2016 Seminars

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.

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.

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.

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.

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.

Chronic infections present a serious threat to the health of humans by decreasing life expectancy and quality. They have more recently been attributed to the existence of persister cells within bacterial populations which constitute a small fraction of the population capable of surviving a wide range of environmental stressors including starvation, DNA damage, and heat shock. Persis- tence also allows the survival of successive applications of antibiotics resulting in chronic infections. Persistence has been strongly linked to so-called toxin-antitoxin (TA) modules, operons with an evolutionarily conserved motif including a toxin that halts cell growth and an antitoxin that under healthy conditions neutralizes the toxin, typically by forming a complex which protects the antitoxin from rapid proteolytic degradation and performs some regulatory action on the operon. While many such modules have been identifed and studied in a wide range of organisms, little consideration of interactions between multiple modules within a single host has been made. Moreover, the multitude of different antitoxin species share a limited number of proteolytic pathways, strongly suggesting competition between antitoxins for degradation machinery. Here we present a theoretical under- standing of the dynamics of multiple toxin-antitoxin modules whose activity is coupled through proteolytic activity. Such indirect coordination between multiple TA modules may be at the heart of bacterial robustness owed to the persistent response.

The ultimate goal of Soft Matter is to synthesize materials of enhanced physical properties from the spontaneous self-organization of their individual units. A prototypical example is the use of colloids. With a typical size of the order of the wavelength of visible light, colloidal particles are not only excellent building blocks for optical materials as they are ideal for experiments, for their trajectories can be resolved using available optical techniques. Unfortunately, self-organization is usually driven out of equilibrium and the relaxation towards equilibrium involves the competition of various mechanisms occurring at different length and time scales. The investigation of these mechanisms provides valuable information on the feasibility of the desired structures while unveiling novel non-equilibrium phases that differ in significant ways from the thermodynamic ones. One focus is on identifying novel phases and constructing the equilibrium phase diagrams, based on the properties of individual particles (shape, size, and chemistry). For example, patchy colloids, characterized by highly directional pairwise interactions, set a maximal valence and determine the local particle arrangements leading to novel thermodynamic phases. The question then is, are these phases kinetically accessible? We address this question by means of Langevin dynamics simulations. We identify a crossover between fast (exponential) and slow (scale free) relaxation regimes at a critical temperature, that it is intimately related to the formation of a percolating gel. An impressive advance of experimental techniques has opened the possibility of exploring alternative assembling routes such as the use of substrates, interfaces and electromagnetic fields to collectively drive the system towards the desired structures. We study self-organization under such constraints combining Brownian dynamics simulations and a simple dynamic density functional theory. We analyze the interplay between the strength of the particle-particle and particle-substrate interactions. In addition, we analyze field driven self-organization, by investigating the switching (field on) dynamics and the relaxation times as a function of the system parameters. We also consider binary suspensions of colloids of different mobilities finding non-equilibrium demixing, where the lifetime of the demixed phase diverges when the high mobility colloids crystallize.