arXiv subjects

Daniel M. Sussman

Publications and source records attributed to Daniel M. Sussman.

At least 37 records · Page 2Linked to original sources

arXiv2020

Interplay of curvature and rigidity in shape-based models of confluent tissue

Rigidity transitions in simple models of confluent cells have been a powerful organizing principle in understanding the dynamics and mechanics of dense biological tissue. In this work we explore the interplay between geometry and rigidity in two-dimensional vertex models confined to the surface of a sphere. By considering shapes of cells defined by perimeters whose magnitude depends on geodesic distances and areas determined by spherical polygons, the critical shape index in such models is affected by the size of the cell relative to the radius of the sphere on which it is embedded. This implies that cells can collectively rigidify by growing the size of the sphere, i.e. by tuning the curvature of their domain. Finite-temperature studies indicate that cell motility is affected well away from the zero-temperature transition point.

cond-mat.soft↗

arXiv2020

Small-scale demixing in confluent biological tissues

Surface tension governed by differential adhesion can drive fluid particle mixtures to sort into separate regions, i.e., demix. Does the same phenomenon occur in confluent biological tissues? We begin to answer this question for epithelial monolayers with a combination of theory via a vertex model and experiments on keratinocyte monolayers. Vertex models are distinct from particle models in that the interactions between the cells are shape-based, as opposed to distance-dependent. We investigate whether a disparity in cell shape or size alone is sufficient to drive demixing in bidisperse vertex model fluid mixtures. Surprisingly, we observe that both types of bidisperse systems robustly mix on large lengthscales. On the other hand, shape disparity generates slight demixing over a few cell diameters, a phenomenon we term micro-demixing. This result can be understood by examining the differential energy barriers for neighbor exchanges (T1 transitions). Experiments with mixtures of wild-type and E-cadherin-deficient keratinocytes on a substrate are consistent with the predicted phenomenon of micro-demixing, which biology may exploit to create subtle patterning. The robustness of mixing at large scales, however, suggests that despite some differences in cell shape and size, progenitor cells can readily mix throughout a developing tissue until acquiring means of recognizing cells of different types.

cond-mat.soft↗

arXiv2019

Fast, scalable, and interactive software for Landau-de Gennes numerical modeling of nematic topological defects

Numerical modeling of nematic liquid crystals using the tensorial Landau-de Gennes (LdG) theory provides detailed insights into the structure and energetics of the enormous variety of possible topological defect configurations that may arise when the liquid crystal is in contact with colloidal inclusions or structured boundaries. However, these methods can be computationally expensive, making it challenging to predict (meta)stable configurations involving several colloidal particles, and they are often restricted to system sizes well below the experimental scale. Here we present an open-source software package that exploits the embarrassingly parallel structure of the lattice discretization of the LdG approach. Our implementation, combining CUDA/C++ and OpenMPI, allows users to accelerate simulations using both CPU and GPU resources in either single- or multiple-core configurations. We make use of an efficient minimization algorithm, the Fast Inertial Relaxation Engine (FIRE) method, that is well-suited to large-scale parallelization, requiring little additional memory or computational cost while offering performance competitive with other commonly used methods. In multi-core operation we are able to scale simulations up to supra-micron length scales of experimental relevance, and in single-core operation the simulation package includes a user-friendly GUI environment for rapid prototyping of interfacial features and the multifarious defect states they can promote. To demonstrate this software package, we examine in detail the competition between curvilinear disclinations and point-like hedgehog defects as size scale, material properties, and geometric features are varied. We also study the effects of an interface patterned with an array of topological point-defects.

cond-mat.soft↗

arXiv2019

Glassy Dynamics in Models of Confluent Tissue with Mitosis and Apoptosis

Recent work on particle-based models of tissues has suggested that any finite rate of cell division and cell death is sufficient to fluidize an epithelial tissue. At the same time, experimental evidence has indicated the existence of glassy dynamics in some epithelial layers despite continued cell cycling. To address this discrepancy, we quantify the role of cell birth and death on glassy states in confluent tissues using simulations of an active vertex model that includes cell motility, cell division, and cell death. Our simulation data is consistent with a simple ansatz in which the rate of cell-life cycling and the rate of relaxation of the tissue in the absence of cell cycling contribute independently and additively to the overall rate of cell motion. Specifically, we find that a glass-like regime with caging behavior indicated by subdiffusive cell displacements can be achieved in systems with sufficiently low rates of cell cycling.

cond-mat.soft↗

arXiv2017

Anomalous glassy dynamics in simple models of dense biological tissue

In order to understand the mechanisms for glassy dynamics in biological tissues and shed light on those in non-biological materials, we study the low-temperature disordered phase of 2D vertex-like models. Recently it has been noted that vertex models have quite unusual behavior in the zero-temperature limit, with rigidity transitions that are controlled by residual stresses and therefore exhibit very different scaling and phenomenology compared to particulate systems. Here we investigate the finite-temperature phase of two-dimensional Voronoi and Vertex models, and show that they have highly unusual, sub-Arrhenius scaling of dynamics with temperature. We connect the anomalous glassy dynamics to features of the potential energy landscape associated with zero-temperature inherent states.

cond-mat.soft↗

arXiv2017

Soft yet sharp interfaces in a vertex model of confluent tissue

How can dense biological tissue maintain sharp boundaries between coexisting cell populations? We explore this question within a simple vertex model for cells, focusing on the role of topology and tissue surface tension. We show that the ability of cells to independently regulate adhesivity and tension, together with neighbor-based interaction rules, lets them support strikingly unusual interfaces. In particular, we show that mechanical- and fluctuation-based measurements of the effective surface tension of a cellular aggregate yield different results, leading to mechanically soft interfaces that are nevertheless extremely sharp.

cond-mat.soft↗

arXiv2017

No unjamming transition in a marginal vertex model of biological tissue

Vertex models are a popular approach to modeling the mechanical and dynamical properties of dense biological tissues, describing the tissue as a network of connected polygons representing the cells. Recently a class of two-dimensional vertex models was shown to exhibit a disordered rigidity transition controlled by the preferred cellular geometry, echoing experimental findings. An attractive variant of these models uses a Voronoi tessellation to describe the cells and endows them with a non-equilibrium model of cellular motility, leading to rich, glassy behavior. This glassy behavior was suggested to be inextricably linked to an underlying jamming transition. We test this conjecture, exploring the low-effective-temperature limit of the Voronoi model by studying cell trajectories from detailed dynamical simulations in combination with rigidity measurements of energy-minimized disordered cell configurations. We find that the zero-temperature limit of this model has no unjamming transition.

cond-mat.soft↗

arXiv2017

cellGPU: massively parallel simulations of dynamic vertex models

Vertex models represent confluent tissue by polygonal or polyhedral tilings of space, with the individual cell interacting via force laws that depend on both the geometry of the cells and the topology of the tessellation. This dependence on the connectivity of the cellular network introduces several complications to performing molecular-dynamics-like simulations of vertex models, and in particular makes parallelizing the simulations difficult. cellGPU addresses this difficulty and lays the foundation for massively parallelized, GPU-based simulations of these models. This article discusses its implementation for a pair of two-dimensional models, and compares the typical performance that can be expected between running cellGPU entirely on the CPU versus its performance when running on a range of commercial and server-grade graphics cards. By implementing the calculation of topological changes and forces on cells in a highly parallelizable fashion, cellGPU enables researchers to simulate time- and length-scales previously inaccessible via existing single-threaded CPU implementations.

physics.bio-ph↗

arXiv2016

Disconnecting structure and dynamics in glassy thin films

Nanometrically thin glassy films depart strikingly from the behavior of their bulk counterparts. We investigate whether the dynamical differences between bulk and thin film glasses can be understood by differences in local microscopic structure. We employ machine-learning methods that have previously identified strong correlations between local structure and particle rearrangement dynamics in bulk systems. We show that these methods completely fail to detect key aspects of thin-film glassy dynamics. Furthermore, we show that no combination of local structural features drawn from a very general set of two- and multi-point functions is able to distinguish between particles at the center of film and those in intermediate layers where the dynamics are strongly perturbed.

cond-mat.soft↗

arXiv2016

Spatial distribution of entanglements in thin free-standing films

We simulate entangled linear polymers in free-standing thin film geometries where the confining dimension is on the same scale or smaller than the bulk chain dimensions. We compare both film-averaged and layer-resolved, spatially inhomogeneous measures of the polymer structure and entanglement network with theoretical models. We find that these properties are controlled by the ratio of both chain- and entanglement-strand length scales to the film thickness. While the film-averaged entanglement properties can be accurately predicted, we identify outstanding challenges in understanding the spatially resolved character of the heterogeneities in the entanglement network, particularly when the scale of both the entanglement strand and the chain end-to-end vector is comparable to or smaller than the film thickness.

cond-mat.soft↗

arXiv2016

Topological boundary modes in jammed matter

Granular matter at the jamming transition is poised on the brink of mechanical stability, and hence it is possible that these random systems have topologically protected surface phonons. Studying two model systems for jammed matter, we find states that exhibit distinct mechanical topological classes, protected surface modes, and ubiquitous Weyl points. The detailed statistics of the boundary modes enable tests of a standard understanding of the detailed features of the jamming transition, and show that parts of this argument are invalid.

cond-mat.soft↗

arXiv2016

A Force-Level Theory of the Rheology of Entangled Rod and Chain Polymer Liquids. II. Perturbed Reptation, Stress Overshoot, Emergent Convective Constraint Release and Steady State Flow

We numerically and analytically analyze the startup continuous shear rheology of heavily entangled rigid rod polymer fluids based on our self-consistent, force-level theory of anharmonic tube confinement. The approach is simplified by neglecting stress-assisted transverse barrier hopping, and irreversible relaxation proceeds solely via deformation-perturbed reptation. This process is self-consistently coupled to tube dilation and macroscopic rheological response. We predict that with increasing strain the tube strongly dilates, entanglements are lost, and reptation speeds up. As a consequence, a stress overshoot emerges not due to affine over-orientation, but rather to strong weakening of the entanglement network. Just beyond the stress overshoot the longest relaxation time is predicted to scale as the inverse shear rate, corresponding to the emergence of a generic form of convective constraint release (CCR). Its origin is a stress-induced local force that self-consistently couples the mesoscopic tube-scale physics with macroscopic mechanical response. Tube weakening at the overshoot occurs via the same qualitative mechanism that leads to microscopic absolute yielding in the nonlinear elastic scenario analyzed in the preceding paper. The stress overshoot and emergent CCR thus correspond to an elastic-viscous crossover due to deformation-induced disentanglement, which at long times and high shear rates results in a quantitatively sensible flow stress plateau and shear thinning behavior. We suggest that the predicted behavior for needles is relevant to flexible chain melts at low Rouse Weissenberg numbers if contour length equilibration is fast. Quantitative predictions for tube dilation in the steady state flow of chains melts are favorably compared to a recent simulation.

cond-mat.soft↗

arXiv2016

A Force-Level Theory of the Rheology of Entangled Rod and Chain Polymer Liquids. I. Tube Deformation, Microscopic Yielding and the Nonlinear Elastic Limit

We employ a first principles, force-level approach to self-consistently construct the anharmonic tube confinement field for entangled fluids of rigid needles and for primitive-path (PP) level chains in two limiting situations where chain stretching is assumed to either completely relax or remain unrelaxed. The influence of shear and extensional deformation and polymer orientation is determined in a nonlinear elastic limit where dissipative relaxation processes are intentionally neglected. For needles and PP-level chains, a Gaussian analysis of transverse polymer dynamical fluctuations predicts that deformation-induced orientation leads to tube dilation. In contrast, for deformed polymers in which chain stretch does not relax we find tube compression. For all three systems, a finite maximum transverse entanglement force localizing the polymers in effective tubes is predicted. The conditions when this entanglement force can be overcome (a force imbalance) by an externally applied force associated with macroscopic deformation can be crisply defined in the nonlinear elastic limit, and the possibility of a "microscopic absolute yielding" event destroying the tube confinement can be analyzed. For needles and contour-relaxed PP chains, this force imbalance is found to occur at a stress of order the equilibrium shear modulus and thus a strain of order unity, corresponding to a mechanically fragile entanglement tube field. However, for unrelaxed stretched chains, tube compression stabilizes transverse polymer confinement, and there appears to be no force imbalance. These results collectively suggest that the crossover from elastic to irreversible viscous response requires chain retraction to initiate disentanglement. We qualitatively discuss comparisons with existing phenomenological models for nonlinear startup shear, step strain, and creep rheology experiments.

cond-mat.soft↗

arXiv2016

Spatial structure of states of self stress in jammed systems

States of self stress, organizations of internal forces in many-body systems that are in equilibrium with an absence of external forces, can be thought of as the constitutive building blocks of the elastic response of a material. In overconstrained disordered packings they have a natural mathematical correspondence with the zero-energy vibrational modes in underconstrained systems. While substantial attention in the literature has been paid to diverging length scales associated with zero- and finite-energy vibrational modes in jammed systems, less is known about the spatial structure of the states of self stress. In this work we define a natural way in which a unique state of self stress can be associated with each bond in a disordered spring network derived from a jammed packing, and then investigate the spatial structure of these bond-localized states of self stress. This allows for an understanding of how the elastic properties of a system would change upon changing the strength or even existence of any bond in the system.

cond-mat.soft↗

arXiv2015

A structural approach to relaxation in glassy liquids

When a liquid freezes, a change in the local atomic structure marks the transition to the crystal. When a liquid is cooled to form a glass, however, no noticeable structural change marks the glass transition. Indeed, characteristic features of glassy dynamics that appear below an onset temperature, T_0, are qualitatively captured by mean field theory, which assumes uniform local structure at all temperatures. Even studies of more realistic systems have found only weak correlations between structure and dynamics. This raises the question: is structure important to glassy dynamics in three dimensions? Here, we answer this question affirmatively by using machine learning methods to identify a new field, that we call softness, which characterizes local structure and is strongly correlated with rearrangement dynamics. We find that the onset of glassy dynamics at T_0 is marked by the onset of correlations between softness (i.e. structure) and dynamics. Moreover, we use softness to construct a simple model of slow glassy relaxation that is in excellent agreement with our simulation results, showing that a theory of the evolution of softness in time would constitute a theory of glassy dynamics.

cond-mat.soft↗

arXiv2015

Strain fluctuations and elastic moduli in disordered solids

Recently there has been a surge in interest in using video-microscopy techniques to infer the local mechanical properties of disordered solids. One common approach is to minimize the difference between particle vibrational displacements in a local coarse-graining volume and the displacements that would result from a best-fit affine deformation. Effective moduli are then be inferred under the assumption that the components of this best-fit affine deformation tensor have a Boltzmann distribution. In this paper, we combine theoretical arguments with experimental and simulation data to demonstrate that the above does not reveal information about the true elastic moduli of jammed packings and colloidal glasses.

cond-mat.soft↗

arXiv2015

Algorithmic Lattice Kirigami: A Route to Pluripotent Materials

We use a regular arrangement of kirigami elements to demonstrate an inverse design paradigm for folding a flat surface into complex target configurations. We first present a scheme using arrays of disclination defect pairs on the dual to the honeycomb lattice; by arranging these defect pairs properly with respect to each other and choosing an appropriate fold pattern a target stepped surface can be designed. We then present a more general method that specifies a fixed lattice of kirigami cuts to be performed on a flat sheet. This single "pluripotent" lattice of cuts permits a wide variety of target surfaces to be programmed into the sheet by changing the folding directions.

cond-mat.soft↗

arXiv2014

Disordered surface vibrations in jammed sphere packings

We study the vibrational properties near a free surface of disordered spring networks derived from jammed sphere packings. In bulk systems, without surfaces, it is well understood that such systems have a plateau in the density of vibrational modes extending down to a frequency scale $ω^*$. This frequency is controlled by $ΔZ = \langle Z \rangle - 2d$, the difference between the average coordination of the spheres and twice the spatial dimension, $d$, of the system, which vanishes at the jamming transition. In the presence of a free surface we find that there is a density of disordered vibrational modes associated with the surface that extends far below $ω^*$. The total number of these low-frequency surface modes is controlled by $ΔZ$, and the profile of their decay into the bulk has two characteristic length scales, which diverge as $ΔZ^{-1/2}$ and $ΔZ^{-1}$ as the jamming transition is approached.

cond-mat.soft↗