Eric Sembrat's Test Bonanza

In ordinary solids, acoustic shocks are extreme mechanical phenomena: they occur when rigid materials are subjected to violent impacts. But in soft materials things are different. Granular media, foams and polymer networks can all be prepared in a state of vanishing rigidity in which even the tiniest perturbation elicits an extreme mechanical response. When that happens these materials are not just soft, they have become fragile.

In this talk, we present simulations in which two-dimensional jammed granular packings are dynamically compressed, and demonstrate that the elementary excitations are strongly nonlinear shocks, rather than ordinary phonons. We capture the full dependence of the shock speed on pressure and impact intensity by a surprisingly simple analytical model.

We also discuss shear shocks within a simplified viscoelastic model of nearly-isostatic random networks comprised of harmonic springs. In this case, anharmonicity does not originate locally from nonlinear interactions between particles, as in granular media. Instead, it emerges from the global architecture of the network. As a result, the diverging width of the shear shocks bears a nonlinear signature of the diverging isostatic length associated with the loss of rigidity in these floppy networks.

Bulk Topological Insulators are a new phase of electronic matter which realizes a non-quantum-Hall-like topological state in the bulk matter and unlike the quantum Hall liquids can be turned into superconductors. In this Lecture, I will first review the basic theory of topological matter and experimental probes that reveal topological order. I will discuss experimental results that demonstrate the fundamental properties of topological insulators such as spin-momentum locking, non-trivial Berry’s phases, mirror Chern number, absence of backscattering or no U-turn rule, protection by time-reversal symmetry and the existence of room temperature topological order (at the level of M.Z.H and C.L. Kane, Rev. of Mod. Phys., 82, 3045 (2010)). I will then discuss the possible exotic roles of broken symmetry phases such as superconductivity and magnetism in doped topological insulators and their potential device applications in connection to our recent results as well as outline the emerging research frontiers of the field as a whole.

Departing from the context of CoGeNT and COUPP, two direct searches for WIMP dark matter, we will inspect the recent landscape of anomalies observed by these and several other detectors. The aim of this talk is to communicate an appreciation for the subtleties inherent to experimental efforts in this field, and for the considerable difficulties that await for those trying to make sense of WIMP search observations (or lack thereof).

This talk will describe new results on the properties of colloidal crystals, both on their solidification and on their melting.  It will describe how hard-sphere like colloids crystallize, and will explore the huge discrepancy between the nucleation rates predicted by theory and measured in simulation and those measured experimentally.  The discrepancy can be as large as 150 orders of magnitude!  A simple modification to the theory, suggested by experiment, is able to account for this behavior and to rectify the discrepancy.  It will also describe how perfect colloidal crystals, formed in a Wigner lattice, melt.  Since there are no grain boundaries for the crystals, melting occurs in a different fashion, one that seems to have some second order character to it.

Self-assembly of amphiphilic peptides designed during the last ten years by different research  groups leads to a large variety of 3D-structures that already found applications in e.g. stabilization of large protein complexes, cell culturing systems etc. Our group has recently suggested a new type of short amphiphilic peptides that exhibits clear charge separation controllable by the pH of the environment. An intricate interplay between electrostatic and hydrophobic interactions and the packing parameter of the peptide molecule leads to a rich pattern of self-assembling behavior ranging from nucleated and pH-dependent self-assembly into tubular and spherical micelles up to pH-independent isodesmic polymerization into thin ribbons.

Another interesting development came from one of the short antimicrobial peptides (AMP), indolicidin. We found that indolicidin, as well as some of its derivatives can assemble on the DNA surface forming smooth and continuous coverage. In nature this phenomenon might be responsible for efficient knocking down the DNA replication and transcription processes in the invading cells while from nanotechnological prospective, it can help designing functional DNA electronics.

1. L. Gurevich, T.W. Poulsen, O. Z. Andersen, N. L. Kildeby and P. Fojan, “pH-dependent self-assembly of the short surfactant-like peptide KA6”, J.Nanoscience and Nanotechnology 10, 7946-7950 (2010)

Embryogenesis and regeneration are among the most striking and beautiful phenomena in nature. For a physicist, this brings together many major themes—pattern formation, information processing, the mechanics of complex fluid-like materials—that are essential for our understanding of life more broadly. In my talk I will give two examples on the important role of tissue mechanics for these phenomena.

First, I will discuss how a macroscopic tissue property, specifically tissue surface tension, is connected to the properties of the constituent cells, such as cortical tension and adhesion. I will directly compare theoretical predictions with experimental data and discuss the relationship between tissue surface tension and tissue dynamics using primarily zebrafish embryonic tissues as the experimental system.

In the second part of my talk, I'll switch gears over to regeneration and asexual reproduction in planarians. Asexual reproduction and the ability to regenerate are intrinsically connected, but despite this important link, little is known about the physical process of reproduction due to experimental difficulties. We have overcome some of these difficulties and I will present preliminary data on the physical mechanisms of dividing planarians. Finally, I will discuss our current understanding of the asexual population dynamics based on a large-scale experiment in which we have been tracking >10,000 reproductive events over the course of >2.5 years and up to 51 generations using a custom-built Scan-Add-Print database system.

The heart is an electro-mechanical system in which, under normal conditions, electrical waves propagate in a coordinated manner to initiate an efficient contraction. In pathologic states, propagation can destabilize and exhibit period-doubling bifurcations that can result in both quasiperiodic and spatiotemporally chaotic oscillations. In turn, these oscillations can lead to single or multiple rapidly rotating spiral or scroll waves that generate complex spatiotemporal patterns of activation that inhibit contraction and can be lethal if untreated. Despite much study, little is known about the actual mechanisms that initiate, perpetuate, and terminate reentrant waves in cardiac tissue.

In this talk, I will discuss experimental and theoretical approaches to understanding the dynamics of cardiac arrhythmias. Then I will show how state-of-the-art voltage-sensitive fluorescent dyes can be used to image the electrical waves present in cardiac tissue, leading to new insights about their underlying dynamics. I will establish a relationship between the response of cardiac tissue to an electric field and the spatial distribution of heterogeneities in the scale-free coronary vascular structure. I will discuss how in response to a pulsed electric field E, these heterogeneities serve as nucleation sites for the generation of intramural electrical waves with a source density ρ(E) and a characteristic time τ for tissue excitation that obeys a power law. These intramural wave sources permit targeting of electrical turbulence near the cores of the vortices of electrical activity that drive complex fibrillatory dynamics. Therefore, rapid synchronization of cardiac tissue and termination of fibrillation can be achieved with a series of low-energy pulses. I will finish with results showing the efficacy and clinical application of this novel mechanism in vitro and in vivo.

Living organisms are capable to sense and adapt to a wide range of environmental changes, which is essential for their survival in nature. Although numerous molecular circuits have been evolved to accomplish this sensory adaptation function in different organisms, these circuits share intrinsically the same logical construct. Using Escherichia coli cells as model system, we combined theoretical techniques with experiments to formulate biological sensory adaptation. We demonstrated that E. coli cells accurately “remember” the chemical environment by differentiating and encoding external signals into molecular modifications on specific sensory receptors. We also discovered that E. coli cells adjust their chemical sensitivity via tuning the sensory machinery assembly according to the environment. Moreover, by evaluating the energetic cost associated with sensory adaptation, we were able to derive the exponential tradeoff relation between the benefit (adaptation accuracy & adaptation speed) and the cost (energy dissipation). We believe that this set of approaches sketch a general framework for studying various biological regulatory circuits and the obtained benefit-to-cost relations could shed light on the design principles and the evolution of regulatory circuits.

Clathrin-coated vesicles are the most prominent carriers of membrane traffic from cell surface to endosomes (endocytosis), a pathway by which hormones, transferrin, immunoglobulins, LDL, viruses, and their receptors enter cells. They are also important for traffic between endosomes and the trans-Golgi network. In this presentation, I will discuss (i) technological and analytical advances that I developed to directly visualize clathrin-mediated membrane traffic in three dimensions and in living cells; (ii) data obtained using these advances that defined a role for actin filament polymerization in counteracting membrane tension during clathrin-coated vesicle budding at the apical surface of polarized epithelial cells; and (iii) how these advances can be used to study a wide variety of biological processes that occur in living cells and tissues.

Cadherins constitute a large family of Ca2+-dependent adhesion molecules in the Inter-cellular junctions that play a pivotal role in the assembly of cells into specific three-dimensional tissues.  Although the molecular mechanisms underlying cadherin-mediated cell adhesion are still not fully understood, it seems likely that both cis dimers that are formed by binding of extracellular domains of two cadherins on the same cell surface, and trans-dimers formed between cadherins on opposing cell surfaces, are critical to trigger the junction formation.

Here we present a new multiscale computational strategy to model the process of junction formation based on the knowledge of cadherin molecular structures and its 3D binding affinities. The cell interfacial region is defined by a simplified system where each of two interacting membrane surfaces is represented as a two-dimensional lattice with each cadherin molecule treated as a randomly diffusing unit. The binding energy for a pair of interacting cadherins in this two-dimensional discrete system is obtained from 3D binding affinities through a renormalization process derived from statistical thermodynamics. The properties of individual cadherins used in the lattice model are based on molecular level simulations. Our results show that within the range of experimentally-measured binding affinities, cadherins condense into junctions driven by the coupling of cis and trans interactions. The key factor appears to be a loss of molecular flexibility during trans dimerization that increases the magnitude of lateral cis interactions.

We have also developed stochastic dynamics to study the adhesion of multiple cells. Each cell in the system is described as a mechanical entity and adhesive properties between two cells are derived from the lattice model. The cellular simulations are used to study the specific problems of tissue morphogenesis and tumor metastasis. The consequent question and upcoming challenge is to understand the functional roles of cell adhesion in intracellular signal transduction.