Eric Sembrat's Test Bonanza

Viruses are ubiquitous in the environment, with densities often ten-fold higher than that of their microbial hosts. Viruses can function like microbial predators, regulating the amount and diversity of hosts present in a community. However, efforts to understand the dynamics of complex virus-microbe communities are still in their infancy. Here, I present examples of the interplay between evolutionary and ecological dynamics arising due to virus-microbe interactions. In the first example, I show how rapid changes in the frequency of bacterial strains that differ in their susceptibility to infection can imprint a novel ecological signature - so-called cryptic dynamics.  Then, in a second example, I show how rapid changes in the frequencies of hosts and viruses that differ in their cross-infectivity can reverse the canonical predictions of Lotka-Volterra (and similar) dynamics, leading to dynamics in which it appears that hosts eat viruses. In both examples, I synthesize insights from theory and models with results from laboratory experiments.  However, applying such insights to the environment requires addressing an ongoing challenge: how to characterize who infects whom when many ubiquitous microbes and associated viruses are not yet culturable.  I close with a discussion of recent innovations that can help shed light on the interactions of viruses and microbes using culture-independent techniques.

Gelation and vitrification are the most common mechanisms for a liquid-to-solid transition in amorphous materials. For both, a heterogeneous, percolating internal structure grows and reduces the mobility of internal constituents. Macroscopic rheological properties are strongly affected but appear to be very similar for gelation and vitrification. Here we propose a novel rheological test to distinguish between gelation and vitrification. The test is based on Boltzmann’s equation of linear viscoelasticity and focuses on the distribution of relaxation modes in samples near the liquid-to-solid transition. Short relaxation modes dominate gelation since the majority of the internal constituents is still unconnected or barely connected while the percolating structure is barely there and too weak to significantly support a macroscopic stress. The relaxation time spectrum of gelation is a decaying function, large for fast modes and small for the slower modes. The opposite is found for vitrification, which originates from large, cooperatively-moving regions which finally connect into a percolating structure at the glass transition. As a consequence, the long relaxation modes dominate the approach of the glass transition. Surprisingly, the relaxation time spectrum, H(tau)~tau^n, adopts the same format for both phenomena near the transition, except that the relaxation exponent, n, is negative for gelation and positive for vitrification (see Macromolecules 46:2425-32, 2013). Mathematically, one is the inverse of the other. The spectrum is cut off by the diverging longest relaxation time. Examples will be shown for these phenomena.

For many viruses, the spontaneous assembly of a capsid shell around the nucleic acid (NA) genome is an essential step in the viral life cycle. Understanding how this process depends on the charge, structure, and sequence of the nucleic acid could promote biomedical efforts to block viral propagation and guide the reengi-neering of capsids for gene therapy applications.

This talk will describe coarse-grained models of capsid proteins and NAs which enable dynamical simulations of the assembly process. With these models, we investigate how assembly efficiency and mechanisms depend on biophysical parameters, such as RNA length and structure, solution conditions, and capsid protein charge. We find that capsids spontaneously ‘overcharge’; that is, the NA length which is kinetically and thermodynamically optimal possesses a negative charge greater than the positive charge of the capsid. When applied to specific virus capsids, the calculated optimal NA lengths closely correspond to the natural viral genome lengths. These results suggest that the features included in this model (i.e. electrostatics, excluded volume, and NA tertiary structure) play key roles in determining assembly thermodynamics and consequently exert selective pressure on viral evolution. We then show that assembly can proceed through two qualitatively different classes of pathways, which can be tuned by controlling solution conditions or changing the capsid protein charge. Time permitting, we will also dis-cuss how viruses assemble on a substrate with a different topology – an enveloping lipid membrane.

We will see how a result in von Neumann algebras (a theory developed by von Neumann to give the mathematical framework for quantum physics) gave rise, rather serendipitously, to an elementary but very useful invariant in the theory of ordinary knots in three dimensional space. Then we'll look at some subsequent developments of the theory, and talk about a thorny problem which remains open.

The nature of dark matter remains one of the most fascinating yet unsolved problems in modern science. A large compelling body of evidence supports the theory that almost 27% of the mass-energy density of the universe is made of cold dark matter. The XENON Project aims at the direct detection of dark matter in the form of Weakly Interacting Massive Particles (WIMPs) via nuclear recoils in a LXe Dual-phase Time Projection Chamber. The third phase of the project XENON1T, a ton scale LXe dark matter detector is currently under construction at the Laboratori Nazionali del Gran Sasso in Italy and aims to achieve unprecedented sensitivities of the cross section of the WIMP-nucleon interaction. Such sensitivity will probe new sectors predicted by Supersymmetry with a high discovery potential. The design of XENON1T and R&D projects such as the XENON1T Demonstrator, as well as the future prospect of the field will be discussed in detail.

Metamaterials are commonly viewed as artificially-structured media capable of realizing arbitrary effective parameters, in which metals and dielectrics are delicately combined to facilitate the index contrast and plasmonic response required for a particular purpose. We aim to drive beyond this limited vision and explore the use of optical metamaterials as a generalizable platform for optoelectronic information technology: Metals will provide tailored plasmonic behavior as before, but will serve double duty by providing electrical functions including voltage input, carrier injection/extraction, and heat sinking, and dielectrics will consist of functional elements such as Kerr materials, electrooptic polymers, and p-n junctions. In this talk I will discuss our preliminary results on several topics in this category, including the electrically induced harmonic generation and optical rectification of light in a perfect metamaterial absorber, the nonlinear spectroscopy and imaging from a chiral metamaterial, and the backward phase-matching in an optical metamaterial where the fundamental and frequency-doubled waves possess opposite indices of refraction.

Biography

Wenshan Cai received his B.S. and M.S. degrees in Electronic Engineering from Tsinghua University, Beijing, China in 2000 and 2002, respectively, and his Ph.D. in Electrical and Computer Engineering from Purdue University, West Lafayette, Indiana, in 2008. He joined the faculty of the Georgia Institute of Technology in January 2012 as an Associate Professor in Electrical and Computer Engineering, with a joint appointment in Materials Science and Engineering. Prior to this, he was a postdoctoral fellow in the Geballe Laboratory for Advanced Materials at Stanford University. His scientific research is in the area of nanophotonic materials and devices, in which he has made a major impact on the evolving field of plasmonics and metamaterials. Dr. Cai has published ~40 papers in peer-reviewed journals, and the total citations of his recent papers have reached ~4,000 within the past few years. He is a reviewer or editorial board member of over 20 scientific journals. In addition, Dr. Cai is the lead author of the book Optical Metamaterials: Fundamentals and Applications (Springer, 2010), a text or a major reference used at many universities around the world, for which he won the 2014 Joseph W. Goodman Book Writing Award from OSA and SPIE.

Understanding the thermal conductivity of bulk crystalline solids is essentially a solved problem and it is well described by the phonon gas model (PGM). The PGM treats individual phonons (e.g., quanta of lattice vibration energy) as gas molecules that carry energy at a certain speed for some averaged distance, termed the mean free path (MFP). This model does an excellent job at explaining the thermal conductivity of crystalline solids and due to advancements in modeling over the last decade, one can now calculate phonon energies, velocities and MFPs fully from first principles. This now allows one to predict the thermal conductivity of virtually any crystalline material with excellent agreement with experiments at virtually all temperatures of technological interest. By employing Monte Carlo methods or the Boltzmann Transport Equation, one can also accurately predict the thermal conductivity of micro and nanostructures due to quantum or classical size effects. As a result of the great success of this model, it has prevailed as the primary physical picture used to understand and interpret all phonon transport related phenomena. However, there are a number of technologically important material classes and molecules that are not well described by the PGM. This talk will discuss several instances where the PGM is inconsistent with the atomic level behaviors observed in molecular dynamics simulations. The talk will also cover several new theoretical modeling developments that offer a different perspective on phonon-phonon interactions and allows for direct calculation of phonon contributions to thermal conductivity and interface conductance.

Fivefold symmetry is incompatible with the translational order in all 17 plane groups and is therefore of fundamental interest for two dimensional crystallization processes. A model study on single crystal surfaces, e.g. Cu(111), has been carried out to better understand the fundamental principles of intermolecular interactions between fivefold symmetric corannulene and its derivatives in two-dimensional clusters and lattices, including those consisting of fivefold bowl-shaped (buckybowl) molecules. Rational molecular design and state of the art surface science methods, e.g. Scanning Tunneling Microscopy, Low Energy Electron Diffraction, X-Ray Photoelectron Spectroscopy, Ultraviolet Photoelectron Spectroscopy, Temperature Programmed Desorption, and Reflection Adsorption Infrared Spectroscopy were applied. Several reversible surface phases were identified, including stripes, zig-zag, rosette and rotator phases. The packings of fivefold symmetric molecules was found to exhibit the same patterns upon adsorption as identified in the closest packings of hard pentagons and five-pointed stars.

 TBD

This is a Webinar

Geographic tongue (GT) is a medical condition affecting approximately 2% of the population, whereby the papillae covering the upper part of the tongue are lost due to a slowly expanding inflammation. The resultant dynamical appearance of the tongue has striking similarities with well known out-of-equilibrium phenomena observed in excitable media, such as forest fires, cardiac dynamics and chemically driven reaction-diffusion systems. We explore the dynamics associated with GT from a dynamical systems perspective, utilizing cellular automata simulations. Our results shed light on the evolution of the inflammation and suggest a practical way to classify the severity of the condition, based on the characteristic patterns observed in GT patients.