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Correlated velocity patterns and associated large length-scale transmission of traction forces have been observed in collective live cell migration as a response to a "wound". We argue that a simple physical model of a force-driven…

Constructing physical models of living cells and tissues is an extremely challenging task because of the high complexities of both intra- and intercellular processes. In addition, the force that a single cell generates vanishes in total due…

Causal inference quantifies cause-effect relationships by estimating counterfactual parameters from data. This entails using \emph{identification theory} to establish a link between counterfactual parameters of interest and distributions…

Membranes regulate transport in a wide variety of industrial and biological applications. The microscale geometry of the membrane can significantly affect overall transport through the membrane, but the precise nature of this multiscale…

We propose a computational framework to study the growth and spread of bacterial biofilms on interfaces, as well as the action of antibiotics on them. Bacterial membranes are represented by boundaries immersed in a fluid matrix and subject…

Nanofluidic systems exhibit transport characteristics that have made technological marvels such as desalination, energy harvesting, and highly sensitive biomolecule sensing possible by virtue of their ability to influence small currents due…

Inferring dynamical models from low-resolution temporal data continues to be a significant challenge in biophysics, especially within transcriptomics, where separating molecular programs from noise remains an important open problem. We…

New text as data techniques offer a great promise: the ability to inductively discover measures that are useful for testing social science theories of interest from large collections of text. We introduce a conceptual framework for making…

Many inference tasks on knowledge graphs, including relation prediction, operate on knowledge graph embeddings -- vector representations of the vertices (entities) and edges (relations) that preserve task-relevant structure encoded within…

In the past two decades a range of fluorescence cell microscopy techniques have been developed which can achieve ~10 nm spatial resolution, i.e. substantially beating the usual limits set by optical diffraction. However, these methods rely…

Biopolymer Networks play an important role in coordinating and regulating collective cellular dynamics via a number of signaling pathways. Here, we investigate the mechanical response of a model biopolymer network due to the active…

Gas transport across cell membrane is a very important process in biochemistry which is essential for many crucial tasks, including cell respiration pH regulation in the cell. In the late 1990's, the suggestion that gasses are transported…

Both classical and quantum electrodynamics predict the existence of dipole-dipole long-range electrodynamic intermolecular forces; however, these have never been hitherto experimentally observed. The discovery of completely new and…

All living cells transport molecules and ions across membranes, often against concentration gradients. This active transport requires continual energy expenditure and is clearly a nonequilibrium process for which standard equilibrium…

The dynamics of biological systems, from proteins to cells to organisms, is complex and stochastic. To decipher their physical laws, we need to bridge between experimental observations and theoretical modeling. Thanks to progress in…

Machine learning classifiers rely on loss functions for performance evaluation, often on a private (hidden) dataset. In a recent line of research, label inference was introduced as the problem of reconstructing the ground truth labels of…

Proteins are the active working horses in our body. These biomolecules perform all vital cellular functions from DNA replication and general biosynthesis to metabolic signaling and environmental sensing. While static 3D structures are now…

The life of a cell is governed by highly dynamical microscopic processes. Two notable examples are the diffusion of membrane receptors and the kinetics of transcription factors governing the rates of gene expression. Different fluorescence…

Bacterial cellulose biofilms are complex networks of strong interwoven nanofibers that control transport and protect bacterial colonies in the film. Design of diverse applications of bacterial cellulose films also relies on understanding…

In vivo, eukaryotic cells are embedded in a matrix environment, where they grow and develop. Generally, this extracellular matrix (ECM) is an anisotropic fibrous structure, through which macromolecules and biochemical signaling molecules at…