• Hindered diffusion becomes

the dominant force of molecular movement in a thrombus. • The thrombus core acts as a selective molecular prison. Hemostatic thrombi formed after a penetrating injury have a heterogeneous architecture in which a core of highly activated, densely packed platelets is covered by a shell of less-activated, loosely packed platelets. In the first manuscript in this series, we show that regional differences in intrathrombus protein transport rates emerge early in the hemo-static response and are preserved as the thrombus develops. Here, we use a theoretical approach to investigate this process and its impact on agonist distribution. The results suggest that hindered diffusion, rather than convection, is the dominant mechanism responsible for molecular movement within the thrombus. The analysis also suggests that the thrombuscore, as comparedwith the shell, providesanenvironment for retaining soluble agonists such as thrombin, affecting the extent of platelet activationby establishing agonist-specific concentrationgradients radiating from the site of injury. This analysis accounts for the observed weaker activation and relative instability of platelets in the shell andpredicts that a failure to forma tightlypacked thrombuscorewill limit thrombinaccumulation, aprediction testedbyanalysis of data from mice with a defect in clot retraction. (Blood. 2014;124(11):1816-1823