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Buddhapriya Chakrabarti

Publications and source records attributed to Buddhapriya Chakrabarti.

29 records · Page 2Linked to original sources
arXiv2012

Dynamic response of open cell dry foams

We study the mechanical response of an open cell dry foam subjected to periodic forcing using experiments and theory. Using the measurements of the static and dynamic stress-strain relationship, we derive an over-damped model of the foam, as a set of infinitesimal non-linear springs, where the damping term depends on the local foam strain. We then analyse the properties of the foam when subjected to large amplitudes periodic stresses and determine the conditions for which the foam becomes optimally absorbing.

cond-mat.soft↗
arXiv2010

Frequency-dependent Chemolocation and Chemotactic Target Selection

Chemotaxis is typically modeled in the context of cellular motion towards a static, exogenous source of chemoattractant. Here, we propose a time-dependent mechanism of chemotaxis in which a self-propelled particle ({\it e.g.}, a cell) releases a chemical that diffuses to fixed particles (targets) and signals the production of a second chemical by these targets. The particle then moves up concentration gradients of this second chemical, analogous to diffusive echolocation. When one target is present, we describe probe release strategies that optimize travel of the cell to the target. In the presence of multiple targets, the one selected by the cell depends on the strength and, interestingly, on the frequency of probe chemical release. Although involving an additional chemical signaling step, our chemical ``pinging'' hypothesis allows for greater flexibility in regulating target selection, as seen in a number of physical or biological realizations.

q-bio.CB↗
arXiv2009

Counterion desorption and globule-coil transition of a polyelectrolyte under tension

We explore the mechanical response of a single polyelectrolyte chain under tension in good and poor solvents using a combination of simulation and theory. In poor solvents, where the equilibrium state of the chain is a collapsed globule, we find that the chain undergoes a globule-coil transition, as the magnitude of the force is increased beyond a critical value. This transition, where the polymer size changes discontinuously from a small to a large value, is accompanied by release of bound counterions from the chain. We explain these results by adhering to a statistical mechanical theory of counter-ion condensation on flexible polyelectrolytes.

cond-mat.soft↗
arXiv2009

Shear Unzipping of DNA

We study theoretically the mechanical failure of a simple model of double stranded DNA under an applied shear. Starting from a more microscopic Hamiltonian that describes a sheared DNA, we arrive at a nonlinear generalization of a ladder model of shear unzipping proposed earlier by deGennes [deGennes P. G. C. R. Acad. Sci., Ser. IV; Phys., Astrophys. 2001, 1505]. Using this model and a combination of analytical and numerical methods, we study the DNA "unzipping" transition when the shearing force exceeds a critical threshold at zero temperature. We also explore the effects of sequence heterogeneity and finite temperature and discuss possible applications to determine the strength of colloidal nanoparticle assemblies functionalized by DNA.

cond-mat.soft↗
arXiv2005

Routes to spatiotemporal chaos in the rheology of nematogenic fluids

With a view to understanding the ``rheochaos'' observed in recent experiments in a variety of orientable fluids, we study numerically the equations of motion of the spatiotemporal evolution of the traceless symmetric order parameter of a sheared nematogenic fluid. In particular we establish, by decisive numerical tests, that the irregular oscillatory behavior seen in a region of parameter space where the nematic is not stably flow-aligning is in fact spatiotemporal chaos. We outline the dynamical phase diagram of the model and study the route to the chaotic state. We find that spatiotemporal chaos in this system sets in via a regime of {\em spatiotemporal intermittency}, with a power-law distribution of the widths of laminar regions, as in H. Chaté and P. Manneville, Phys. Rev. Lett. {\bf 58}, 112 (1987). Further, the evolution of the histogram of band sizes shows a growing length-scale as one moves from the chaotic towards the flow aligned phase. Finally we suggest possible experiments which can observe the intriguing behaviors discussed here.

cond-mat.soft↗
arXiv2004

The nonlinear elasticity of an $α$-helical polypeptide: Monte Carlo studies

We perform Monte Carlo simulations to study the elastic properties of the helix-coil worm-like chain model of alpha-helical polypeptides. In this model the secondary structure enters as a scalar (Ising like) variable that controls the local chain bending modulus. We compute numerically the bending and stretching compliances of this molecule as well as the nonlinear interaction between stretching and torque over a wide range of model parameters. The numerical results agree well with previous mean-field and perturbative calculations where they are expected to do so. The Monte Carlo simulations allow us to examine the response of the chain to large forces and torques where the perturbative approaches fail. In addition we extend our mean-field analysis by studying the fluctuation dominated regime at the force-induced denaturation transition.

cond-mat.soft↗
arXiv2004

Interplay of instabilities in mounded surface growth

We numerically study a one-dimensional conserved growth equation with competing linear (Ehrlich-Schwoebel) and nonlinear instabilities. As a control parameter is varied, this model exhibits a non-equilibrium phase transition between two mounded states, one of which exhibits slope selection and the other does not. The coarsening behavior of mounds in these two phases is studied in detail. In the absence of noise the steady-state configuration depends crucially on which of the two instabilities dominates the early time behavior.

cond-mat.mtrl-sci↗
arXiv2004

The nonlinear elasticity of an $α$-helical polypeptide

We study a minimal extension of the worm-like chain to describe polypeptides having alpha-helical secondary structure. In this model presence/absence of secondary structure enters as a scalar variable that controls the local chain bending modulus. Using this model we compute the extensional compliance of an alpha-helix under tensile stress, the bending compliance of the molecule under externally imposed torques, and the nonlinear interaction of such torques and forces on the molecule. We find that, due to coupling of the ``internal'' secondary structure variables to the conformational degrees of freedom of the polymer, the molecule has a highly nonlinear response to applied stress and force couples. In particular we demonstrate a sharp lengthening transition under applied force and a buckling transition under applied torque. Finally, we speculate that the inherent bistability of the molecule may underlie protein conformational change \emph{in vivo}.

cond-mat.stat-mech↗
arXiv2003

Spatiotemporal rheochaos in nematic hydrodynamics

Motivated by the observation of rheochaos in sheared wormlike micelles [Bandyopadhyay et al., Phys. Rev. Lett, 84 2022, (2000); Europhys. Lett. 56, 447 (2001); Pramana 53, 223 (1999)] we study the coupled nonlinear partial differential equations for the hydrodynamic velocity and order parameter fields in a sheared nematogenic fluid. In a suitable parameter range, we find irregular, dynamic shear-banding and establish by decisive numerical tests that the chaos we observe in the model is spatiotemporal in nature.

cond-mat.soft↗
arXiv2003

Mound formation and coarsening from a nonlinear instability in surface growth

We study a class of one-dimensional, nonequilibrium, conserved growth equations for both nonconserved and conserved noise statistics using numerical integration. An atomistic version of these growth equations is also studied using stochastic simulation. The models with nonconserved noise statistics are found to exhibit mound formation and power-law coarsening with slope selection for a range of values of the model parameters. Unlike previously proposed models of mound formation, the Ehrlich-Schwoebel step-edge barrier, usually modeled as a linear instability in growth equations, is absent in our models. Mound formation in our models occurs due to a nonlinear instability in which the height (depth) of spontaneously generated pillars (grooves) increases rapidly if the initial height (depth) is sufficiently large. When this instability is controlled by the introduction of an infinite number of higher-order gradient nonlinearities, the system exhibits a first-order dynamical phase transition from a rough self-affine phase to a mounded one as the value of the parameter that measures the effectiveness of control is decreased. We define a new ``order parameter'' that may be used to distinguish between these two phases. In the mounded phase, the system exhibits power-law coarsening of the mounds in which a selected slope is retained at all times. The coarsening exponents for the continuum equation and the discrete model are found to be different. An explanation of this difference is proposed and verified by simulations. In the growth equation with conserved noise, we find the curious result that the kinetically rough and mounded phases are both locally stable in a region of parameter space. In this region, the initial configuration of the system determines its steady-state behavior.

cond-mat.stat-mech↗