title: Time-Dependent Markov State Models for Single Molecule Force Spectroscopy.
abstract: This Letter demonstrates that using time-dependent Markov state models (TD-MSMs) one can obtain molecular-scale insights into force-extension curves for a variety of stretching experiments. A master-MSM constructed at a reference extension forms the basis for generating the required TD-MSM, i.e., the TD-MSM that is appropriate for the stretching experiment can be constructed from a single master-MSM. In addition, the availability of state-specific force models enable calculation of force-extension behavior in a variety of ensembles. Changes in the network topology upon stretching are related through a thermodynamic quantity termed the mechanical disposition. Proof-of-principle is provided using a stretched alanine decapeptide under a time-varying pulling force.
authors.affiliation: Department of Physics, Indian Institute of Technology Guwahati , Guwahati 781039, India.
authors.forename: Susmita
authors.initials: S
authors.lastname: Ghosh
authors.affiliation: Department of Chemical Engineering, Indian Institute of Technology Bombay , Mumbai 400076, India.
authors.forename: Abhijit
authors.identifier: http://orcid.org/0000-0002-3747-8433
authors.initials: A
authors.lastname: Chatterjee
authors.affiliation: Department of Physics, Indian Institute of Technology Guwahati , Guwahati 781039, India.|Department of Chemical Engineering, Indian Institute of Technology Bombay , Mumbai 400076, India.
authors.forename: Swati
authors.identifier: http://orcid.org/0000-0003-1960-443X
authors.initials: S
authors.lastname: Bhattacharya
mesh_terms: D000409:Alanine / Q000737:chemistry; D008390:Markov Chains; D018625:Microscopy, Atomic Force; D008958:Models, Molecular; D009842:Oligopeptides / Q000737:chemistry; D011487:Protein Conformation; D013997:Time Factors
chemical_list: D009842:Oligopeptides; D000409:Alanine