Abstract: Understanding the processes that govern the behavior of a system is a central goal in the natural and social sciences. In some cases, the systems studied by natural and social scientists are complicated and the equations dictating the system’s behavior are unknown. In other cases, scientists wish to use data in order to develop or test a predictive model for a particular system. Time series analysis provides a set of tools which can be used to understand the dynamics of a system by examining data measured from the system.  The tools of time series analysis can be used to develop or test predictive models. In addition, time series analysis algorithms can be used to shed light on the dynamics of a complicated system. In this talk, I will discuss some methods of determining the nature of the dynamics governing a system by analyzing time series data measured from the system. Specifics tests covered in the talk include a test for determinism (the permutation spectrum test) and several tests for detecting chaos.

Abstract: Nematic liquid crystals, widely used in LCD screens, are anisotropic fluids: the molecules orient along a common direction called the director field. In chiral nematic liquid crystals, this director field twists spontaneously in a helix with a preferred pitch, creating apparent “layers” whose Bragg reflection properties prove useful in both technology and biology. However, when the chiral nematic is distorted away from its ground state, it's no longer clear how to define the twist “layers”, or even how to identify the “pitch axis” about which twist is locally occurring. I will present a mathematical approach to identifying the pitch axis field in arbitrarily distorted chiral nematic textures. This approach yields insights not only into the geometry of chiral nematics but also their topology, namely, the topological defects where the pitch axis field suffers from singularities. Furthermore, the results clarify in what sense chiral nematics are truly “layered” even when strongly distorted. 

Abstract: We study adaptations in blood vessel networks, particularly how these networks respond to damage in order to maintain adequate distribution of oxygen. Our primary case study is a section of an experimentally observed arterial network in a mouse. Using the diameters, lengths and relative directions of flow obtained from intravital microscopy, we implement a Monte Carlo simulated annealing process to recover the unknown pressures at the boundaries of the observed network as well as the uncertainties in the recovered pressures. These boundary pressures give us a basis on which to study the redistribution of flow throughout the network if a blood vessel near the center of the observed network is damaged and is no longer able to support flow. To study the effects of these damaged central vessels in a larger scale network, we create synthetic networks similar in structure to the experimental network and observe the relationship between the changes in a vessel’s flow and its proximity to the damage. We find that the density of closed loops in the network plays a critical role in determining the resilience of vascular networks to damage. Our study provides insights into stroke, heart disease and vascular tumors.

Abstract: We have developed an experimental approach to automatically adjust multiple electrostatic and/or magnetic elements on an ion optical beamline, while analyzing the profile of the beam on a detector at the image point, until an optimal tune is found. This approach dramatically simplifies beamline tuning, thus allowing more efficient use of experimental equipment; ensures a more optimal tune is found, providing a more focused beam spot without a significant loss of beam transmission; and will allow the development of specialized optical tunes based on the needs of any given experiment. The approach was tested directly on the D-Line at the National Superconducting Cyclotron Laboratory at Michigan State University in several real-time optimization runs. The initial experiments demonstrate the ability of the optimizer to focus the beam while preserving transmission within a one-hour optimization run. With further research we plan to generalize the approach to work on any given beamline, including particularly for higher order tunes of fragment separators.

Abstract: Lipids, cholesterol, and proteins collaborate to organize the plasma membrane of our cells for functional ends, such as signaling and transfer of cargo. New microscopy and imaging techniques are beginning to reveal the structure and dynamics of lipid mixtures on lengthscales well below the diffraction limit, permitting the development and testing of models for cellular organization at the scale of individual signaling events. Chemically detailed molecular simulations reveal an unexpected nanoscale structure in lipid membranes (verified by NMR data), in which cholesterol mediates local hexagonal packing of hydrocarbon chains, which are nonetheless fluid on longer length and timescales. Lipid diffusion is non-Fickian, with subdiffusion observed on timescales that matter for the encounter of signaling partners in the membrane. These results are verified by recent iSCAT single particle tracking experiments, and motivate the development of stochastic subdiffusive models for signaling. Remarkably, subdiffusion offers unexpected advantages for regulating cellular responses from clustered receptors.

Abstract: Eighty years ago, geneticist Timoféeff-Rssovsky, radiation physicist Zimmer and theoretical physicist Delbrück co-authored the famous three-man paper “On the nature of gene mutation and gene structure”, marking not only one of the earliest interdisciplinary collaborations, but also the start of biophysics. Since then, there are more and more interactions among physicists, mathematicians and biologists to try to build a quantitative framework towards appreciating the complexity in living organisms. In this talk, I will use a few examples to illustrate the emerging field of biophysics and introduce the biophysics course (PHYS 340) we will offer in the coming spring semester.

Abstract: Complex fluids play an important role in many applications ranging from biological to industrial. Colloidal suspensions have long been studied for their complex behavioral dynamics in shear flow. In this research, we study the physical properties of suspensions of bacterial flagella from Salmonella typhimurium prepared in a variety of rigid polymorphic shapes. Flagella act as a rigid colloidal particle that can exhibit non-trivial geometry including helices of varying dimensions, straight rods, or a combination of the two in the same filament. By utilizing a variety of experimental techniques, the polymorphic shape that the filament assumes can be controlled. Utilizing different polymorphic shapes, we combine results from observing individual filament dynamics optically with bulk rheological measurements to help understand the role that constituent colloidal geometry plays in bulk complex behavior.

Abstract: A century ago, during November 1915, Albert Einstein presented a series of four papers to the Prussian Academy of Natural Sciences. This talk traces the difficulties and triumphs -- both scientific and personal -- experienced by Einstein that month on the way to formulating his now famous Einstein Field Equations for general relativity. While there is certainly some mathematical physics involved, most of the talk should be appropriate for first-year physics students.

Abstract: We present the results of experimental studies of the effects of fluid flows on various dynamical processes. Much of our research during the past few years has involved the motion of chemical reaction fronts in vortex flows. Several experiments have revealed the presence of invisible barriers (“burning invariant manifolds” or BIMs) that block the motion of reaction fronts in two-dimensional fluid flows. We will present preliminary results from some experiments that extend these ideas to three-dimensional fluid flows. The same theory that explains BIMs that block reaction fronts also predicts barriers that impede the motion of self-propelled swimmers in a flow. We will present experiments studying these barriers in a microfluidic flow. The swimmers are the bacteria bacillus subtilis that have been mutated so that they swim in only one direction.

Abstract: In introductory quantum mechanics, quantum measurement is described as an instantaneous operation that projects an initial quantum state $|\psi_i\rangle = \sum_n c_n |\psi_n\rangle$ into a final state $|\psi_n\rangle$ with a probability $P_n = |c_n|^2$. But what precisely is this mysterious process, and how does it physically manifest outside of a mathematical construction? Recent advances in low-noise amplifiers allow us to probe this question directly, using artificial atoms cooled to 20 milliKelvin. In this talk, I will discuss how to experimentally realize and interpret a quantum measurement, and will explore connections between measurement, noise, and uncertainty. I will also introduce a quantum toolbox made out of superconducting quantum bits, resonators, and quantum-limited amplifiers, and will demonstrate how we can use measurement as a powerful means for generating entanglement between remote quantum objects.

Abstract: Those faculty in the Department of Physics & Astronomy who will be taking students for summer research will give short (5 minute) presentations of their research area. Additional information will be provided about summer research opportunities that are available beyond Bucknell and how to apply for them.