arXiv subjects

Kranthi K. Mandadapu

Publications and source records attributed to Kranthi K. Mandadapu.

At least 37 records · Page 2Linked to original sources

arXiv2023

Emergent Facilitation and Glassy Dynamics in Supercooled Liquids

In supercooled liquids, dynamical facilitation refers to a phenomenon where microscopic motion begets further motion nearby, resulting in spatially heterogeneous dynamics. This is central to the glassy relaxation dynamics of such liquids, which show super-Arrhenius growth of relaxation timescales with decreasing temperature. Despite the importance of dynamical facilitation, there is no theoretical understanding of how facilitation emerges and impacts relaxation dynamics. Here, we present a theory that explains the microscopic origins of dynamical facilitation. We show that dynamics proceeds by localized bond-exchange events, also known as excitations, resulting in the accumulation of elastic stresses with which new excitations can interact. At low temperatures, these elastic interactions dominate and facilitate the creation of new excitations near prior excitations. Using the theory of linear elasticity and Markov processes, we simulate a model, which reproduces multiple aspects of glassy dynamics observed in experiments and molecular simulations, including the stretched exponential decay of relaxation functions, the super-Arrhenius behavior of relaxation timescales as well as their two-dimensional (2D) finite-size effects. The model also predicts the subdiffusive behavior of the mean squared displacement (MSD) on short, intermediate timescales. Furthermore, we derive the phonon contributions to diffusion and relaxation, which when combined with the excitation contributions produce the two-step relaxation processes, and the ballistic-subdiffusive-diffusive crossover MSD behaviors commonly found in supercooled liquids.

cond-mat.stat-mech↗

arXiv2023

The $(2 + δ)$-dimensional theory of the electromechanics of lipid membranes: I. Electrostatics

The coupling of electric fields to the mechanics of lipid membranes gives rise to intriguing electromechanical behavior, as, for example, evidenced by the deformation of lipid vesicles in external electric fields. Electromechanical effects are relevant for many biological processes, such as the propagation of action potentials in axons and the activation of mechanically-gated ion channels. Currently, a theoretical framework describing the electromechanical behavior of arbitrarily curved and deforming lipid membranes does not exist. Purely mechanical models commonly treat lipid membranes as two-dimensional surfaces, ignoring their finite thickness. While holding analytical and numerical merit, this approach cannot describe the coupling of lipid membranes to electric fields and is thus unsuitable for electromechanical models. In a sequence of articles, we derive an \textit{effective} surface theory of the electromechanics of lipid membranes, named a $(2+δ)$-dimensional theory, which has the advantages of surface descriptions while accounting for finite thickness effects. The present article proposes a new, generic dimension-reduction procedure relying on low-order spectral expansions. This procedure is applied to the electrostatics of lipid membranes to obtain a $(2+δ)$-dimensional theory that captures potential differences across and electric fields within lipid membranes. This new model is tested on different geometries relevant for lipid membranes, showing good agreement with the corresponding three-dimensional electrostatics theory.

cond-mat.soft↗

arXiv2022

Supervised Learning and the Finite-Temperature String Method for Computing Committor Functions and Reaction Rates

A central object in the computational studies of rare events is the committor function. Though costly to compute, the committor function encodes complete mechanistic information of the processes involving rare events, including reaction rates and transition-state ensembles. Under the framework of transition path theory (TPT), recent work [1] proposes an algorithm where a feedback loop couples a neural network that models the committor function with importance sampling, mainly umbrella sampling, which collects data needed for adaptive training. In this work, we show additional modifications are needed to improve the accuracy of the algorithm. The first modification adds elements of supervised learning, which allows the neural network to improve its prediction by fitting to sample-mean estimates of committor values obtained from short molecular dynamics trajectories. The second modification replaces the committor-based umbrella sampling with the finite-temperature string (FTS) method, which enables homogeneous sampling in regions where transition pathways are located. We test our modifications on low-dimensional systems with non-convex potential energy where reference solutions can be found via analytical or the finite element methods, and show how combining supervised learning and the FTS method yields accurate computation of committor functions and reaction rates. We also provide an error analysis for algorithms that use the FTS method, using which reaction rates can be accurately estimated during training with a small number of samples. The methods are then applied to a molecular system in which no reference solution is known, where accurate computations of committor functions and reaction rates can still be obtained.

cond-mat.stat-mech↗

arXiv2022

Inherent-State Melting and the Onset of Glassy Dynamics in Two-Dimensional Supercooled Liquids

Below the onset temperature $T_\text{o}$, the equilibrium relaxation time of most glass-forming liquids exhibits glassy dynamics characterized by super-Arrhenius temperature dependence. In this supercooled regime, the relaxation dynamics also proceeds through localized elastic excitations corresponding to hopping events between inherent states, i.e., potential-energy minimizing configurations of the liquid. Despite its importance in distinguishing the supercooled regime from the high-temperature regime, the microscopic origin of $T_\text{o}$ is not yet known. Here, we construct a theory for the onset temperature in two dimensions and find that inherent-state melting transition, described by the binding-unbinding transition of dipolar elastic excitations, delineates the supercooled regime from the high-temperature regime. The corresponding melting transition temperature is in good agreement with the onset temperature found in various two-dimensional atomistic models of glass formers. We discuss the predictions of our theory on the displacement and density correlations of two-dimensional supercooled liquids, which are consistent with observations of the Mermin-Wagner fluctuations in recent experiments and molecular simulations.

cond-mat.stat-mech↗

arXiv2022

Time reversal symmetry breaking and odd viscosity in active fluids: Green-Kubo and NEMD results

Active fluids, which are driven at the microscale by non-conservative forces, are known to exhibit novel transport phenomena due to the breaking of time reversal symmetry. Recently, Epstein and Mandadapu [arXiv:1907.10041] obtained Green-Kubo relations for the full set of viscous coefficients governing isotropic chiral active fluids, including the so-called odd viscosity, invoking Onsager's regression hypothesis for the decay of fluctuations in active non-equilibrium steady states. In this Communication, we test these Green-Kubo relations using molecular dynamics simulations of a canonical model system consisting of actively torqued dumbbells. We find the resulting odd and shear viscosity values from the Green-Kubo relations to be in good agreement with values measured independently through non-equilibrium molecular dynamics (NEMD) flow simulations. This provides a test of the Green-Kubo relations, and lends support to the application of the Onsager regression hypothesis in relation to viscous behaviors of active matter systems.

cond-mat.stat-mech↗

arXiv2022

Odd Diffusivity of Chiral Random Motion

Diffusive transport is characterized by a diffusivity tensor which may, in general, contain both a symmetric and an antisymmetric component. Although the latter is often neglected, we derive Green-Kubo relations showing it to be a general characteristic of random motion breaking time-reversal and parity symmetries, as encountered in chiral active matter. In analogy with the odd viscosity appearing in chiral active fluids, we term this component the odd diffusivity. We show how odd diffusivity emerges in a chiral random walk model, and demonstrate the applicability of the Green-Kubo relations through molecular dynamics simulations of a passive tracer particle diffusing in a chiral active bath.

cond-mat.stat-mech↗

arXiv2022

Absolute vs Convective Instabilities and Front Propagation in Lipid Membrane Tubes

We analyze the stability of biological membrane tubes, with and without a base flow of lipids. Membrane dynamics are completely specified by two dimensionless numbers: the well-known Föppl--von Kármán number $Γ$ and the recently introduced Scriven--Love number $SL$, respectively quantifying the base tension and base flow speed. For unstable tubes, the growth rate of a local perturbation depends only on $Γ$, whereas $SL$ governs the absolute or convective nature of the instability. Furthermore, nonlinear simulations of unstable tubes reveal an initially localized disturbance results in propagating fronts, which leave a thin atrophied tube in their wake. Depending on the value of $Γ$, the thin tube is connected to the unperturbed regions via oscillatory or monotonic shape transitions -- reminiscent of recent experimental observations on the retraction and atrophy of axons. We elucidate our findings through a weakly nonlinear analysis, which shows membrane dynamics may be approximated by a model of the class of extended Fisher--Kolmogorov equations. Our study sheds light on the pattern selection mechanism in axonal shapes by recognizing the existence of two Lifshitz points, at which the front dynamics undergo steady-to-oscillatory bifurcations.

cond-mat.soft↗

arXiv2021

A Theory of Localized Excitations in Supercooled Liquids

A new connection between structure and dynamics in glass-forming liquids is presented. We show how the origin of spatially localized excitations, as defined by dynamical facilitation (DF) theory, can be understood from a structure-based framework. This framework is constructed by associating excitation events in DF theory to hopping events between energy minima in the potential energy landscape (PEL). By reducing the PEL to an equal energy well picture and applying a harmonic approximation, we develop a field theory to describe elastic fluctuations about inherent states, which are energy minimizing configurations of the PEL. We model an excitation as a shear transformation zone (STZ) inducing a localized pure shear deformation onto an inherent state. We connect STZs to T1 transition events that break the elastic bonds holding the local structure of an inherent state. A formula for the excitation energy barrier, denoted as $J_σ$, is obtained as a function of inherent-state elastic moduli and radial distribution function. The energy barrier from the current theory is compared to one predicted by the DF theory where good agreement is found in various two-dimensional continuous poly-disperse atomistic models of glass formers. These results strengthen the role of structure and elasticity in driving glassy dynamics through the creation and relaxation of localized excitations.

cond-mat.stat-mech↗

arXiv2021

A chemo-mechano-thermodynamical contact theory for adhesion, friction and (de)bonding reactions

This work presents a self-contained continuum formulation for coupled chemical, mechanical and thermal contact interactions. The formulation is very general and hence admits arbitrary geometry, deformation and material behavior. All model equations are derived rigorously from the balance laws of mass, momentum, energy and entropy in the framework of irreversible thermodynamics, thus exposing all the coupling present in the field equations and constitutive relations. In the process, the conjugated kinematic and kinetic variables for mechanical, thermal and chemical contact are identified, and the analogies between mechanical, thermal and chemical contact are highlighted. Particular focus is placed on the thermodynamics of chemical bonding distinguishing between exothermic and endothermic contact reactions. Distinction is also made between long-range, non-touching surface interactions and short-range, touching contact. For all constitutive relations examples are proposed and discussed comprehensively with particular focus on their coupling. Finally, three analytical test cases are presented that illustrate the thermo-chemo-mechanical contact coupling and are useful for verifying computational models. While the main novelty is the extension of existing contact formulations to chemical contact, the presented formulation also sheds new light on thermo-mechanical contact, since it is consistently derived from basic principles using only few assumptions.

physics.class-ph↗

arXiv2021

Quadrupole-mediated dielectric response and the charge-asymmetric solvation of ions in water

Treating water as a linearly responding dielectric continuum on molecular length scales allows very simple estimates of solvation structure and thermodynamics for charged and polar solutes. While this approach can successfully account for basic length and energy scales of ion solvation, computer simulations indicate not only its quantitative inaccuracies but also its inability to capture some basic and important aspects of microscopic polarization response. Here we consider one such shortcoming, a failure to distinguish the solvation thermodynamics of cations from that of otherwise-identical anions, and we pursue a simple, physically inspired modification of the dielectric continuum model to address it. The adaptation is motivated by analyzing the orientational response of an isolated water molecule whose dipole is rigidly constrained. Its free energy suggests a Hamiltonian for dipole fluctuations that accounts implicitly for the influence of higher-order multipole moments, while respecting constraints of molecular geometry. We propose a field theory with the suggested form, whose nonlinear response breaks the charge symmetry of ion solvation. An approximate variational solution of this theory, with a single adjustable parameter, yields solvation free energies that agree closely with simulation results over a considerable range of solute size and charge.

cond-mat.stat-mech↗

arXiv2020

Entropy production fluctuations encode collective behavior in active matter

We derive a general lower bound on distributions of entropy production in interacting active matter systems. The bound is tight in the limit that interparticle correlations are small and short-ranged, which we explore in four canonical active matter models. In all models studied, the bound is weak where collective fluctuations result in long-ranged correlations, which subsequently links the locations of phase transitions to enhanced entropy production fluctuations. We develop a theory for the onset of enhanced fluctuations and relate it to specific phase transitions in active Brownian particles. We also derive optimal control forces that realize the dynamics necessary to tune dissipation and manipulate the system between phases. In so doing, we uncover a general relationship between entropy production and pattern formation in active matter, as well as ways of controlling it.

cond-mat.stat-mech↗

arXiv2020

Transport phenomena in electrolyte solutions: Non-equilibrium thermodynamics and statistical mechanics

The theory of transport phenomena in multicomponent electrolyte solutions is presented here through the integration of continuum mechanics, electromagnetism, and non-equilibrium thermodynamics. The governing equations of irreversible thermodynamics, including balance laws, Maxwell's equations, internal entropy production, and linear laws relating the thermodynamic forces and fluxes, are derived. Green-Kubo relations for the transport coefficients connecting electrochemical potential gradients and diffusive fluxes are obtained in terms of the flux-flux time correlations. The relationship between the derived transport coefficients and those of the Stefan-Maxwell and infinitely dilute frameworks are presented, and the connection between the transport matrix and experimentally measurable quantities is described. To exemplify application of the derived Green-Kubo relations in molecular simulations, the matrix of transport coefficients for lithium and chloride ions in dimethyl sulfoxide is computed using classical molecular dynamics and compared with experimental measurements.

cond-mat.stat-mech↗

arXiv2020

An adaptive space-time phase field formulation for dynamic fracture of brittle shells based on LR NURBS

We present an adaptive space-time phase field formulation for dynamic fracture of brittle shells. Their deformation is characterized by the Kirchhoff-Love thin shell theory using a curvilinear surface description. All kinematical objects are defined on the shell's mid-plane. The evolution equation for the phase field is determined by the minimization of an energy functional based on Griffith's theory of brittle fracture. Membrane and bending contributions to the fracture process are modeled separately and a thickness integration is established for the latter. The coupled system consists of two nonlinear fourth-order PDEs and all quantities are defined on an evolving two-dimensional manifold. Since the weak form requires $C^1$-continuity, isogeometric shape functions are used. The mesh is adaptively refined based on the phase field using Locally Refinable (LR) NURBS. Time is discretized based on a generalized-$α$ method using adaptive time-stepping, and the discretized coupled system is solved with a monolithic Newton-Raphson scheme. The interaction between surface deformation and crack evolution is demonstrated by several numerical examples showing dynamic crack propagation and branching.

cs.CE↗

arXiv2020

Geometry and dynamics of lipid membranes: The Scriven--Love number

The equations governing lipid membrane dynamics in planar, spherical, and cylindrical geometries are presented here. Unperturbed and first-order perturbed equations are determined and non-dimensionalized. In membrane systems with a nonzero base flow, perturbed in-plane and out-of-plane quantities are found to vary over different length scales. A new dimensionless number, named the Scriven--Love number, and the well-known Föppl--von Kármán number result from a scaling analysis. The Scriven--Love number compares out-of-plane forces arising from the in-plane, intramembrane viscous stresses to the familiar elastic bending forces, while the Föppl--von Kármán number compares tension to bending forces. Both numbers are calculated in past experimental works, and span a wide range of values in various biological processes across different geometries. In situations with large Scriven--Love and Föppl--von Kármán numbers, the dynamical response of a perturbed membrane is dominated by out-of-plane viscous and surface tension forces---with bending forces playing a negligible role. Calculations of non-negligible Scriven--Love numbers in various biological processes and in vitro experiments show in-plane intramembrane viscous flows cannot generally be ignored when analyzing lipid membrane behavior.

cond-mat.soft↗

arXiv2020

Arbitrary Lagrangian--Eulerian finite element method for curved and deforming surfaces. I. General theory and application to fluid interfaces

An arbitrary Lagrangian--Eulerian (ALE) finite element method for arbitrarily curved and deforming two-dimensional materials and interfaces is presented here. An ALE theory is developed by endowing the surface with a mesh whose in-plane velocity need not depend on the in-plane material velocity, and can be specified arbitrarily. A finite element implementation of the theory is formulated and applied to curved and deforming surfaces with in-plane incompressible flows. Numerical inf--sup instabilities associated with in-plane incompressibility are removed by locally projecting the surface tension onto a discontinuous space of piecewise linear functions. The general isoparametric finite element method, based on an arbitrary surface parametrization with curvilinear coordinates, is tested and validated against several numerical benchmarks. A new physical insight is obtained by applying the ALE developments to cylindrical fluid films, which are computationally and analytically found to be stable to non-axisymmetric perturbations, and unstable with respect to long-wavelength axisymmetric perturbations when their length exceeds their circumference. A Lagrangian scheme is attained as a special case of the ALE formulation. Though unable to model fluid films with sustained shear flows, the Lagrangian scheme is validated by reproducing the cylindrical instability. However, relative to the ALE results, the Lagrangian simulations are found to have spatially unresolved regions with few nodes, and thus larger errors.

physics.comp-ph↗

arXiv2020

Motility-induced buckling and glassy dynamics regulate three-dimensional transitions of bacterial monolayers

Many mature bacterial colonies and biofilms are complex three-dimensional (3D) structures. One key step in their developmental program is a transition from a two-dimensional (2D) monolayer into a 3D architecture. Despite the importance of controlling the growth of microbial colonies and biofilms in a variety of medical and industrial settings, the underlying physical mechanisms behind single-cell dynamics, collective behaviors of densely-packed cells, and 3D complex colony expansion remain largely unknown. In this work, we explore the mechanisms behind the 2D-to-3D transition of motile Pseudomonas aeruginosa colonies; we provide a new motility-induced, rate-dependent buckling mechanism for their out-of-plane growth. We find that swarming of motile bacterial colonies generate sustained in-plane flows. We show that the viscous shear stresses and dynamic pressures arising from these flows allow cells to overcome cell-substrate adhesion, leading to buckling of bacterial monolayers and growth into the third dimension. Modeling bacterial monolayers as 2D fluid films, we identify universal relationships that elucidate the competition between in-plane viscous stresses, pressure and cell-substrate adhesion. Furthermore, we show that bacterial monolayers can exhibit crossover from swarming to kinetically-arrested, glassy-like states above an onset density, resulting in distinct 2D-to-3D transition mechanisms. Combining experimental observations of P. aeruginosa colonies at single-cell resolution, molecular dynamics simulations of active systems, and theories of glassy dynamics and 2D fluid films, we develop a dynamical state diagram that predicts the state of the colony, and the mechanisms governing their 2D-to-3D transitions.

cond-mat.soft↗

arXiv2019

Time reversal symmetry breaking in two-dimensional non-equilibrium viscous fluids

We study the rheological signatures of departure from equilibrium in two-dimensional viscous fluids with and without internal spin. Under the assumption of isotropy, we provide the most general linear constitutive relations for stress and couple stress in terms of the velocity and spin fields. Invoking Onsager's regression hypothesis for fluctuations about steady states, we derive the Green-Kubo formulae relating the transport coefficients to time correlation functions of the fluctuating stress. In doing so, we verify the claim that one of the non-equilibrium transport coefficients, the odd-viscosity, requires time reversal symmetry breaking in the case of systems without internal spin. However, the Green-Kubo relations for systems with internal spin also show that there is a possibility for non-vanishing odd viscosity even when time reversal symmetry is preserved. Furthermore, we find that breakdown of equipartition in non-equilibrium steady states results in the decoupling of the two rotational viscosities relating the vorticity and the internal spin.

cond-mat.stat-mech↗

arXiv2019

Statistical Mechanics of Transport Processes in Active Fluids II: Equations of Hydrodynamics for Active Brownian Particles

We perform a coarse-graining analysis of the paradigmatic active matter model, Active Brownian Particles, yielding a continuum description in terms of balance laws for mass, linear and angular momentum, and energy. The derivation of the balance of linear momentum reveals that the active force manifests itself directly as a continuum-level body force proportional to an order parameter-like director field, which therefore requires its own evolution equation to complete the continuum description of the system. We derive this equation, demonstrating in the process that bulk currents may be sustained in homogeneous systems only in the presence of inter-particle aligning interactions. Further, we perform a second coarse-graining of the balance of linear momentum and derive the expression for active or swim pressure in the case of mechanical equilibrium.

cond-mat.soft↗