Eric Sembrat's Test Bonanza

Biological flows are vital for the conservation of life and indispensable commodity of living organisms. Morphological structures of living organisms and biological flow phenomena in nature have been evolved through a long history. The basic biophysics of several biofluid flow phenomena and the hidden secrets of nature such as blood flow in chicken embryos, blood sucking of mosquitoes, and sap flows in plants have been investigated experimentally by using advanced flow visualization techniques, such as X-ray PIV (particle image veocimetry), holographic PTV (particle tracking veocimetry), time-resolved micro-PIV, etc. Biological samples include insects (blood-sucking mosquitoes, liquid-feeding butterflies), fishes (zebra fish, planktons), animals (blood flows in chicken embryos or rats) and plants (sap flow in xylem vessels of rice or Arabidopsis). Gold nanoparticles developed as tracer particles transmit membranes of organisms without destroying the surrounding tissues. Detailed understanding on these biofluid flow phenomena are helpful to develop creative nature-inspired technologies for practical applications in biomedical science, microfluidics and renewable energy, etc. For example, a micropump consisting of serial-connected two-pump chambers and three diffuser elements was developed based on the revealed blood-sucking mechanism of a female mosquito. When the two pump chambers are operated in a well coordinated manner with a certain phase shift, the bio-inspired pump exhibits a good pumping performance, as appeared in the blood-sucking mosquitoes. The nature-inspired micropump would be utilized in various bio-chips as a liquid-phase sample supplying system. In addition, another bio-inspired micropump that can produce a large pressure gradient was developed by bio-inspiring a liquid-feeding butterfly through a long proboscis.

We present and discuss, in the context of the drug discovery pipeline, recent computational developments that enable the virtual screening of massive databases of chemicals against a large number of protein structures. We present "ensemble docking" applications of virtual screening in multiple protein structures that identify new protein ligands and explore biochemical pathways. We also discuss fundamental and challenging aspects of these very large virtual screening approaches.

Given that many diverse astrophysical systems are susceptible to relativistic hydromagnetic turbulence, it is surprising how little is presently known about how they manifest chaotic flow. Of primary interest is to establish a basic understanding of how the small-scale turbulent dynamo, whereby kinetic energy of the flow is converted into magnetic energy, operates in these systems. This process is thought to be instrumental in both stellar and galactic magnetogenesis, and may also be at work in relativistic astrophysical jets and their central engines.

Of equal importance is to understand how magnetic energy decays in the absence of continued stirring by external forces. For example, if magnetic fluctuations are driven locally (in a pulsar magnetosphere for instance) what fraction of the Poynting flux survives to infinity, and how much is trapped by collisions with ambient Alfven waves? Similarly, can turbulent magnetic fields produced by plasma instabilities upstream of a relativistic blast-wave survive long enough into the downstream to be consistent with synchrotron models for GRB afterglow emission?

I will present results from large-scale numerical simulations which are providing answers to some of these questions, and discuss ongoing efforts to answer others. If there is time, I will also explain how simulations of relativistic turbulence can be used to synthesize images of polarized synchrotron emission from giant radio lobes, thereby assessing the possibility that they are in a state of turbulence.

We utilize electroconvecting liquid crystal samples as a test bed from non-equilibrium driven systems. I will discuss results from the application of a novel mathematical analysis that incorporates time-delay embedding and diffusion maps to elucidate the underlying geometry in this system. This analysis permits the discrimination of different dynamical states from empirical data and is used to demonstrate multistability in this system. In addition we investigate the effects of an abrupt transition to defect turbulence on the structure and energy flow in this system.

Intrinsically disordered proteins (IDPs), which form over a third of human proteins, challenge the structure-function paradigm because they function without ever folding into a unique three-dimensional structure. A particularly fascinating example of IDP function is the gating mechanism of the nuclear pore complex (NPC). The NPC is a large macromolecular structure that gates nanoscale pores in the nuclear envelope and controls all nucleo-cytoplasmic traffic such as the import of proteins from the cytoplasm and the export of RNA from the nucleus. The NPC forms a highly selective barrier composed of a large number of IDPs that fill the pore and potentially interact with each other and the cargo.

However, despite numerous studies, the actual structure of the complex within the nuclear pore and its mechanism of operation are poorly understood primarily because of the disordered nature of these proteins. I will present our “bottom-up” approach to understanding the higher-order architecture formed by these proteins using coarse-grained simulations and polymer brush theory. Our results indicate that different regions or “blocks” of an individual NPC protein can have distinctly different forms of disorder and properties and our bioinformatic analysis indicates that this appears to be a conserved feature across all of eukarya. Furthermore, this block structure at the individual protein level is critical to the formation of a unique higher-order polymer brush architecture. Our results indicate that there exist transitions between distinct brush morphologies, which can be triggered by the presence of cargo with specific surface properties which points to a novel form of gated transport in operation within the nuclear pore complex. Insights into this system can potentially be applied to the design of bio-mimetic filters that can achieve highly regulated transport across biological or in vitro membranes.

Bio:

Ajay Gopinathan is currently an Associate Professor and Chair of the Physics Graduate Group at UC Merced. He received his Ph.D in Physics in 2003, from the University of Chicago, working under the supervision of Tom Witten on various problems in soft condensed matter physics including crumpling, colloids and polymers. Following this, he was a joint postdoctoral fellow at UCLA and UCSB with Andrea Liu and Phil Pincus working on biopolymers with a focus on actin dynamics. His current research involves using theoretical and computational methods to understand biological transport at the molecular, cellular and multicellular scales. Examples include understanding cooperative behavior in molecular motor-driven intracellular transport; the role of membrane pore geometry and environment in gated transport through nuclear pores; actin based cellular motility; bacterial cell division and collective motility; optimal foraging in groups and swarming in the presence of behavioral heterogeneity and in disordered environments. Honors include the James S. McDonnell Foundation 21^st Century Science Initiative Award, the George E. Brown, Jr. award and the UC Merced Chancellor's award.

Note: This is a WEBINAR

The theory of Lagrangian Coherent Structures (LCSs) has advanced significantly over recent years, and now covers both hyperbolic and elliptic material surfaces in unsteady flow. Parabolic (i.e., jet-type) LCSs have, however, remained outside the reach of the theory, despite their significance in oceanic and atmospheric transport.

Here I discuss a new variational approach to general shearless transport barriers in two-dimensional unsteady flows, which covers both hyperbolic and parabolic LCSs. I also describe a computational implementation of this new theory, and show applications to model flows and geophysical data sets.

After a general introduction to the Lagrangian of QCD (Quantum Chromodynamics) and its symmetries, I will present the QCD Sum Rules approach for studying hadronic properties. This will be generalized to a finite temperature scenario, where we expect that phase transitions like deconfinement and/or chiral symmetry restorations should occur. In particular we will present our results for the rho meson spectrum, reconstructed from the dimuon spectrum in heavy ion collisions, and for charmonium resonances which could survive beyond the critical temperature. I will try to avoid technical details, emphasizing the physical and general aspects of our approach.

The syntax of theoretical physics and modern finance is deceptively similar, but the semantics is very different. I present a short introduction to the principles of modern finance, and compare and contrast the field to physics.

One of the deepest and most controversial questions of our time is that of the origin of life. In this lecture a hypothesis is presented, according to which the temperature gradients existing deep in the earth (which leads to plate tectonics and the formation of undersea thermal vents), also led to the origin and evolution of life around those vents. Movies and data will be shown of experiments in which various stages of this scenario are presented: how thermal gradients led to plate tectonics, to DNA possible amplification in the thermal vents, and to huge increase of molecular concentration in the early soup. In this scenario the Carnot cycle, at the origin of the first industrial revolution, might have also be relevant at the origin of life.