Center for Soft Matter and Biological Physics Seminars

Fall 2016

Organizers: Will Mather and Vinh Nguyen

Refreshments are served before the seminars (unless otherwise indicated)

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August 2016
August 29

Monday 4:00pm
304 Robeson Hall

(poster)

Dr. Ting Ge
University of North Carolina at Chapel Hill

Nanoparticle Motion in Entangled Melts of Linear and Non-Concatenated Ring Polymers

Fabrication and processing of polymer nanocomposites, a prominent class of hybrid materials that integrate nanoparticles (NPs) with desirable properties into polymer matrices, requires a good understanding of their viscoelastic behavior. Central to the viscoelasticity of polymer nanocomposites is the dynamical coupling between the motion of NPs and the relaxation dynamics of matrix polymers. We perform large-scale molecular dynamics simulations to compare the motion of NPs in entangled melts of linear polymers and non-concatenated ring polymers. This comparison provides a paradigm for the effects of polymer architecture on the dynamical coupling between NPs and polymers. Strongly suppressed motion of NPs with diameter d larger than the entanglement spacing a is observed in linear polymer melts before the onset of Fickian NP diffusion. The strong suppression of NP motion occurs progressively as d exceeds a, and is related to the hopping diffusion of NPs in the entanglement network. In contrast, the motion of NPs with d>a in ring polymers is not as strongly suppressed prior to Fickian diffusion. The sub-diffusive motion of NPs in ring polymers is understood through a scaling analysis of the coupling between NP motion and the self-similar entangled dynamics of non-concatenated rings.

Host: Shengfeng Cheng

September 2016
September 5

Monday 4:00pm
304 Robeson Hall

(poster)

Prof. Hans Werner Diehl
University Duisburg-Essen

Fluctuation-induced forces in confined He and ideal and imperfect Bose gases

When condensed-matter systems in which low-energy thermal fluctuations occur are confined by a pair of parallel planes or walls to a film geometry, effective forces between the planes are generated by these fluctuations. Familiar examples are 4He near the λ transition and Bose gases near the condensation transition. The cases of He or Bose gases in a 3D film geometry are particularly challenging since nontrivial dimensional crossovers of 3D bulk systems exhibiting long-range order at low temperatures to effective 2D systems without long-range order must be handled in addition to bulk, boundary, and finite-size critical behaviors. We show that exact results can be obtained for analogous n-component φ4 models in the limit n→∞ via inverse-scattering theory and other methods, and show that these results apply directly to the so-called imperfect Bose gas.

Host: Uwe Täuber

October 2016
October 24

Monday 4:00pm
304 Robeson Hall

(poster)

Prof. David Odde  
Department of Biomedical Engineering, University of Minnesota

Mechanisms of microtubule kinetic stabilization by the anticancer drugs paclitaxel and vinblastine

Microtubule-targeting agents (MTAs), widely used as biological probes and chemotherapeutic drugs, bind directly to tubulin subunits and suppress the characteristic microtubule self-assembly process of dynamic instability. This "kinetic stabilization" of microtubules is a universal phenotype of MTAs even though they have generally been separated based on tendency to promote either assembly or disassembly at high concentrations. Despite years of study, the molecular-level mechanisms of kinetic stabilization are still unclear. Here we integrate a computational model for microtubule assembly with nanometer-scale fluorescence microscopy measurements to identify the kinetic and thermodynamic basis of kinetic stabilization by the MTAs paclitaxel, an assembly promoter, and vinblastine, a disassembly promoter. Acquiring the highest resolution data across the largest drug concentration range in live cells to date, we identify two distinct modes of kinetic stabilization. One is truly a suppression of tubulin on-off kinetics, characteristic of vinblastine, and the other is a 'pseudo' kinetic stabilization, characteristic of paclitaxel, that nearly eliminates the energy difference between the tubulin nucleotide states. In this work we outline a kinetic and thermodynamic description of kinetic stabilization by the drugs paclitaxel and vinblastine, and further put constraints on the molecular mechanisms of other MTAs that promote in this universal phenotype. These results may help guide development of new microtubule-directed therapies for cancer and neurodegeneration.

Host: Shengfeng Cheng

November 2016
November 14

Monday 4:00pm
304 Robeson Hall

Joint with Condensed Matter

(poster)

Prof. Nicholas J. Mayhall
Department of Chemistry, Virginia Tech

Using simple ab initio methods to construct even simpler Hamiltonians: applying spin-flip methods for strong correlation and excited states.

Although ab initio quantum chemistry can be used routinely to accurately calculate energies and properties of a rather vast array of chemical systems, when the system size grows too large, or the structure too complex, standard approximations breakdown. Strong electron correlation and multiply excited electronic states represent two examples where our current methods fail to provide a robust toolset for applications. In this talk, I will discuss some recent work toward extending the spin-flip family of approximations to larger classes of problems, including exchange coupled transition metal complexes, and multiexciton states of organic molecule clusters.

Host: Vinh Nguyen

November 28

Monday 4:00pm
304 Robeson Hall

Joint with Condensed Matter

(poster)

Prof. Jing Chen
Department of Biological Sciences, Virginia Tech

Mathematical modeling of myxobacterial motility

Myxobacterium glides on substrate with two motility systems: a pili-driven, in-pack Social(S)-Motility and a single-cell based Adventurous(A)-Motility. To carry out complex "social" behaviors on the colony level, such as fruiting body formation, the myxobacteria periodically reverse, and the reversal frequency is modulated by cell-cell contact. In each single cell, motility regulators exhibit intriguing spatiotemporal patterns, including polar localization that oscillates in coordination with cell reversals, and cluster formation at the substrate interface. Previously we built a helical rotor model, which explains the cluster formation as a necessary force generation element in the A-motility mechanism. Currently we are developing an integrated model for myxobacteria motility that coherently links force generation and spatiotemporal patterns to the modulation of cell reversals. Ultimately we aim for understanding how intercellular contact confers intracellular signal to coordinate neighboring cells.

Host: Shengfeng Cheng

December 2016
December 5

Monday 4:00pm
304 Robeson Hall

Joint with Condensed Matter

(poster)

Prof. Dmitry Matyushov
Department of Physics and Molecular Sciences, Arizona State University

Electrostatic soup of biology: Production of biological energy by the fluctuating protein-water interface

Energy comes to living systems through electrons occupying high-energy states, either from food (respiratory chains) or light (photosynthesis). Electrons are transferred across the cellular membrane in a sequence of hopping events, with an overall small loss of free energy. Biology employs electrostatic fluctuations produced by the protein-water interface to overcome activation barriers for individual electron hops. Ergodicity is often broken in protein-driven reactions and thermodynamic free energies become irrelevant. Breaking the grip of thermodynamics allows for an efficient optimization between the rates of individual electron-transfer steps and the spectrum of relaxation times. Time, it appears, plays as significant role as the free energy in optimizing biology's performance.

Host: Vinh Nguyen

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