Session Y36: Soft Mechanics in Biological Systems

Intermediate response of complex fluids with biophysical implications

Over sufficiently large distances any complex fluid responds as a continuous medium, characterized by bulk viscoelastic moduli. But how large is ``sufficiently large"? Close examination of the competing sub-asymptotic term reveals a distinctive spatio-temporal regime, intermediate between the small-scale and large-scale responses. In materials such as semiflexible polymer networks this regime governs the dynamics over a broad range of distances, pushing the crossover to the bulk behavior to a distance much larger than the structural correlation length. The validity of these findings has been confirmed by two-point microrheology of entangled F-actin networks, where the crossover distance was found to be of micron scale\,---\,i.e., relevant to biological cells.\footnote{A. Sonn-Segev, A. Bernheim-Groswasser, H. Diamant, Y. Roichman, Phys. Rev. Lett. {\bf 112}, 088301 (2014).} We discuss consequences of the intermediate response for the fluctuations of small objects and membranes inside actin networks.   

Mechanical response of biopolymer double networks

We investigate a double network model of articular cartilage (AC) and characterize its equilibrium mechanical response. AC has very few cells and the extracellular matrix mainly determines its mechanical response. This matrix can be thought of as a double polymer network made of collagen and aggrecan. The collagen fibers are stiff and resist tension and compression forces, while aggrecans are flexible and control swelling and hydration. We construct a microscopic model made of two interconnected disordered polymer networks, with fiber elasticity chosen to qualitatively mimic the experimental system. We study the collective mechanical response of this double network as a function of the concentration and stiffness of the individual components as well as the strength of the connection between them using rigidity percolation theory. Our results may provide a better understanding of mechanisms underlying the mechanical resilience of AC, and more broadly may also lead to new perspectives on the mechanical response of multicomponent soft materials.   

The mechanics of endothelial gap formation

The vascular endothelium is a layer of specialized cells, referred to as endothelial cells (EC) that line the internal surfaces of blood vessels and are largely responsible for regulating the transit of fluids, solutes and immune system cells from the circulation, across the vessel wall, and into the tissues. We investigate the physics of the mechanical events that may proceed and eventually lead to dramatic increase of its permeability, leading to serious illness. In combination with experiments measuring local stresses and gap formation in EC in different conditions, we devise a minimal model based on an amorphous assembly of adhesive particles, subjected to an imposed tension. Numerical simulations of the model show that, as a function of the rate at which the tension is imposed, the system goes from an elastic regime in which small gaps increase in number to a “plastic” one, where pre-existing gaps increase in size, and internal stresses display large hetereogeneities and long range correlations. This second regime bears intriguing similarities with the experimental finding in EC monolayers.   

A simple polymeric model describes cell nuclear mechanical response

The cell nucleus must continually resist inter- and intracellular mechanical forces, and proper mechanical response is essential to basic cell biological functions as diverse as migration, differentiation, and gene regulation. Experiments probing nuclear mechanics reveal that the nucleus stiffens under strain, leading to two characteristic regimes of force response. This behavior depends sensitively on the intermediate filament protein lamin A, which comprises the outer layer of the nucleus, and the properties of the chromatin interior. To understand these mechanics, we study a simulation model of a polymeric shell encapsulating a semiflexible polymer. This minimalistic model qualitatively captures the typical experimental nuclear force-extension relation and observed nuclear morphologies. Using a Flory-like theory, we explain the simulation results and mathematically estimate the force-extension relation. The model and experiments suggest that chromatin organization is a dominant contributor to nuclear mechanics, while the lamina protects cell nuclei from large deformations.   

The Effect of Predators on Cholera Biofilms: If it Lyses, We Can Smash It

Many microbes form biofilms—dense clumps of cells and proteins—on surfaces. Biofilms are complex communities that facilitate the study of biological competition (e.g., two types of microbes may compete to form a biofilm in the same location) and interesting physics (e.g., the source of a biofilm’s rigidity). \emph{Vibrio cholerae} can produce biofilms which have a network-like structure—however, cholera can be genetically engineered to kill other cholera with different genotypes, which leaves behind a structureless “slime” rather than such a biofilm. Through mechanical creep testing of both predator-prey and non-predator populations, we found that the predator-prey population responds viscously and decreases in height with repeated compression, whereas the non-predator population responds elastically and maintains its original height. The current work suggests that cell lysis after killing disrupts biofilm formation, preventing microbial colonies from forming rigid networks.   

Mechanical Properties of a Primary Cilium Measured by Resonant Oscillation

Primary cilia are ubiquitous mammalian cellular substructures implicated in an ever-increasing number of regulatory pathways. The well-established `ciliary hypothesis' states that physical bending of the cilium (for example, due to fluid flow) initiates signaling cascades, yet the mechanical properties of the cilium remain incompletely measured, resulting in confusion regarding the biological significance of flow-induced ciliary mechanotransduction. In this work we measure the mechanical properties of a primary cilium by using an optical trap to induce resonant oscillation of the structure. Our data indicate 1), the primary cilium is not a simple cantilevered beam, 2), the base of the cilium may be modeled as a nonlinear rotatory spring, the linear spring constant `k' of the cilium base calculated to be (4.6 $+$/- 0.62)*10$^{\mathrm{-12}}$ N/rad and nonlinear spring constant `$\alpha $' to be (-1 $+$/- 0.34) *10$^{\mathrm{-10}}$ N/rad$^{\mathrm{2}}$ , and 3) the ciliary base may be an essential regulator of mechanotransduction signalling. Our method is also particularly suited to measure mechanical properties of nodal cilia, stereocilia, and motile cilia, anatomically similar structures with very different physiological functions.   

Composition and Humidity Response of the Black Widow Spider's Gumfoot Silk and its Implications on Adhesion

Humidity plays an important part in the performance of biomaterials such as pollen, gecko toe, wheat awns, bird feathers and dragline silk. Capture silk produced by web building spiders form an interesting class of humidity responsive biological glues. The adhesive properties of the widely studied `viscid silk' produced by orbweb-weaving spiders is highly humidity sensitive. On the other hand, relatively less is known about the dependence of composition and humidity response towards adhesion for `gumfoot' silk produced by cobweb-weaving spiders. In the present study, we investigate the gumfoot silk produced by Black Widow using adhesion mechanics, microscopy and spectroscopic methods. The results show the presence of hygroscopic salts, glycoproteins and previously known spider coating peptides in silk and their importance in the humidity response and adhesion. The current study elucidates the role of constituents of capture silk in its adhesion mechanism and offers insights to novel ways for fabricating bio-inspired adhesives.   

Flexibility of bacterial type IV pili determined using atomic force microscopy

Type IV pili (T4P) are very thin protein filaments extended and retracted from the surface of certain Gram-negative bacteria. Pili play a major role in processes such as adhesion, twitching motility and biofilm formation. We used atomic force microscopy (AFM) to perform force spectroscopy measurements on T4P of \textit{P. aeruginosa}. Bacteria were adhered to the end of an AFM cantilever that was brought into contact with a substrate, allowing the pili to adhere. Force-separation curves were collected by retracting the cantilever, corresponding to the stretching of the T4P that was well described by the worm-like chain (WLC) model. Distinct peaks were observed in the distributions of the best-fit values of the persistence length \textsl{L$_{p}$} on two different surfaces, providing strong evidence for close-packed bundling of very flexible T4P [1]. Surprisingly, the most prominent value of \textit{L$_{p}$} $\sim$ 1 nm is significantly less than the $\sim$ 8 nm length of the PilA subunit. We have investigated this intriguing result by refining our protocol to combine AFM with fluorescence microscopy to isolate a single bacterium on a colloidal probe, as well as critically examining the applicability of the WLC model. [1] S. Lu et al., Biophys. J. {\bf 108}, 2865 (2015).   

Passage times of confined cancer cells and deformable particles flowing through a microfluidic channel

Circulating tumor cells, the primary cause of cancer metastasis, have to navigate through tight extracellular matrix and capillaries. Unfortunately, understanding of the hydrodynamic interactions between cells and narrow vessel walls is lacking. Using a microfluidic channel of rectangular cross-section, we investigate cell hydrodynamic behavior by measuring cell confinement, passage time through the microchannel, and excess pressure drop. Testing with highly and lowly aggressive cancer cells shows that passage time may not always be indicative of cancer cell aggressiveness as the relationship among passage time, friction and rheology is complex. Transport of deformable particles including droplets of varying viscosity and interfacial tension, as well as elastic particles of different elastic moduli, reveals that passage times depend on particle size and, contrary to prior claims, on viscosity but not on elastic modulus. We also find that particle viscosity and not modulus controls the friction force and lubrication film thickness, suggesting that cancer cell viscosity rather than elasticity controls cell transport on short time-scales.   

Mechanics governs single-cell signaling and multi-cell robustness in biofilm infections.

In biofilms, bacteria and other microbes are embedded in extracellular polymers (EPS). Multiple types of EPS can be produced by a single bacterial strain - the reasons for this redundancy are not well-understood. Our work suggests that different polymers may confer distinct mechanical benefits. Our model organism is \textit{Pseudomonas aeruginosa}, an opportunistic human pathogen that forms chronic biofilm infections associated with increased antibiotic resistance and evasion of the immune defense. Biofilms initiate when bacteria attach to a surface, sense the surface, and change their gene expression. Changes in gene expression are regulated by a chemical signal, cyclic-di-GMP. We find that one EPS material, called ``PEL,'' enhances surface sensing by increasing mechanical coupling of single bacteria to the surface. Measurements of bacterial motility suggest that PEL may increase frictional interactions between the surface and the bacteria. Consistent with this, we show that bacteria increase cyclic-di-GMP signaling in response to mechanical shear stress. Mechanosensing has long been known to be important to the function of cells in higher eukaryotes, but this is one of only a handful of studies showing that bacteria can sense and respond to mechanical forces. For the mature biofilm, the embedding polymer matrix can protect bacteria both chemically and mechanically. \textit{P. aeruginosa} infections in the cystic fibrosis (CF) lung often last for decades, ample time for the infecting strain(s) to evolve. Production of another EPS material, alginate, is well-known to tend to increase over time in CF infections. Alginate chemically protects biofilms, but also makes them softer and weaker. Recently, it is being increasingly recognized that bacteria in chronic CF infections also evolve to increase PSL production. We use oscillatory bulk rheology to determine the unique contributions of EPS materials to biofilm mechanics. Unlike alginate, increased PSL stiffens biofilms. Increasing both PSL and alginate expression increases the energy cost to break the biofilm. We compare the elastic moduli of biofilms to estimated stresses exerted by phagocytotic immune cells, and infer that increased PSL could confer a mechanical fitness benefit.   

Suspended Solid-state Membranes on Glass Chips with Sub 1-pF Capacitance for Biomolecule Sensing Applications

Solid-state membranes are finding use in many applications in nanoelectronics and nanomedicine, from single molecule sensors to water filtration, and yet many of their electronics applications are limited by the current noise and low bandwidth stemming from the relatively high capacitance (more than 10 pF) of the membrane chips. To address this problem, we devised an integrated fabrication process to grow and define circular silicon nitride membranes on glass chips that successfully lower the chip capacitance to below 1 pF. We use these devices to demonstrate low-noise, high-bandwidth DNA translocation measurements. We also make use of this versatile, low-capacitance platform to suspend other thin, two-dimensional membranes such as graphene.