Marino Arroyo

An atomistic-based finite deformation membrane for single layer crystalline films

A general methodology to develop hyper-elastic membrane models applicable to crystalline films one-atom thick is presented. In this method, an extension of the Born rule based on the exponential map is proposed. The exponential map accounts for the fact that the lattice vectors of the crystal lie along the chords of the curved membrane, and consequently a tangent map like the standard Born rule is inadequate. In order to obtain practical methods, the exponential map is locally approximated. The effectiveness of our approach is demonstrated by numerical studies of carbon nanotubes. Deformed configurations as well as equilibrium energies of atomistic simulations are compared with those provided by the continuum membrane resulting from this method discretized by finite elements.

Elastic bending modulus of monolayer graphene

An analytic formula is derived for the elastic bending modulus of monolayer graphene based on an empirical potential for solid-state carbon atoms. Two physical origins are identified for the non-vanishing bending stiffness of the atomically thin graphene sheet, one due to the bond-angle effect and the other resulting from the bond-order term associated with the dihedral angles. The analytical prediction compares closely with ab initio energy calculations. Pure bending of graphene monolayers into cylindrical tubes is simulated by a molecular mechanics approach, showing slight nonlinearity and anisotropy in the tangent bending modulus as the bending curvature increases. An intrinsic coupling between bending and in-plane strain is noted for graphene monolayers rolled into carbon nanotubes.

A finite deformation membrane based on inter-atomic potentials for the transverse mechanics of nanotubes

A finite deformation hyper-elastic membrane theory based on inter-atomic potentials for crystalline films composed of a single atomic layer is developed. For this purpose, an extension of the standard Born rule that exploits the differential geometry concept of the exponential map is proposed to deal with the curvature of surfaces. The exponential map is approximated locally and strain measures based on the stretch and the curvature of the membrane arise. The methodology is first particularized to atomic chains in two dimensions, and then to graphene sheets. A reduced model for the transverse mechanics of carbon nanotubes is developed in detail. This model is a hyper-elastic constrained membrane which fully exploits the symmetry of the transverse deformation. Additionally, a continuum version of the non-bonded interactions is provided. The continuum model is discretized using finite elements and very good agreement with molecular mechanics simulations is obtained. Finally, several simulations illustrate the strong effect of the van der Waals interactions in the transverse deformation of carbon nanotubes.

Reverse engineering the euglenoid movement

Euglenids exhibit an unconventional motility strategy amongst unicellular eukaryotes, consisting of large-amplitude highly concerted deformations of the entire body (euglenoid movement or metaboly). A plastic cell envelope called pellicle mediates these deformations. Unlike ciliary or flagellar motility, the biophysics of this mode is not well understood, including its efficiency and molecular machinery. We quantitatively examine video recordings of four euglenids executing such motions with statistical learning methods. This analysis reveals strokes of high uniformity in shape and pace. We then interpret the observations in the light of a theory for the pellicle kinematics, providing a precise understanding of the link between local actuation by pellicle shear and shape control. We systematically understand common observations, such as the helical conformations of the pellicle, and identify previously unnoticed features of metaboly. While two of our euglenids execute their stroke at constant body volume, the other two exhibit deviations of about 20% from their average volume, challenging current models of low Reynolds number locomotion. We find that the active pellicle shear deformations causing shape changes can reach 340%, and estimate the velocity of the molecular motors. Moreover, we find that metaboly accomplishes locomotion at hydrodynamic efficiencies comparable to those of ciliates and flagellates. Our results suggest new quantitative experiments, provide insight into the evolutionary history of euglenids, and suggest that the pellicle may serve as a model for engineered active surfaces with applications in microfluidics.

Importance of Force Decomposition for Local Stress Calculations in Biomembrane Molecular Simulations.

Local stress fields are routinely computed from molecular dynamics trajectories to understand the structure and mechanical properties of lipid bilayers. These calculations can be systematically understood with the Irving-Kirkwood-Noll theory. In identifying the stress tensor, a crucial step is the decomposition of the forces on the particles into pairwise contributions. However, such a decomposition is not unique in general, leading to an ambiguity in the definition of the stress tensor, particularly for multibody potentials. Furthermore, a theoretical treatment of constraints in local stress calculations has been lacking. Here, we present a new implementation of local stress calculations that systematically treats constraints and considers a privileged decomposition, the central force decomposition, that leads to a symmetric stress tensor by construction. We focus on biomembranes, although the methodology presented here is widely applicable. Our results show that some unphysical behavior obtained with previous implementations (e.g. nonconstant normal stress profiles along an isotropic bilayer in equilibrium) is a consequence of an improper treatment of constraints. Furthermore, other valid force decompositions produce significantly different stress profiles, particularly in the presence of dihedral potentials. Our methodology reveals the striking effect of unsaturations on the bilayer mechanics, missed by previous stress calculation implementations.

Adhesion and friction control localized folding in supported graphene

Graphene deposited on planar surfaces often exhibits sharp and localized folds delimiting seemingly planar regions, as a result of compressive stresses transmitted by the substrate. Such folds alter the electronic and chemical properties of graphene, and therefore, it is important to understand their emergence, to either suppress them or control their morphology. Here, we study the emergence of out-of-plane deformations in supported and laterally strained graphene with high-fidelity simulations and a simpler theoretical model. We characterize the onset of buckling and the nonlinear behavior after the instability in terms of the adhesion and frictional material parameters of the graphene-substrate interface. We find that localized folds evolve from a distributed wrinkling linear instability due to the nonlinearity in the van der Waals graphene-substrate interactions. We identify friction as a selection mechanism for the separation between folds, as the formation of far apart folds is penalized by the work of friction. Our systematic analysis is a first step towards strain engineering of supported graphene, and is applicable to other compressed thin elastic films weakly coupled to a substrate.

Adaptivity based on error estimation for viscoplastic softening materials

This paper focuses on the numerical simulation of strain softening mechanical problems. Two problems arise: (1) the constitutive model has to be regular and (2) the numerical technique must be able to capture the two scales of the problem (the macroscopic geometrical representation and the microscopic behaviour in the localization bands). The Perzyna viscoplastic model is used in order to obtain a regularized softening model allowing to simulate strain localization phenomena. This model is applied to quasistatic examples. The viscous regularization of quasistatic processes is also discussed: in quasistatics, the internal length associated with the obtained band width is no longer only a function of the material parameters but also depends on the boundary value problem (geometry and loads, specially loading velocity). An adaptive computation is applied to softening viscoplastic materials showing strain localization. As the key ingredient of the adaptive strategy, a residual-type error estimator is generalized to deal with such highly non-linear material model. In several numerical examples the adaptive process is able to detect complex collapse modes that are not captured by a first, even if fine, mesh. Consequently, adaptive strategies are found to be essential to detect the collapse mechanism and to assess the optimal location of the elements in the mesh. Copyright

Hydraulic fracture during epithelial stretching

The origin of fracture in epithelial cell sheets subject to stretch is commonly attributed to excess tension in the cells’ cytoskeleton, in the plasma membrane, or in cell-cell contacts. Here we demonstrate that for a variety of synthetic and physiological hydrogel substrates the formation of epithelial cracks is caused by tissue stretching independently of epithelial tension. We show that the origin of the cracks is hydraulic; they result from a transient pressure build-up in the substrate during stretch and compression maneuvers. After pressure equilibration cracks heal readily through actomyosin-dependent mechanisms. The observed phenomenology is captured by the theory of poroelasticity, which predicts the size and healing dynamics of epithelial cracks as a function of the stiffness, geometry and composition of the hydrogel substrate. Our findings demonstrate that epithelial integrity is determined in a tension-independent manner by the coupling between tissue stretching and matrix hydraulics.

Computational evaluation of the flexoelectric effect in dielectric solids

Flexoelectricity is a size-dependent electromechanical mechanism coupling polarization and strain gradient. It exists in a wide variety of materials, and is most noticeable for nanoscale objects, where strain gradients are higher. Simulations are important to understand flexoelectricity because experiments at very small scales are difficult, and analytical solutions are scarce. Here, we computationally evaluate the role of flexoelectricity in the electromechanical response of linear dielectric solids in two-dimensions. We deal with the higher-order coupled partial differential equations using smooth meshfree basis functions in a Galerkin method, which allows us to consider general geometries and boundary conditions. We focus on the most common setups to quantify the flexoelectric response, namely, bending of cantilever beams and compression of truncated pyramids, which are generally interpreted through approximate solutions. While these approximations capture the size-dependent flexoelectric electromechanical coupling, we show that they only provide order-of-magnitude estimates as compared with a solution fully accounting for the multidimensional nature of the problem. We discuss the flexoelectric mechanism behind the enhanced size-dependent elasticity in beam configurations. We show that this mechanism is also responsible for the actuation of beams under purely electrical loading, supporting the idea that a mechanical flexoelectric sensor also behaves as an actuator. The predicted actuation-induced curvature is in a good agreement with experimental results. The truncated pyramid configuration highlights the critical role of geometry and boundary conditions on the effective electromechanical response. Our results suggest that computer simulations can help understanding and quantifying the physical properties of flexoelectric devices.

An adaptive meshfree method for phase-field models of biomembranes. Part I

We present an adaptive meshfree method for phase-field models of biomembranes.Max-ent smooth approximants can deal with the high-order phase-field equations.The method resolves adaptively the models at an affordable computational cost.Convergence to sharp interface limit is shown with small regularization parameters. We present an adaptive meshfree method to approximate phase-field models of biomembranes. In such models, the Helfrich curvature elastic energy, the surface area, and the enclosed volume of a vesicle are written as functionals of a continuous phase-field, which describes the interface in a smeared manner. Such functionals involve up to second-order spatial derivatives of the phase-field, leading to fourth-order Euler-Lagrange partial differential equations (PDE). The solutions develop sharp internal layers in the vicinity of the putative interface, and are nearly constant elsewhere. Thanks to the smoothness of the local maximum-entropy (max-ent) meshfree basis functions, we approximate numerically this high-order phase-field model with a direct Ritz-Galerkin method. The flexibility of the meshfree method allows us to easily adapt the grid to resolve the sharp features of the solutions. Thus, the proposed approach is more efficient than common tensor product methods (e.g. finite differences or spectral methods), and simpler than unstructured C 0 finite element methods, applicable by reformulating the model as a system of second-order PDE. The proposed method, implemented here under the assumption of axisymmetry, allows us to show numerical evidence of convergence of the phase-field solutions to the sharp interface limit as the regularization parameter approaches zero. In a companion paper, we present a Lagrangian method based on the approximants analyzed here to study the dynamics of vesicles embedded in a viscous fluid.