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Biomolecular condensates self-assemble when proteins and nucleic acids spontaneously demix to form droplets within the crowded intracellular milieu. This simple mechanism underlies the formation of a wide variety of membraneless…
Based on recent experiments with time-lapse fluorescent imaging, we propose a cellular automaton model for the dynamics of vascular endothelial cells (ECs) in angiogenic morphogenesis. The model successfully reproduces cell mixing behavior,…
How much information does a cell inherit from its ancestors beyond its genetic sequence? What are the epigenetic mechanisms that allow this? Despite the rise in available epigenetic data, how such information is inherited through the cell…
Temperature dependent photodegradation and recovery studies of Dipserse Orange 11 (DO11) dye dissolved in poly(methyl methacrylate) and polystyrene polymer hosts are used as a test of the recently proposed correlated chromophore domain…
In the recent decade, the emergence of liquid biopsy has significantly improved cancer monitoring and detection. Dying cells, including those originating from tumors, shed their DNA into the bloodstream and contribute to a pool of…
The understanding of mechanisms that control epigenetic changes is an important research area in modern functional biology. Epigenetic modifications such as DNA methylation are in general very stable over many cell divisions. DNA…
Understanding protein motion within the cell is crucial for predicting reaction rates and macromolecular transport in the cytoplasm. A key question is how crowded environments affect protein dynamics through hydrodynamic and direct…
This study presents an enhanced method for analyzing cluster dynamics, with a particular focus on tracking clusters' continuity over time using time-series data from molecular dynamics (MD) simulation. The proposed method was applied to…
The baseline level of transcription, which is variable and difficult to quantify, seriously complicates the normalization of comparative transcriptomic data, but its biological importance remains unappreciated. We show that this currently…
We propose a novel framework for ID-preserving generation using a multi-modal encoding strategy rather than injecting identity features via adapters into pre-trained models. Our method treats identity and text as a unified conditioning…
Biomolecular condensates formed through the phase separation of proteins and nucleic acids are widely observed, offering a fundamental means of organizing intracellular materials in a membrane-less fashion. Traditionally, these condensates…
Understanding chromatin dynamics across multiple spatiotemporal scales requires models that reconcile biological specificity with physics-based interactions and computational tractability. We present a modular, recognition-enabled…
Epigenetic Tracking (ET) is an Artificial Embryology system which allows for the evolution and development of large complex structures built from artificial cells. In terms of the number of cells, the complexity of the bodies generated with…
Investigating the dynamics of chromatin and the factors that are affecting it, has provided valuable insights into the organization and functionality of the genome in the cell nucleus. We control the expression of Lamin-A, an important…
Heterogeneity is ubiquitous in stem cells (SC), cancer cells (CS), and cancer stem cells (CSC). SC and CSC heterogeneity is manifested as diverse sub-populations with self-renewing and unique regeneration capacity. Moreover, the CSC progeny…
Organic molecular crystals are appealing for next-generation optoelectronic applications, most notably due to their multiexciton generation process that can increase the efficiency of photovoltaic devices. However, a general understanding…
Recent high resolution experiments have provided a quantitative description of the statistical properties of interphase chromatin at large scales. These findings have stimulated a search for generic physical interactions that give rise to…
With the advent of digital scanners and deep learning, diagnostic operations may move from a microscope to a desktop. Hematoxylin and Eosin (H&E) staining is one of the most frequently used stains for disease analysis, diagnosis, and…
The mechanism and driving forces of chromosome segregation in the bacterial cell cycle of E. coli is one of the least understood events in its life cycle. Using principles of entropic repulsion between polymer loops confined in a cylinder,…
Segmentation of nuclei regions from histological images is an important task for automated computer-aided analysis of histological images, particularly in the presence of impermissible color variation in the color appearance of stained…