Energy and topology of heteropolymers

The properties of biological polymers are controlled by two fundamental aspects: the energetic interactions, and the topological properties due to the fact that they are chains of connected monomers. In this thesis I study the interplay of topological and energetic properties in heteropolymers. We first study the problem of aggregation of polymers in solution. We find that aggregation is slowed by a transient topological force that exists on time scales shorter than the reptation time. We then study the translocation of a polymer through a membrane. Our key finding is that the dynamics of translocation occur on the same time scale as diffusion, and are affected only weakly by the entropic barrier created by the hole. Next we survey the energetics of random sequence heteropolymers, searching for "typical" properties of a sequence using lattice models. By enumerating the states and energies of compact 18, 27, and 36mers on a 3-d square lattice with an ensemble of random sequences, we test the validity of the self-averaging approximation. We find that fluctuations in the free energy between sequences are weak, and that self-averaging is a valid approximation at the length scale of real proteins. We then examine the validity of the Random Energy Model for these same lattice heteropolymers, through an analysis of the density of states. We see that the shape of the density of states is dependent on the sequence, and that this dependence is stronger for certain types of interactions between monomers.

Department dc:contributor.department

Massachusetts Institute of Technology. Dept. of Physics.

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2001

Author dc:creator

• Chuang, Jeffrey Hsu-Min, 1974-

Advisor dc:contributor.advisor

• Mehran Kardar.

• Physics.

Statement dc:rights

• M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/8285

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/8285