Dimensional Magnetic Systems with Heisenberg Interaction"

This project aims to explore the initial relaxation dynamics of Heisenberg ferro and anti-ferromagnets. It involves a new simulation technique of combining reversible mode coupling dynamics with the simple diffusive relaxation dynamics in order to obtain the correct dynamic exponent and identify the correct universality class. The system undergoes critical aging and relevant exponents identified. Finally, for a system with non-conserved order-parameter, i.e., the anti-ferromagnet, theory predicts non-universal initial slip exponent. This work aims to study its dependence on the width of the initial distribution of the conserved quantities. This is a work in progress, at best just beginning to show promising results.

Organizer: Vinh Nguyen

April 20

Friday 4:00pm
304 Robeson Hall
(poster)

Physics Faculty Meeting (No CSMB Discussion Meeting)

Organizer: Vinh Nguyen

April 27

Friday 4:00pm
304 Robeson Hall
(poster)

Physics Faculty Meeting (No CSMB Discussion Meeting)

Organizer: Vinh Nguyen

May 2018
May 4

Friday 4:00pm
304 Robeson Hall
(poster)

Exam Week (No CSMB Discussion Meeting)

Organizer: Vinh Nguyen