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1. Fibrin-modulating nanogels for treatment of disseminated intravascular coagulation

   https://doi.org/10.1182/bloodadvances.2020003046  

   Mihalko, Emily P.; Sandry, Megan; Mininni, Nicholas; Nellenbach, Kimberly; Deal, Halston; Daniele, Michael; Ghadimi, Kamrouz; Levy, Jerrold H.; Brown, Ashley C. (February 2021, Blood Advances)

   null (Ed.)

   Abstract Disseminated intravascular coagulation (DIC) is a pathological coagulopathy associated with infection that increases mortality. In DIC, excessive thrombin generation causes symptoms from formation of microthrombi to multiorgan failure; bleeding risks can also be a concern because of clotting factor consumption. Different clinical events lead to DIC, including sepsis, trauma, and shock. Treatments for thrombotic episodes or bleeding presentation in DIC oppose each other, thus creating therapeutic dilemmas in management. The objective of this study was to develop fibrin-specific core-shell nanogels (FSNs) loaded with tissue-type plasminogen activator (tPA) to treat the microcirculatory complications of DIC, which would facilitate targeted clot dissolution to manage microthrombi and the potential consumptive coagulopathy that causes bleeding. FSNs enhance formation of actively polymerizing clots by crosslinking fibrin fibers, but they can also target preexisting microthrombi and, when loaded with tPA, facilitate targeted delivery to lyse the microthrombi. We hypothesized that this dual action would simultaneously address bleeding and microthrombi with DIC to improve outcomes. In vivo, tPA-FSNs decreased the presentation of multiorgan microthrombi, recovered platelet counts, and improved bleeding outcomes in a DIC rodent model. When incorporated with human DIC patient plasma, tPA-FSNs restored clot structure and clot growth under flow. Together, these data demonstrate that a fibrinolytic agent loaded into fibrin-targeting nanogels could improve DIC outcomes. 

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2. The Art and Science of Building a Computational Model to Understand Hemostasis

   https://doi.org/10.1055/s-0041-1722861  

   Leiderman, Karin; Sindi, Suzanne S.; Monroe, Dougald M.; Fogelson, Aaron L.; Neeves, Keith B. (February 2021, Seminars in Thrombosis and Hemostasis)

   null (Ed.)

   Abstract Computational models of various facets of hemostasis and thrombosis have increased substantially in the last decade. These models have the potential to make predictions that can uncover new mechanisms within the complex dynamics of thrombus formation. However, these predictions are only as good as the data and assumptions they are built upon, and therefore model building requires intimate coupling with experiments. The objective of this article is to guide the reader through how a computational model is built and how it can inform and be refined by experiments. This is accomplished by answering six questions facing the model builder: (1) Why make a model? (2) What kind of model should be built? (3) How is the model built? (4) Is the model a “good” model? (5) Do we believe the model? (6) Is the model useful? These questions are answered in the context of a model of thrombus formation that has been successfully applied to understanding the interplay between blood flow, platelet deposition, and coagulation and in identifying potential modifiers of thrombin generation in hemophilia A. 

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3. Mathematical modeling to understand the role of bivalent thrombin-fibrin binding during polymerization

   https://doi.org/10.1371/journal.pcbi.1010414  

   Kelley, Michael A.; Leiderman, Karin (September 2022, PLOS Computational Biology)

   Vavylonis, Dimitrios (Ed.)

   Thrombin is an enzyme produced during blood coagulation that is crucial to the formation of a stable clot. Thrombin cleaves soluble fibrinogen into fibrin, which polymerizes and forms an insoluble, stabilizing gel around the growing clot. A small fraction of circulating fibrinogen is the variant γ A / γ ′, which has been associated with high-affinity thrombin binding and implicated as a risk factor for myocardial infarctions, deep vein thrombosis, and coronary artery disease. Thrombin is also known to be strongly sequestered by polymerized fibrin for extended periods of time in a way that is partially regulated by γ A / γ ′. However, the role of γ A / γ ′-thrombin interactions during fibrin polymerization is not fully understood. Here, we present a mathematical model of fibrin polymerization that considered the interactions between thrombin, fibrinogen, and fibrin, including those with γ A / γ ′. In our model, bivalent thrombin-fibrin binding greatly increased thrombin residency times and allowed for thrombin-trapping during fibrin polymerization. Results from the model showed that early in fibrin polymerization, γ ′ binding to thrombin served to localize the thrombin to the fibrin(ogen), which effectively enhanced the enzymatic conversion of fibrinogen to fibrin. When all the fibrin was fully generated, however, the fibrin-thrombin binding persisted but the effect of fibrin on thrombin switched quickly to serve as a sink, essentially removing all free thrombin from the system. This dual role for γ ′-thrombin binding during polymerization led to a paradoxical decrease in trapped thrombin as the amount of γ ′ was increased. The model highlighted biochemical and biophysical roles for fibrin-thrombin interactions during polymerization and agreed well with experimental observations. 

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4. Transient particle tracking microrheology of plasma coagulation via the intrinsic pathway

   https://doi.org/10.1515/arh-2022-0129  

   Mao, Yating; Tan, Mingyang; Kohs, Tia C.; Sylman, Joanna L.; Ngo, Anh T.; Puy, Cristina; McCarty, Owen J.; Walker, Travis W. (January 2023, Applied Rheology)

   Abstract The maintenance of hemostasis to ensure vascular integrity is dependent upon the rapid conversion of zymogen species of the coagulation cascade to their enzymatically active forms. This process culminates in the generation of the serine protease thrombin and polymerization of fibrin to prevent vascular leak at sites of endothelial cell injury or loss of cellular junctions. Thrombin generation can be initiated by the extrinsic pathway of coagulation through exposure of blood to tissue factor at sites of vascular damage, or alternatively by the coagulation factor (F) XII activated by foreign surfaces with negative charges, such as glass, through the contact activation pathway. Here, we used transient particle tracking microrheology to investigate the mechanical properties of fibrin in response to thrombin generation downstream of both coagulation pathways. We found that the structural heterogeneity of fibrin formation was dependent on the reaction kinetics of thrombin generation. Pharmacological inhibition of FXII activity prolonged the time to form fibrin and increased the degree of heterogeneity of fibrin, resulting in fibrin clots with reduced mechanical properties. Taken together, this study demonstrates a dependency of the physical biology of fibrin formation on activation of the contact pathway of coagulation. 

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5. Approximation of Anisotropic Pair Potentials Using Multivariate Interpolation

   https://doi.org/10.1021/acs.jpcb.5c01451  

   Fakhraei, Mohammadreza; Kieslich, Chris A; Howard, Michael P (July 2025, The Journal of Physical Chemistry B)

   The interaction between two particles with shape or interaction anisotropy can be modeled using a pairwise potential energy function that depends on their relative position and orientation; however, this function is often challenging to mathematically formulate. Data-driven approaches for approximating anisotropic pair potentials have gained significant interest due to their flexibility and generality but often require large sets of training data, potentially limiting their feasibility when training data is computationally demanding to collect. Here, we investigate the use of multivariate polynomial interpolation to approximate anisotropic pair potentials from a limited set of prescribed particle configurations. We consider both standard Chebyshev polynomial interpolation as well as mixed-basis polynomial interpolation that uses trigonometric polynomials for coordinates along which the pair potential is known to be periodic. We exploit mathematical reasoning and physical knowledge to refine the interpolation domain and to design our interpolants. We test our approach on two-dimensional and three-dimensional model anisotropic nanoparticles, finding satisfactory approximations can be constructed in all cases. 

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