abstract: Bio-molecules and proteins are building blocks of life as is known, and understanding
their dynamics and functions are necessary to better understand life and improve its
quality. While ergodicity and fluctuation dissipation theorem (FDT) are fundamental
and crucial concepts regarding study of dynamics of systems in equilibrium, biological
function is not possible in equilibrium.
In this work, dynamical and orientational structural crossovers in low-temperature
glycerol are investigated. A sudden and notable increase in the orientational Kirk-
wood factor and the dielectric constant is observed, which appears in the same range
of temperatures that dynamic crossover of translational and rotational dynamics oc-
cur.
Theory and electrochemistry of cytochrome c is also investigated. The seeming
discrepancy in reorganization energies of protein electron transfer produced by atom-
istic simulations and those reported by protein electrochemistry (which are smaller)
is resolved. It is proposed in this thesis that ergodicity breaking results in an effective
reorganization energy (0.57 eV) consistent with experiment.
Ergodicity breaking also affects the iron displacement in heme proteins. A model
for dynamical transition of atomic displacements in proteins is provided. Different
temperatures for rotational and translational crossovers of water molecules are re-
ported, which all are ergodicity breaking transitions depending on the corresponding
observation windows. The comparison with Mössbauer spectroscopy is presented.
Biological function at low temperatures and its termination is also investigated in
this research. Here, it is proposed that ergodicity breaking gives rise to the violation
of the FDT, and this violation is maintained in the entire range of physiological
temperatures for cytochrome c. Below the crossover temperature, the protein returns
to the FDT, which leads to a sudden jump in the activation barrier for electron
itransfer.
Finally the interaction of charges in dielectric materials is discussed. It is shown
that the potential of mean force between ions in polar liquids becomes oscillatory at
short distances. / Dissertation/Thesis / Doctoral Dissertation Physics 2018
| Identifer | oai:union.ndltd.org:asu.edu/item:51639 |
| Date | January 2018 |
| Contributors | Seyedi, seyed salman (Author), Matyushov, Dmitry V (Advisor), Beckstein, Oliver (Committee member), Vaiana, Sara M (Committee member), Ros, Robert (Committee member), Arizona State University (Publisher) |
| Source Sets | Arizona State University |
| Language | English |
| Detected Language | English |
| Type | Doctoral Dissertation |
| Format | 245 pages |
| Rights | http://rightsstatements.org/vocab/InC/1.0/ |
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