Protein Mechanics:From Amino Acid to Swimming Cells

This proceedings paper contains a review of the work presented in the Sectional Lecture in Solids on August 25 at ICTAM 2016. - Proteins are long polypeptide chains of amino acids and their structure and biological function are directly related to their amino acid sequence. I will discuss three different biological functions that are dominated by protein mechanics, each at their own specific time and length scale. To relate structure to function, multiscale computational models have been developed for (i) cilia and flagella, (ii) actin filament networks and (iii) the nuclear pore complex

Micromechanics of creep fracture: simulation of intergranular crack growth

A computational model is presented to analyze intergranular creep crack growth in a polycrystalline aggregate in a discrete manner and based directly on the underlying physical micromechanisms. A crack tip process zone is used in which grains and their grain boundaries are represented discretely, while the surrounding undamaged material is described as a continuum. The constitutive description of the grain boundaries accounts for the relevant physical mechanisms, i.e. viscous grain boundary sliding, the nucleation and growth of grain boundary cavities, and microcracking by the coalescence of cavities. Discrete propagation of the main crack occurs by linking up of neighbouring facet microcracks. Assuming small-scale damage conditions, the model is used to simulate the initial stages of crack growth under C* controlled, model I loading conditions. Initially sharp or blunted cracks are considered. The emphasis in this study is on the effect of the grain microstructure on crack growth.

Topographical changes in photo-responsive liquid crystal films:a computational analysis

Switchable materials in response to external stimuli serve as building blocks to construct microscale functionalized actuators and sensors. Azobenzene-modified liquid crystal (LC) polymeric networks, that combine liquid crystalline orientational order and elasticity, reversibly undergo conformational changes powered by light. We present a computational framework to describe photo-induced topographical transformations of azobenzene-modified LC glassy polymer coatings. A nonlinear light penetration model is combined with an opto-mechanical constitutive relation to simulate various ordered and corrugated topographical textures resulting from aligned or randomly distributed LC molecule orientations. Our results shed light on the fundamental physical mechanisms of light-triggered surface undulations and can be used as guidelines to optimize surface modulation and roughness in emerging fields that involve haptics interfacing, friction control and wetting manipulation.</p

Structure–property relations of three-dimensional nanoporous template-based graphene foams

Recently, much attention has been directed to 3D graphene structures due to their potential of retaining intrinsic 2D graphene properties, in combination with structural flexibility and tunable porosity. From a theoretical point of view, however, it is challenging to build 3D graphene foam structures that accurately represent experimental topological configurations. Here, we generate open-cell 3D graphene structures that closely reflect template-based manufacturing techniques and investigate their mechanical properties. We use all-atom molecular dynamics simulations to relate the overall stiffness, collapse stress and fracture properties to the underlying graphene microstructure represented by the graphene relative density, template relative density and number of graphene layers. We do so for four different template morphologies: gyroids, regular foam (BCC), random foam and nanoporous gold. The overall mechanical properties as a function of graphene relative density are analyzed in terms of power law relations to probe the microstructural deformation modes. Our results show that the open-cell 3D graphene structures feature bending as the dominant deformation mode, with regular graphene foams having the highest stiffness and strength and random foams the lowest. For gyroids we found that a higher template relative density leads to reduced mechanical properties but improved ductility. A similar trend was observed when the number of graphene layers was increased: enhanced ductility but at the expense of a reduced strength. Interestingly, we found that for low graphene density, the gyroids feature a strong self-stiffening response, leading to improvements in both strength as well as ductility. Our findings can be used as a guideline for the experimental design of innovate and lightweight graphene structures with strongly enhanced mechanical properties

Microfluidic propulsion by the metachronal beating of magnetic artificial cilia: a numerical analysis

In this work we study the effect of metachronal waves on the flow created by magnetically-driven plate-like artificial cilia in microchannels using numerical simulations. The simulations are performed using a coupled magneto-mechanical solid-fluid computational model that captures the physical interactions between the fluid flow, ciliary deformation and applied magnetic field. When a rotating magnetic field is applied to super-paramagnetic artificial cilia, they mimic the asymmetric motion of natural cilia, consisting of an effective and recovery stroke. When a phase-difference is prescribed between neighbouring cilia, metachronal waves develop. Due to the discrete nature of the cilia, the metachronal waves change direction when the phase difference becomes sufficiently large, resulting in antiplectic as well as symplectic metachrony. We show that the fluid flow created by the artificial cilia is significantly enhanced in the presence of metachronal waves and that the fluid flow becomes unidirectional. Antiplectic metachrony is observed to lead to a considerable enhancement in flow compared to symplectic metachrony, when the cilia spacing is small. Obstruction of flow in the direction of the effective stroke for the case of symplectic metachrony was found to be the key mechanism that governs this effect

Bi-directional locomotion of a magnetically-actuated jellyfish-inspired soft robot

Biomimetic compliant untethered robots find a plethora of applications in biomedical engineering, microfluidics, soft robotics, and deep-sea exploration. Flexible miniature robots in the form of magnetically actuated compliant swimmers are increasingly used for targeted drug delivery, robotic surgery, laparoscopy, and microfluidic device design. These applications require an in-depth understanding of the nonlinear large deformation structural mechanics, non-invasive remote-control and untethered actuation mechanisms, and associated fluid-structure interactions that arise between a soft smart robot and its surrounding fluid. The present work obtains numerical solutions for the temporal evolution of structural and flow variables using a fictitious domain method that employs a robust multi-physics computational model involving both fluid-structure interaction and magneto-elasto-dynamics. The magnetically-actuated soft robotic swimmer (jellyfishbot) is inspired by the most efficient aquatic swimmer, the jellyfish. The swimming kinematics and bi-directional locomotion are obtained for different waveforms and gradients of the external magnetic actuation. The breaking of temporal symmetry and its relative dominance is discussed as well

Transport and mixing by metachronal waves in nonreciprocal soft robotic pneumatic artificial cilia at low Reynolds numbers

Cilia are widely employed by living systems to manipulate fluid flow in various functions, such as feeding, pumping, and locomotion. Mimicking the intricate ciliary asymmetry in combination with collective metachronal beating may find wide application in fluid transport and mixing in microfluidic systems. Here, we numerically analyze the metachronal beating of pneumatic artificial cilia. We specifically address three aspects of ciliary motion: (i) pumping in the backflow region, (ii) mixing in the cilia region, and (iii) the transport—mixing transition region. Our results show that antiplectic metachrony leads to the highest mixing efficiency and transport rate in two distinct regions, i.e., below and above the ciliary surface, respectively. We find that the ciliary motion strongly enhances the diffusivity when advection is dominant at high Péclet numbers, with a factor 3 for symplectic metachrony and a factor 4 for antiplectic metachrony and synchronous beating. In addition, we find an increase with a factor 1.5 for antiplectic metachrony and a decrease with a factor 2.5 for symplectic metachrony compared with synchronous beating for fluid pumping. To investigate the higher transport rate compared to symplectic metachrony, we develop a simple two-cilia model and demonstrate that the shielding of flow between neighboring cilia is the main reason for the higher antiplectic transport rate

Travelling waves on photo-switchable patterned liquid crystal polymer films directed by rotating polarized light

\u3cp\u3eNature employs travelling waves to generate propulsion of fluids, cells and organisms. This has inspired the development of responsive material systems based on different external triggers. Especially light-actuation is suitable because of its remote control and scalability, but often complex, moving light sources are required. Here, we developed a method that only requires flood exposure by rotating the linear polarization of light to generate propagating surface waves on azobenzene-modified liquid crystalline polymer films. We built a photomechanical computational model that accounts for the attenuation of polarized light and trans-to-cis isomerization of azobenzene. A non-uniform in-plane distribution of the liquid crystal molecules allows for the generation of travelling surface waves whose amplitude, speed and direction can be controlled through the intensity, rotation direction and rotation speed of the linear polarization of a light source. Our method opens new avenues for motion control based on light-responsive topographical transformations for application in microfluidic lab-on-chip systems and soft robotics.\u3c/p\u3

Phase separation of intrinsically disordered FG-Nups is driven by highly dynamic FG motifs

The intrinsically disordered FG-Nups in the central channel of the nuclear pore complex (NPC) form a selective permeability barrier, allowing small molecules to traverse by passive diffusion, while large molecules can only translocate with the help of nuclear transport receptors. The exact phase state of the permeability barrier remains elusive. In vitro experiments have shown that some FG-Nups can undergo phase separation into condensates that display NPC-like permeability barrier properties. Here, we use molecular dynamics simulations at amino acid resolution to study the phase separation characteristics of each of the disordered FG-Nups of the yeast NPC. We find that GLFG-Nups undergo phase separation and reveal that the FG motifs act as highly dynamic hydrophobic stickers that are essential for the formation of FG-Nup condensates featuring droplet-spanning percolated networks. Additionally, we study phase separation in an FG-Nup mixture that resembles the NPC stoichiometry and observe that an NPC condensate is formed containing multiple GLFG-Nups. We find that the phase separation of this NPC condensate is also driven by FG-FG interactions, similar to the homotypic FG-Nup condensates. Based on the observed phase separation behavior, the different FG-Nups of the yeast NPC can be divided into two classes: The FG-Nups (mostly GLFG-type) located in the central channel of the NPC form a highly dynamic percolated network formed by many short-lived FG-FG interactions, while the peripheral FG-Nups (mostly FxFG-type) at the entry and exit of the NPC channel likely form an entropic brush.</p