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Kranthi K. Mandadapu

Publications and source records attributed to Kranthi K. Mandadapu.

50 records · Page 3Linked to original sources
arXiv2019

An isogeometric finite element formulation for phase transitions on deforming surfaces

This paper presents a general theory and isogeometric finite element implementation for studying mass conserving phase transitions on deforming surfaces. The mathematical problem is governed by two coupled fourth-order nonlinear partial differential equations (PDEs) that live on an evolving two-dimensional manifold. For the phase transitions, the PDE is the Cahn-Hilliard equation for curved surfaces, which can be derived from surface mass balance in the framework of irreversible thermodynamics. For the surface deformation, the PDE is the (vector-valued) Kirchhoff-Love thin shell equation. Both PDEs can be efficiently discretized using $C^1$-continuous interpolations without derivative degrees-of-freedom (dofs). Structured NURBS and unstructured spline spaces with pointwise $C^1$-continuity are utilized for these interpolations. The resulting finite element formulation is discretized in time by the generalized-$α$ scheme with adaptive time-stepping, and it is fully linearized within a monolithic Newton-Raphson approach. A curvilinear surface parameterization is used throughout the formulation to admit general surface shapes and deformations. The behavior of the coupled system is illustrated by several numerical examples exhibiting phase transitions on deforming spheres, tori and double-tori.

math.NA↗
arXiv2019

Theory for Glassy Behavior of Supercooled Liquid Mixtures

We present a model for glassy dynamics in supercooled liquid mixtures. Given the relaxation behavior of individual supercooled liquids, the model predicts the relaxation times of their mixtures as temperature is decreased. The model is based on dynamical facilitation theory for glassy dynamics, which provides a physical basis for relaxation and vitrification of a supercooled liquid. This is in contrast to empirical linear interpolations such as the Gordon-Taylor equation typically used to predict glass transition temperatures of liquid mixtures. To understand the behavior of supercooled liquid mixtures we consider a multi-component variant of the kinetically constrained East model in which components have a different energy scale and can also diffuse when locally mobile regions, i.e., excitations, are present. Using a variational approach we determine an effective single component model with a single effective energy scale that best approximates a mixture. When scaled by this single effective energy, we show that experimental relaxation times of many liquid mixtures all collapse onto the 'parabolic law' predicted by dynamical facilitation theory. The model can be used to predict transport properties and glass transition temperatures of mixtures of glassy materials, with implications in atmospheric chemistry, biology, and pharmaceuticals.

cond-mat.stat-mech↗
arXiv2018

On the Polar Nature and Invariance Properties of a Thermomechanical Theory for Continuum-on-Continuum Homogenization

This paper makes a rigorous case for considering the homogenized continuum derived by the Irving-Kirkwood procedure as a polar medium in which the balances of angular momentum and energy contain contributions due to body couples and couple stresses defined in terms of the underlying microscopic state. The paper also addresses the question of invariance of macroscopic stress and heat flux and form-invariance of the macroscopic balance laws.

physics.class-ph↗
arXiv2018

Mechanisms for bacterial gliding motility on soft substrates

The motility mechanism of certain rod-shaped bacteria has long been a mystery, since no external appendages are involved in their motion which is known as gliding. However, the physical principles behind gliding motility still remain poorly understood. Using myxobacteria as a canonical example of such organisms, we identify here the physical principles behind gliding motility, and develop a theoretical model that predicts a two-regime behavior of the gliding speed as a function of the substrate stiffness. Our theory describes the elastic, viscous, and capillary interactions between the bacterial membrane carrying a traveling wave, the secreted slime acting as a lubricating film, and the substrate which we model as a soft solid. Defining the myxobacterial gliding as the horizontal motion on the substrate under zero net force, we find the two-regime behavior is due to two different mechanisms of motility thrust. On stiff substrates, the thrust arises from the bacterial shape deformations creating a flow of slime that exerts a pressure along the bacterial length. This pressure in conjunction with the bacterial shape provides the necessary thrust for propulsion. However, we show that such a mechanism cannot lead to gliding on very soft substrates. Instead, we show that capillary effects lead to the formation of a ridge at the slime-substrate-air interface, which creates a thrust in the form of a localized pressure gradient at the tip of the bacteria. To test our theory, we perform experiments with isolated cells on agar substrates of varying stiffness and find the measured gliding speeds to be in good agreement with the predictions from our elasto-capillary-hydrodynamic model. The physical mechanisms reported here serve as an important step towards an accurate theory of friction and substrate-mediated interaction between bacteria in a swarm of cells proliferating in soft media.

physics.bio-ph↗
arXiv2018

Solvation in Space-Time: Pre-transition Effects in Trajectory Space

We demonstrate pre-transition effects in space-time in trajectories of systems in which the dynamics displays a first-order phase transition between distinct dynamical phases. These effects are analogous to those observed for thermodynamic first-order phase transitions, most notably the hydrophobic effect in water. Considering the (infinite temperature) East model as an elementary example, we study the properties of "space-time solvation" by examining trajectories where finite space-time regions are conditioned to be inactive in an otherwise active phase. Analogous to ideal hydrophobic solutes in water, we show that solvating an inactive region of space-time within an active trajectory shows two regimes in the dynamical equivalent of solvation free energy: an "entropic" small solute regime in which uncorrelated fluctuations are sufficient to evacuate activity from the solute, and an "energetic" large solute regime which involves the formation of a solute-induced inactive domain with an associated active-inactive interface bearing a dynamical interfacial tension. We also show that as a result of this dynamical interfacial tension there is a dynamical analog of the hydrophobic collapse that drives the assembly of large hydrophobes in water. We discuss the general relevance of these results to the properties of dynamical fluctuations in systems with slow collective relaxation such as glass formers.

cond-mat.stat-mech↗
arXiv2018

On the nature of the glass transition in atomistic models of glass formers

We study the nature of the glass transition by cooling model atomistic glass formers at constant rate from a temperature above the onset of glassy dynamics to $T=0$. Motivated by the East model, a kinetically constrained lattice model with hierarchical relaxation, we make several predictions about the behavior of the supercooled liquid as it passes through the glass transition. We then compare those predictions to the results of our atomistic simulations. Consistent with our predictions, our results show that the relaxation time $τ$ of the material undergoes a crossover from super-Arrhenius to Arrhenius behavior at a cooling-rate-dependent glass transition temperature $T_\text{g}$. The slope of $\lnτ$ with respect to inverse temperature exhibits a peak near $T_\text{g}$ that grows more pronounced with slower cooling, matching our expectations qualitatively. Additionally, the limiting value of this slope at low temperature shows remarkable quantitative agreement with our predictions. Our results also show that the rate of short-time particle displacements deviates from the equilibrium linear scaling around $T_\text{g}$, asymptotically approaching a different linear scaling. To our surprise, these short-time displacements, the dynamic indicators of the underlying excitations responsible for structural relaxation, show no spatial correlations beyond a few particle diameters, both above and below $T_\text{g}$. This final result is contrary to our expectation, based on previous results for East model glasses formed by cooling, that inter-excitation correlations should emerge as the liquid vitrifies.

cond-mat.stat-mech↗
arXiv2018

The irreversible thermodynamics of curved lipid membranes

The theory of irreversible thermodynamics for arbitrarily curved lipid membranes is presented here. The coupling between elastic bending and irreversible processes such as intra-membrane lipid flow, intra-membrane phase transitions, and protein binding and diffusion is studied. The forms of the entropy production for the irreversible processes are obtained, and the corresponding thermodynamic forces and fluxes are identified. Employing the linear irreversible thermodynamic framework, the governing equations of motion along with appropriate boundary conditions are provided.

cond-mat.soft↗
arXiv2017

Generalized hydrodynamics of active polar suspensions

We utilize a generalized Irving-Kirkwood procedure to derive the hydrodynamic equations of an active matter suspension with internal structure and driven by internal torque. The internal structure and torque of the active Brownian particles give rise to a balance law for internal angular momentum density, making the hydrodynamic description a polar theory of continuum mechanics. We derive exact microscopic expressions for the stress tensor, couple stress tensor, internal energy density, and heat flux vector. Unlike passive matter, the symmetry of the stress tensor is broken explicitly due to active internal torque and the antisymmetric component drives the internal angular momentum density. These results provide a molecular basis to understand the transport characteristics and collectively provide a strategy to develop the theory of linear irreversible thermodynamics of active matter.

cond-mat.stat-mech↗
arXiv2017

Topological localization in out-of-equilibrium dissipative systems

In this paper we report that notions of topological protection can be applied to stationary configurations that are driven far from equilibrium by active, dissipative processes. We show this for physically two disparate cases : stochastic networks governed by microscopic single particle dynamics as well as collections of driven, interacting particles described by coarse-grained hydrodynamic theory. In both cases, the presence of dissipative couplings to the environment that break time reversal symmetry are crucial to ensuring topologically protection. These examples constitute proof of principle that notions of topological protection, established in the context of electronic and mechanical systems, do indeed extend generically to processes that operate out of equilibrium. Such topologically robust boundary modes have implications for both biological and synthetic systems.

cond-mat.stat-mech↗
arXiv2016

A stabilized finite element formulation for liquid shells and its application to lipid bilayers

This paper presents a new finite element (FE) formulation for liquid shells that is based on an explicit, 3D surface discretization using $C^1$-continuous finite elements constructed from NURBS interpolation. Both displacement-based and mixed FE formulations are proposed. The latter is needed for area-incompressible material behavior, where penalty-type regularizations can lead to misleading results. In order to obtain quasi-static solutions, several numerical stabilization schemes are proposed based on either stiffness, viscosity or projection. Several numerical examples are considered in order to illustrate the accuracy and the capabilities of the proposed formulation, and to compare the different stabilization schemes. The presented formulation is capable of simulating non-trivial surface shapes associated with tube formation and protein-induced budding of lipid bilayers. In the latter case, the presented formulation yields non-axisymmetric solutions, which have not been observed in previous simulations. It is shown that those non-axisymmetric shapes are preferred over axisymmetric ones.

cs.CE↗
arXiv2015

Pre-transition effects mediate forces of assembly between transmembrane proteins

We present a mechanism for a generic and powerful force of assembly and mobility for transmembrane proteins in lipid bilayers. This force is a pre-transition (or pre-melting) effect for the first-order transition between ordered and disordered phases in the host membrane. Using large scale molecular simulation, we show that a protein with hydrophobic thickness equal to that of the disordered phase embedded in an ordered bilayer stabilizes a microscopic order-disorder interface, and the stiffness of that interface is finite. When two such proteins approach each other, they assemble because assembly reduces the net interfacial free energy. In analogy with the hydrophobic effect, we refer to this phenomenon as the "orderphobic effect". The effect is mediated by proximity to the order-disorder phase transition and the size and hydrophobic mismatch of the protein. The strength and range of forces arising from the orderphobic effect are significantly larger than those that could arise from membrane elasticity for the membranes we examine.

cond-mat.soft↗
arXiv2015

The order-disorder transition in model lipid bilayers is a first-order hexatic to liquid phase transition

We characterize the order-disorder transition in a model lipid bilayer using molecular dynamics simulations. We find that the ordered phase is hexatic. In particular, in-plane structures possess a finite concentration of 5-7 disclination pairs that diffuse throughout the plane of the bilayer, and further, in-plane structures exhibit long-range orientational order and short-range translational order. In contrast, the disordered phase is liquid. The transition between the two phases is first order. Specifically, it exhibits hysteresis, and coexistence exhibits an interface with capillary scaling. The location of the interface and its spatial fluctuations are analyzed with a spatial field constructed from a rotational-invariant for local 6-fold orientational order. As a result of finite interfacial tension, there necessarily exist associated forces of assembly between membrane-bound solutes that pre-melt the ordered phase.

cond-mat.soft↗
arXiv2015

Mechanics of torque generation in the bacterial flagellar motor

The bacterial flagellar motor (BFM) is responsible for driving bacterial locomotion and chemotaxis, fundamental processes in pathogenesis and biofilm formation. In the BFM, torque is generated at the interface between transmembrane proteins (stators) and a rotor. It is well-established that the passage of ions down a transmembrane gradient through the stator complex provides the energy needed for torque generation. However, the physics involved in this energy conversion remain poorly understood. Here we propose a mechanically specific model for torque generation in the BFM. In particular, we identify two fundamental forces involved in torque generation: electrostatic and steric. We propose that electrostatic forces serve to position the stator, while steric forces comprise the actual 'power stroke'. Specifically, we predict that ion-induced conformational changes about a proline 'hinge' residue in an $α$-helix of the stator are directly responsible for generating the power stroke. Our model predictions fit well with recent experiments on a single-stator motor. Furthermore, we propose several experiments to elucidate the torque-speed relationship in motors where the number of stators may not be constant. The proposed model provides a mechanical explanation for several fundamental features of the flagellar motor, including: torque-speed and speed-ion motive force relationships, backstepping, variation in step sizes, and the puzzle of swarming experiments.

physics.bio-ph↗