Center for Soft Matter and Biological Physics Seminars

Spring 2019

Organizer: Vinh Nguyen

These meetings occur on Mondays from 4:00pm to 5:00pm in Robeson 304.
Refreshments are served before the semnars (unless otherwise indicated)

January 2019
January 21

Monday 4:00pm
304 Robeson Hall
(poster)

"Martin Luther King Holiday (No Classes-University Offices Closed)

Host:

January 25

"Special Seminar"
Friday, 4:00pm
304 Robeson Hall
(poster)

Prof. Xinqi Gong (Renmin University of China)

"Mathematical Intelligence Applications for Bio-Marcromolecular Problems"

The intersection among mathematics, information and biology has becoming more and more interesting and important. Many studies in this direction have led to developments of theories, methods and applications. But the too fast advancing of nowadays forefront information technology and biology knowledge, have triggered two obviously emerging phenomena, tremendous brand-new peaks accessible by new kinds of efforts, randomly meaningless results by in-correct intersections. Here I will show some of our recent results in developing and distinguishing efficiently intelligent approaches and applications for computational molecular biology and medical problems, such as protein structure-function-interaction prediction and pancreas cancer CT image analysis using algorithms like Fast Fourier transform, Monte Carlo, and deep learning, and some new designed physical and geometrical features.

Host: Shengfeng Cheng

January 28

"Special Colloquium" Monday 4:00pm
190 Goodwin Halll
(poster)

Dr. Rui Zhang (University of Chicago)

"Structure and Dynamics of Topological Defects in Active Liquid Crystals"

Topological defects in nematic liquid crystals exhibit unique optical and physicochemical properties that have led to emerging applications in directed self-assembly of colloids and macromolecules. Recent experiments have demonstrated that active matter that consists of a dense collection of self-propelled rods can form an active nematic liquid crystal in which defects bind and unbind in a chaotic-like manner. Abundant examples of active nematics are found in different animate and inanimate systems, including flocking animals, bacteria, tissue cells, biopolymer suspensions, and even vibrating granular rods. However, the material properties of and seemingly chaotic-like defect dynamics in these non-equilibrium systems are poorly understood, limiting their applications. In this talk, I will discuss our recent work on unraveling defect behavior in active nematics. Specifically, we have adopted a hydrodynamic model to explain how the morphology, structure and dynamics of defects are determined by the interplay between elasticity and activity. Our model predictions are successfully confirmed by actomyosin-based experiments, shedding light on understanding and further control of topological defects in active liquid crystals.

Host: Shengfeng Cheng

February 2019
February 1

"Special Colloquium" Friday, 2:30pm
210 Robeson Hall
(poster)

Dr. Ting Ge (Duke University)

"Rheology and Nanorheology of Entangled Melts of Non-Concatenated Ring Polymers"

Rheology is the branch of science that studies how matter deforms and flows. Rheology of polymers is characterized by viscoelasticity that exhibits both solid-like elastic and liquid-like viscous features depending on the relevant time scales. Understanding and controlling the macromolecular dynamics underlying the viscoelastic response of polymers is one of the great challenges in polymer science. Complementary to experiments, theoretical and computational approaches provide deep physical insight into polymer dynamics. We use scaling theory and molecular dynamics simulation to study the rheology of non-concatenated ring polymers [1], a prominent example of polymers with non-linear architectures. The study of ring polymers sheds light on the effects of polymer architecture on polymer dynamics and rheology. Additionally, the melt of non-concatenated ring polymers serves as a good model for the de-swollen polymer network that possesses super-elasticity and for the organization of chromosomes critical to the gene expression and regulation in cell nucleus. Unlike their linear counterparts, ring polymers do not form long-lived entanglement network. Their viscoelastic response is characterized by a power-law stress relaxation prior to terminal viscous flow. The theoretical description and simulation results agree with each other and are in consistence with experimental observations of ring polymers. We further use molecular simulations to study nanorheology, which employs embedded nanoparticles to explore local viscoelasticity of polymers [2]. Nanorheology is important to the processing of nanoparticle polymer composites and the design of particle-based drug delivery systems in living cells as well. We find that the motion of large nanoparticles is not strongly suppressed in ring polymers as in linear polymers, because there is no long-lived entanglement network that traps nanoparticles. With increasing nanoparticle size, the local viscoelasticity experienced by the particle approaches the bulk viscoelasticity of ring polymers. We estimate that the bulk viscoelasticity is reached for nanoparticle size about twice the average spanning size of ring polymers. References [1]. “Self-Similar Conformations and Dynamics in Entangled Melts and Solutions of Nonconcatenated Ring Polymers”, T. Ge, S. Panyukov, and M. Rubinstein, Macromolecules 49, 708 (2016) [2]. “Nanorheology of Entangled Polymer melts”, T. Ge, G. S. Grest, and M. Rubinstein, Phys. Rev. Lett. 120, 057801 (2018) .

Host: Shunsaku Horiuchi

February 4

Monday 4:00pm
304 Robeson Hall
(poster)

Bart Brown (Virginia Tech)

“Coarsening with non-trivial in-domain dynamics and dynamically generated hierarchies in predator-prey games”

Spatial many-species predator-prey systems have been shown to yield very rich space-time patterns. We study the effects of non-trivial in-domain pattern formations in the context of a six-species predator prey game which exhibits growing domains composed of three species in a rock-paper-scissors relationship. Through the investigation of different quantities, such as space-time correlations and the characteristic length, and interface width we demonstrate that the non-trivial dynamics inside the domains affects the coarsening process as well as the properties of the interfaces separating the domains. A nine-species game is also introduced characterized by the spontaneous formation of spirals within spirals. The properties of these nested spirals are investigated through similar quantities including the temporal Fourier analysis of species density.

Host: Michel Pleimling

February 8

"Special Colloquium" Friday, 2:30pm
210 Robeson Hall
(poster)

Dr. Daniel Sussman (Duke University)

"Anomalous Interfaces in Biological Matter"

What can we learn about dense biological tissue by viewing it as a soft, active matter system? The mechanical and dynamical properties of dense collections of cells help govern processes ranging from wound healing to embryonic development to cancer progression, and an outstanding challenge is developing tractable models that can predict and explain the amazing variety of complex phenomena that even simple cellular systems can exhibit. Recent experiments have shown, for example, that many tissues lie close to a collective rigidity transition, and I will briefly discuss how simple coarse-grained models of dense tissue can support unusual forms of mechanical integrity. I will then show that these models exhibit anomalous interfacial properties, with different measurements of the surface tension between two tissues types differing by orders of magnitude. This departure from equilibrium behavior can be understood as a generic consequence of certain topological features of the cell-cell interactions, and I will discuss the potential relevance of this mechanism for both biological processes (such as cell sorting and compartmentalization) and for designing new materials with exotic bulk and boundary behavior.

Host: Michel Pleimling

February 11

Monday 4:00pm
304 Robeson Hall
Condensed Matter Seminar
(poster)

Sam Carter (Naval Research Lab)

"Spins in InAs quantum dots: qubits, sensors, and photon sources "

Over the past few decades a number of exciting applications of quantum coherence and entanglement have been developed that promise fundamental improvements in computing, secure communications, and sensing. A team of scientists at the Naval Research Laboratory are working to develop a physical implementation for these quantum information applications using semiconductor indium arsenide quantum dots (QDs). This system has the advantages of a robust solid state host, strong optical transitions, mature device fabrication, tunable properties, and a scalable, monolithic architecture. A single electron or hole spin within a QD acts as a stationary quantum bit that can be optically controlled on a picosecond timescale. In this presentation, I will discuss how a spin in a QD or in a pair of coupled QDs can also be used for sensing mechanical motion and for generating tunable single photons. To sense motion, QDs have been incorporated into mechanical resonators, which couple to the dots through strain. When mechanical resonators are driven, the optical transitions of QDs shift significantly [1], and the spin states shift as well [2]. In single QDs, the hole spin shows much stronger coupling to strain than electrons spins, due to the stronger spin-orbit interaction. In coupled QDs, a pair of interacting electron spins can be made highly sensitive to strain gradients that change the relative QD energies. To generate photons, we make use of the Raman spin-flip process, which has the advantage of generating photons with properties determined by the drive laser and the spin properties. In this way, we are able to demonstrate spectral and temporal control over single photon wavepackets [3], with very low two photon emission probability and high indistinguishability. Finally, I will briefly discuss efforts that combine these topics, in which highly localized strain is used to tune multiple QD photon emitters into resonance within nanophotonic waveguides [4]. This work is supported by the U.S. Office of Naval Research and the OSD Quantum Sciences and Engineering Program. [1] Carter, S. G. et al. Sensing flexural motion of a photonic crystal membrane with InGaAs quantum dots. Appl. Phys. Lett. 111, 183101 (2017). [2] Carter, S. G. et al. Spin-mechanical coupling of an InAs quantum dot embedded in a mechanical resonator. Phys. Rev. Lett. 121, 246801 (2018). [3] Pursley, B. C., Carter, S. G., Yakes, M. K., Bracker, A. S. & Gammon, D. Picosecond pulse shaping of single photons using quantum dots. Nat. Commun. 9, 115 (2018). [4] Grim, J. Q. et al. Scalable in operando strain tuning of multiple quantum dots within a photonic waveguide architecture. arXiv 1810.05195 (2018).

Host: Sophia Economou

February 15

"Special Colloquium" Friday, 2:30pm
210 Robeson Hall
(poster)

Dr. Antonia Statt (Princeton University)

"Pathways to Structure Formation in Colloid and Polymer Mixtures"

Soft matter is important in technological applications, biology and everyday life. Its behavior on mesoscopic scales is challenging to predict because dominant energy scales are of the magnitude of thermal fluctuations. I will present simulation results for two examples of structure formation in soft matter: colloidal crystal nucleation and inverted stratification in drying polymer mixtures. We developed a novel method to determine nucleation barriers without calculating the anisotropic interfacial tension or locating the interface precisely. By demonstrating the importance of hydrodynamic interactions during evaporation, we show that hydrodynamics need to be incorporated when predicting the structure of drying films.

Host: Uwe Tauber

February 18

"Special Colloquium" Monday 4:00pm
190 Goodwin Hall

(poster)

Dr. Cihan Nadir Kaplan (Harvard University)

"Morphing hard and soft matter by reaction-transport dynamics"

Engineering next-generation materials that can grow into efficient multitasking agents, move rapidly, or discern environmental cues greatly benefits from inspiration from biological systems. In the first part of my talk, I will present a geometrical theory that explains the biomineralization-inspired growth and form of carbonate-silica microarchitectures in a dynamic reaction-diffusion system. The theory predicts new self-assembly pathways of intricate morphologies and thereby guides the synthesis of light-guiding optical structures. The second part is dedicated to a soft matter analog of controlled actuation and complex sensing in living systems. Specifically, I will introduce a continuum framework of a simple hydrogel system that is activated upon transport and reaction of chemical stimuli. The hydrogel exhibits unique cascades of mechanical and optical responses, suggesting that common gels have a much larger sensing space than currently employed. The theoretical work presented in my talk is intimately connected to modern materials science. The effective convergence of theory and experiment paves the way for optimized hard or soft biomimetic materials for applications ranging from bottom-up manufacturing to soft robotics.

Host: Rana Ashkar

February 25

"Special Colloquium" Monday 4:00pm
190 Goodwin Halll

(poster)

Dr. Trung Dac Nguyen (Northwestern University)

"Engineering materials from bottom up for bioremediation applications"

The accumulation of mismanaged organic waste and toxins in insecticides and warfare agents poses serious environmental threats to the ecosystem and human health. Bioremediation provides an effective means to address these issues, for instance, by using cleaning agents containing enzymes that break down the pollutants into more bio-friendly products. The ability to maximize the catalytic activity of those enzymes out of their native media will enable industry-scale bioremediation applications for a wider variety of pollutants. In this talk, I will discuss a recently proposed bottom-up approach for stabilizing enzymes in organic solvents, where the enzymes are mixed with copolymers that are composed of hydrophobic and hydrophilic monomers arranged in disordered sequences. These so-called random heteropolymers possess a rich diversity in monomer sequences, which plays a vital role in reducing the enzymes’ exposure the unfavorable solvent. This helps explain why the proposed approach is superior to the often-used reverse-micelle techniques in retaining the activity of numerous types of enzymes in toluene. Furthermore, the collectivity in the interaction between the polymers and enzymes upon assembly is predicted to lead to the uniform size of the assembled complexes, which is important for their solubility and delivery. These outstanding features of the random heteropolymer approach suggests new possibilities for engineering protein-based materials for applications much beyond bioremediation.

Host: Daniel Capelluto

February 26

"Special Seminar"
Tuesday, 5:00pm
304 Robeson Hall

(poster)

Prof. Nuno Araujo (University Lisbon, Portugal)

"Dynamics of Colloidal Particles on Surface and Interfaces"

Colloidal particles are considered ideal building blocks to produce materials with enhanced physical properties. The state-of-the-art techniques for synthesizing these particles provide control over shape, size, and directionality of the interactions. In spite of these advances, there is still a huge gap between the synthesis of individual components and the management of their spontaneous organization towards the desired structures. The main challenge is the control over the dynamics of self-organization. In their kinetic route towards thermodynamically stable structures, colloidal particles self-organize into intermediate structures that are much larger than the individual particles and become the relevant units for the dynamics. To follow the dynamics and identify kinetically trapped structures, one needs to develop new theoretical and numerical tools. In this seminar, we will discuss the self-organization of colloidal particles under confinement. Experiments with suspensions of ellipsoidal colloidal particles suggest a transition in the statistical properties of the stain left by an evaporating drop, depending on the eccentricity of the particles [1]. We proposed a stochastic model to show that the very-strong anisotropic capillary attraction between particles stemming from the deformation of the interface can be responsible for such transition [2,3]. We will discuss the main mechanisms involved and compare the quantitative results with experiments. With the experimental groups of Erika Eiser (Univ. Cambridge) and Jasna Bruijc (New York University), we have shown that the long-range capillary attraction and consequent formation of kinetically trapped structures of colloidal particles at interfaces can be avoided using DNA-coated colloids on complementary functionalized interfaces (oil droplet) [4], where we keep the irreversible interfacial binding but suppress the strong attraction, resulting in a fully ergodic colloidal dynamics. We will discuss how the coverage of the oil droplet by colloidal particles and the self-assembled structures depend on different system parameters, such as, temperature and bulk concentration of colloidal particles. [1] P. J. Yunker et al. Physical Review Letters 110, 035501 (2013). [2] C. S. Dias et al., Soft Matter 14, 1903 (2018). [3] C. S. Dias, N. A. M. Araújo, M. M. Telo da Gama, EPL 107, 56002 (2014). [4] D. Joshi et al. Science Advances 2, e1600881 (2016). * with M. M. Telo da Gama, C. S. Dias, A. S. Nunes, and D. Pinto

Host: Uwe Tauber

March 2019
March 4

Monday 4:00pm
304 Robeson Hall

(poster)

APS Meeting (No Seminar)

Host:

March 11

Monday, 4:00pm
304 Robeson Hall

(poster)

Prof. Subir Das (J. Nehru Institute, Bangalore, India)

"TBD"

Host: Uwe Tauber

March 18

Monday 4:00pm
304 Robeson Hall

(poster)

Host:

March 25

Monday 4:00pm
304 Robeson Hall

(poster)

Host:

April 2019
April 1

Monday 4:00pm
304 Robeson Hall
Condensed Matter Seminar
(poster)

Prof. Herbert Fotso (University at Albany)

"TBD"

Host: Ed Barnes

April 8

Monday 4:00pm
304 Robeson Hall
Joint CM Seminar

(poster)

Prof. Chih Kuan Tung (North Carolina A&T State University)

"TBD"

Host: Shengfeng Cheng

April 15

Monday 4:00pm
304 Robeson Hall

(poster)

Dr. Ulrich Dobramsyl (University of Cambridge)

"TBD"

Host: Uwe Tauber

April 22

Monday 4:00pm
304 Robeson Hall

(poster)

Host:

April 29

Monday 4:00pm
304 Robeson Hall

(poster)

Host:

May 2019
May 6

Monday 4:00pm
304 Robeson Hall
(poster)

Host:

May 13

Wednesday,
210 Robeson Hall
(poster)

Final Exam Week
(No Seminars)