COLLECTIONS

Documents published in Scipedia

• Combined molecular/continuum modeling reveals the role of friction during fast unfolding of coiled-coil proteins

  A. Torres-Sánchez, J. Vanegas, P. Purohit, M. Arroyo

  Soft Matter (2019). Vol. 15, pp. 4961-4975 (Preprint)

  
  

  Abstract

  Coiled-coils are filamentous proteins that form the basic building block of important force-bearing cellular elements, such as intermediate filaments and myosin motors. In addition to their biological importance, coiled-coil proteins are increasingly used in new biomaterials including fibers, nanotubes, or hydrogels. Coiled-coils undergo a structural transition from an a-helical coil to an unfolded state upon extension, which allows them to sustain large strains and is critical for their biological function. By performing equilibrium and out-of-equilibrium all-atom molecular dynamics (MD) simulations of coiledcoils in explicit solvent, we show that two-state models based on Kramers’ or Bell’s theories fail to predict the rate of unfolding at high pulling rates. We further show that an atomistically informed continuum rod model accounting for phase transformations and for the hydrodynamic interactions with the solvent can reconcile two-state models with our MD results. Our results show that frictional forces, usually neglected in theories of fibrous protein unfolding, reduce the thermodynamic force acting on the interface, and thus control the dynamics of unfolding at different pulling rates. Our results may help interpret MD simulations at high pulling rates, and could be pertinent to cytoskeletal networks or protein-based artificial materials subjected to shocks or blasts.

  Abstract
  Coiled-coils are filamentous proteins that form the basic building block of important force-bearing cellular elements, such as intermediate filaments and myosin motors. In [...]

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• Swimming Euglena respond to confinement with a behavioural change enabling effective crawling

  G. Noselli, A. Beran, M. Arroyo, A. DeSimone

  Nature physics (2019). Vol. 15, pp. 496-502 (Preprint)

  
  

  Abstract

  Some euglenids, a family of aquatic unicellular organisms, can develop highly concerted, large-amplitude peristaltic body deformations. This remarkable behaviour has been known for centuries. Yet, its function remains controversial, and is even viewed as a functionless ancestral vestige. Here, by examining swimming Euglena¿gracilis in environments of controlled crowding and geometry, we show that this behaviour is triggered by confinement. Under these conditions, it allows cells to switch from unviable flagellar swimming to a new and highly robust mode of fast crawling, which can deal with extreme geometric confinement and turn both frictional and hydraulic resistance into propulsive forces. To understand how a single cell can control such an adaptable and robust mode of locomotion, we developed a computational model of the motile apparatus of Euglena cells consisting of an active striated cell envelope. Our modelling shows that gait adaptability does not require specific mechanosensitive feedback but instead can be explained by the mechanical self-regulation of an elastic and extended motor system. Our study thus identifies a locomotory function and the operating principles of the adaptable peristaltic body deformation of Euglena cells.

  Abstract
  Some euglenids, a family of aquatic unicellular organisms, can develop highly concerted, large-amplitude peristaltic body deformations. This remarkable behaviour has been [...]

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• Smart helical structures inspired by the pellicle of euglenids

  G. Noselli, M. Arroyo, A. DeSimone

  Journal of the Mechanics and Physics of Solids (2019). Vol. 123, pp. 234-246 (Preprint)

  
  

  Abstract

  This paper deals with a concept for a reconfigurable structure bio-inspired by the cell wall architecture of euglenids, a family of unicellular protists, and based on the relative sliding of adjacent strips. Uniform sliding turns a cylinder resulting from the assembly of straight and parallel strips into a cylinder of smaller height and larger radius, in which the strips are deformed into a family of parallel helices. We examine the mechanics of this cylindrical assembly, in which the interlocking strips are allowed to slide freely at their junctions, and compute the external forces (axial force and axial torque at the two ends, or pressure on the lateral surface) necessary to drive and control the shape changes of the composite structure. Despite the simplicity of the structure, we find a remarkably complex mechanical behaviour that can be tuned by the spontaneous curvature or twist of the strips.

  Abstract
  This paper deals with a concept for a reconfigurable structure bio-inspired by the cell wall architecture of euglenids, a family of unicellular protists, and based on the [...]

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• Active superelasticity in three-dimensional epithelia of controlled shape

  E. Latorre, S. Kale, L. Casares, M. Gómez-González, M. Uroz, L. Valon, R. Nair, E. Garreta, N. Monstserrat, A. Campo, B. Ladoux, M. Arroyo, X. Trepat

  Nature (2018). Vol. 563 (7730), pp. 203-208 (Preprint)

  
  

  Abstract

  Fundamental biological processes are carried out by curved epithelial sheets that enclose a pressurized lumen. How these sheets develop and withstand three-dimensional deformations has remained unclear. Here we combine measurements of epithelial tension and shape with theoretical modelling to show that epithelial sheets are active superelastic materials. We produce arrays of epithelial domes with controlled geometry. Quantification of luminal pressure and epithelial tension reveals a tensional plateau over several-fold areal strains. These extreme strains in the tissue are accommodated by highly heterogeneous strains at a cellular level, in seeming contradiction to the measured tensional uniformity. This phenomenon is reminiscent of superelasticity, a behaviour that is generally attributed to microscopic material instabilities in metal alloys. We show that in epithelial cells this instability is triggered by a stretch-induced dilution of the actin cortex, and is rescued by the intermediate filament network. Our study reveals a type of mechanical behaviour—which we term active superelasticity—that enables epithelial sheets to sustain extreme stretching under constant tension.

  Abstract
  Fundamental biological processes are carried out by curved epithelial sheets that enclose a pressurized lumen. How these sheets develop and withstand three-dimensional deformations [...]

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• A variational model of fracture for tearing brittle thin sheets

  B. Li, D. Millán, A. Torres-Sánchez, B. Roman, M. Arroyo

  Journal of the Mechanics and Physics of Solids (2018). Vol. 119, pp. 334-348 (Preprint)

  
  

  Abstract

  Tearing of brittle thin elastic sheets, possibly adhered to a substrate, involves a rich interplay between nonlinear elasticity, geometry, adhesion, and fracture mechanics. In addition to its intrinsic and practical interest, tearing of thin sheets has helped elucidate fundamental aspects of fracture mechanics including the mechanism of crack path selection. A wealth of experimental observations in different experimental setups is available, which has been often rationalized with insightful yet simplified theoretical models based on energetic considerations. In contrast, no computational method has addressed tearing in brittle thin elastic sheets. Here, motivated by the variational nature of simplified models that successfully explain crack paths in tearing sheets, we present a variational phase-field model of fracture coupled to a nonlinear Koiter thin shell model including stretching and bending. We show that this general yet straightforward approach is able to reproduce the observed phenomenology, including spiral or power-law crack paths in free standing films, or converging/diverging cracks in thin films adhered to negatively/positively curved surfaces, a scenario not amenable to simple models. Turning to more quantitative experiments on thin sheets adhered to planar surfaces, our simulations allow us to examine the boundaries of existing theories and suggest that homogeneous damage induced by moving folds is responsible for a systematic discrepancy between theory and experiments. Thus, our computational approach to tearing provides a new tool to understand these complex processes involving fracture, geometric nonlinearity and delamination, complementing experiments and simplified theories.

  Abstract
  Tearing of brittle thin elastic sheets, possibly adhered to a substrate, involves a rich interplay between nonlinear elasticity, geometry, adhesion, and fracture mechanics. [...]

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• Coexistence of wrinkles and blisters in supported graphene

  K. Zang, M. Arroyo

  Extreme Mechanics Letters (2017). Vol. 14, pp. 23-30 (Preprint)

  
  

  Abstract

  Blisters induced by gas trapped in the interstitial space between supported graphene and the substrate are commonly observed. These blisters are often quasi-spherical with a circular rim, but polygonal blisters are also common and coexist with wrinkles emanating from their vertices. Here, we show that these different blister morphologies can be understood mechanically in terms of free energy minimization of the supported graphene sheet for a given mass of trapped gas and for a given lateral strain. Using a nonlinear continuum model for supported graphene closely reproducing experimental images of blisters, we build a morphological diagram as a function of strain and trapped mass. We show that the transition from quasi-spherical to polygonal of blisters as compressive strain is increased is a process of stretching energy relaxation and focusing, as many other crumpling events in thin sheets. Furthermore, to characterize this transition, we theoretically examine the onset of nucleation of short wrinkles in the periphery of a quasi-spherical blister. Our results are experimentally testable and provide a framework to control complex out-of-plane motifs in supported graphene combining blisters and wrinkles for strain engineering of graphene.

  Abstract
  Blisters induced by gas trapped in the interstitial space between supported graphene and the substrate are commonly observed. These blisters are often quasi-spherical with [...]

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• Hydraulic fracturing in cells and tissues: fracking meets cell biology

  M. Arroyo, X. Trepat

  Current opinion in cell biology (2017). Vol. 44, pp. 1-6 (Preprint)

  
  

  Abstract

  The animal body is largely made of water. A small fraction of body water is freely flowing in blood and lymph, but most of it is trapped in hydrogels such as the extracellular matrix (ECM), the cytoskeleton, and chromatin. Besides providing a medium for biological molecules to diffuse, water trapped in hydrogels plays a fundamental mechanical role. This role is well captured by the theory of poroelasticity, which explains how any deformation applied to a hydrogel causes pressure gradients and water flows, much like compressing a sponge squeezes water out of it. Here we review recent evidence that poroelastic pressures and flows can fracture essential biological barriers such as the nuclear envelope, the cellular cortex, and epithelial layers. This type of fracture is known in engineering literature as hydraulic fracturing or ‘fracking’.

  Abstract
  The animal body is largely made of water. A small fraction of body water is freely flowing in blood and lymph, but most of it is trapped in hydrogels such as the extracellular [...]

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• Sticking and sliding of lipid bilayers on deformable substrates

  L. Stubbington, M. Arroyo, M. Staykova

  Soft Matter (2017). Vol. 13 (1), pp. 181-186

  
  

  Abstract

  We examine here the properties of lipid bilayers coupled to deformable substrates. We show that by changing the extent of the substrate hydrophilicity, we can control the membrane–substrate coupling and the response of the bilayer to strain deformation. Our results demonstrate that lipid bilayers coupled to flexible substrates can easily accommodate large strains, form stable protrusions and open reversibly pores. These properties, which differ significantly from those of free standing membranes, can extend the applications of the current lipid technologies. Moreover, such systems better capture the mechanical architecture of the cell interface and can provide insights into the capacity of cells to reshape and respond to mechanical perturbations.

  Abstract
  We examine here the properties of lipid bilayers coupled to deformable substrates. We show that by changing the extent of the substrate hydrophilicity, we can control the [...]

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• Fourth order phase-field model for local max-ent approximants applied to crack propagation

  F. Amiri, D. Millán, M. Arroyo, M. Silani, T. Rabczuk

  Comput. Methods Appl. Mech. Engrg., (2016). Vol. 312, pp. 254-275 (Preprint)

  
  

  Abstract

  We apply a fourth order phase-field model for fracture based on local maximum entropy (LME) approximants. The higher order continuity of the meshfree LME approximants allows to directly solve the fourth order phase-field equations without splitting the fourth order differential equation into two second order differential equations. We will first show that the crack surface can be captured more accurately in the fourth order model. Furthermore, less nodes are needed for the fourth order model to resolve the crack path. Finally, we demonstrate the performance of the proposed meshfree fourth order phase-field formulation for 5 representative numerical examples. Computational results will be compared to analytical solutions within linear elastic fracture mechanics and experimental data for three-dimensional crack propagation.

  Abstract
  We apply a fourth order phase-field model for fracture based on local maximum entropy (LME) approximants. The higher order continuity of the meshfree LME approximants allows [...]

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• Charting molecular free-energy landscapes with an atlas of collective variables

  B. Hashemian, D. Millán, M. Arroyo

  Journal of chemical physics (2016). Vol. 145 (17), pp. 1-33 (Preprint)

  
  

  Abstract

  Collective variables (CVs) are a fundamental tool to understand molecular flexibility, to compute free energy landscapes, and to enhance sampling in molecular dynamics simulations. However, identifying suitable CVs is challenging, and is increasingly addressed with systematic data-driven manifold learning techniques. Here, we provide a flexible framework to model molecular systems in terms of a collection of locally valid and partially overlapping CVs: an atlas of CVs. The specific motivation for such a framework is to enhance the applicability and robustness of CVs based on manifold learning methods, which fail in the presence of periodicities in the underlying conformational manifold. More generally, using an atlas of CVs rather than a single chart may help us better describe different regions of conformational space. We develop the statistical mechanics foundation for our multi-chart description and propose an algorithmic implementation. The resulting atlas of data-based CVs are then used to enhance sampling and compute free energy surfaces in two model systems, alanine dipeptide and ß-D-glucopyranose, whose conformational manifolds have toroidal and spherical topologies.

  Abstract
  Collective variables (CVs) are a fundamental tool to understand molecular flexibility, to compute free energy landscapes, and to enhance sampling in molecular dynamics simulations. [...]

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