Models for Brownian and biomolecular motors
| dc.contributor.author | Craig, Erin Michelle, 1980- | |
| dc.date.accessioned | 2009-02-17T23:09:47Z | |
| dc.date.available | 2009-02-17T23:09:47Z | |
| dc.date.issued | 2008-09 | |
| dc.description | xiv, 171 p. ; ill. (some col.) A print copy of this title is available through the UO Libraries. Search the library catalog for the location and call number. | en |
| dc.description.abstract | Biological molecular motors, which use chemical energy from ATP hydrolysis to generate mechanical force, are involved in a variety of important mechanical processes in eukaryotic cells, such as intracellular transport, cell division and muscle contraction. These motors, which produce motion on the nanoscale, operate in the presence of substantial thermal noise. In this dissertation, two approaches are used to model the physics of nanoscale motors: (1) A theoretically established type of Brownian motor called the "flashing ratchet" is studied. This motor transports diffusive particles in a preferred direction. (2) A coarse-grained mechanical model for the biological molecular motor myosin-V is developed, and used to study the role of Brownian diffusion, and the interaction between chemical and mechanical degrees of freedom, in the transport mechanism of this motor. In chapter III, Brownian dynamics simulations and analytical calculations demonstrate that the average velocity of rigid chains of particles in a flashing ratchet reverses direction in response to changing the size of the chain or the temperature of the heat bath. Recent studies have introduced policies for "closed-loop" control of a flashing ratchet, in which the system is controlled based on information about its internal state (such as the positional distribution of particles). In chapter IV, the effect of time delay on the implementation of closed-loop control of a flashing ratchet is investigated. For a large ensemble, a well-chosen delay time improves the ratchet performance (increasing the velocity) by synchronizing into a quasi-stable mode that takes advantage of the semi-deterministic nature of the time development of average quantities for a large ensemble. I n chapter V, a coarse-grained mechanical model is presented for the transport mechanism of myosin-V, which walks along intracellular filaments. The model is well constrained by experimental data on the mechanical properties of myosin V and on the kinetic cycle. An experimentally motivated model for the intramolecular coordination of the motor's steps is proposed and tested. | en |
| dc.description.sponsorship | Adviser: Heiner Linke | en |
| dc.identifier.uri | https://hdl.handle.net/1794/8565 | |
| dc.language.iso | en_US | en |
| dc.publisher | University of Oregon | en |
| dc.relation.ispartofseries | University of Oregon theses, Dept. of Physics, Ph. D., 2008; | |
| dc.subject | Biophysics | en |
| dc.subject | Feedback control | en |
| dc.subject | Molecular motors | en |
| dc.subject | Brownian motors | en |
| dc.subject | Biomolecular motors | en |
| dc.title | Models for Brownian and biomolecular motors | en |
| dc.type | Thesis | en |
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