Combined computational modeling and experimental study of the biomechanical mechanisms of platelet-driven contraction of fibrin clots

While blood clot formation has been relatively well studied, little is known about the mechanisms underlying the subsequent structural and mechanical clot remodeling called contraction or retraction. Impairment of the clot contraction process is associated with both life-threatening bleeding and thrombotic conditions, such as ischemic stroke, venous thromboembolism, and others. Recently, blood clot contraction was observed to be hindered in patients with COVID-19. A three-dimensional multiscale computational model is developed and used to quantify biomechanical mechanisms of the kinetics of clot contraction driven by platelet-fibrin pulling interactions. These results provide important biological insights into contraction of platelet filopodia, the mechanically active thin protrusions of the plasma membrane, described previously as performing mostly a sensory function. The biomechanical mechanisms and modeling approach described can potentially apply to studying other systems in which cells are embedded in a filamentous network and exert forces on the extracellular matrix modulated by the substrate stiffness.

Characterization of fibronectin properties by integrated micro-fluidic experiments and fluid-structure interaction simulations

Fibronectin (Fn) has been observed to assemble in the extracellular matrix (ECM) of cell culture and stretch in response to the external force. The alteration of molecule domain functions generally follows the extension of Fn. Several researchers have investigated fibronectin extensively in molecular architecture and conformation structure. However, the bulk material behavior of the Fn in the ECM has not been fully depicted at the cell scale, and many studies have ignored physiological conditions. Conversely, microfluidic techniques that explore cellular properties based on cell deformation and adhesion have emerged as a powerful and effective platform to study cell rheological transformation in a physiological environment. However, directly quantifying properties from microfluidic measurements remains a challenge. Therefore, it is an efficient way to combine experimental measurements with a robust and reliable numerical framework to calibrate the mechanical stress distribution in the test sample. In this paper, we present a monolithic Lagrangian fluid-structure interaction (FSI) approach within the Optimal Transportation Meshfree (OTM) framework that enables the investigation of the adherent Red Blood Cell (RBC) interacting with fluid and overcomes the drawbacks of the traditional computational tools such as the mesh entanglement and interface tracking, etc. This study aims to assess the material properties of the RBC and Fn fiber by calibrating the numerical predictions to experimental measurements. Moreover, a physical-based constitutive model will be proposed to describe the bulk behavior of the Fn fiber inflow, and the rate-dependent deformation and separation of the Fn fiber will be discussed.

Development of a novel hybrid method combining finite difference method and dissipative particle dynamics to simulate thrombus formation on orifice flow

In our previous works, the transport of activated platelets (APs) on orifice flow has been simulated by finite difference method (FDM). And the distribution of AP concentration on the flow was obtained. However, the effect of platelet aggregation on the distribution of AP concentration can't be investigated by FDM because FDM can't simulate platelet aggregation. On the other hand, platelet aggregation has been simulated by dissipative particle dynamics (DPD). In this paper, a hybrid method combining FDM and DPD is proposed to investigate the effect of platelet aggregation on the distribution of AP concentration. And the hybrid method is used to simulate thrombus formation on orifice flow. As for the effect of platelet aggregation, it is found that the distribution of AP concentration in the hybrid method is different from the distribution in FDM at the places of platelet aggregation. It is considered that the difference is induced by platelet aggregation. As for the distribution of thrombus, higher AP concentration and more aggregated APs are found around the reattachment point and in the recirculation area. It is considered that thrombus is mainly distributed at these places in the simulation. And according to our previous experimental results, thrombus is mainly distributed around the reattachment point and in the recirculation area. It is concluded that the effect of platelet aggregation on the distribution of AP concentration can be investigated by the hybrid method, and the computational results agree with our previous experimental results.

The key events of thrombus formation: platelet adhesion and aggregation

Thrombus formation is a complex, dynamic and multistep process, involving biochemical reactions, mechanical stimulation, hemodynamics, and so on. In this study, we concentrate on its two crucial steps: (i) platelets adhered to a vessel wall, or simply platelet adhesion, and (ii) platelets clumping and arrested to the adherent platelets, named platelet aggregation. We report the first direct simulation of three modes of platelet adhesion, detachment, rolling adhesion and firm adhesion, as well as the formation, disintegration, arrestment and consolidation of platelet plugs. The results show that the bond dissociation in the detachment mode is mainly attributed to a high probability of rupturing bonds, such that any existing bond can be quickly ruptured and all bonds would be completely broken. In the rolling adhesion, however, it is mainly attributed to the strong traction from the shear flow or erythrocytes, causing that the bonds are ruptured at the trailing edge of the platelet. The erythrocytes play an important role in platelet activities, such as the formation, disintegration, arrestment and consolidation of platelet plugs. They exert an aggregate force on platelets, a repulsion at a near distance but an attraction at a far distance to the platelets. This aggregate force can promote platelets to form a plug and/or bring along a part of a platelet plug causing its disintegration. It also greatly influences the arrestment and consolidation of platelet plugs, together with the adhesive force from the thrombus.

A Multiscale Model for Recruitment Aggregation of Platelets by Correlating with In Vitro Results

Introduction

We developed a multiscale model to simulate the dynamics of platelet aggregation by recruitment of unactivated platelets flowing in viscous shear flows by an activated platelet deposited onto a blood vessel wall. This model uses coarse grained molecular dynamics (CGMD) for platelets at the microscale and dissipative particle dynamics (DPD) for the shear flow at the macroscale. Under conditions of relatively low shear, aggregation is mediated by fibrinogen via αIIbβ3 receptors.

Methods

The binding of αIIbβ3 and fibrinogen is modeled by a molecular-level hybrid force field consisting of Morse potential and Hooke law for the nonbonded and bonded interactions, respectively. The force field, parametrized in two different interaction scales, is calculated by correlating with the platelet contact area measured in vitro and the detaching force between αIIbβ3 and fibrinogen.

Results

Using our model, we derived, the relationship between recruitment force and distance between the centers of mass of two platelets, by integrating the molecular-scale inter-platelet interactions during recruitment aggregation in shear flows. Our model indicates that assuming a rigid-platelet model, underestimates the contact area by 89% and the detaching force by 93% as compared to a model that takes into account the platelet deformability leading to a prediction of a significantly lower attachment during recruitment.

Conclusions

The molecular-level predictive capability of our model sheds a light on differences observed between transient and permanent platelet aggregation patterns. The model and simulation framework can be further adapted to simulate initial thrombus formation involving multiple flowing platelets as well as deposition and adhesion onto blood vessels.

Model predictions of deformation, embolization and permeability of partially obstructive blood clots under variable shear flow

Thromboembolism, one of the leading causes of morbidity and mortality worldwide, is characterized by formation of obstructive intravascular clots (thrombi) and their mechanical breakage (embolization). A novel two-dimensional multi-phase computational model is introduced that describes active interactions between the main components of the clot, including platelets and fibrin, to study the impact of various physiologically relevant blood shear flow conditions on deformation and embolization of a partially obstructive clot with variable permeability. Simulations provide new insights into mechanisms underlying clot stability and embolization that cannot be studied experimentally at this time. In particular, model simulations, calibrated using experimental intravital imaging of an established arteriolar clot, show that flow-induced changes in size, shape and internal structure of the clot are largely determined by two shear-dependent mechanisms: reversible attachment of platelets to the exterior of the clot and removal of large clot pieces. Model simulations predict that blood clots with higher permeability are more prone to embolization with enhanced disintegration under increasing shear rate. In contrast, less permeable clots are more resistant to rupture due to shear rate-dependent clot stiffening originating from enhanced platelet adhesion and aggregation. These results can be used in future to predict risk of thromboembolism based on the data about composition, permeability and deformability of a clot under specific local haemodynamic conditions.

Probing eukaryotic cell mechanics via mesoscopic simulations

Cell mechanics has proven to be important in many biological processes. Although there is a number of experimental techniques which allow us to study mechanical properties of cell, there is still a lack of understanding of the role each sub-cellular component plays during cell deformations. We present a new mesoscopic particle-based eukaryotic cell model which explicitly describes cell membrane, nucleus and cytoskeleton. We employ Dissipative Particle Dynamics (DPD) method that provides us with the unified framework for modeling of a cell and its interactions in the flow. Data from micropipette aspiration experiments were used to define model parameters. The model was validated using data from microfluidic experiments. The validated model was then applied to study the impact of the sub-cellular components on the cell viscoelastic response in micropipette aspiration and microfluidic experiments.

GPU-accelerated Red Blood Cells Simulations with Transport Dissipative Particle Dynamics

Mesoscopic numerical simulations provide a unique approach for the quantification of the chemical influences on red blood cell functionalities. The transport Dissipative Particles Dynamics (tDPD) method can lead to such effective multiscale simulations due to its ability to simultaneously capture mesoscopic advection, diffusion, and reaction. In this paper, we present a GPU-accelerated red blood cell simulation package based on a tDPD adaptation of our red blood cell model, which can correctly recover the cell membrane viscosity, elasticity, bending stiffness, and cross-membrane chemical transport. The package essentially processes all computational workloads in parallel by GPU, and it incorporates multi-stream scheduling and non-blocking MPI communications to improve inter-node scalability. Our code is validated for accuracy and compared against the CPU counterpart for speed. Strong scaling and weak scaling are also presented to characterizes scalability. We observe a speedup of 10.1 on one GPU over all 16 cores within a single node, and a weak scaling efficiency of 91% across 256 nodes. The program enables quick-turnaround and high-throughput numerical simulations for investigating chemical-driven red blood cell phenomena and disorders.

Shear-induced platelet aggregation and distribution of thrombogenesis at stenotic vessels

OBJECTIVE

SIPA, which is mediated by vWF, is a key mechanism in arterial thrombosis under an abnormally high shear rate of blood flow. We investigated the influence of SIPA on thrombogenesis, focusing on alterations in blood flow at stenotic vessels.

METHODS

We carried out a computer simulation of thrombogenesis in stenotic vessels at three different injury positions (ie, upstream, apex, and downstream of the stenosis) to evaluate the effect of SIPA.

RESULTS

The results demonstrated that thrombus volume increased downstream of the stenosis. In particular, growth was enhanced significantly as blood flow velocity and severity of stenosis increased. The influence of SIPA was induced by continuous exposure to high shear rate; thus, SIPA had a greater effect from the apex to downstream of the stenosis along the vessel wall. The asymmetry of the impact of SIPA contributed to the distribution of the thrombus. Furthermore, we found that the degree of SIPA was prolonged in a stenotic vessel with a distal injury, whereas it was moderate with thrombus growth in a nonstenosed vessel. This occurred because platelets and vWF that underwent a high shear rate around the apex were transported to the region downstream of the stenosis.

CONCLUSIONS

These results suggest that thrombus formation downstream of the stenosis is easily affected by SIPA and hemodynamics.

In vitro measurement of particle margination in the microchannel flow: effect of varying hematocrit

It has long been known that platelets undergo margination when flowing in blood vessels, such that there is an excess concentration near the vessel wall. We conduct experiments and three-dimensional boundary integral simulations of platelet-sized spherical particles in a microchannel 30 μm in height to measure the particle-concentration distribution profile and observe its margination at 10%, 20%, and 30% red blood cell hematocrit. The experiments involved adding 2.15-μm-diameter spheres into a solution of red blood cells, plasma, and water and flowing this mixture down a microfluidic channel at a wall shear rate of 1000 s(-1). Fluorescence imaging was used to determine the height and velocity of particles in the channel. Experimental results indicate that margination has largely occurred before particles travel 1 cm downstream and that hematocrit plays a role in the degree of margination. With simulations, we can track the trajectories of the particles with higher resolution. These simulations also confirm that margination from an initially uniform distribution of spheres and red blood cells occurs over the length scale of O(1 cm), with higher hematocrit showing faster margination. The results presented here, from both experiments and 3D simulations, may help explain the relationship between bleeding time in vessel trauma and red blood cell hematocrit as platelets move to a vessel wall.

Transport dissipative particle dynamics model for mesoscopic advection-diffusion-reaction problems

We present a transport dissipative particle dynamics (tDPD) model for simulating mesoscopic problems involving advection-diffusion-reaction (ADR) processes, along with a methodology for implementation of the correct Dirichlet and Neumann boundary conditions in tDPD simulations. tDPD is an extension of the classic dissipative particle dynamics (DPD) framework with extra variables for describing the evolution of concentration fields. The transport of concentration is modeled by a Fickian flux and a random flux between tDPD particles, and the advection is implicitly considered by the movements of these Lagrangian particles. An analytical formula is proposed to relate the tDPD parameters to the effective diffusion coefficient. To validate the present tDPD model and the boundary conditions, we perform three tDPD simulations of one-dimensional diffusion with different boundary conditions, and the results show excellent agreement with the theoretical solutions. We also performed two-dimensional simulations of ADR systems and the tDPD simulations agree well with the results obtained by the spectral element method. Finally, we present an application of the tDPD model to the dynamic process of blood coagulation involving 25 reacting species in order to demonstrate the potential of tDPD in simulating biological dynamics at the mesoscale. We find that the tDPD solution of this comprehensive 25-species coagulation model is only twice as computationally expensive as the conventional DPD simulation of the hydrodynamics only, which is a significant advantage over available continuum solvers.

Modelling of platelet-fibrin clot formation in flow with a DPD-PDE method

The paper is devoted to mathematical modelling of clot growth in blood flow. Great complexity of the hemostatic system dictates the need of usage of the mathematical models to understand its functioning in the normal and especially in pathological situations. In this work we investigate the interaction of blood flow, platelet aggregation and plasma coagulation. We develop a hybrid DPD-PDE model where dissipative particle dynamics (DPD) is used to model plasma flow and platelets, while the regulatory network of plasma coagulation is described by a system of partial differential equations. Modelling results confirm the potency of the scenario of clot growth where at the first stage of clot formation platelets form an aggregate due to weak inter-platelet connections and then due to their activation. This enables the formation of the fibrin net in the centre of the platelet aggregate where the flow velocity is significantly reduced. The fibrin net reinforces the clot and allows its further growth. When the clot becomes sufficiently large, it stops growing due to the narrowed vessel and the increase of flow shear rate at the surface of the clot. Its outer part is detached by the flow revealing the inner part covered by fibrin. This fibrin cap does not allow new platelets to attach at the high shear rate, and the clot stops growing. Dependence of the final clot size on wall shear rate and on other parameters is studied.

Fluid Mechanics of Blood Clot Formation

Intravascular blood clots form in an environment in which hydrodynamic forces dominate and in which fluid-mediated transport is the primary means of moving material. The clotting system has evolved to exploit fluid dynamic mechanisms and to overcome fluid dynamic challenges to ensure that clots that preserve vascular integrity can form over the wide range of flow conditions found in the circulation. Fluid-mediated interactions between the many large deformable red blood cells and the few small rigid platelets lead to high platelet concentrations near vessel walls where platelets contribute to clotting. Receptor-ligand pairs with diverse kinetic and mechanical characteristics work synergistically to arrest rapidly flowing cells on an injured vessel. Variations in hydrodynamic stresses switch on and off the function of key clotting polymers. Protein transport to, from, and within a developing clot determines whether and how fast it grows. We review ongoing experimental and modeling research to understand these and related phenomena.

Hemodynamics in the microcirculation and in microfluidics

Hemodynamics in microcirculation is important for hemorheology and several types of circulatory disease. Although hemodynamics research has a long history, the field continues to expand due to recent advancements in numerical and experimental techniques at the micro-and nano-scales. In this paper, we review recent computational and experimental studies of blood flow in microcirculation and microfluidics. We first focus on the computational studies of red blood cell (RBC) dynamics, from the single cellular level to mesoscopic multiple cellular flows, followed by a review of recent computational adhesion models for white blood cells, platelets, and malaria-infected RBCs, in which the cell adhesion to the vascular wall is essential for cellular function. Recent developments in optical microscopy have enabled the observation of flowing blood cells in microfluidics. Experimental particle image velocimetry and particle tracking velocimetry techniques are described in this article. Advancements in micro total analysis system technologies have facilitated flowing cell separation with microfluidic devices, which can be used for biomedical applications, such as a diagnostic tool for breast cancer or large intestinal tumors. In this paper, cell-separation techniques are reviewed for microfluidic devices, emphasizing recent advances and the potential of this fast-evolving research field in the near future.

Where do the platelets go? A simulation study of fully resolved blood flow through aneurysmal vessels

Despite the importance of platelets in the formation of a thrombus, their transport in complex flows has not yet been studied in detail. In this paper we simulated red blood cells and platelets to explore their transport behaviour in aneurysmal geometries. We considered two aneurysms with different aspect ratios (AR = 1.0, 2.0) in the presence of fast and slow blood flows (Re = 10, 100), and examined the distributions of the cells. Low velocities in the parent vessel resulted in a large stagnation zone inside the cavity, leaving the initial distribution almost unchanged. In fast flows, an influx of platelets into the aneurysm was observed, leading to an elevated concentration. The connection of the platelet-rich cell-free layer (CFL) with the outer regions of the recirculation zones leads to their increased platelet concentration. These platelet-enhanced recirculation zones produced a diverse distribution of cells inside the aneurysm, for the different aspect ratios. A thin red blood CFL that was occupied by platelets was observed on the top of the wide-necked aneurysm, whereas a high-haematocrit region very close to the vessel wall was present in the narrow-necked case. The simulations revealed that non-trivial distributions of red blood cells and platelets are possible inside aneurysmal geometries, giving rise to several hypotheses on the formation of a thrombus, as well as to the wall weakening and the possible rupture of an aneurysm.

Simulation of platelets suspension flowing through a stenosis model using a dissipative particle dynamics approach

Stresses on blood cellular constituents induced by blood flow can be represented by a continuum approach down to the μm level; however, the molecular mechanisms of thrombosis and platelet activation and aggregation are on the order of nm. The coupling of the disparate length and time scales between molecular and macroscopic transport phenomena represents a major computational challenge. In order to bridge the gap between macroscopic flow scales and the cellular scales with the goal of depicting and predicting flow induced thrombogenicity, multi-scale approaches based on particle methods are better suited. We present a top-scale model to describe bulk flow of platelet suspensions: we employ dissipative particle dynamics to model viscous flow dynamics and present a novel and general no-slip boundary condition that allows the description of three-dimensional viscous flows through complex geometries. Dissipative phenomena associated with boundary layers and recirculation zones are observed and favorably compared to benchmark viscous flow solutions (Poiseuille and Couette flows). Platelets in suspension, modeled as coarse-grained finite-sized ensembles of bound particles constituting an enclosed deformable membrane with flat ellipsoid shape, show self-orbiting motions in shear flows consistent with Jeffery's orbits, and are transported with the flow, flipping and colliding with the walls and interacting with other platelets.

Computational analysis on the mechanical interaction between a thrombus and red blood cells: possible causes of membrane damage of red blood cells at microvessels

Previous studies investigating thrombus formation have not focused on the physical interaction between red blood cells (RBCs) and thrombus, although they have been speculated that some pathological conditions such as microangiopathic hemolytic anemia (MAHA) stem from interactions between RBCs and thrombi. In this study, we investigated the mechanical influence of RBCs on primary thrombi during hemostasis. We also explored the mechanics and aggravating factors of intravascular hemolysis. Computer simulations of primary thrombogenesis in the presence and the absence of RBCs demonstrated that RBCs are unlikely to affect the thrombus height and coverage, although their presence may change microvessel hemodynamics and platelet transportation to the injured wall. Our results suggest that intravascular hemolysis owing to RBC membrane damage would be promoted by three hemodynamic factors: (1) dispersibility of platelet thrombi, because more frequent spatial thrombus formation decreases the time available for an RBC to recover its shape and enforces more severe deformation; (2) platelet thrombus stiffness, because a stiffer thrombus increases the degree of RBC deformation upon collision; and (3) vessel size and hemocyte density, because a smaller vessel diameter and higher hemocyte density decrease the room for RBCs to escape as they come closer to a thrombus, thereby enhancing thrombus-RBC interactions.

Time-dependent and outflow boundary conditions for Dissipative Particle Dynamics

We propose a simple method to impose both no-slip boundary conditions at fluid-wall interfaces and at outflow boundaries in fully developed regions for Dissipative Particle Dynamics (DPD) fluid systems. The procedure to enforce the no-slip condition is based on a velocity-dependent shear force, which is a generalized force to represent the presence of the solid-wall particles and to maintain locally thermodynamic consistency. We show that this method can be implemented in both steady and time-dependent fluid systems and compare the DPD results with the continuum limit (Navier-Stokes) results. We also develop a force-adaptive method to impose the outflow boundary conditions for fully developed flow with unspecified outflow velocity profile or pressure value. We study flows over the backward-facing step and in idealized arterial bifurcations using a combination of the two new boundary methods with different flow rates. Finally, we explore the applicability of the outflow method in time-dependent flow systems. The outflow boundary method works well for systems with Womersley number of O(1), i.e., when the pressure and flowrate at the outflow are approximately in-phase.