Dataset Information

Diffusion-Reaction Models of Genipin Incorporation into Fibrin Networks.

ABSTRACT: Genipin is a naturally derived small molecule that crosslinks compounds containing primary amines including many natural biopolymers. A diffusion-reaction model to predict the rates of delivery and incorporation of genipin into fibrin networks is presented. Genipin crosslink formation within fibrin hydrogels is a multi-step process that requires genipin diffusion and reaction with primary amines in hydrated networks. The reaction rate of genipin into fibrin gels was measured via spectroscopy while the rate of marginal crosslink formation was measured by rheology. Covalent coupling between genipin and primary amines in fibrin gels obeys second-order kinetics in genipin concentration with an effective activation energy of -71.9 ± 3.2 kJ-mol-1. Genipin diffusion-reaction within fibrin gels exhibits Thiele moduli between 0.02-0.28, which suggests that the systems studied herein are reaction-limited. Genipin-crosslinked fibrin clots are resistant to fibrinolytic degradation as measured by rheology. Finally, active genipin can be delivered from poly(D,L-lactide-co-glycolide) matrices to gels at rates that are comparable to the characteristic rate of incorporation in fibrin networks. Taken together, this work establishes a quantitative framework to engineer controlled release systems for genipin delivery into protein-based hydrogel networks.

SUBMITTER: Ninh C

PROVIDER: S-EPMC6157746 | biostudies-literature | 2015 Jun

REPOSITORIES: biostudies-literature

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Diffusion-Reaction Models of Genipin Incorporation into Fibrin Networks.

Ninh Chi C Iftikhar Aimon A Cramer Madeline M Bettinger Christopher J CJ

Journal of materials chemistry. B 20150512 22

Genipin is a naturally derived small molecule that crosslinks compounds containing primary amines including many natural biopolymers. A diffusion-reaction model to predict the rates of delivery and incorporation of genipin into fibrin networks is presented. Genipin crosslink formation within fibrin hydrogels is a multi-step process that requires genipin diffusion and reaction with primary amines in hydrated networks. The reaction rate of genipin into fibrin gels was measured via spectroscopy whi ...[more]

PMID: 30271605

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Project description:BACKGROUND: Models of cellular molecular systems are built from components such as biochemical reactions (including interactions between ligands and membrane-bound proteins), conformational changes and active and passive transport. A discrete, stochastic description of the kinetics is often essential to capture the behavior of the system accurately. Where spatial effects play a prominent role the complex morphology of cells may have to be represented, along with aspects such as chemical localization and diffusion. This high level of detail makes efficiency a particularly important consideration for software that is designed to simulate such systems. RESULTS: We describe STEPS, a stochastic reaction-diffusion simulator developed with an emphasis on simulating biochemical signaling pathways accurately and efficiently. STEPS supports all the above-mentioned features, and well-validated support for SBML allows many existing biochemical models to be imported reliably. Complex boundaries can be represented accurately in externally generated 3D tetrahedral meshes imported by STEPS. The powerful Python interface facilitates model construction and simulation control. STEPS implements the composition and rejection method, a variation of the Gillespie SSA, supporting diffusion between tetrahedral elements within an efficient search and update engine. Additional support for well-mixed conditions and for deterministic model solution is implemented. Solver accuracy is confirmed with an original and extensive validation set consisting of isolated reaction, diffusion and reaction-diffusion systems. Accuracy imposes upper and lower limits on tetrahedron sizes, which are described in detail. By comparing to Smoldyn, we show how the voxel-based approach in STEPS is often faster than particle-based methods, with increasing advantage in larger systems, and by comparing to MesoRD we show the efficiency of the STEPS implementation. CONCLUSION: STEPS simulates models of cellular reaction-diffusion systems with complex boundaries with high accuracy and high performance in C/C++, controlled by a powerful and user-friendly Python interface. STEPS is free for use and is available at http://steps.sourceforge.net/

Dataset Information

Diffusion-Reaction Models of Genipin Incorporation into Fibrin Networks.

Publications

Diffusion-Reaction Models of Genipin Incorporation into Fibrin Networks.

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