Thesis (Ph. D.)--Virginia Polytechnic Institute and State University, 1990. / Vita. Abstract. Includes bibliographical references (leaves 188-191). Also available via the Internet.

Thesis (M. Phil.)--University of Hong Kong, 2000. / Includes bibliographical references (leaves 140-141).

Thesis (M.Phil.)--University of Hong Kong, 2000. / Includes bibliographical references (leaves 140-141) Also available in print.

Integral Membrane Proteins (IMPs) are an important and scientifically interesting class of protein which span the lipid bilayer surrounding cells, cell compartments and many viruses. Molecular Dynamics (MD) simulation has revealed intimate and often highly specific relationships between membrane lipids and IMPs critical to many metabolic and signalling pathways. Meanwhile, the use of Coarse-Grained (CG) MD techniques has extended capabilities of biomolecular simulation to larger proteins over longer time periods. Several tools and resources for biomolecular simulations of IMPs are presented here, as well as two MD studies of specific IMPs. The previously developed MemProtMD pipeline automates the setup of MD simulations of IMPs; major extensions to this are presented here with the MemProtMD database and web server, automating the analysis of IMP simulations. The results of this can be viewed using the MemProtMD web server, an interactive, searchable online resource containing data from simulations of over 3000 experimentally determined IMP structures in explicit lipid bilayers. Using data from analysis of the entire MemProtMD database, MemProtMetrics has been developed to automate identification and orientation of IMP structures from Protein DataBank (PDB) depositions. This is shown to effectively predict membrane protein orientations seen in MD simulations. A tool for identification and classification of membrane lipids is also described, and used to identify over 500 IMPs structures with resolved lipids. CGMD simulations have also been used to assess dependence on side-chain ionisation state of interactions between lipids and two IMPs observed in mass spectrometry experiments. The simulations reveal similar trends to those seen in experiments. Finally, using multi-scale simulations, and through the development of a novel method for altering membrane composition in MD simulations, lipid-specific scramblase activity was shown for a novel structure of the TMEM16K scramblase IMP.

Thesis (Ph. D.)--University of Washington, 1998. / Vita. Includes bibliographical references (leaves [127]-134).

Thesis (Ph. D.)--University of Texas at Austin, 2004. / Supervisor: Jeffrey K. Bennighof. Vita. Includes bibliographical references.

Thesis (Ph. D.)--University of Chicago, Department of Chemistry, March 2001. / Includes bibliographical references. Also available on the Internet.

Thesis (Ph. D.)--Drexel University, 2006. / Includes abstract and vita. Includes bibliographical references (leaves 155-163).

This thesis addresses the problem of identifying the modal properties of a system based only on measurements of the system responses. This situation is frequently encountered in structural dynamics and is particularly relevant for systems where the in-service excitation is not artificially reproducible. The inherent non-linearities in these systems mean that the modal properties estimated using traditional input/output techniques will be different to those exhibited in operation. A common example from the literature is an aircraft in flight where the modal properties are heavily influenced by the operating point, i.e. the combination of load, speed, altitude etc., at which the aircraft is travelling. The process of identifying the modal properties of systems in-service is called Operational Modal Analysis (OMA). Not knowing the input complicates the analysis. Most of the techniques in the literature overcome the lack of knowledge about the unmeasured excitations by assuming they are both spatially and frequentially white, i.e. of equal magnitude and with a flat autospectrum. This thesis presents a new technique for OMA which relaxes these constraints, requiring only that the system is excited by a so called cyclostationary input with a unique cyclic frequency, and that the log spectrum of the second order component of this input is frequentially smooth, as will be explained. Such systems include vehicles with internal combustion engines as the vibration from such an engine exhibits cyclostationary statistics. In this thesis, the technique is applied to a laboratory test rig and a passenger train both using an artificial input, and to a race car using the engine as the excitation. By combining cyclostationary signal processing and the concept of the cepstrum, the technique identifies the resonances and anti-resonances in the transfer functions between each response and the cyclostationary source. These resonances and antiresonances can be used to regenerate Frequency Response Functions (FRFs) and it is shown how the unknown scaling of the system can be recovered by employing finite element model updating in conjunction with this regeneration. In addition, the contribution made to model updating by the anti-resonances is also investigated. Finally, the potential of OMA to inform a model updating process is demonstrated using an experimental case study on a diesel railcar.

The METU Gait Analysis System employs a computer program called Kiss-GAIT for the calculation of joint angles, moments and powers using force plate data and marker trajectories as input. Kiss-GAIT was developed using Delphi and is confined to calculations related to the standard gait protocol. Because the code lacks the flexibility required to carry out various test cases, the inverse dynamics formulation being used could not be verified and the extent of the error propagation problem could not be determined so far. The first aim of this study was to develop a code for the inverse dynamics model of the METU Gait Analysis System making use of the flexible programming environment provided by MATLAB. Verified and more reliable analysis results, obtained by reformulating the inverse dynamics algorithm in a new code, are presented. Secondly, data smoothing and differentiation techniques conventionally used in gait analysis were critically reviewed. A common tool used for filtering marker trajectories is the Butterworth digital filter. This thesis presents a modified, adaptive version of this classical tool that can handle non-stationary signals owing to its coefficients which are functions of local signal structure. The results of this thesis indicate the dominancy of ground reactions as compared to inertial effects in normal human gait. This implies that the accuracy needed in body segment inertial parameter estimation is not a critical factor. On the other hand, marker trajectories must be as accurate as possible for meaningful kinetic patterns. While any smoothing and differentiation routine that produces reasonable estimates is sufficient for joint moment calculation purposes, the estimation performance becomes a key requirement for the calculation of joint powers.