Biology subjects

Shaqfeh, E. S. G.

Publications and source records attributed to Shaqfeh, E. S. G..

3 recordsLinked to original sources

bioRxiv2026

Rapid simulation of organ-scale oxygen transport for tissue ischemia prediction

A densely vascularized tissue can still be starved of oxygen. Tissue oxygenation depends heavily on vessel arrangement, blood flow distributions, and cellular metabolism. Resolving these effects from individual constituent vessels to whole organs has historically been computationally prohibitive. We introduce the Cardiovascular Analysis and Simulation of Circulatory Advection, Diffusion, and Exchange (CASCADE) toolkit, which makes vessel-resolved oxygen transport tractable at the organ scale through a novel screened Green's-function formulation. On laptop-class hardware, CASCADE simulates networks containing thousands of vessels in under one second and a full biventricular human heart model in about two minutes. We validate spatial oxygen and cell-survival predictions against experiments in perfused engineered tissues and matched finite-element simulations. In engineered tissues, sweeps across thousands of network designs and physiological conditions reveal when vessel density, oxygen supply, or network architecture limits viability, establishing design rules for sustaining thick constructs. In a human heart model, CASCADE translates coronary occlusion, anemia, polycythemia, and hypoxemia into distinct myocardial oxygenation patterns, revealing where oxygen delivery fails and how much tissue is at risk.

bioengineering↗

bioRxiv2026

Photopatterned Sacrificial Vascular Architectures for Large Tissue-Scale Oxygenation

The engineering of thick, metabolically active tissues is constrained by the lack of scalable methods to create perfusable vasculature. This hinders effective metabolite transport in large tissue volumes, posing a critical barrier for regenerative tissue applications. In this study, we introduce photopatterned Channel Architectures with Sacrificial Templates (pCAST), an additive manufacturing strategy for generating three dimensional (3D), interconnected vascular networks with precisely defined negative space. Water-soluble sacrificial templates were fabricated using scalable Continuous Liquid Interface Production (CLIP), embedded within tissue constructs, and flushed away to yield 50 {micro}m perfusable channels spanning centimeter-scale tissue constructs. We then apply experimental oxygen mapping and viability analysis to pCAST constructs to build finite-element models that predict patterns of oxygen availability and tissue survival are governed by the balance between metabolic demand and vascular architecture, consistent with reaction-diffusion theory. This computational framework quantitatively predicts oxygen distributions and viability boundaries across vascular geometries and is validated experimentally. Together, these results establish pCAST as a scalable design framework linking vascular architecture, perfusion, and metabolic support for engineering large, 3D perfused tissue constructs. SignificanceThe ability to engineer thick, living tissues is limited by poor oxygen and nutrient delivery, which causes cell death before tissues can function or integrate with the body. This work addresses that fundamental barrier by introducing photopatterned Channel Architecture with Sacrificial Templates (pCAST), a scalable manufacturing strategy that creates precisely defined, perfusable vascular networks inside 3D tissues. By combining high-resolution 3D printing, sacrificial templating, and quantitative oxygen mapping, this research establishes design rules that link vascular geometry, perfusion, and tissue viability. These insights provide a general framework for building large, metabolically active tissues, with direct relevance to cardiac patches and other regenerative medicine applications.

bioengineering↗

bioRxiv2019

Simulation of Red Blood Cell Migration in Small Arterioles: Effect of Cytoplasmic Viscosity

The dynamics of red blood cells in small arterioles are important as these dynamics affect many physiological processes such as hemostasis and thrombosis. However, studying red blood cell flows via computer simulations is challenging due to the complex shapes and the non-trivial viscosity contrast of a red blood cell. To date, little progress has been made studying small arteriole flows (20-40m) with a hematocrit (red blood cell volume fraction) of 10-20% and a physiological viscosity contrast. In this work, we present the results of large-scale simulations that show how the channel size, viscosity contrast of the red blood cells, and hematocrit affect cell distributions and the cell-free layer in these systems. We utilize a massively-parallel immersed boundary code coupled to a finite volume solver to capture the particle resolved physics. We show that channel size qualitatively changes how the cells distribute in the channel. Our results also indicate that at a hematocrit of 10% that the viscosity contrast is not negligible when calculating the cell free layer thickness. We explain this result by comparing lift and collision trajectories of cells at different viscosity contrasts.

biophysics↗