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Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 31 for “"Normal mode analysis"”.
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Applications of normal mode analysis to ocean acoustic tomography
Thesis: Ph. D., Massachusetts Institute of Technology, Department of Physics, 1987
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Linear normal mode analysis of baroclinic instability in a meridional channel
Numerical solutions of the unstable, growing modes are found for the two-layer inviscid quasigeostrophic equations in a meridional channel. A steady mean flow in the N-S direction is imposed in the upper layer, and it is assumed that changes in planetary vorticity following this mean flow are …
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Ocean Surface Maps From Blending Disparate Data Through Normal Mode Analysis
… the large and meso-scale circulations. Spectral analysis of high resolution current meter and drifter data reveals the significant forcing features detectable by readily available observing techniques. These observations are combined with boundary data extracted from the U.S. Navy's Modular Ocean …
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Linear normal mode analysis of baroclinic instability in a meridional channel
Numerical solutions of the unstable, growing modes are found for the two-layer inviscid quasigeostrophic equations in a meridional channel. A steady mean flow in the N-S direction is imposed in the upper layer, and it is assumed that changes in planetary vorticity following this mean flow are …
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Investigating the effects of different force fields on spring-based normal mode analysis
<p>Classical normal mode analysis (CNMA) has been widely acknowledged as one of the most useful simulation tools for studying protein dynamics. CNMA uses a fine-grained all-atom model of proteins and a complex empirical potential. In addition, CNMA requires a structure that must be energetically …
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Normal Mode Analysis Of Single Bunch, Charge Density Dependent Behavior In Electron/Positron Beams
… and direct space charge. CesrTA design and analysis is conducted in a normal mode coordinates environment which allows for natural handling of coupling. To that end, we develop a 6D normal modes decomposition of the linear beam optics. Multi-particle effects are also important for Energy …
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Development of an Accurate and Efficient Method for Normal Mode Analysis in Extended Molecular Systems: the Mobile Block Hessian Method
… the spectrum consists of a number of close-lying normal modes, which result from normal mode analysis (NMA). This is the diagonalization of the full mass-weighted molecular Hessian matrix, which contains the second derivatives of the total potential energy with respect to Cartesian nuclear …
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Human testis angiotensin-converting enzyme: crystal structure of a glycosylation mutant and investigation of a putative hinge-mechanism by normal mode analysis
… constrained regions, involved in the hinge. Normal mode analysis reveals the intrinsic flexibility of tACE, and further suggests that a putative open form of tACE would behave similarly to the open form of ACE2. Based on these indications, a conservation of the ACE2 hinge-bending mechanism is …
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Deep Neural Networks for Learning Protein Vibrational Behaviors to Characterize Structure and Function
… associated with metabolism and disease. Normal mode analysis is a powerful method that allows us to understand the mechanisms of these functions in high detail, but not without significant cost. Replacing this method with inference by a machine learning model could potentially eliminate …
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Modeling the flexibility of alpha helices in protein interfaces : structure based design and prediction of helix-mediated protein-protein interactions
… using computational methods requires models that can be used to efficiently sample structural variation. This thesis identifies methods that can be used to sample an important sub-space of protein structure: alpha helices that participate in protein interfaces. Helices, the global …
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The Conformational Dynamics of the Polymorphic Amyloid β Protofilaments
… between amyloid β (Aβ) protofilaments and model bilayers.|The community, as a whole, does not know the 3D structure of the Aβ protofilament. Therefore, we studied two polymorphic Aβ (9-40) structures [1] as likely conformations. We relaxed the structures through normal mode analysis. In …
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A modal analysis of acoustic propagation in the changing Arctic environment
… through the double duct system is analyzed using normal mode analysis, through the Kraken normal mode code. A simulated lower duct is introduced in order to isolate only those modes which travel within the lower duct. Propagation through the lower duct is compared to propagation in traditional …
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Kelvin-Helmholtz instability in aluminium reduction cells
… role of the basic steady flow is focused in this analysis, while most previous MHD analyses neglect it and emphasise on the interaction between the interface wave and the electromagnetic field by the electromagnetic perturbation. The stationary magnetic field is considered important as a strong …
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Energy landscape statistics and coarsening in liquids: a relaxation mode analysis
… in this work, we developed a relaxation mode analysis (RMA) for liquids under a framework analogous to the normal mode analysis for solids. Using RMA, complicated relaxations of liquids are decoupled into a distribution of relaxation modes, from which important statistics of relaxation …
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Ultracold Rydberg Atoms in Structured and Disordered Environments
… atom, were investigated in the framework of normal mode analysis. This exotic ultralong-range triatomic bound state exists despite that the Rydberg-ground-state interaction is repulsive. Their lifetimes were estimated using both quantum scattering calculations and semi-classical …
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Application of simulation methods for the identification of allosteric binding site in human glucokinase
… approaches, molecular dynamics (MD) and normal mode analysis (NMA) have been applied to an allosteric enzyme human glucokinase (GLK) for which known allosteric activators have been discovered, as a test-case. First an X-ray structure, bound to glucose and an allosteric activator, has been …
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Contributions to the analysis of proteins
… role in almost every biological process. The analysis of the conformational dynamics and mechanics of proteins using numerical methods, such as normal mode analysis (NMA), provides insight into their functional mechanisms. However, despite the fact that much effort has been focused on …
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Dynamics and structures of linear and supercoiled DNAs
A normal mode theory is developed for the Brownian dynamics of weakly bending rods with preaveraged hydrodynamic interactions. An expression is given for the mean squared angular displacement $$ of the $m\sp{th}$ bond-vector around the instantaneous x-axis (perpendicular to the end-to-end vector …
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An Efficient Reduced Order Modeling Method for Analyzing Composite Beams Under Aeroelastic Loading
… aeroelastic tailoring. Due to the complexity of modeling composites, designers often select safe, simple geometry and layup schedules for their wing/blade cross-sections. An example of this might be a box-beam made up of 4 laminates, all of which are quasi-isotropic. This results in neglecting …
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