TY - JOUR
T1 - Wet and dry internal friction can be measured with the Jarzynski equality
AU - Ramalingam Kailasham, null
AU - Chakrabarti, Rajarshi
AU - Prakash, J. Ravi
N1 - Publisher Copyright:
© 2020 authors. Published by the American Physical Society.
Copyright:
Copyright 2021 Elsevier B.V., All rights reserved.
PY - 2020/3
Y1 - 2020/3
N2 - The existence of two types of internal friction-wet and dry-is revisited, and a simple protocol is proposed for distinguishing between the two types and extracting the appropriate internal friction coefficient. The scheme requires repeatedly stretching a polymer molecule and measuring the average work dissipated in the process by applying the Jarzynski equality. The internal friction coefficient is then estimated from the average dissipated work in the extrapolated limit of zero solvent viscosity. The validity of the protocol is established through analytical calculations on a one-dimensional free-draining Hookean spring-dashpot model for a polymer, and Brownian dynamics simulations of (a) a single-mode nonlinear spring-dashpot model for a polymer and (b) a finitely extensible bead-spring chain with cohesive intrachain interactions, both of which incorporate fluctuating hydrodynamic interactions. Well-established single-molecule manipulation techniques, such as optical tweezer-based pulling, can be used to implement the suggested protocol experimentally.
AB - The existence of two types of internal friction-wet and dry-is revisited, and a simple protocol is proposed for distinguishing between the two types and extracting the appropriate internal friction coefficient. The scheme requires repeatedly stretching a polymer molecule and measuring the average work dissipated in the process by applying the Jarzynski equality. The internal friction coefficient is then estimated from the average dissipated work in the extrapolated limit of zero solvent viscosity. The validity of the protocol is established through analytical calculations on a one-dimensional free-draining Hookean spring-dashpot model for a polymer, and Brownian dynamics simulations of (a) a single-mode nonlinear spring-dashpot model for a polymer and (b) a finitely extensible bead-spring chain with cohesive intrachain interactions, both of which incorporate fluctuating hydrodynamic interactions. Well-established single-molecule manipulation techniques, such as optical tweezer-based pulling, can be used to implement the suggested protocol experimentally.
KW - Biomolecular dynamics
KW - Fluctuation Theorems
KW - Polymer conformation changes
KW - Brownian dynamics simulations
KW - Proteins
KW - Nonequilibrium and irreversible thermodynamics
UR - http://www.scopus.com/inward/record.url?scp=85089367535&partnerID=8YFLogxK
U2 - 10.1103/PhysRevResearch.2.013331
DO - 10.1103/PhysRevResearch.2.013331
M3 - Article
AN - SCOPUS:85089367535
SN - 2643-1564
VL - 2
JO - Physical Review Research
JF - Physical Review Research
IS - 1
M1 - 013331
ER -