Eric Sembrat's Test Bonanza

Abstract

Optical tweezers allow us to probe the interactions of proteins with single DNA molecules and apply very small forces. Measurement of force-dependent DNA conformations allows us to quantify interactions that govern cellular function. Here we investigate the DNA interactions of human APOBEC3G, an innate antiviral immunity protein that functions as a cytidine deaminase.

Our results show that the process of interconversion between monomeric and dimeric states regulates APOBEC3G’s deamination-dependent and deamination-independent inhibition of HIV-1 replication. I will then discuss the role of eukaryotic HMGB proteins in determining nucleosome accessibility, an important mechanism for regulating protein expression.

We construct an array of nucleosomes on a single DNA molecule, measuring nucleosome stability in the presence of HMGB proteins. We find significant unwrapping of nucleosomes due to HMBG-DNA binding, the extent of which differs between different types of HMGB proteins. The extent of observed destabilization correlates with the presence of nucleosome-free regions in cells, revealing distinct functions for regulation of nucleosome accessibility by different HMGB proteins.

Abstract

In this talk I will discuss the scaling laws governing the stochastic growth dynamics of individual cells and populations, in and out of steady-steady. Time permitting, I will make connections with energetic costs of cellular information processing.

Abstract

Graphene based electronic and spintronic devices require understanding the growth of metals on graphene. Several metals (Gd, Dy, Eu, Fe,Pb) deposited on epitaxial graphene were studied with STM, SPA-LEED and DFT. For practically all metals the growth mode is 3-d[1,2].This is a result of the low ratio of the metal adsorption to metal cohesive energy and repulsive interactions between unscreened charges at the metal-graphene interface that favor islands of small “footprint". It is an open challenge to find ways to modify the growth to layer–by–layer for high quality metal contacts and graphene applications as a spin filter. By growing Dy at low temperatures or high flux rates it is found that upward adatom transfer is kinetically suppressed and layer-by-layer is possible[3]. These results are also relevant for metal growth on other 2-d van der Vaals materials that also have weak bonding with metals and favor 3-d metal growth.

The graphene-metal interaction is also important for metal intercalation which provides a novel way to tune graphene’s properties, besides doping. However many issues related to the intercalation process itself are poorly understood, i.e., the temperature and entry points where atoms move below graphene, different intercalation phases, their coverage, etc. SPA-LEED and STM were used to study these questions for Dy intercalation. Spot profiles of several spots (specular, 6sq(3), graphene) are studied as function of temperature and electron energy to deduce the kinetics of intercalation and the layer where the intercalated atoms reside. 

Dy nucleation experiments were performed on graphene partially intercalated with Dy. The results show that nucleation is preferred on the intercalated than on the pristine areas. Difference in doping between the two areas generates an electric field that transforms random walk to directional diffusion and accounts for the guided nucleation[4]. This can be a general method to control patterning of metallic films on graphene. 

References

1.M. Hupalo et al Advanc. Mater. 23 2082 (2011) 2.X. Liu, et al. Progr. Surf. Sci. 90 397 (2015) 3. D. Mc Dougall et al Carbon 108 283 (2016)) 4. X. Liu et al. Nano Research 9(5): 1434 (2016)

Abstract: 

After a brief overview of quantum gravity as a whole, Dr. Ashtekar will explain the basics of Loop Quantum Gravity and its applications to some long standing questions: the nature of the very early universe and the ultimate fate of black holes in the process of their quantum evaporation. 

Please join us for a special CRA Seminar, where we will have our very own Jim Sowell on the hot seat. For one hour, the students, postdocs, faculty, and friends can ask Prof. Sowell about his research and life. Refreshments will be provided and students are encouraged to participation questions! 

Abstract

I will talk about ongoing efforts in my lab at the University of Utah in one, two and three dimensional mesoscopic material systems.

In 1D, we study longer ultraclean carbon nanotubes than studied previously and observe new conductance oscillations versus gate voltage on top of the commonly observed Fabry-Perot conductance oscillations. These new oscillations are slower than the Fabry-Perot oscillations and up to an order of magnitude more robust in temperature, surviving up to 100K in our devices. Further using structurally characterized nanotubes, we find that the new oscillations are a fingerprint of the structure and allow identification of carbon nanotube chirality from a transport measurement for the first time.

In 2D, we study thermal transport in two-dimensional metal-organic graphene analogues and find promising thermoelectric figures of merit for potential application as thermoelectrics.

In 3D topological insulators (TIs), we create van der Waals heterostructures with boron nitride and top/bottom graphite gates for top/bottom surfaces of 3D TIs. Using these structures, we observe individually tunable half-integer quantum Hall effects in TI surfaces at lower magnetic fields than previous groups.

I will discuss implications of these measurements and other measurements we are performing on these systems in my lab.

Abstract

Dynamic networks are found in a majority of natural materials, but also in engineering materials, such as entangled polymers and physically cross-linked gels. Owing to their transient bond dynamics, these networks display a rich class of behaviors, from elasticity, rheology, self-healing or growth. Although classical theories in rheology and mechanics have enabled us to characterize these materials, there is still a gap in our understanding on how individuals (i.e., the mechanics of each building blocks and its connection with others) affect the emerging response of the network.

In this presentation, I will discuss an alternative way to think about these networks from a statistical point of view. More specifically, a network will be seen as a collection of individual building blocks connected by elastic chains that can associate and dissociate over time. From the knowledge of these individual chains (elasticity, transient attachment, and detachment events), we will construct a statistical description of the population and derive an evolution equation of their distribution based on applied deformation and their local interactions. Upon appropriate averaging operations, I will then show that these distributions can be used to determine important macroscopic measures such as stress, energy storage and dissipation in the network.

Based on this approach, I will then illustrate how different behaviors at the scale of individual chains lead to well-known macroscopic response such as Newtonian and non-Newtonian behaviors, shear thinning, shear thickening, and viscoelasticity. The case of active networks will finally be discussed in the context of plant growth and the force-sensitivity of non-muscle cells. 

Bio:

Dr. Vernerey is an associate professor in the Department of Mechanical Engineering at the University of Colorado, Boulder. He received his Ph.D. from Northwestern University in 2006 in the field of theoretical and applied mechanics. His interests are in understanding the emerging response of soft matter based on the mechanical interactions between its building blocks, with particular emphasis on the deformation, flow, and growth mechanisms in soft shells, soft particles, and cellular gels. Dr. Vernerey is the author of about 60 scientific publications in peer-reviewed journals and book chapters and is the recipient of the NSF career award in 2014 and the Presidential Early Career Award for Scientists and Engineers (PECASE) in 2017. 

Public nights at the Georgia Tech Observatory have resumed for the 2017-2018 season. During the fall and spring semesters, the observatory will be open one Thursday each month (except December) for people to observe various celestial bodies.

The viewing on Sept. 28 includes a 30-minute talk with Kate Napier at 8:30 pm. Topic: Asteroids: Past, Present, and Future. 

Public nights are contingent on clear weather.

Potential closures and driving directions are on the official website.

Go here for the full schedule.

ALL ARE WELCOME.

 Abstract

There are now a number of experimental platforms for fabricating self-folding origami structures. In these platforms, individual folds on an initially flat sheet are patterned so that the structure folds autonomously into a desired three dimensional shape.

The dream is to develop a system in which three-dimensional structures can be fabricated from a rapid roll-to-roll process. Yet, in our experiments with self-folding origami, structures sometimes misfold, especially as they become more complicated.

In this talk, I will discuss a model to understand why self-folding origami misfolds by counting the number of folding pathways of “random” origami. Finally, I will discuss methods that may circumvent the problem and suppress misfolds.

 Abstract

Simple rules can create complex patterns and dynamics. This connection is routinely used by living systems to create complex rhythms, spatio-temporal structures, and high-performance materials with surprising design features at meso- and macroscopic length scales that seem to defy their molecular origins.

In my lecture, I will present several examples that illustrate this point and demonstrate that many phenomena that appear to be unique to life processes actually occur in non-biological, often simple chemical systems.

Specifically, I will discuss nonlinear wave patterns in reaction-diffusion media and examples of life-like structures in chemical reactions that form polycrystalline or amorphous solids. The unexpectedness of some of these universalities has profound consequences in a wide range of scientific disciplines ranging from the misidentification of early microfossils to deadly cardiac arrhythmias.