UMD Theses and Dissertations

Permanent URI for this collectionhttp://hdl.handle.net/1903/3

New submissions to the thesis/dissertation collections are added automatically as they are received from the Graduate School. Currently, the Graduate School deposits all theses and dissertations from a given semester after the official graduation date. This means that there may be up to a 4 month delay in the appearance of a given thesis/dissertation in DRUM.

More information is available at Theses and Dissertations at University of Maryland Libraries.

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Now showing 1 - 4 of 4
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    EPIGENETICS TUNE CHROMATIN MECHANICS, A COMPUTATIONAL APPROACH
    (2021) Pitman, Mary; Papoian, Garegin A; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    The base unit of DNA packaging in eukaryotes, the nucleosome, is adaptively modified for epigenetic control. Given the vast chemical space of chromatin and complexity of signaling and expression, much of our knowledge about genetic regulation comes from a biochemical or structural perspective. However, the architecture and function of chromatin also mechanically responds to non-equilibrium forces. Mechanical and biochemical properties are not independent of one another and the interplay of both of these material properties is an area of chromatin physics with many remaining questions. Therefore, I set out to determine how the material properties of chromatin are altered by biochemical variations of nucleosomes. All-atom molecular dynamics is employed coupled with new computational and theoretical tools. My findings and predictions were collaboratively validated and biologically contextualized through multiscale experimental methods. First, I computationally discover that epigenetic switches buried within the nucleosome core alter DNA accessibility and the recruitment of essential proteins for mitosis. Next, using new computational tools, I report that centromeric nucleosomes are more elastic than their canonical counterparts and that centromeric nucleosomes rigidify when seeded for kinetochore formation. We conclude that the material properties of variants and binding events correlate with modified loading of transcriptional machinery. Further, I present my theoretical approach called Minimal Cylinder Analysis (MCA) that uses strain fluctuations to determine the Young's modulus of nucleosomes from all-atom molecular dynamics simulations. I show and explain why MCA achieves quantitative agreement with experimental measurements. Finally, the elasticity of hybrid nucleosomes in cancer is measured from simulation, and I implicate this oncogenic variant in potential neocentromere formation. Together, these data link the physics of nucleosome variations to chromatin states' plasticity and biological ramifications.
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    Investigation into the Aerodynamics of Swashplateless Rotors Using CFD-CSD Analysis
    (2012) Jose, Arun Isaac; Baeder, James D; Aerospace Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    This study obtains a better understanding of the aerodynamics of integrated trailing edge flap (TEF) based swashplateless rotors. Both two dimensional (2D) and three dimensional (3D) analysis/simulations are performed to understand the behavior of TEF airfoils and integrated TEF based swashplateless rotors. The 2D aerodynamics of TEF airfoils is explored in detail. A semi-empirical approach is developed for modeling drag for TEF airfoils in steady flows based on baseline airfoil drag data alone. Extensive 2D CFD simulations are performed for a wide range of flow conditions in order to better understand various aspects of the aerodynamics of TEF airfoils. The trends in the airloads (lift, drag, pitching moment, hinge moment) for TEF airfoils are obtained. Nonlinear phenomena such as flow separation, shocks and unsteady vortex shedding are investigated, and the flow conditions and trends associated with them are studied. The effect of airfoil properties such as thickness and overhang are studied. Various approaches are used to model the effect of gaps at the leading edge of the flap. An approximate ``gap averaging'' technique is developed, which provides good predictions of steady airloads at almost the same computational cost as a simulation where the gap is not modeled. Direct modeling of the gap is done by using a patched mesh in the gap region. To solve problems (such as poor grid quality/control and poor convergence) that are associated with the patched mesh simulations, an alternate approach using overlapping meshes is used. It is seen that for TEF airfoils, the presence of gaps adversely affects the effectiveness of the flap. The change in airloads is not negligible, especially at the relatively higher flap deflections associated with swashplateless TEF rotors. Finally, uncoupled and coupled computational fluid/structural dynamics (CFD-CSD) simulations of conventional (baseline) and swashplateless TEF rotors is performed in hovering flight. The CFD-CSD code is validated against experiment and good agreement is observed. It is observed that the baseline UH-60 rotor performs better than the swashplateless UH-60 rotor. For an untwisted NACA0012 airfoil based rotor, the performance is similar for the baseline and swashplateless configurations. The effect of gaps on the performance of swashplateless TEF rotors is also investigated. It is seen that the presence of chordwise gaps significantly affects the effectiveness of the TEF to control the rotor. Spanwise gaps also affect the performance of swashplateless rotors but their effect is not as significant.
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    On the Development of Postural Stability During Infancy as a Process of Growth and Active, Exploratory Sensorimotor Tuning
    (2007-12-04) Metcalfe, Jason Scott; Clark, Jane E; Kinesiology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    The process by which humans stabilize bipedal stance represents a confluence of changes associated with musculoskeletal maturation and experience-based sensorimotor learning. While investigations have documented a variety of changes with increased bipedal experience, such as reduced velocity and frequency of postural sway and concomitant refinements in muscle activation sequences, the extent to which these changes may be ascribed to growth versus learning processes has not been well characterized. For example, reduced sway frequency is a natural consequence of increasing body height but alternatively, may be explained by active modulations in motor commands specifying the timing and magnitude of muscular activation sequences. It is clear that both types of influences are needed to explain postural development. However, a parsimonious framework for understanding and explaining postural development has yet to be clearly articulated and validated against empirical observations. As such, the purpose of this dissertation was to initiate the development of such an account through a combination of empirical and computational studies. In this dissertation, data are presented from a longitudinal study of upright posture in infants ranging from the onset of independent sitting until 9 months of walking experience; this dissertation focused on the particular period spanning from walk onset onward. Infants participated in a quiet stance task involving hand contact with a surface that was either static or dynamic as well as an independent stance condition. Empirical analyses were performed to estimate the statistical properties of sway and characterize adaptations to static and dynamic manipulations utilizing the touch surface. An unexpected lack of significance for sway magnitude was observed in all conditions. Robust effects, however, were found across measures of rate properties of sway. Taken in the context of previous literature, the empirical observations were used to guide a final study utilizing computational techniques to test hypotheses regarding potential sources of change in postural development. First, the mechanical and computational requirements for postural stabilization were systematically assessed through a review of extant models of both stance and motor learning. Armed with insights from this review, the final study examined an autonomous reinforcement learning algorithm, that was designed to capture the essence of how a human may stabilize his or her posture under the tutelage of exploratory action. Simulation results provided evidence in support of conclusions regarding changes in rate-properties of postural sway and underlying associations with physical growth as well as calibration of both sensory and motor system parameters. Further, simulations emphasized the importance of inclusion of noise in biologically-relevant aspects of the model, such as in sensory and motor processes, as well as the need to consider physical morphology as a primary constraint on sensorimotor learning in the context of upright postural development.
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    The ADI-FDTD Method for High Accuracy Electrophysics Applications
    (2006-11-24) Haeri Kermani, Mohammad; Ramahi, Omar M; Electrical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    The Finite-Difference Time-Domain (FDTD) is a dependable method to simulate a wide range of problems from acoustics, to electromagnetics, and to photonics, amongst others. The execution time of an FDTD simulation is inversely proportional to the time-step size. Since the FDTD method is explicit, its time-step size is limited by the well-known Courant-Friedrich-Levy (CFL) stability limit. The CFL stability limit can render the simulation inefficient for very fine structures. The Alternating Direction Implicit FDTD (ADI-FDTD) method has been introduced as an unconditionally stable implicit method. Numerous works have shown that the ADI-FDTD method is stable even when the CFL stability limit is exceeded. Therefore, the ADI-FDTD method can be considered an efficient method for special classes of problems with very fine structures or high gradient fields. Whenever the ADI-FDTD method is used to simulate open-region radiation or scattering problems, the implementation of a mesh-truncation scheme or absorbing boundary condition becomes an integral part of the simulation. These truncation techniques represent, in essence, differential operators that are discretized using a distinct differencing scheme which can potentially affect the stability of the scheme used for the interior region. In this work, we show that the ADI-FDTD method can be rendered unstable when higher-order mesh truncation techniques such as Higdon's Absorbing Boundary Condition (ABC) or Complementary Derivatives Method (COM) are used. When having large field gradients within a limited volume, a non-uniform grid can reduce the computational domain and, therefore, it decreases the computational cost of the FDTD method. However, for high-accuracy problems, different grid sizes increase the truncation error at the boundary of domains having different grid sizes. To address this problem, we introduce the Complementary Derivatives Method (CDM), a second-order accurate interpolation scheme. The CDM theory is discussed and applied to numerical examples employing the FDTD and ADI-FDTD methods.