Exploring the energy landscape of biopolymers using single molecule force spectroscopy and molecular simulations (1009.3697v1)

Abstract: In recent years, single molecule force techniques have opened a new avenue to decipher the folding landscapes of biopolymers by allowing us to watch and manipulate the dynamics of individual proteins and nucleic acids. In single molecule force experiments, quantitative analyses of measurements employing sound theoretical models and molecular simulations play central role more than any other field. With a brief description of basic theories for force mechanics and molecular simulation technique using self-organized polymer (SOP) model, this chapter will discuss various issues in single molecule force spectroscopy (SMFS) experiments, which include pulling speed dependent unfolding pathway, measurement of energy landscape roughness, the in uence of molecular handles in optical tweezers on measurement and molecular motion, and folding dynamics of biopolymers under force quench condition.