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We present feature finding and tracking algorithms in 3D in living cells, and demonstrate their utility to measure metrics important in cell biological processes. We developed a computational imaging hybrid approach that combines automated…
Deep learning approaches to the segmentation of magnetic resonance images have shown significant promise in automating the quantitative analysis of brain images. However, a continuing challenge has been its sensitivity to the variability of…
Exactly solvable neural network models with asymmetric weights are rare, and exact solutions are available only in some mean-field approaches. In this article we find exact analytical solutions of an asymmetric spin-glass-like model of…
Various biological phenomena, like cell differentiation and pattern formation in multicellular organisms, are explained using the bifurcation theory. Molecular network motifs like positive feedback and mutual repressor exhibit bifurcation…
In this paper we develop a directional search-and-capture model of cytoneme-based morphogenesis. We consider a single cytoneme nucleating from a source cell and searching for a set of $N$ target cells $\Omega_k\subset \R^d$, $k=1,\ldots,N$,…
In the past several years, the problem of genome assembly has received considerable attention from both biologists and computer scientists. An important component of current assembly methods is the scaffolding process. This process involves…
Motivated by recent experiments probing shape, size and dynamics of bacterial chromosomes in growing cells, we consider a polymer model consisting of a circular backbone to which side-loops are attached, confined to a cylindrical cell. Such…
A binary mixture of particles interacting with spherically-symmetric potentials leading to microsegregation is studied by theory and molecular dynamics (MD) simulations. We consider spherical particles with equal diameters and volume…
Kinesin-8 motor proteins destabilize microtubules. Their absence during cell division is associated with disorganized mitotic chromosome movements and chromosome loss. Despite recent work studying effects of kinesin 8s on microtubule…
We study how confinement transforms the chaotic dynamics of bulk microtubule-based active nematics into regular spatiotemporal patterns. For weak confinements, multiple continuously nucleating and annihilating topological defects…
Segmentation of abdominal organs has been a comprehensive, yet unresolved, research field for many years. In the last decade, intensive developments in deep learning (DL) have introduced new state-of-the-art segmentation systems. In order…
Planning of radiotherapy involves accurate segmentation of a large number of organs at risk, i.e. organs for which irradiation doses should be minimized to avoid important side effects of the therapy. We propose a deep learning method for…
Based on extensive study of a dynamical systems model of the development of a cell society, a novel theory for stem cell differentiation and its regulation is proposed as the ``chaos hypothesis''. Two fundamental features of stem cell…
Particles with directional interactions are promising building blocks for new functional materials and may serve as models for biological structures. Mutually attractive nanoparticles that are deformable due to flexible surface groups, for…
Self-assembly is the autonomous organization of components into patterns or structures: an essential ingredient of biology and a desired route to complex organization. At equilibrium, the structure is encoded through specific interactions,…
Measurement of the life time of attachments formed by a single microtubule (MT) with a single kinetochore (kt) {\it in-vitro} under force-clamp conditions had earlier revealed a catch-bond-like behavior. In the past the physical origin of…
Network of nonlinear dynamical elements often show clustering of synchronization by chaotic instability. Relevance of the clustering to ecological, immune, neural, and cellular networks is discussed, with the emphasis of partially ordered…
When the motion of a motile cell is observed closely, it appears erratic, and yet the combination of nonequilibrium forces and surfaces can produce striking examples of organization in microbial systems. While most of our current…
Myxococcus xanthus cells self-organize into aligned groups, clusters, at various stages of their lifecycle. Formation of these clusters is crucial for the complex dynamic multi-cellular behavior of these bacteria. However, the mechanism…
Metabolic heterogeneity is widely recognised as the next challenge in our understanding of non-genetic variation. A growing body of evidence suggests that metabolic heterogeneity may result from the inherent stochasticity of intracellular…