Center for Soft Matter and Biological Physics Seminars

Spring 2017

Organizers: Will Mather and Vinh Nguyen

Refreshments are served before the seminars (unless otherwise indicated)

< S2017 | January | February | March | April | May | June | S2018 >

January 2017
January 16

Monday 4:00pm
304 Robeson Hall

(poster)

 

Martin Luther King Holiday. No talk scheduled.

January 20

Friday 2:30pm
210 Robeson Hall

Special Colloquium

(poster)

Dr. Rana Ashkar  
Oak Ridge National Lab

Towards Switchable Topography and Tunable Fluctuations in Biomimetic Lipid Bilayers

Lipid bilayers are ubiquitous in nature; they form the backbone of cell membranes and are responsible for vital biological processes, including the regulation of protein functions and the exchange of nutrients in and out of the cell. In order to understand the function of lipid membranes and fully utilize their potential in biotechnologies, it is imperative to investigate the factors that control essential membrane processes, such as domain formation and protein recruitment. While decades of research have remarkably furthered our understanding of lipid membranes, the role of local curvature and nanoscale fluctuations remain to be the least understood. In this talk, I will present recent progress in developing a platform for topographic control of lipid bilayers, using thermoresponsive nanostructured polymer scaffolds, to explore curvature-mediated membrane phenomena, such as domain reorganization and switchable protein binding. I will also discuss ongoing experimental and computational studies on tuning nanoscale membrane fluctuations and investigating their effects on protein binding/insertion mechanisms.


Host:Vicki Soghomonian

January 27

Friday 2:30pm
210 Robeson Hall

Special Colloquium

(poster)

Dr. Liheng Cai  
Harvard University

Soft matter approaches to biology: A tale of mucus hydrogel in human lung defense

Biological systems are featured by their ability to defend themselves against external challenges. While these defense mechanisms are extensively studied in the context of life sciences, their physical aspects have largely been overlooked, although they are implicated in many important biological processes. Using knowledge and tools in soft matter and physical science, we can not only provide unique insights to biological questions that directly impact healthcare, but also in turn create new directions that broaden the scope of soft matter research. In this talk, I will discuss how soft matter physics can help understand a long-standing question for human lung defense: Why can the human lung fight against numerous inhaled infectious particulates and maintain functional through its lifetime? Contrary to the widely accepted dogma that the epithelium of human airway is lined by a physiological liquid, I discover that it is covered by a gel-like polymer brush. This brush layer protects the epithelium from small, infectious particulates that sneak through mucus hydrogel. Moreover, the brush layer enables efficient clearance of mucus out of lung by stabilizing itself against osmotic compression from the mucus. Furthermore, I will show that chronic osmotic stress from diseased mucus likely affects airway remodeling. It slows down the proliferation of epithelial cells, and more strikingly, directs the differentiation of epithelial cells to mucus producing cells, a hallmark of mucus obstructive lung diseases such as asthma, chronic obstructive pulmonary disease (COPD) and cystic fibrosis. These findings suggest that the osmotic pressure of mucus hydrogel provides a unified measure of pathogenesis of mucus obstructive lung diseases, and open new directions for the development of novel therapeutics to teat these diseases.



Host:Will Mather

February 2017
February 6

Monday 4:00pm
145 Goodwin Hall

Special Colloquium

(poster)

Dr. Jejoong Yoo  
University of Illinois Urbana-Champaign

The physics of chromosomes: from DNA loops to nucleus-scale structures

Human chromosomes in a cell's nucleus have long been thought to behave like encapsulated random polymers. Recent experiments, however, have shown that chromosomes organize into well-defined three-dimensional structures thereby controlling the cell's state. The very presence of such structures implies existence of yet unknown physical interactions that de-fine the free energy of chromosomes in a cell's nucleus and govern the free-energy change during processes such as cell development and cancer. Using high-through put molecular dynamics simulations and single-molecule experiments, we determined the free energy landscape of the fundamental structural unit of chromosome organization-a nucleosome, which is a fragment of DNA wrapped around a protein core. At a single nucleosome level, we found the nucleotide sequence of DNA and its CpG methylation to uniquely determine the orientation of the DNA loop with respect to the protein core, offering a simple physical mechanism of controlling DNA accessibility to DNA reader machinery. At a multi-nucleosome level, we found the AT content of the DNA sequence and the methylation of either DNA or the nucleosome proteins to govern association of nucleosomes into clusters. Overall, our findings suggest that intrinsic properties of DNA may play a considerable role in defining the free energy landscape and the nucleus-scale organization of chromosomes.


Host: Shengfeng Cheng

February 13

Monday 4:00pm
145 Goodwin Hall

Special Colloquium

(poster)

Dr. Maxim Lavrentovich  
University of Pennsylvania

Putting Patterns on Spheres: Pollen Grains and Cholesteric Liquid Crystal Shells

Insect egg shells, mite carapaces, pollen grain surfaces, and many other biological materials exhibit intri-cate surface patterns including stripes, spikes, pores, and ridges. Beautiful surface patterning occurs in cho-lesteric liquid crystals (CLCs), as well. I will discuss how to understand such surface patterning as a phase transition to a spatially modulated state on a sphere. On infinite, flat surfaces, the patterned states consist of uniform strips or hexagons. On the sphere, however, the patterns are more varied because they must have topological defects, which may be accommodated in many ways. In these phase transition models, the patterns have a characteristic wavelength, which has important consequences for the thermal fluctua-tions in the system, including a fluctuation-driven qualitative change in the behavior near the phase transi-tion. Focusing on spherical pollen grain development, I will describe what sets the characteristic wave-length, the influence of fluctuations, and how our simple model may be tested experimentally. CLCs also have an intrinsic, characteristic wavelength associated with the twist in the stacking of their constituent molecules. These compounds also exhibit phase transitions to spatially modulated states, over which we have good experimental control. I will discuss the behavior of spherical CLC shells and their surface patterns by drawing insights from experiments and simulations. We will end with a discussion of the nu-cleation and growth of such patterns.


Host: Vicki Soghomonian

February 20

Monday 4:00pm
145 Goodwin Hall

Special Colloquium

(poster)

Dr. Edward Banigan  
Northwestern University

Emergent length scales of the cell nucleus

The interiors of living cells are highly organized, and this internal order is critical to robust cell biological function. However, it is not well understood how few-nanometer-sized proteins dynamically generate spatiotemporal order over length scales spanning several nanometers to tens of microns. The cell nucleus and the genome contained within exemplify this problem: the same ~1 meter of DNA is packed into each ~10 micron cell nucleus, and yet, different cells differ dramati-cally in function and activity. Thus, biological function is largely governed by genome organization, and it is critical to establish biophysical mechanisms for measuring length in the nucleus. I will discuss several models for DNA on differ-ent length scales that reveal different physical mechanisms underlying intracellu-lar organization. Specifically, I will discuss experimentally motivated models for non-equilibrium DNA twist dynamics, spatial partitioning of catalytic macromol-ecules, and whole nuclear deformation. These models show how DNA mechan-ics, biomolecule diffusion and catalytic activity, and nuclear geometry and archi-tecture each determine distinct lengths for cellular phenomena on multiple scales. Together, these models illustrate how mechanical and biochemical effects at small scales may be integrated to lead to emergent phenomena that control cell nuclear and genome organization.


Host: Shengfeng Cheng

February 27

Monday 4:00pm
304 Robeson Hall

(poster)

 

Faculty Meeting. No talk scheduled.

March 2017
March 6

Monday 4:00pm
304 Robeson Hall

(poster)

 

Spring Break Week. No talk scheduled.

March 13

Monday 4:00pm
304 Robeson Hall

(poster)

 

APS March Meeting. No talk scheduled.

March 20

Monday 4:00pm
304 Robeson Hall

Joint Condensed Matter Seminar

(poster)

Prof. Christian Ray  
University of Kansas

Regulation of Bacterial Growth in Discrete Steps and Structured Lineages


Prodigious growth is a defining feature of bacterial life. Systems of networks change growth rates in bacteria dynamically in response to changing environments. This includes surviving stresses such as antibiotics and starvation via slowing of growth. Phenotypic heterogeneity allows a small fraction of cells to enter growth arrest by randomly crossing an internal molecular threshold, a form of bet-hedging that allows the population of cells to survive even if future environments are inhospitable to actively growing cells. Therapeutic targeting of growth arrested bacteria is a critical emerging strategy during the current rising problem of antibiotic resistance and the continued challenge of treating stubborn, chronic infections. We are taking a multifaceted approach that has opened new avenues for understanding persister formation with time-lapse microscopy and computational models. Our experiments have shown a novel persister-forming condition. In this condition, bacterial cells undergo discrete shifts in growth rate that correspond to fast molecular reshuffling events. Analysis of cellular lineages in these conditions demonstrates that cellular transitions into growth arrest are not statistically independent: closely related cells are more likely to transition together. Computational models reproduce lineage correlations with a remarkably simple set of assumptions. We discuss implications of the novel persister phenotype for pathogens surviving in changing environments, and new questions raised by our results.

Host: Will Mather

March 27

Monday 4:00pm
304 Robeson Hall

Joint Condensed Matter Seminar

(poster)

Prof. Katie Mitchell-Koch  
Dept. of Chemistry, Wichita State University

How do bio molecular surfaces influence small molecule dynamics?


Our group has been using molecular dynamics simulations to study the interactions and dynamics of small molecules-solvent and substrate-at the surfaces of biomolecules. Simulations of aldehyde and alcohol substrates in the presence of the aldehyde reductase YqhD have revealed a substrate access channel that is not evident in the crystal structure. Collaborative work with Prof. Vinh Nguyen (Virginia Tech) has investigated the hydration layer dynamics around DPC micelles. Simulations coupled with GHz-to-THz measurements have shown that the slowest waters are hydrogen-bonded to the anionic phosphatidyl oxygen's, while only a modest slowdown in hydration dynamics is observed around the cationic trimethylamine groups of the zwitterionic lipids. Hydration dynamics around the enzyme Candida Antarctica lipase B (CALB) have been simulated, indicating heterogeneity in protein-water hydrogen bond lifetimes at the surface. CALB is an enzyme that is also used in organic solvents for the production of fine chemicals such as flavoring agents. Work is underway to characterize the solvation layer of CALB in organic solvents, connecting solvent dynamics to protein structure and dynamics.

Host: Vinh Nguyen

April 2017
April 3

Monday 4:00pm
304 Robeson Hall

Joint Condensed Matter Seminar

(poster)

Prof. Ting Lu  
University of Illinois at Urbana-Champaign

Bottom-up Assembly of Microbial Communities: Modeling, Analysis and Engineering


Microbes are of fundamental importance to human health, environment and agriculture. To ultimately exploit their potential for various purposes, a fundamental challenge is to decipher the basic rules of microbial community organization that is heterogeneous in space and time. My lab aims to address the challenge using a bottom-up approach that combines biophysical modeling with experimental synthetic biology. Recently, we developed a computational platform that enables individual-based simulation of microbial communities across multiple scales. We also explored how the modes of cellular social interaction and the spatial scale of interaction contribute to microbial assemblages using the platform, both of which were subsequently determined using experimental ecosystems. Using engineered cellular interactions, we further demonstrated the utility of synthetic microbial consortia for metabolic engineering applications. Our studies provide insights into the organization of complex microbial communities and illustrate the potential of synthetic communities for practical goals.

Host: Will Mather

April 10

Monday 4:00pm
304 Robeson Hall

Joint Condensed Matter Seminar

(poster)

Prof. Jiadong Zang  
University of New Hampshire

Skyrmions in Helimagnets

A Skyrmion is a topological configuration in which local spins wrap around the unit sphere for an integer number of times. After decades of theoretical discussions in high energy physics, it has been recently observed in a series of non-centrosymmetric chiral magnets. Several experiments by neutron scattering or transmission electron microscopy confirm the presence of skyrmions in a crystalline state at a finite window of magnetic field and temperature. Skyrmions show various novel properties inherent to its topological nature, such as topological Hall effect, topological stability, and ultralow critical current for movement, which offer the skyrmion promising prospects for next generation spintronic devices and information storage. In this talk, I will explain the physical origin of skyrmions in chiral magnets, and discuss our recent progress on the skyrmion physics, including skyrmions in confined geometries, new skyrmion materials, and electron transports of the skyrmion materials.

Host: Uwe Täuber

April 17

Monday 4:00pm
304 Robeson Hall

(poster)

 

Condensed Matter Seminar. No CSB seminar scheduled.

April 24

Monday 4:00pm
304 Robeson Hall


(poster)



No talk scheduled.

May 2017
May 1

Monday 4:00pm
304 Robeson Hall

(poster)

 

Condensed Matter Seminar. No CSB seminar scheduled.

May 8

Monday 4:00pm
304 Robeson Hall

(poster)

 

Final Exam Week. No talk scheduled.

June 2017
June 2

Friday, 1:30pm
304 Robeson Hall

Special Date / Time

(poster)

Prof. P. S. Krishnaprasad  
University of Maryland

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.

Host: Uwe Täuber

   
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