In this paper we make the first attempt to decipher the free energy landscape of homopolymer using the external force as reaction coordinate. The impact of the quenched force on the free energy landscape was studied using simplified coarsegrain Go model. Similar to protein, we have obtained a clear switch from the thermal regime to force-driven regime. | Vietnam Journal of Science and Technology 55 (6A) (2017) 1-8 REFOLDING OF HOMOPOLYMER UNDER QUENCHED FORCE Maksim Kouza1, 2, *, Andrzej Kloczkowski2, Pham Dang Lan3, Mai Suan Li4, * 1 Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland Nationwide Childrens Hospital, Battelle Center for Mathematical Medicine, Columbus, OH 43215 USA 2 3 Institute for Computational Science and Technology, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Viet Nam 4 Institute of Physics, Polish Academy of Science, Al. Lotnikow 32/46 02-668 Warsaw, Poland * Email: mkouza@; masli@ Received: 15 July 2017; Accepted for publication: 15 December 2017 ABSTRACT Recently single molecule force spectroscopy has become an useful tool to study protein, DNA and RNA. However, very little attention was paid to homopolymer which plays an important role in many domains of science. In this paper we make the first attempt to decipher the free energy landscape of homopolymer using the external force as reaction coordinate. The impact of the quenched force on the free energy landscape was studied using simplified coarsegrain Go model. Similar to protein, we have obtained a clear switch from the thermal regime to force-driven regime. The distance between the denatured state and transition state in the temperature-driven regime is smaller than in the force-driven one. Having a rugged free energy landscape without a pronounced funnel the homopolymer folding is much slower than that of protein making study of homopolymer very time consuming. Keywords: protein refolding, folding pathways, free energy landscape, distance between denaturate and transition states, Go model. 1. INTRODUCTION Recently great advance in understanding free energy landscape (FEL) of biomolecules has been achieved [1 - 3], but very little was known about FEL of homopolymer which is important not only for basic research but also for application. In single molecule force .
