Physics Faculty Works

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    Physical Guidance of Cultured Retinal Neurons Using Zig-zag Surface Patterns
    (American Journal of Biomedical Science & Research, 2020-12-18) Moslehi, Saba; Watterson, William J.; Rowland, Conor; Smith, Julian H.; Perez, Maria-Thereza; Taylor, Richard P.
    The use of physical cues to control and guide various types of cells in vitro, especially neurons and their processes, has been the focus of a large amount of research. The response of neuronal processes to artificial surfaces depends on a number of factors including the cell type, the surface chemistry of the material, and the surface’s topological features [1,2]. In this Opinion piece, we investigate the extent to which retinal neuronal processes can be made to follow straight lines patterned into a surface. We show they can follow lines with relatively shallow heights of 2 μm and be made to undergo directional changes as great as 50°. However, some processes leave the lines and assume a weaving trajectory as they grow into the surface’s unpatterned regions. Based on these findings, we propose that neuronal processes will follow lines more closely if their shapes mimic the fractal weave patterns of unrestricted neurons. In addition to exploring the fundamental behavior of neurons interacting with artificial surfaces, the results inform the design of bio-inspired electrodes for human implants.
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    Temporal mode transformations by sequential time and frequency phase modulation for applications in quantum information science
    (Optica Publishing Group, 2020-12-04) Ashby, James; Thiel, Valérian; Allgaier, Markus; d'Ornellas, Peru; Davis, Alex O. C.; Smith, Brian J.
    Controlling the temporal mode shape of quantum light pulses has wide ranging application to quantum information science and technology. Techniques have been developed to control the bandwidth, allow shifting in the time and frequency domains, and perform mode-selective beam-splitter-like transformations. However, there is no present scheme to perform targeted multimode unitary transformations on temporal modes. Here we present a practical approach to realize general transformations for temporal modes. We show theoretically that any unitary transformation on temporal modes can be performed using a series of phase operations in the time and frequency domains. Numerical simulations show that several key transformations on temporal modes can be performed with greater than 95% fidelity using experimentally feasible specifications.
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    Structured environments foster competitor coexistence by manipulating interspecies interfaces
    (PLOS, 2021-01) Ursell, Tristan
    Natural environments, like soils or the mammalian gut, frequently contain microbial consor- tia competing within a niche, wherein many species contain genetically encoded mecha- nisms of interspecies competition. Recent computational work suggests that physical structures in the environment can stabilize local competition between species that would otherwise be subject to competitive exclusion under isotropic conditions. Here we employ Lotka-Volterra models to show that interfacial competition localizes to physical structures, stabilizing competitive ecological networks of many species, even with significant differ- ences in the strength of competitive interactions between species. Within a limited range of parameter space, we show that for stable communities the length-scale of physical structure inversely correlates with the width of the distribution of competitive fitness, such that physi- cal environments with finer structure can sustain a broader spectrum of interspecific compe- tition. These results highlight the potentially stabilizing effects of physical structure on microbial communities and lay groundwork for engineering structures that stabilize and/or select for diverse communities of ecological, medical, or industrial utility.
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    Resource Letter Biological Physics
    (The American Journal of Physics, 2021-06-05) Parthasarathy, Raghuveer
    This resource letter provides an overview of the literature in biological physics, a vast, active, and expanding field that links the phenomena of the living world to the tools and perspectives of physics. While no survey of this area could be complete, this list and commentary are intended to help provide an entry point for upper level undergraduates, graduate students, researchers new to biophysics, or workers in subfields of biophysics who wish to expand their horizons. Topics covered include subcellular structure and function, cell-scale mechanics and organization, collective behaviors and embryogenesis, genetic networks, and ecological dynamics.
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    Diffuse optics for glaciology
    (Optical Society of America, 2021-06) Allgaier, Markus; Smith, Brian J.
    Optical probing of glaciers has the potential for tremendous impact on environmental science. However, glacier ice is turbid, which prohibits the use of most established optical measurements for determining a glacier’s interior structure. Here, we propose a method for determining the depth, scattering and absorption length based upon diffuse propagation of short optical pulses. Our model allows us to extract several characteristics of the glacier. Performing Monte Carlo simulations implementing Mie scattering and mixed boundary conditions, we show that the proposed approach should be feasible with current technology. The results suggest that the optical properties and geometry of the glacier can be extracted from realistic measurements, which could be implemented with a low cost and small footprint.