CyberSec Research

Recent works indicate that heterogeneous response and non-Markovianity may yield recognizable hallmarks in the microrheology of semisolid viscoelastic materials. Here we perform numerical simulations using a non-Markovian overdamped Langevin approach to explore how the microrheology experienced by probe particles immersed in an effective semisolid material can be influenced by its micro-heterogeneities. Our results show that, besides affecting the mean squared displacement, the time-dependent diffusion coefficient, and the shear moduli, the micro-heterogeneities lead to displacement distributions that deviate from the usual Gaussian behavior. In addition, our study provides an analytical way to characterize the micro-heterogeneities of semisolid viscoelastic materials through their microrheology.

Proliferation and motility are ubiquitous drivers of activity in biological systems. Here, we study a dense binary mixture of motile and proliferating particles with exclusively repulsive interactions, where homeostasis in the proliferating subpopulation is maintained by pressure-induced removal. Using computer simulations, we show that phase separation emerges naturally in this system at high density and weak enough self-propulsion. We show that condensation is caused by interactions between motile particles induced by the growing phase, and recapitulate this behavior in an effective model of only motile particles with attractive interactions. Our results establish a new type of phase transition and pave a way to reinterpret the physics of dense cellular populations, such as bacterial colonies or tumors, as systems of mixed active matter.

We numerically investigate the shear rheology of mixtures of active and passive Brownian particles, with varying fractions of active components. We find that even a small fraction of active dopants triggers fluidization with comparable efficiency to fully active systems. A combined parameter, active energy, given by dopant fraction multiplied by propulsion speed squared controls the shear rheology and glass transition of the active-passive mixtures. These results together provide a quantitative strategy for fine-tuning the mechanical properties of a soft material with small amounts of active dopants.

Suspensions, which exhibit complex behaviors such as shear thickening, thinning, and jamming, are prevalent in nature and industry. However, predicting the mechanical properties of concentrated suspensions, in both steady state and the transient regime, remains a significant challenge, impacting product quality and process efficiency. In this study, we focus on developing a robust theoretical framework to explain how flow history governs the anisotropy of mechanical responses in suspensions of hard particles under unsteady flow conditions. Our starting point is the Gillissen-Wilson constitutive model, which we confront to DEM simulation data of the micro-structure during steady shear, and shear rotations where the shear axis is rotated by a specific angle around the flow gradient direction. We introduce a simple modification to the Gillissen-Wilson model which leads to a model with higher predictive power in steady state and during shear rotations.

Skin tension plays a pivotal role in clinical settings, it affects scarring, wound healing and skin necrosis. Despite its importance, there is no widely accepted method for assessing in vivo skin tension or its natural pre-stretch. This study aims to utilise modern machine learning (ML) methods to develop a model that uses non-invasive measurements of surface wave speed to predict clinically useful skin properties such as stress and natural pre-stretch. A large dataset consisting of simulated wave propagation experiments was created using a simplified two-dimensional finite element (FE) model. Using this dataset, a sensitivity analysis was performed, highlighting the effect of the material parameters and material model on the Rayleigh and supersonic shear wave speeds. Then, a Gaussian process regression model was trained to solve the ill-posed inverse problem of predicting stress and pre-stretch of skin using measurements of surface wave speed. This model had good predictive performance (R2 = 0.9570) and it was possible to interpolate simplified parametric equations to calculate the stress and pre-stretch. To demonstrate that wave speed measurements could be obtained cheaply and easily, a simple experiment was devised to obtain wave speed measurements from synthetic skin at different values of pre-stretch. These experimental wave speeds agree well with the FE simulations and a model trained solely on the FE data provided accurate predictions of synthetic skin stiffness. Both the simulated and experimental results provide further evidence that elastic wave measurements coupled with ML models are a viable non-invasive method to determine in vivo skin tension.

Liquid crystal mesophases of achiral molecules are normally achiral, yet in a few materials they spontaneously deracemize and form right- and left-handed chiral domains. One mechanism that drives deracemization is molecular shape fluctuations between axial chiral conformations, where molecular interactions favor matching chirality and promote helical twist. Cooperative chiral ordering may also play a role in chirality amplification, as when a tiny fraction of chiral dopant drives a nematic phase to become cholesteric. We present a model of cooperative chiral ordering in liquid crystals using Maier-Saupe theory, and predict a phase diagram with a deracemized cholesteric phase as well as racemic nematic and isotropic phases. Our model also predicts chirality amplification in the nematic phase, which may be observed even in materials where the deracemization transition is preempted by a transition to another phase. We compare these results with Monte Carlo simulation studies of the switchable chiral Lebwohl-Lasher model, where each spin switches between right- and left-handed chiral states. Simulation results validate the predicted phase diagram, demonstrate chiral amplification in the racemic nematic phase, and reveal coarsening dynamics in the deracemized phase. Our results suggest that cooperative chiral ordering via molecular shape transitions is a common mechanism in liquid crystals.

The description of complex physical phenomena often involves sophisticated models that rely on a large number of parameters, with many dimensions and scales. One practical way to simplify that kind of models is to discard some of the parameters, or terms of underlying equations, thus giving rise to reduced models. Here, we propose a general approach to obtaining such reduced models. The method is independent of the model in use, i.e., equation-free, depends only on the interplay between the scales and dimensions involved in the description of the phenomena, and controls over-parametrization. It also quantifies conditions for asymptotic models by providing explicitly computable thresholds on values of parameters that allow for reducing complexity of a model, while preserving essential predictive properties. Although our focus is on complexity reduction, this approach may also help with calibration by mitigating the risks of over-parameterization and instability in parameter estimation. The benefits of this approach are discussed in the context of the classical projectile model.

We study theoretically the closure of a wound in a layer of epithelial cells in a living tissue after damage. Our analysis is informed by our recent experiments observing re-epithelialisation in vivo of Drosophila pupae. On time and length-scales such that the evolution of the epithelial tissue near the wound is well captured by that of a 2D active fluid with local nematic order, we consider the free-surface problem of a hole in a bounded region of tissue, and study the role that active stresses far from the hole play in the closure of the hole. For parallel anchored nematic order at the wound boundary (as we observe in our experiments), we find that closure is accelerated when the active stresses are contractile and slowed down when the stresses are extensile. Parallel anchoring also leads to the appearance of topological defects which annihilate upon wound closure.

Phase separation of biomolecular condensates is ubiquitous in living cells, promoting colocalization of enzymes and their substrates as well as achieving membrane-free compartmentalization. Energy-consuming processes are routinely used to regulate biocondensate growth by opposing the thermodynamic tendency toward coarsening. At the same time, cells often use energy to instead accelerate thermodynamic processes. Here, we theoretically explore the possibility of utilizing chemical reactions to accelerate biocondensate coarsening. We combine Lifshitz-Slyozov theory with a reaction-diffusion approach, wherein particles interconvert between phase-separating and inert forms. We find that mass conservation restricts the volume growth to be linear in time (as in the passive case) despite activity, though if reactions are restricted to occur only outside droplets, the rate of Ostwald ripening can be increased by an arbitrarily large factor. Our acceleration theory is quantitatively supported by recent experiments on ripening in the presence of fueled interconversion reactions, under precisely the predicted conditions. We posit that the ability to induce rapid biocondensate coarsening can be advantageous in synthetic-biological contexts as a regulator of metabolic channeling.

Sedimentation of particulate suspensions in horizontal pipes can lead to formation, growth and consolidation of a solid-like bed which can severely retard pipeline performance. As stagnant flow conditions frequently arise during industrial processes, critical operational questions are: (i) at what rate and extent does sedimentation proceed, and (ii) can the sedimentation dynamics be predicted from conventional suspension characterisation methods? We address these questions by characterising the sedimentation properties of an aqueous Kaolin suspension via batch settling tests and comparing predictions from 1D sedimentation theory with experiments in a horizontally oriented cylindrical pipe. We show that particulate sedimentation can be accurately predicted, indicating that the estimated sedimentation properties are representative material properties, and that transient effects such as gravity currents are not significant. Conversely, we find that the consolidation of the sediment is not well predicted by 1D theory, suggesting that the stress state is not 1D and likely involves contributions from the pipe walls. These stagnant cylindrical pipe results provide a basis for the development of methods to predict pipeline sedimentation under more general (laminar and turbulent) flow conditions.

Materials with negative Poisson's ratio, also known as auxetic materials, display exotic properties such as expansion in all directions under uni-axial tension. For their unique properties, these materials find a broad range of applications in robotic, structural, aerospace, and biomedical engineering. In this work we study the wrinkling behavior of thin and soft auxetic membranes, subjected to edge tractions. We show that spatial inhomogeneities of the Young modulus and of the Poisson ratio can be suitably tailored to produce non-trivial wrinkling patterns, with wrinkled regions that can appear, broaden, merge, and eventually disappear again, as the magnitude of applied tractions is increased monotonically. To model wrinkling in a functionally graded membrane, we employ the mathematically elegant and physically transparent tension field theory, an approximated method that we implement in commercially available software. Beyond unveiling the challenging technological potential to achieve non-standard wrinkling on-demand in auxetic membranes, our study also confirms the potential of using tension field theory to study, analytically and numerically, instabilities in functionally graded materials.

Confluent tissues are a type of foam-like biological active matter. There is a recent interest in using active nematic liquid crystal framework to understand confluent cells, where topological (orientational) defects are believed to play a crucial role. However, how to reconcile the physical picture of lattice defects in Voronoi polygons with that of orientational defects in the nematic field$-$particularly in the context of cellular transport$-$remains elusive. Here, we employ the Active Vertex model to investigate the physics of lattice and orientational defects in the dynamics of confluent cells. We find a spatio-orientational correlation between lattice defects and $+1/2$ defects, unveiling a correspondence between the two physical perspectives. Next, we simulate the behavior of a dragged cell within a hexagonal-lattice tissue. Our results reveal that while the drag coefficient is anisotropic, the threshold drag force to mobilize the cell is isotropic, indicating the presence of a caging energy barrier. We further analyze the defect pattern in the wake of the dragged cell or cells. Remarkably, we discover that dragging two neighboring cells along the least-drag direction can substantially minimize the destruction of the lattice structure during cell transport. We find that this is due to the cooperative and periodic self-healing of the lattice defects. Taken together, our work sheds new light on the topological structure of confluent cells during their collective motion, advancing our physical understanding of cellular transport in processes such as wound healing, cancer cell metastasis, and other physiological events.

Structural-Maintenance-of-Chromosome (SMC) complexes such as condensins are well-known to dictate the folding and entanglement of interphase and mitotic chromosomes. However, their role in modulating the rheology and viscoelasticity of entangled DNA is not fully understood. In this work, we discover that physiological concentrations of yeast condensin increase both the effective viscosity and elasticity of dense solutions of $\lambda$-DNA even in absence of ATP. By combining biochemical assays and single-molecule imaging, we discover that yeast condensin can proficiently bind double-stranded DNA through its hinge domain, in addition to its heads. We further discover that presence of ATP fluidifies the entangled solution possibly by activating loop extrusion. Finally, we show that the observed rheology can be understood by modelling SMCs as transient crosslinkers in bottle-brush-like entangled polymers. Our findings help us to understand how SMCs affect the rheology and dynamics of the genome.

Complex flow fields govern the deformation of polymers in various manufacturing processes. However, high flow rates may trigger reaction events (i.e., bond breaking or undesirable reaction of mechanophores) in raw polymeric materials, leading to the mechanical or functional debasement of manufactured structures. Additionally, it is difficult to fully characterize such molecular-level flow in the laboratory due to time- and length-scale limits. In this study, we perform non-equilibrium molecular dynamics (NEMD) simulations to explore the rheological and mechanical degradation of unentangled polymer melts under uniaxial extensional flow (UEF), allowing for chain breaking. Our simulations demonstrate shear thickening-thinning-thickening stages with the increase of UEF extension rates, resulting from flow-induced changes of chain conformation. With further increasing UEF extension rates, a bond-breaking potential leads to another flow thinning stage. Interestingly, fracture kinetics is originally first-order owing to the need for highly stretched polymer chains before bond fracture. It is no longer first-order when bond fracture is instigated before chains are stretched. Our computational work provides insight into the optimal design of the manufacturing process for polymeric materials.

The Poynting effect is a paragon of nonlinear soft matter mechanics. It is the tendency (found in all incompressible, isotropic, hyperelastic solids) exhibited by a soft block to expand vertically when sheared horizontally. It can be observed whenever the length of the cuboid is at least four times its thickness. Here we show that the Poynting effect can be easily reversed and the cuboid can shrink vertically, simply by reducing this aspect ratio. In principle, this discovery means that for a given solid, say one used as a seismic wave absorber under a building, an optimal ratio exists where vertical displacements and vibrations can be completely eliminated. Here we first recall the classical theoretical treatment of the positive Poynting effect, and then show experimentally how it can be reversed. Using Finite Element simulations, we then investigate how the effect can be suppressed. We find that cubes always provide a reverse Poynting effect, irrespective of their material properties (in the third-order theory of weakly nonlinear elasticity).

Supercooled liquids exhibit intricate flow behaviors, which progressively become nonlinear as flow rate increases. Conceptually, this complexity can be understood by the solid-liquid duality in Maxwell's understanding of materials' response to external load. Nevertheless, the microscopic foundation of this duality in supercooled liquids remains elusive, thereby impeding the modeling of flow behaviors from a microscopic viewpoint. The existence of dynamic heterogeneity adds to this difficulty. To tackle these problems, we propose the concept of local configurational relaxation time $\tau_\rm{LC}$, which is defined at the particle level. The spatial distribution of $\tau_\rm{LC}$ in flow is heterogeneous. Depending on the comparison between the local mobility measured by $\tau_\rm{LC}$ and the external shear rate, the response of local regions is either solid-like or liquid-like. In this way, $\tau_\rm{LC}$ plays a role similar to the Maxwell time. By applying this microscopic solid-liquid duality to different conditions of shear flow, we describe the emergence of shear thinning in steady shear, and predict the major characteristics of the transient response to start-up shear. Furthermore, we reveal a clear structural foundation for $\tau_\rm{LC}$ and the solid-liquid duality associated with it by introducing an order parameter extracted from local configuration. Thus, we establish a framework that connects microscopic structure, dynamics, local mechanical response, and flow behaviors for supercooled liquids. Finally, we rationalize our framework by leveraging the connection among structure, dynamics, and potential energy landscape (PEL). The PEL model illustrates how local structure, convection and thermal activation collectively determine $\tau_\rm{LC}$. Notably, it predicts two distinct response groups, which well correspond to the microscopic solid-liquid duality.

Mechanical stresses in soft materials across different length scales play a fundamental role in understanding the function of biological systems and in the use of artificial materials for engineering soft machines and biomedical devices. Yet it remains a great challenge to probe local mechanical stresses in situ in a non-invasive, non-destructive manner, in particular when the mechanical properties are unknown. To address this challenge, we propose an acoustoelastic imaging-based method to infer the local mechanical stresses in soft materials by measuring the speed of shear waves induced by custom-programmed acoustic radiation force. Using a medical ultrasound transducer to excite and track the shear waves remotely, we demonstrate the application of the method by imaging uniaxial stress and bending stress in an isotropic hydrogel, and the passive uniaxial stress in a skeletal muscle. These measurements were all done without the knowledge of the constitutive parameters of the materials. These examples indicate that our method will find broad applications, ranging from health monitoring of soft structures and machines, to the diagnosis of diseases that alter stresses in soft tissues.

Biological active matter like the cytoskeleton or tissues are characterized by their ability to transform chemical energy into mechanical stress. In addition, it often exhibits orientational order, which is essential for many cellular and morphogenetic processes. Experimental evidence suggests that defects in the orientational order field play an important role in organizing active stress. However, defects tend to annihilate unless the material is in a chaotic state or hydrodynamic interactions are suppressed. Using a hydrodynamic description of compressible active polar fluids, we show that turnover readily leads to a stabilization of defects. Depending on the turnover rate, topological defects arrange in a multitude of different phases, including lattices, active foams, and vortex glasses. Our work suggests that turnover plays a crucial role for organizing biological active matter.