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Broken ergodicity in myoglobin

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Title: Broken ergodicity in myoglobin
Author(s): Shyamsunder, Erramilli
Doctoral Committee Chair(s): Frauenfelder, H.
Department / Program: Physics
Discipline: Physics
Degree: Ph.D.
Genre: Dissertation
Subject(s): biomolecules Gibbs free energy myoglobin
Abstract: Biomolecules need long-lived far from equilibrium states to function. These states have a high Gibbs free energy that is used for biologically important functions such as catalysis and they need to live for a sufficiently long time, comparable to reactant diffusion times that vary from 100 ns on up, to enable the system to use this free energy. Many theories have been put forth to explain the longevity of these states, such as "Bose condensation", "spontaneous symmetry breakdown", "dissipative structures", solitons and so on. We have isolated such transient far-from equilibrium states in sperm whale myoglobin and measured the decays of these states as a function of time under vastly different conditions. Our studies have led us to a completely different mechanism for the longevity of these long-lived states, which is based on the idea that non-equilibrium states are examples of "broken ergodicity". Our experiments at low temperatures and high pressures prove the existence at short times are in broken ergodic states even at room temperature. These broken ergodic states give us a new mechanism for excited states to live long. The dynamics of these states in proteins involve structural hierarchies. The motions take so long because the system has to go through many levels of relaxation. This concept of "getting lost" in a hierarchy is quantified precisely through an unusual idea: we show that the number of proteins participating in the recombination reaction obeys a second order linear differential equation and use this to define and experimentally determine a frequency dependent friction coefficient The idea of using such a number as a generalized coordinate is consistent with modern ideas of friction. We can now make the following alternative statement: the motions are so slow because friction slows them down. There is no need for solitons. The idea that friction is the mechanism by which an excited state lives longer is a little startling because we are used to thinking of friction as a dissipative mechanism. Here, friction is used to stabilize excited states, an idea that is applicable to glasses and spin glasses as well.
Issue Date: 1986
Genre: Dissertation / Thesis
Type: Text
Language: English
URI: http://hdl.handle.net/2142/25254
Rights Information: 1986 Erramilli Shyamsunder
Date Available in IDEALS: 2011-06-03
Identifier in Online Catalog: 977321
 

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