Wet and dry internal friction can be measured with the Jarzynski equality

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 intra-chain 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.Comment: 27 pages, 17 figure

Endoplasmic reticulum stress, degeneration of pancreatic islet β-cells, and therapeutic modulation of the unfolded protein response in diabetes.

BackgroundMyriad challenges to the proper folding and structural maturation of secretory pathway client proteins in the endoplasmic reticulum (ER) - a condition referred to as "ER stress" - activate intracellular signaling pathways termed the unfolded protein response (UPR).Scope of reviewThrough executing transcriptional and translational programs the UPR restores homeostasis in those cells experiencing manageable levels of ER stress. But the UPR also actively triggers cell degeneration and apoptosis in those cells that are encountering ER stress levels that exceed irremediable thresholds. Thus, UPR outputs are "double-edged". In pancreatic islet β-cells, numerous genetic mutations affecting the balance between these opposing UPR functions cause diabetes mellitus in both rodents and humans, amply demonstrating the principle that the UPR is critical for the proper functioning and survival of the cell.Major conclusionsSpecifically, we have found that the UPR master regulator IRE1α kinase/endoribonuclease (RNase) triggers apoptosis, β-cell degeneration, and diabetes, when ER stress reaches critical levels. Based on these mechanistic findings, we find that novel small molecule compounds that inhibit IRE1α during such "terminal" UPR signaling can spare ER stressed β-cells from death, perhaps affording future opportunities to test new drug candidates for disease modification in patients suffering from diabetes

Exact analytical evaluation of time dependent transmission coefficient from the method of reactive flux for an inverted parabolic barrier

In this paper we derive a general expression for the transmission coefficient using the method of reactive flux for a particle coupled to a harmonic bath surmounting a one dimensional inverted parabolic barrier. Unlike Kohen and Tannor [J. Chem. Phys. 103, 6013 (1995)] we use a normal mode analysis where the unstable and the other modes have a complete physical meaning. Importantly our approach results a very general expression for the time dependent transmission coefficient not restricted to overdamped limit. Once the spectral density for the problem is know one can use our formula to evaluate the time dependent transmission coefficient. We have done the calculations with time dependent friction used by Xie [Phys. Rev. Lett 93, 180603 (2004)] and also the one used by Kohen and Tannor [J. Chem. Phys. 103, 6013 (1995)]. Like the formula of Kohen and Tannor our formula also reproduces the results of transition state theory as well as the Kramers theory in the limits t->0 and t->infinity respectively

Experimental Observations of Group Synchrony in a System of Chaotic Optoelectronic Oscillators

We experimentally demonstrate group synchrony in a network of four nonlinear optoelectronic oscillators with time-delayed coupling. We divide the nodes into two groups of two each, by giving each group different parameters and by enabling only inter-group coupling. When coupled in this fashion, the two groups display different dynamics, with no isochronal synchrony between them, but the nodes in a single group are isochronally synchronized, even though there is no intra-group coupling. We compare experimental behavior with theoretical and numerical results

Thermodynamics of the PNJL model with nonzero baryon and isospin chemical potentials

We have extended the Polyakov-Nambu-Jona-Lasinio (PNJL) model for two degenerate flavours to include the isospin chemical potential ($\mu_I$). All the diagonal and mixed derivatives of pressure with respect to the quark number (proportional to baryon number) chemical potential ($\mu_0$) and isospin chemical potential upto sixth order have been extracted at $\mu_0 = \mu_I = 0$. These derivatives give the generalized susceptibilities with respect to quark and isospin numbers. Similar estimates for the flavour diagonal and off-diagonal susceptibilities are also presented. Comparison to Lattice QCD (LQCD) data of some of these susceptibilities for which LQCD data are available, show similar temperature dependence, though there are some quantitative deviations above the crossover temperature. We have also looked at the effects of instanton induced flavour-mixing coming from the $U_A(1)$ chiral symmetry breaking 't Hooft determinant like term in the NJL part of the model. The diagonal quark number and isospin susceptibilities are completely unaffected. The off-diagonal susceptibilities show significant dependence near the crossover. Finally we present the chemical potential dependence of specific heat and speed of sound within the limits of chemical potentials where neither diquarks nor pions can condense.Comment: 15 pages, 7 figures, Added discussions and references, version to appear in Phys. Rev.

Preface - Personal perspectives in nonlinear science : Looking back, looking forward

Peer reviewedPublisher PD

How important are fluctuations in the treatment of internal friction in polymers?

The Rouse model with internal friction (RIF), a widely used theoretical framework to interpret the effects of internal friction on conformational transitions in biomolecules, is shown to be an approximate treatment that is based on preaveraging internal friction. By comparison with Brownian dynamics simulations of an exact coarse-grained model that incorporates fluctuations in internal friction, the accuracy of the preaveraged model predictions is examined both at and away from equilibrium. While the two models predict intrachain autocorrelations that approach each other for long enough chain segments, they differ in their predictions for shorter segments. Furthermore, the two models differ qualitatively in their predictions for the chain extension and viscosity in shear flow, which is taken to represent a prototypical out-of-equilibrium condition.Comment: 10 pages, 5 figures, additional supplemental materia

Shear viscosity for finitely extensible chains with fluctuating internal friction and hydrodynamic interactions

An exact solution of coarse-grained polymer models with fluctuating internal friction and hydrodynamic interactions has not been proposed so far due to a one-to-all coupling between the connector vector velocities that precludes the formulation of the governing stochastic differential equations. A methodology for the removal of this coupling is presented, and the governing stochastic differential equations, obtained by attaching a kinetic interpretation to the Fokker-Planck equation for the system, are integrated numerically using Brownian dynamics simulations. The proposed computational route eliminates the calculation of the divergence of the diffusion tensor which appears in models with internal friction, and is about an order of magnitude faster than the recursion-based algorithm for the decoupling of connector-vector velocities previously developed [J. Rheol., 65, 903 (2021)] for the solution of freely draining models with internal friction. The effects of the interplay of various combinations of finite extensibility, internal friction and hydrodynamic interactions on the steady-shear-viscosity is examined. While finite extensibility leads solely to shear-thinning, both internal friction and hydrodynamic interactions result in shear-thinning followed by shear-thickening. The shear-thickening induced by internal friction effects are more pronounced than that due to hydrodynamic interactions.Comment: Comments: To appear in the Journal of Rheology, 20 pages, 9 figures, includes Supplemental Materia

Rheological consequences of wet and dry friction in a dumbbell model with hydrodynamic interactions and internal viscosity

The effect of fluctuating internal viscosity and hydrodynamic interactions on a range of rheological properties of dilute polymer solutions is examined using a finitely extensible dumbbell model for a polymer. Brownian dynamics simulations are used to compute both transient and steady state viscometric functions in shear flow. The results enable a careful differentiation of the influence, on rheological properties, of solvent-mediated friction from that of a dissipative mechanism that is independent of solvent viscosity. In particular, hydrodynamic interactions have a significant influence on the magnitude of the stress jump at the inception of shear flow, and on the transient viscometric functions, but a negligible effect on the steady state viscometric functions at high shear rates. Zero-shear rate viscometric functions of free-draining dumbbells remain essentially independent of the internal viscosity parameter, as predicted by the Gaussian approximation, but the inclusion of hydrodynamic interactions induces a dependence on both the hydrodynamic interaction and the internal viscosity parameter. Large values of the internal viscosity parameter lead to linear viscoelastic predictions that mimic the behavior of rigid dumbbell solutions. On the other hand, steady-shear viscometric functions at high shear rates differ in general from those for rigid dumbbells, depending crucially on the finite extensibility of the dumbbell spring.Comment: 26 pages, 19 figures, to appear in J. Chem. Phy