Related papers: Tensegrity structures and data-driven analysis for…
A direct numerical simulation of the three-dimensional elektrokinetic instability near a charge selective surface (electric membrane, electrode, or system of micro-/nanochannels) is carried out and analyzed. A special finite-difference…
In developing organisms, internal cellular processes generate mechanical stresses at the tissue scale. The resulting deformations depend on the material properties of the tissue, which can exhibit long-ranged orientational order and…
Understanding mechanosensitivity, i.e. how cells sense the stiffness of their environment is very important, yet there is a fundamental difficulty in understanding its mechanism: to measure an elastic modulus one requires two points of…
Synthetic generation of three-dimensional cell models from histopathological images aims to enhance understanding of cell mutation, and progression of cancer, necessary for clinical assessment and optimal treatment. Classical reconstruction…
Multiphase field models have emerged as an important computational tool for understanding biological tissue while resolving single-cell properties. While they have successfully reproduced many experimentally observed behaviors of living…
We present a practical algorithm for partially relaxing multiwell energy densities such as pertain to materials undergoing martensitic phase transitions. The algorithm is based on sequential lamination, but the evolution of the…
Single and collective cell migration are fundamental processes critical for physiological phenomena ranging from embryonic development and immune response to wound healing and cancer metastasis. To understand cell migration from a physical…
Strength, ductility, and failure properties of metals are tailored by plastic deformation routes. Predicting these properties requires modeling of the structural dynamics and stress evolution taking place on several length scales. Progress…
One of the essential questions in the area of granular matter is, how to obtain macroscopic tensorial quantities like stress and strain from ``microscopic'' quantities like the contact forces in a granular assembly. Different averaging…
Analysis of microscopy images can provide insight into many biological processes. One particularly challenging problem is cell nuclear segmentation in highly anisotropic and noisy 3D image data. Manually localizing and segmenting each and…
A severe application of stress on articular cartilage can initiate a cascade of biochemical reactions that can lead to the development of osteoarthritis. We constructed a multiscale mathematical model of the process with three components:…
There is compelling evidence that substrate stiffness affects cell adhesion as well as cytoskeleton organization and contractile activity. This work was designed to study the cytoskeletal contractile activity of cells plated on microposts…
Previous models of the cerebrovascular smooth muscle cell have not addressed the interaction between the electrical, chemical and mechanical components of cell function during the development of active tension. These models are primarily…
We investigate image segmentation of cells under the lens of scalar fields. Our goal is to learn a continuous scalar field on image domains such that its segmentation produces robust instances for cells present in images. This field is a…
We present a continuum model trained on molecular dynamics (MD) simulations for cellular membranes composed of an arbitrary number of lipid types. The model is constructed within the formalism of dynamic density functional theory and can be…
Computer simulations can aid in understanding how collective materials properties emerge from interactions between simple constituents. Here, we introduce a coarse-grained model that enables simulation of networks of actin filaments, myosin…
Cells in tissues can organize into a broad spectrum of structures according to their function. Drastic changes of organization, such as epithelial-mesenchymal transitions or the formation of spheroidal aggregates, are often associated…
Photoelasticity enables full-field stress analysis in transparent objects through stress-induced birefringence. Existing techniques are limited to 2D slices and require destructively slicing the object. Recovering the internal 3D stress…
Methods allowing the synthesis of realistic cell shapes could help generate training data sets to improve cell tracking and segmentation in biomedical images. Deep generative models for cell shape synthesis require a light-weight and…
This article considers the problem of 3-dimensional genome reconstruction for single-cell data, and the uniqueness of such reconstructions in the setting of haploid organisms. We consider multiple graph models as representations of this…