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You searched for subject:(Subdiffusion). Showing records 1 – 2 of 2 total matches.

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University of Texas – Austin

1. Satija, Rohit. Understanding structural transitions and dynamics in biomolecules at a single molecule level.

Degree: PhD, Cell and Molecular Biology, 2020, University of Texas – Austin

Transition paths are fleeting events when a molecule crosses a barrier separating stable configurational basins. Recent advances in single molecule experiments, including optical tweezers-based force spectroscopy and FRET-based techniques, and data analysis methods have allowed detection of various statistical properties of transition paths. These observations have highlighted an important limitation in their current theoretical interpretation – a model of diffusive dynamics of the reaction coordinate along a one-dimensional free energy landscape is often unable to account for measurements of transition path time distributions in single molecule experiments. Here, we report similar observations in a long all-atom simulation of a small fast folding protein that exhibits multiple folding and unfolding transitions. Specifically, we discovered that the distribution of transition path times in this case is much broader than the prediction of the one-dimensional diffusion model. Moreover, direct analysis of the dynamics of the reaction coordinate in this simulation as well as in several other polypeptide simulations revealed that those dynamics are not diffusive, but subdiffusive. To explain these observations, we developed and tested several non-Markovian models, which include memory effects in the dynamics of the reaction coordinate in the form of time-dependent transport coefficients. We invented a novel technique, based on an overdamped generalized Langevin equation, to extract conformational memory directly from one-dimensional trajectories in single molecule experiments and simulations. Finally, we tested our theories on loop formation kinetics in intrinsically disordered proteins and found that, while mean first passage times to loop closure are well described by both one-dimensional diffusion and generalized Langevin equation, neither of them can capture long-time tails observed in distributions of transition path times in all-atom simulations. Advisors/Committee Members: Makarov, Dmitrii E. (advisor), Elber, Ron (committee member), Russell, Rick (committee member), Ren, Pengyu (committee member), Florin, Ernst L (committee member).

Subjects/Keywords: Theoretical chemical physics; Reaction dynamics; Kinetics; Transition path time; Single molecule force spectroscopy; FRET; Subdiffusion; Non-Markovian models; Memory kernel; Loop closure; Protein folding

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APA (6th Edition):

Satija, R. (2020). Understanding structural transitions and dynamics in biomolecules at a single molecule level. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://dx.doi.org/10.26153/tsw/9031

Chicago Manual of Style (16th Edition):

Satija, Rohit. “Understanding structural transitions and dynamics in biomolecules at a single molecule level.” 2020. Doctoral Dissertation, University of Texas – Austin. Accessed October 29, 2020. http://dx.doi.org/10.26153/tsw/9031.

MLA Handbook (7th Edition):

Satija, Rohit. “Understanding structural transitions and dynamics in biomolecules at a single molecule level.” 2020. Web. 29 Oct 2020.

Vancouver:

Satija R. Understanding structural transitions and dynamics in biomolecules at a single molecule level. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2020. [cited 2020 Oct 29]. Available from: http://dx.doi.org/10.26153/tsw/9031.

Council of Science Editors:

Satija R. Understanding structural transitions and dynamics in biomolecules at a single molecule level. [Doctoral Dissertation]. University of Texas – Austin; 2020. Available from: http://dx.doi.org/10.26153/tsw/9031

2. Schulz, Maximilian. Non-equilibrium quantum dynamics : interplay of disorder, interactions and confinement.

Degree: PhD, 2019, University of St Andrews

The study of collective behaviour in many-body systems often explores fundamentally new ideas absent from the mere constituents of such a system. A paradigmatic model for these studies is the spin-1/2 XXZ chain and its fermionic equivalent. This thesis can be broadly divided into the study of two fundamental aspects of this model. Firstly, we discuss localisation phenomena in one dimensional lattices as often experimentally realised in cold atom systems. Secondly, we investigate how disorder and symmetry influence heat transport in spin chains. More specifically, in the first part we consider a system of non-interacting fermions in one dimension subject to a single-particle potential consisting of a strong optical lattice, a harmonic trap, and uncorrelated on-site disorder. We investigate a global inhomogeneous quantum quench and present numerical and analytical results for static and dynamical properties. We show that the approach to the non-thermal equilibrium state is extremely slow and that it implies a sensitivity to disorder parametrically stronger than that expected from Anderson localisation. We also consider the above system in a strong non-uniform electric field. In the non-interacting case, due to Wannier-Stark localisation, the single-particle wave functions are exponentially localised without quenched disorder. We show that this system remains localised in the presence of nearest-neighbour interactions and exhibits physics analogous to models of conventional many-body localisation. The second part explores the hydrodynamics of the disordered XYZ spin chain. Using time-evolving block decimation on open chains of up to 400 spins attached to thermal baths, we probe the energy transport of this system. Our principal findings are as follows. For weak disorder there is a stable diffusive region that persists up to a critical disorder strength that depends on the XY anisotropy. Then, for disorder strengths above this critical value energy transport becomes increasingly subdiffusive.

Subjects/Keywords: Condensed matter; Cold atoms; Many-body localization; Localization; Confinement; Transport; Subdiffusion; Spin chains; QC173.454S8; Quantum theory; Many-body problem

…spin chain with broken U(1) symmetry: diffusion, subdiffusion, and many-body… 

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Schulz, M. (2019). Non-equilibrium quantum dynamics : interplay of disorder, interactions and confinement. (Doctoral Dissertation). University of St Andrews. Retrieved from http://hdl.handle.net/10023/17345

Chicago Manual of Style (16th Edition):

Schulz, Maximilian. “Non-equilibrium quantum dynamics : interplay of disorder, interactions and confinement.” 2019. Doctoral Dissertation, University of St Andrews. Accessed October 29, 2020. http://hdl.handle.net/10023/17345.

MLA Handbook (7th Edition):

Schulz, Maximilian. “Non-equilibrium quantum dynamics : interplay of disorder, interactions and confinement.” 2019. Web. 29 Oct 2020.

Vancouver:

Schulz M. Non-equilibrium quantum dynamics : interplay of disorder, interactions and confinement. [Internet] [Doctoral dissertation]. University of St Andrews; 2019. [cited 2020 Oct 29]. Available from: http://hdl.handle.net/10023/17345.

Council of Science Editors:

Schulz M. Non-equilibrium quantum dynamics : interplay of disorder, interactions and confinement. [Doctoral Dissertation]. University of St Andrews; 2019. Available from: http://hdl.handle.net/10023/17345

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