Browsing by Subject "particle tracking"

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    Data supporting 'Subdiffusion of loci and cytoplasmic particles are different in compressed E. coli cells'
    (2018-05-15) Yu, Shi; Sheats, Julian; Cicuta, Pietro; Sclavi, Bianca; Cosentino Lagomarsino, Marco; Dorfman, Kevin D; dorfman@umn.edu; Dorfman, Kevin D
    The complex physical nature of the bacterial intracellular environment remains largely unknown, and has relevance for key biochemical and biological processes of the cell. While recent work has addressed the role of non-equilibrium drives and crowding, the consequences of mechanical perturbations are relatively less explored.We have used a microfabricated valve system to track both fluorescently labeled chromosomal loci and cytoplasmic particles in E.~coli cells shortly after the application of a compressive force on time scales that are too sudden to allow for biochemical response from the cell. While cytoplasmic diffusion is slowed down significantly under compression, the mobility of DNA loci is much less affected. These results suggest that the dynamics of the bacterial chromosome are decoupled from the viscoelastic environment of the cytoplasm under such short time scales, and that DNA elasticity and nucleoid organization play a more important role in loci subdiffusion than cytoplasmic viscoelasticity.
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    A Study Of Particle Entrainment In Two Common Particle-Fluid Flows In Nature: Bedload Transport In Rivers And Debris Flows In Upland Regions
    (2020-05) Ghasemi, Amirreza
    This work performed for the research describes in this dissertation concerns particle entrainment in two common particle-fluid flows in nature: 1) bedload transport in rivers, and 2) debris flows in steep upland regions. The bedload transport work addressed here concerns height-dependent entrainment from a bed of a channelized flow. Towards this, we perform distinct element method (DEM) simulations to study the roles of particle size and fluid flow on the transport rate, bed surface variations, and depth-dependent particle entrainment. We do so in the context of a theoretical probabilistic formulation derived to better capture spatial variation in sediment exchange between bed material load and alluvial deposits (Parker et al. (2000)). Our findings allow us to provide a link between the longitudinal bedload transport rate with vertical bed surface statistics and provide closure for a theoretical model designed to model transport and bed-surface exchange in the presence of bed variabilities. The debris flow erosion work here focuses on the effect of grain size distribution of a debris flow on the rate of entrainment of bed material. Towards this, we perform several experiments in a laboratory flume where we measure the relative roles of inclination angle, bed composition, and average flow composition on average and instantaneous erosion dynamics. Most significantly, we find that the infiltration of fine particles into a coarse bed can markedly increase the rate of erosion. Further, the infiltration rate is maximized for intermediate concentrations of small particles in the flow. We show this is due to the interplay of two simultaneous mechanisms: (1) segregation dynamics known as kinetic sieving in the shear flow when there is sufficient agitation of the coarse particles to allow the small particles to sink into the bed and (2) correlated interparticle forces which create sufficient agitation only with an adequately high concentration of coarse particles. In this presentation, we demonstrate how a better understanding of these two processes can contribute to a better understanding of the "sediment cycle" in earth-surface dynamics.