Biology subjects

Bannish, B.

Publications and source records attributed to Bannish, B..

2 recordsLinked to original sources

bioRxiv2026

Nonlinear Relationships of Fibrin Network Structure as a Function of Fibrinogen and Thrombin Concentrations for Purified Fibrinogen and Plasma Clots

BackgroundFibrinogen levels are associated with bleeding disorders and thrombotic disease. Thrombin converts fibrinogen to fibrin, producing the load-bearing fibrin scaffold that governs clot mechanics and transport. ObjectiveQuantitatively map how initial fibrinogen and thrombin concentrations, [Fgn]0 and [T[h]r]0, determine fibrin architecture in human plasma and a purified fibrinogen system. MethodsScanning electron microscopy was used to quantify single-fiber morphology--fiber diameter and branch-to-branch segment length from a standardized sample-preparation protocol. Confocal microscopy was used to quantify network architecture--projected fiber density and pore/bubble size. Results and ConclusionsAcross plasma and purified systems, fibrin structural parameters were quantitatively captured by compact multiplicative scaling laws of the form Y = k[Fgn]0[T[h]r]0{beta}. Unlike prior studies, which examined narrower condition ranges without establishing predictive equations across a systematic fibrinogen-thrombin concentration matrix, this framework defines distinct, quantitative roles for fibrinogen and thrombin in fibrin assembly. The magnitudes and signs of the exponents and {beta} indicate that thrombin primarily controls individual fiber growth kinetics, strongly shortening branch-to-branch segment length and modestly thinning fibers, whereas fibrinogen primarily controls space filling, strongly increasing fiber density, reducing pore/bubble size, and thickening fibers. For matched [Fgn]0 and [T[h]r]0, compared to plasma clots, purified fibrinogen formed denser networks with thinner and shorter fibers, suggesting that the plasma biochemical environment partially inhibits thrombin activity. Fiber length analysis further suggests that each thrombin molecule nucleates one fiber segment. Together, these parameterized scaling relations provide a predictive quantitative framework linking clot composition to fibrin microstructure in plasma and purified fibrinogen clots.

biophysics↗

bioRxiv2020

Connecting actin polymer dynamics across multiple scales

Actin is an intracellular protein that constitutes a primary component of the cellular cytoskeleton and is accordingly crucial for various cell functions. Actin assembles into semi-flexible filaments that cross-link to form higher order structures within the cytoskeleton. In turn, the actin cytoskeketon regulates cell shape, and participates in cell migration and division. A variety of theoretical models have been proposed to investigate actin dynamics across distinct scales, from the stochastic nature of protein and molecular motor dynamics to the deterministic macroscopic behavior of the cytoskeleton. Yet, the relationship between molecular-level actin processes and cellular-level actin network behavior remains understudied, where prior models do not holistically bridge the two scales together. In this work, we focus on the dynamics of the formation of a branched actin structure as observed at the leading edge of motile eukaryotic cells. We construct a minimal agent-based model for the microscale branching actin dynamics, and a deterministic partial differential equation model for the macroscopic network growth and bulk diffusion. The microscale model is stochastic, as its dynamics are based on molecular level effects. The effective diffusion constant and reaction rates of the deterministic model are calculated from averaged simulations of the microscale model, using the mean displacement of the network front and characteristics of the actin network density. With this method, we design concrete metrics that connect phenomenological parameters in the reaction-diffusion system to the biochemical molecular rates typically measured experimentally. A parameter sensitivity analysis in the stochastic agent-based model shows that the effective diffusion and growth constants vary with branching parameters in a complementary way to ensure that the outward speed of the network remains fixed. These results suggest that perturbations to microscale rates can have significant consequences at the macroscopic level, and these should be taken into account when proposing continuum models of actin network dynamics.

biophysics↗