Related papers: Coarse-graining the vertex model and its response …
Cell layers eliminate unwanted cells through the extrusion process, which underlines healthy versus flawed tissue behaviors. Although several biochemical pathways have been identified, the underlying mechanical basis including the forces…
We review a few representative examples of granular experiments or models where phase separation, accompanied by domain coarsening, is a relevant phenomenon. We first elucidate the intrinsic non-equilibrium, or athermal, nature of granular…
We describe a systematic approach to construct coarse-grained Markov state models from molecular dynamics data of systems driven into a non-equilibrium steady state. We apply this method to study the globule-stretch transition of a single…
A model of multicellular systems with several types of cells is developed from the phase field model. The model is presented as a set of partial differential equations of the field variables, each of which expresses the shape of one cell.…
Tissue fluidity regulates many critical biological processes, including embryonic development, wound healing, and cancer metastasis. In confluent epithelia, where cell packing fraction is effectively fixed, the prevailing paradigm…
Collective cell motions underlie structure formation during embryonic development. Tissues exhibit emergent multicellular characteristics such as jamming, rigidity transitions, and glassy dynamics, but there remain questions about how those…
Morphogenesis involves complex shape changes of biological tissues. Yet, tissue shape changes depend on tissue rheology, which in turn arises from the interplay of large numbers of cells. Here, we link cell- and tissue-scale mechanics by…
The Single Chain Mean Field theory is used to simulate the equilibrium structure of phospholipid membranes at the molecular level. Three levels of coarse-graining of DMPC phospholipid surfactants are present: the detailed 44-beads double…
Coordinated and cooperative motion of cells is essential for embryonic development, tissue morphogenesis, wound healing and cancer invasion. A predictive understanding of the emergent mechanical behaviors in collective cell motion is…
Animal morphogenesis often involves significant shape changes of epithelial tissue sheets. Great progress has been made in understanding the underlying cellular driving forces and their coordination through biomechanical feedback loops.…
Molecular dynamics simulations provide theoretical insight into the microscopic behavior of materials in condensed phase and, as a predictive tool, enable computational design of new compounds. However, because of the large temporal and…
The relationship between velocities, tractions, and intercellular stresses in the migrating epithelial monolayer are currently unknown. Ten years ago, a method known as Monolayer Stress Microscopy (MSM) was suggested from which the…
The conformational dynamics of a single protein molecule in a shear flow is investigated using Brownian dynamics simulations. A structure-based coarse grained model of a protein is used. We consider two proteins, ubiquitin and integrin, and…
Atomistic or ab-initio molecular dynamics simulations are widely used to predict thermodynamics and kinetics and relate them to molecular structure. A common approach to go beyond the time- and length-scales accessible with such…
A two-dimensional lattice model for the formation and evolution of shear bands in granular media is proposed. Each lattice site is assigned a random variable which reflects the local density. At every time step, the strain is localized…
We study a coarsening process of one-dimensional cell complexes. We show that if cell boundaries move with velocities proportional to the difference in size of neighboring cells, then the average cell size grows at a prescribed exponential…
Understanding the activity of large populations of neurons is difficult due to the combinatorial complexity of possible cell-cell interactions. To reduce the complexity, coarse-graining had been previously applied to experimental neural…
We report the results of three-dimensional molecular dynamics simulations of sheared granular system in a Couette geometry.\cite{movies} The simulations use realistic boundary conditions that may be expected in physical experiments. For a…
Mathematical modelling of biological population dynamics often involves proposing high fidelity discrete agent-based models that capture stochasticity and individual-level processes. These models are often considered in conjunction with an…
We develop a machine-learning method for coarse-graining condensed-phase molecular systems using anisotropic particles. The method extends currently available high-dimensional neural network potentials by addressing molecular anisotropy. We…