Eric Sembrat's Test Bonanza

Computational fluid dynamic simulations are providing new insights into the connections between patient-specific hemodynamic flows and the initiation, progression and treatment of cerebral aneurysms. Recent studies linking aneurysm rupture to the formation of vortices have motivated the need for a more fundamental understanding of swirling blood flow patterns and their evolution during the cardiac cycle. In this talk, I describe how dynamical systems theory is being used to advance our knowledge of vortex dynamics within cerebral aneurysms.

Well-controlled experiments in pipe flow began at least as early as those by Reynolds himself (1883).  Forming a model for transition to turbulence, however, has taken a long time to develop.  The first nonlinear solutions to the equations governing fluid flow in a pipe were discovered only 10 years ago (Faisst and Eckhardt 2003), but since this time our understanding of the underlying nonlinear dynamics has developed thick and fast.  I begin by reviewing some of the progress that followed the discovery of travelling wave solutions.  For the future, it will be necessary to isolate periodic orbits, which will require some development in computational methodology.

Holographic duality, which relates ordinary quantum systems without gravity to systems with gravity, has recently provided an exciting new perspective on quantum many-body physics.  However, the results obtained thus far are still relatively far from experimental reality.  I will show how a version of holography applies even to very conventional quantum systems that are routinely encountered in the laboratory.  I will also discuss progress starting from the gravity side in understanding certain highly entangled compressible states which may be relevant for experiments. 

Entanglement has recently emerged as an important conceptual tool in quantum many-body physics.  I will explain why we care about entanglement in quantum matter and why we are interested in the physics of highly ntangled quantum states.  I will also show how entanglement has led us to new phases of matter, new ways to characterize phases and phase transitions, novel numerical techniques, and useful conceptual advances. I will conclude with a discussion of the prospects for measuring entanglement in many-body systems.

Quantum Simulation with cold atoms is a very ambitious program in AMO research that is being pursued in many laboratories worldwide. The goal is to use cold atoms in optical lattices and in different environment to simulate important yet unsolved theoretical models. In this talk, I shall review the current progress of this effort, its success, and the serious challenges it faces. I shall discuss the possible solutions and the exciting future it holds.

Flows of particulate material, such as sand discharging in an hourglass, are ubiquitous in nature and industry. The flow and transport of granules, powders, or grains is complex and can differ considerably from that associated with a single-phase material. This presentation will highlight some unique features of granular materials (such as the discharge from an orifice) and describe some recent work at Caltech on wave propagation, booming sand dunes, and granular flow rheology.   

The centimeter-long DNAs in our cells are folded up into micron-scale chromosomes through an array of protein-DNA interactions.  Our group uses single-DNA micromanipulation – stretching and twisting of the double helix – as a tool to analyze a variety of enzymes acting on DNA.  I will describe a few different kinds of “magnetic tweezers” experiments we are doing that are aimed at understanding enzymes that help to package DNA and to change its topology. We also use analogous but larger-scale micropipette-based micromanipulation approaches to study the large-scale structure of metaphase chromosomes; I will discuss experiments that tell us the metaphase chromosomes behave as “chromatin gels”, apparently stabilized in part by DNA entanglement. Recent experiments on effects of depletion of condensin SMC complexes - thought to be major "crosslinkers" of chromosomes - will also be discussed.

DNA coils undergo  striking conformational transitions when it is confined to volumes with dimensions smaller than one of the characteristic lengths of the molecule.  We are particularly interested in confinement to channels less than two persistence length wide, and hundreds of microns long.  In these channels, DNA extends to 50 % of its contour length and more, thus establishing a clear connection between location and the linear "genetic address" expressed in base pairs. We can fabricate nanochannel systems with arbitrary configurations in two dimensions using fused silica, and thus are able to directly observe DNA configurations through fluorescence microscopy.

This talk will explore the physics of confined DNA, the application to epigenetic mapping, the interactions of electric fields with DNA, and the dynamic analysis of functional DNA-modifying enzymes.  In particular, we have studies the fluctuation spectrum of nanoconfined DNA, have mapped cytosine methylation levels, histone modification profiles, have discovered that a collapse of DNA in high electric fields that hints at the complete breakdown of linear theory, have studied the migration of DNA through nanochannel systems, have observed single-molecule restriction mapping, have detected DNA at nanoelectrode junctions, and have observed a previously unknown pre-catalytic compaction of DNA by a widely used DNA-binding protein.

Characterization of the mechanical properties of cells, as well as the tissues and extracellular matrices (ECM) in which they reside, requires microscale manipulation platforms that allow precise measurement of their local rheology. To achieve this, my laboratory has developed a suite of NdFeB-based magnetic tweezers devices optimized for biomaterials characterization. In this talk, I will present the design and construction of three new microscope-mounted magnetic tweezers devices that allow controlled forces to be applied locally to networks, cells, and tissues while their deformation is determined with nanometer accuracy: (1) high-force devices that enable the application of nN forces; (2) ring magnet devices that enable oscillatory microrheology without prestress; and (3) portable magnetic tweezers that enable visualization of the microscale deformation of soft materials under applied force through simultaneous fluorescence imaging. The utility of these devices will be demonstrated by measuring the mechanics of dense networks of microtubules, which are rigid cytoskeletal polymers. We find that crosslinker dynamics profoundly affect network elasticity and dynamics, and that it is possible to predict macroscale stiffness, strength, and stress propagation from the force-sensitive unbinding kinetics and compliance of single crosslinkers.

With the availability of spectrally pure lasers and the ability to precisely measure optical frequencies, it appears the era of optical atomic clocks has begun.  At the expense of signal-to-noise ratio, in one project at NIST we have used single trapped atomic ions because uncertainties in systematic effects are smallest, reaching Df/f₀ = 0.8 x 10^-17.  At this level, many effects, including those due to special and general relativity, must be calibrated and corrected for.