Phase boundaries as agents of structural change in macromolecules

Raj, Ritwik; Purohit, Prashant K.

doi:10.1016/j.jmps.2011.07.003

Cited by 17 publications

(13 citation statements)

References 29 publications

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“…To examine the role of viscous friction during fast unfolding of coiled-coils, we model the protein as a one-dimensional phasetransforming continuum rod. This framework has been previously used to rationalize materials exhibiting phase transitions including rod-like macromolecules such as DNA 61,62 or beam-like nanoscale materials such as multi-walled carbon nanotubes 63 . It has also been applied to the α-helix to β -sheet transition in muscle protein titin 64 or in the whelk egg capsule biopolymer 65,66 .…”

Section: A Continuum Model Of Phasetransforming Rodsmentioning

confidence: 99%

Combined molecular/continuum modeling reveals the role of friction during fast unfolding of coiled-coil proteins

et al. 2019

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Section: A Continuum Model Of Phasetransforming Rodsmentioning

confidence: 99%

Combined molecular/continuum modeling reveals the role of friction during fast unfolding of coiled-coil proteins

et al. 2019

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“…The described competition between the entropic energy of the unfolded fraction and the b-sheet unfolding energy has been analysed in [35,36] via Monte Carlo simulations combining a worm-like chain (WLC) with a two-state bell-type model for the unfolding. Finally, we recall the fully phenomenological continuum approaches recently proposed in [37,38] where the authors show the possibility of describing the protein unfolding as an energy minimization of a continuum system with a non-convex internal energy. In particular in [37], based on the general approach of [24,39] for the description of the mechanical behaviour of bistable discrete chains, the authors obtain an interesting characterization of an optimality condition of the number of b-sheet domains with respect to the toughness of the macromolecule.…”

Section: Introductionmentioning

confidence: 99%

An energetic model for macromolecules unfolding in stretching experiments

Tommasi

Millardi

Puglisi

et al. 2013

J. R. Soc. Interface.

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We propose a simple approach, based on the minimization of the total (entropic plus unfolding) energy of a two-state system, to describe the unfolding of multidomain macromolecules (proteins, silks, polysaccharides, nanopolymers). The model is fully analytical and enlightens the role of the different energetic components regulating the unfolding evolution. As an explicit example, we compare the analytical results with a titin atomic force microscopy stretch-induced unfolding experiment showing the ability of the model to quantitatively reproduce the experimental behaviour. In the thermodynamic limit, the sawtooth force-elongation unfolding curve degenerates to a constant force unfolding plateau.

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“…where ρ(x, t) is the mass per unit length and and T (x, t) is the tension in the rod [22,24,23]. If we localize this equation to a discontinuity s(t) (with x 1 ≤ s(t) ≤ x 2 ) then we get the linear momentum jump condition…”

Section: Balance Lawsmentioning

confidence: 99%

“…All these examples involve filaments whose lengths are microns or smaller and they are usually surrounded by a viscous fluid, so that inertia forces are 2 negligible. We have studied the propagation of phase boundaries in such rods earlier [24,37]. Recently, however, macroscopic yarns (called 'artificial muscles') have been fabricated to perform actuation in which inertia forces cannot be neglected [17].…”

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(Adiabatic) phase boundaries in a bistable chain with twist and stretch

Zhao

Purohit

2016

Journal of the Mechanics and Physics of Solids

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Mass-spring chains with only extensional degrees of freedom have provided insights into the behavior of crystalline solids, including those capable of phase transitions. Here we add rotational degrees of freedom to the masses in a chain and study the dynamics of phase boundaries across which both the twist and stretch can jump. We solve impact and Riemann problems in the chain by numerical integration of the equations of motion and show that the solutions are analogous to those in a phase transforming rod whose stored energy function depends on both twist and stretch. From the dynamics of phase boundaries in the chain we extract a kinetic relation whose form is familiar from earlier studies involving chains with only extensional degrees of freedom. However, for some combinations of parameters characterizing the energy landscape of our springs we find propagating phase boundaries for which the rate of dissipation, as calculated using isothermal expressions for the driving force, is negative. This suggests that we cannot neglect the energy stored in the oscillations of the masses in the interpretation of the dynamics of mass-spring chains. Keeping this in mind we define a local temperature of our chain and show that it jumps across phase boundaries, but not across sonic waves. Hence, impact problems in our mass-spring chains are analogous to those on continuum thermoelastic bars with Mie-Gruneisen type constitutive laws. At the end of the paper we use our chain to shed some light on experiments involving yarns that couple twist and stretch to perform useful work in response to various stimuli.

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Phase boundaries as agents of structural change in macromolecules

Cited by 17 publications

References 29 publications

Combined molecular/continuum modeling reveals the role of friction during fast unfolding of coiled-coil proteins

Combined molecular/continuum modeling reveals the role of friction during fast unfolding of coiled-coil proteins

An energetic model for macromolecules unfolding in stretching experiments

(Adiabatic) phase boundaries in a bistable chain with twist and stretch

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