Far-from-equilibrium phenomena in protein dynamics [electronic resource]
- Jeffrey Kurt Weber.
- Physical description
- 1 online resource.
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|3781 2014 W||In-library use|
- The diverse physical principles that govern living things conform to one common precept: all biological processes operate, to some extent, out-of equilibrium. As our understanding of biological pathways advances at the nanoscale, theoretical and simulation techniques that function under non-equilibrium conditions will play an important role in elucidating the working environment of the cell. In this research, large-scale molecular dynamics simulations, discrete dynamical network models, and sophisticated non-equilibrium theories are synthesized to study glassy and dissipative processes facilitated by protein molecules. Leveraging atomistic molecular dynamics data derived from the Folding@home distributed computing project, a number of detailed biophysical systems are examined. I first describe glassy solvent structures that emerge as functional components of a protein chaperone, and I connect such observations to the theory of disordered systems. By coupling Folding@home data, Markov state models of biomolecular dynamics, and the theory of large deviations, I go on to characterize [beta] sheet-rich, amyloid-like misfolded states that appear on protein folding landscapes; I explore the relationship between these misfolded states and so-called dynamical glass transitions. Applying theory related to the Crooks fluctuation theorem, I next explicate the dissipative dynamics in detailed models of signaling proteins, and I illustrate how the input of external energy harmonizes with equilibrium fluctuations to yield functional signaling components. Lastly, I discuss methods by which protein landscapes can be sampled in an adaptive fashion and means for recovering equilibrium kinetics from biased, non-equilibrium simulation data.
- Publication date
- Submitted to the Department of Chemistry.
- Thesis (Ph.D.)--Stanford University, 2014.
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