Medical Insights, Now Available on Your Wrist
Jessilyn Dunn gathers biometric data from smartwatches to study and predict health changes. Read the article
Activity-driven chromatin organization during interphase: Compaction, segregation, and entanglement suppression
In mammalian cells, the cohesin protein complex is believed to translocate along chromatin during interphase to form dynamic loops through a process called active loop extrusion. Chromosome conformation capture and imaging experiments have suggested that chromatin adopts a compact structure with limited interpenetration between chromosomes and between chromosomal sections. We developed a theory demonstrating that…
Theory of chromatin organization maintained by active loop extrusion
The active loop extrusion hypothesis proposes that chromatin threads through the cohesin protein complex into progressively larger loops until reaching specific boundary elements. We build upon this hypothesis and develop an analytical theory for active loop extrusion which predicts that loop formation probability is a nonmonotonic function of loop length and describes chromatin contact probabilities….
Establishing a massively parallel computational model of the adaptive immune response
Parallel agent-based models of the adaptive immune response can efficiently recapitulate emerging spatiotemporal properties of T-cell motility during clonal selection across multiple length and time scales. Here, we present a distributed, three-dimensional (3D) computational model of T-cell priming, and associated parallel data structures and algorithms that enable fully deterministic cell simulations at scale. We demonstrate…
A method for intelligent allocation of diagnostic testing by leveraging data from commercial wearable devices: a case study on COVID-19
Mass surveillance testing can help control outbreaks of infectious diseases such as COVID-19. However, diagnostic test shortages are prevalent globally and continue to occur in the US with the onset of new COVID-19 variants and emerging diseases like monkeypox, demonstrating an unprecedented need for improving our current methods for mass surveillance testing. By targeting surveillance…
Enhancing Adaptive Physics Refinement Simulations Through the Addition of Realistic Red Blood Cell Counts
Simulations of cancer cell transport require accurately modeling mm-scale and longer trajectories through a circulatory system containing trillions of deformable red blood cells, whose intercellular interactions require submicron fidelity. Using a hybrid CPU-GPU approach, we extend the advanced physics refinement (APR) method to couple a finely-resolved region of explicitly-modeled red blood cells to a coarsely-resolved…