טכניון מכון טכנולוגי לישראל
הטכניון מכון טכנולוגי לישראל - בית הספר ללימודי מוסמכים  
M.Sc Thesis
M.Sc StudentShoham Asael
SubjectMechanics of Macromolecules with Bistable Domains
undergoing Hard-Soft Transitions
DepartmentDepartment of Mechanical Engineering
Supervisor Professor Josef Givli
Full Thesis textFull thesis text - English Version


Abstract

Many macromolecules such as DNA, spider silk, biopolymers, titin and more, exhibit bistable or mulit-stable behaviour. While many experiments have been performed to fully understand the rate-dependent behaviour of such macromolecules, under force- or length-control conditions, the interpretation of these experimental results is still under debate. A common assumption in the literature is that the typical energy barrier at transition does not depend on the number of unfolded domains and the overall number of domains in the macromolecule. Therefore, the transition should occur (statistically) at the same force, regardless of the number of unfolded or folded domains.

 In this study we develop a rigorous theoretical model that enables fundamental understanding of the behavior of such molecules when subjected to length-control experiments. To do so, the study uses a mathematical model to describe the behavior of a single domain of the macromolecule. Then, the response of the entire molecule is studied by means of a chain model comprised from several such domains. This enables a rigorous study of the energy barriers that separate between metastable configurations. In addition, by introducing thermal fluctuations and formulating the governing equations for the evolution in time of the probability to find the system in each metastable configuration, we are able to simulate the response of the molecule to various conditions and strain rates. Our results show that the assumption mentioned above is inaccurate, especially for small number of domains, and has to be carefully evaluated before performing experiments or interpreting their results.

 In addition, we find a single quantity that sets a universal scale for rates depending on temperature, strain rate and typical energy barriers. This quantity allows for deeper understanding of the behaviour of such macromolecules, and enables far more accurate predictions in experiments, without the need of any other simulations performed beforehand.