Computer Science – Performance
Scientific paper
Jan 1995
adsabs.harvard.edu/cgi-bin/nph-data_query?bibcode=1995phdt........15s&link_type=abstract
Thesis (PH.D.)--HARVARD UNIVERSITY, 1995.Source: Dissertation Abstracts International, Volume: 56-07, Section: B, page: 3779.
Computer Science
Performance
Phase Transitions
Scientific paper
We present a theoretical study of phase transitions in random heteropolymers using the sequence mode. In this model the random sequence is represented by a set of quenched variables {sigma_i} that correspond to the different chemical nature of each monomer i. The interaction potential is short-range in three dimensions and all monomers are allowed to interact independent of their position along the sequence. We find that the flexibility of the chain is a crucial factor that controls frustration in the system. There is a critical temperature below which the number of thermodynamically relevant conformations is of order unity. This temperature is called freezing temperature and the free energy of the system in the frozen phase does not depend on temperature. In the two-letter model with preference for microphase separation between the two kinds of monomers, the freezing transition can preempt the microphase separation transition in the case of stiff chains. Then microphase separation is never observed. With increasing flexibility the freezing temperature decreases and microphase separation can be observed. The flexibility of the chain can be rescaled by the number of letters used in the sequence and the increasing heterogeneity facilitates the freezing transition. The analogy between the frozen phase and the native state of proteins is discussed. The microphase separation transition is investigated beyond mean field for sequences with chemical correlations along the chain. For symmetric compositions, we find a fluctuationally induced first order transition with size of domains strongly depending on temperature, in contrast to the case of periodic diblock copolymers. We find that long-range order is thermodynamically possible. For non -symmetric compositions we find a critical value f ~0.173 at which the nature of the transition changes. We present a numerical simulation of protein folding with the aid of a chaperone mechanism. We qualitatively reproduce experimental results of selective yield enhancement in sequences with certain properties. The results are explained with a simple double-exponential model and conditions for maximum performance of the mechanism are estimated.
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