Biology subjects

Niloy, R. A.

Publications and source records attributed to Niloy, R. A..

2 recordsLinked to original sources

bioRxiv2025

Reduced-order modeling of solute transport within physiologically realistic solid tumor microenvironment

AO_SCPLOWBSTRACTC_SCPLOWSolid tumors are characterized by densely packed extracellular matrices and limited vascularization, creating significant resistance to both diffusive and convective transport. In this study, we developed an integration of numerical computations with a theoretical modeling framework that couples three phase viscous-laminar transient simulations of glycocalyx-patched tumor vessel resolving plasma, red blood cells (RBCs), and white blood cells (WBCs) and tracking their volume fractions to a calibrated reverse advection-diffusion (RAD) model for intratumoral plasma transport. The reduced-order tumor microenvironment model uses histology-informed extracellular matrix (ECM) tumor domain and packing fraction, together with explicit glycocalyx-patch electrohydrodynamics (EHD) at the tumor vessel wall. At the fenestra, EHD increases inlet plasma intensity relative to a non-EHD framework across all models (means: 0.576 non-EHD vs 0.722 EHD; gain 25.34%). Numerical simulations of plasma perfusion in both the tumor ECM domain and a microfluidic benchmark exhibit two-stage kinetics, with an initial advection-dominated regime. The RAD model reproduces this behavior and, after a simple temporal calibration to account for pore-scale hydrodynamic acceleration resolved by computational fluid dynamics (CFD), matches the observed propagation. By using fully resolved, EHD-inclusive multiphase CFD simulations to calibrate a reduced-order RAD model parameterized by measurable geometric features, we bridge the gap between classical Darcy-Starling tissue perfusion models and fully resolved CFD. The resulting framework provides a tractable, mechanism-grounded tool for quantifying plasma progression in dense solid tumors.

physiology↗

bioRxiv2024

The role of local and long-range stresses in cephalic furrow formation in the Drosophila melanogaster embryo

Cephalic furrow (CF) is a transient epithelial invagination that forms during early gastrulation in the Drosophila melanogaster embryo. The initial stage of cephalic furrow formation (CFF) involves a shortening of initiator cells, generation of a localized asymmetric protrusion inwards, and then subsequent descent of cells into the yolk sac area. We present an analysis of how local forces associated with cell-membrane tensions and cell pressures interact with the long-range tensile stress developing along the furrow to generate the invagination. We propose two numerical models which capture different aspects of CFF. First, we formulate a force-center model of CF to show how the spatiotemporal heterogeneity of initiator-cell activation observed in vivo is a result of tensile-stress-feedback-based intercellular coordination. We also argue that this kind of mechanical stress-based activation mechanism likely contributes to robustness of the overall process. Second, we use our multi-node lateral vertex model to analyze the mechanical dynamics of the anterior-posterior cross-section of CF. This approach allows us to quantify the balance between cortical membrane tension forces, cellular pressures, and the inward force produced by the tension along the curved apical surface of the embryo. Comparing our simulations to experimental images, we discuss the crucial and indispensable role of the tension-induced inward force, especially during the initial stages of CFF where the localized asymmetric protrusion is formed. We argue that without this inward force the initial descent of the initiator cells into the furrow would not be possible, and that at later stages the inward force provides redundancy to this process and thus aids CFF robustness.

biophysics↗