Eric Sembrat's Test Bonanza

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.

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.

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.

Effects of dipolar and spin-exchange interactions are entangled in spin-1 Bose-Einstein condensates, due to their coexistence. We propose to independently manipulate the magnetic dipolar and the spin-exchange interactions by applying generalized WAHUHA sequences of rf pulses and by applying periodic dynamical decoupling sequences of optical Feshbach resonance pulses, respectively. While suppressing one interaction, we can make the other interaction dominate the spin dynamics in the condensates. Furthermore, by suppressing both interactions, this method can be harnessed to realize spinor-condensate-based magnetometers with a higher sensitivity.

Reference: [1] W. Zhang, B. Sun, M. S. Chapman, and L. You, Phys. Rev. A 81, 033602 (2010). [2] Bo-Yuan Ning, J. Zhuang, J. Q. You, W. Zhang£¬ Phys. Rev. A 84, 013606 (2011). [3] Bo-Yuan Ning, S. Yi, J. Zhuang, J. Q. You, and W. Zhang, Phys. Rev. A 85, 053646 (2012).

Bio:

Dr. Wenxian Zhang received his Bachelor and Master of Science degree in Fudan University in 1997 and 2000, respectively. He obtained his Ph. D degree in Georgia Institute of Technology in 2005. After that he did post-doctoral research in Ames Lab and Iowa State University in 2005-2007 and in Department of Physics and Astronomy of Dartmouth College in 2007-2008.  He worked in the department of Optical Science and Technology of Fudan University as an associate researcher in 2008-2011. He visited Department of Physics of the Chinese University of Hong Kong in 2009 and RIKEN, Japan in 2010/2011 for several months. He moved to School of Physics and Technology of Wuhan University as a professor in 2012.

 Wenxian's research interests include quantum optics, quantum computation and quantum information processing, light and matter interaction, and so on. He has published over 40 peer-reviewed journal papers, including 1 Nat. Phys. and 3 Phys. Rev. Lett., with a total 1000+ citations and H-index of 16. He has been funded by MOST, NSFC, MOE, etc..

Previous studies of women in physics mostly focused on the lack of women in the field. The Global Survey of Physics goes beyond the obvious shortage of women and shows that there are much deeper issues. For the first time, a multinational study was conducted with 15000 respondents from 130 countries, showing that problems for women in physics transcend national borders. Across all countries, women have fewer resources and opportunities and are more affected by cultural expectations concerning child care. We show that limited resources and opportunities hurt career progress, and because women have fewer opportunities and resources, their careers progress more slowly. We also show the disproportionate effects of children on women physicists' careers. Cultural expectations about home and family are difficult to change. However, for women to have successful outcomes and advance in physics, they must have equal access to resources and opportunities.

An article based on these findings can be found at: http://www.physicstoday.org/resource/1/phtoad/v65/i2/p47_s1


Bio:

Rachel Ivie is Associate Director of the Statistical Research Center (SRC) at the American Institute of Physics. She received her PhD in sociology from the University of North Carolina at Chapel Hill, where she specialized in research methods, statistics, gender, and the life course. Over the past sixteen years at SRC, she has studied careers of physicists, particularly the careers of women in physics. She authored the first ever thematic report on women in physics (Ivie and Stowe, 2000), bringing together data from AIP’s surveys with data from outside sources. She has designed and carried out numerous studies: from the impact of tenure and promotion practices on male and female faculty to a longitudinal study of astronomy graduate students.

In this talk we will bring parallels of science and cooking to the fore.  Using a wide variety of kitchen cooking techniques whose inner workings on the molecular level can be explained through chemistry and physics we hope to make the science and the food more easily understandable.  We will cover topics ranging from surface tension, diffusion processes, gelation, crystallization and viscoelasticity. The overall goal of the talk is to make you a better cook by better understanding your ingredients and how to manipulate them and to learn science through the prism of cooking.

Bio:

William (Bill) Yosses held the prestigious title of the White House Executive Pastry Chef from 2006 to 2014. Other executive pastry chef experience includes, The Dressing Room in Westport Connecticutt, Tavern on the Green and Bouley Restaurant in New York City. Yosses spent his early career in France in such highly recognized landmarks as Fauchon, La Maison du Chocolat, and LeNotre.

As Pastry Chef of the White House, he was closely involved with Mrs Obama’s Let’s Move initiative, with the goal of reducing childhood health problems related to diet, and conducted bi-weekly tours of the White House vegetable garden for school groups. In a related project, he has given lectures on Science and Cooking in the School of Engineering and Applied Sciences at Harvard University, and was instrumental in building a program in the Physics Department of Harvard University in conjunction with Chop Chop Magazine called Camp Chop Chop, in which healthy foods and innovative exercise are used to introduce scientific concepts to 4th and 5th graders.

Bill earned his A.A.S. degree at New York City College of Technology in Hotel Management, a Master of Arts at Rutgers University in French Language and a Bachelor of Arts at the University of Toledo in French Language. He has published two books, Desserts for Dummies 1997, and The Perfect Finish, Special Desserts for Every Occasion, 2010. He is the recipient of the James Beard Who’s Who Award and Food Arts Magazine Silver Spoon Award.

In Kondo insulator samarium hexaboride SmB6, strong correlation and band hybridization lead to a diverging resistance at low temperature. The resistance divergence ends at about 3 Kelvin, a behavior recently demonstrated to arise from the surface conductance. However, questions remain whether and where a topological surface state exists. Quantum oscillations have not been observed to map the Fermi surface. We solve the problem by resolving the Landau Level quantization and Fermi surface topology using torque magnetometry. The observed angular dependence of the Fermi surface cross section suggests two-dimensional surface states on the (101) and (100) plane. Furthermore, similar to the quantum Hall states for graphene, the tracking of the Landau Levels in the infinite magnetic field limit points to -1/2, the Berry phase contribution from the 2D Dirac electronic state.

Black holes are perhaps the most mysterious and enigmatic objects that one can imagine. Their gravitational fields are so strong that light is unable to escape their grasp, and even fundamental quantities such as space and time are severely disrupted by their presence.  Yet, despite their fantastical nature, astronomers have compiled significant evidence that black holes are actually quite common and are lying at the centers of almost all massive galaxies. Therefore, black holes are no longer the theoretical subjects of mathematical physicists; they are now known to be crucial to our understanding of how galaxies and other structures in the Universe formed and evolved. This talk will provide an overview of our understanding of black holes in the observable universe, and outline how astrophysicists are using them to probe some of the deepest questions in the cosmos.