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\n\n \n \n Gao, C.; Zhang, P.; Marom, G.; Deng, Y.; and Bluestein, D.\n\n\n \n \n \n \n \n Reducing the effects of compressibility in DPD-based blood flow simulations through severe stenotic microchannel.\n \n \n \n \n\n\n \n\n\n\n
J. Comp. Phys., 335: 812–827. 2017.\n
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\n\n \n \n ![\"Reducing](\"//bibbase.org/img/filetypes/link.svg\"\n\t "\\"")
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@Article{a14,\r\n author = {Gao, C. and Zhang, P. and Marom, G. and Deng, Y. and Bluestein, D.},\r\n title = {Reducing the effects of compressibility in DPD-based blood flow simulations through severe stenotic microchannel},\r\n journal = {J. Comp. Phys.},\r\n year = {2017},\r\n volume = {335},\r\n pages = {812–827},\r\n abstract = {Viscous fluid flow simulations based on dissipative particle dynamics (DPD) may bear compressible flow effects when flowing through severe stenotic geometries. This is caused by the soft repulsive potential employed in the DPD force field, which limits the particle-based fluid system ability to sustain a large degree of compression. To mitigate this problem, a Morse potential was added to the DPD force field. We studied the fluid properties of the modified fluid model (DPD–Morse) and compared it with a previously published conventional DPD based fluid model. Our DPD–Morse model demonstrated reduced compressibility while preserving other fluid properties such as the fluid density and viscosity. We further investigated the fluid flow properties for a severe 3D stenotic microchannel with a 67% stenosis, using the two models. The DPD fluid model presented a significant density gradient along the flow direction, where the fluid density increased upstream towards the stenosis and decreased downstream from the stenosis before regaining its initial value. In contrast, the DPD–Morse model demonstrated a far better uniform fluid density distribution along the flow direction. We compared both solutions with CFD simulations. The DPD–Morse fluid resembled the behavior of the continuum fluid model whereas DPD fluid deviated from it. To estimate the effect that the difference between the two DPD formulations may have on the platelet activation potential, we have further embedded a platelet model within the flow field and investigated the shear stress accumulation along the platelet transport trajectory. In the stenotic section, the DPD fluid demonstrated a larger stress gradient than the DPD–Morse fluid. The platelet transport period was shorter for the DPD fluid as it generated a larger fluid density gradient that overestimated the acceleration of the platelet through the stenosis. With reduced fluid compressibility, our modified DPD–Morse fluid model was more accurate than the DPD fluid model when computing the platelet activation potential in a severe stenosis.},\r\n url_Link = {https://dx.doi.org/10.1016/j.jcp.2017.01.062},\r\n project = {Multiscale},\r\n type = {1. Peer-Reviewed Journal Papers},\r\n}\r\n\r\n\n
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\n Viscous fluid flow simulations based on dissipative particle dynamics (DPD) may bear compressible flow effects when flowing through severe stenotic geometries. This is caused by the soft repulsive potential employed in the DPD force field, which limits the particle-based fluid system ability to sustain a large degree of compression. To mitigate this problem, a Morse potential was added to the DPD force field. We studied the fluid properties of the modified fluid model (DPD–Morse) and compared it with a previously published conventional DPD based fluid model. Our DPD–Morse model demonstrated reduced compressibility while preserving other fluid properties such as the fluid density and viscosity. We further investigated the fluid flow properties for a severe 3D stenotic microchannel with a 67% stenosis, using the two models. The DPD fluid model presented a significant density gradient along the flow direction, where the fluid density increased upstream towards the stenosis and decreased downstream from the stenosis before regaining its initial value. In contrast, the DPD–Morse model demonstrated a far better uniform fluid density distribution along the flow direction. We compared both solutions with CFD simulations. The DPD–Morse fluid resembled the behavior of the continuum fluid model whereas DPD fluid deviated from it. To estimate the effect that the difference between the two DPD formulations may have on the platelet activation potential, we have further embedded a platelet model within the flow field and investigated the shear stress accumulation along the platelet transport trajectory. In the stenotic section, the DPD fluid demonstrated a larger stress gradient than the DPD–Morse fluid. The platelet transport period was shorter for the DPD fluid as it generated a larger fluid density gradient that overestimated the acceleration of the platelet through the stenosis. With reduced fluid compressibility, our modified DPD–Morse fluid model was more accurate than the DPD fluid model when computing the platelet activation potential in a severe stenosis.\n
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\n\n \n \n Zhang, P.; Zhang, L.; Slepian, M. J.; Deng, Y.; and Bluestein, D.\n\n\n \n \n \n \n \n A Multiscale Biomechanical Model of Platelets: Correlating with In-Vitro Results.\n \n \n \n \n\n\n \n\n\n\n
J. Biomech, 50: 26–33. 2017.\n
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@article{a11,\r\n author = {Zhang, P. and Zhang, L. and Slepian, M. J. and Deng, Y. and Bluestein, D.},\r\n year = {2017},\r\n title = {A Multiscale Biomechanical Model of Platelets: Correlating with In-Vitro Results},\r\n journal = {J. Biomech},\r\n volume = {50},\r\n pages = {26–33},\r\n abstract = {Using dissipative particle dynamics (DPD) combined with coarse grained molecular dynamics (CGMD) approaches, we developed a multiscale deformable platelet model to accurately describe the molecular-scale intra-platelet constituents and biomechanical properties of platelets in blood flow. Our model includes the platelet bilayer membrane, cytoplasm and an elaborate elastic cytoskeleton. Correlating numerical simulations with published in-vitro experiments, we validated the biorheology of the cytoplasm, the elastic response of membrane to external stresses, and the stiffness of the cytoskeleton actin filaments, resulting in an accurate representation of the molecular-level biomechanical microstructures of platelets. This enabled us to study the mechanotransduction process of the hemodynamic stresses acting onto the platelet membrane and transmitted to these intracellular constituents. The platelets constituents continuously deform in response to the flow induced stresses. To the best of our knowledge, this is the first molecular-scale platelet model that can be used to accurately predict platelets activation mechanism leading to thrombus formation in prosthetic cardiovascular devices and in vascular disease processes. This model can be further employed to study the effects of novel therapeutic approaches of modulating platelet properties to enhance their shear resistance via mechanotransduction pathways.},\r\n project = {Multiscale},\r\n url_Link = {https://dx.doi.org/10.1016/j.jbiomech.2016.11.019},\r\n type = {1. Peer-Reviewed Journal Papers}\r\n}\r\n\r\n\n
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\n Using dissipative particle dynamics (DPD) combined with coarse grained molecular dynamics (CGMD) approaches, we developed a multiscale deformable platelet model to accurately describe the molecular-scale intra-platelet constituents and biomechanical properties of platelets in blood flow. Our model includes the platelet bilayer membrane, cytoplasm and an elaborate elastic cytoskeleton. Correlating numerical simulations with published in-vitro experiments, we validated the biorheology of the cytoplasm, the elastic response of membrane to external stresses, and the stiffness of the cytoskeleton actin filaments, resulting in an accurate representation of the molecular-level biomechanical microstructures of platelets. This enabled us to study the mechanotransduction process of the hemodynamic stresses acting onto the platelet membrane and transmitted to these intracellular constituents. The platelets constituents continuously deform in response to the flow induced stresses. To the best of our knowledge, this is the first molecular-scale platelet model that can be used to accurately predict platelets activation mechanism leading to thrombus formation in prosthetic cardiovascular devices and in vascular disease processes. This model can be further employed to study the effects of novel therapeutic approaches of modulating platelet properties to enhance their shear resistance via mechanotransduction pathways.\n
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\n\n \n \n Zhang, P.; Zhang, N.; Gao, C.; Zhang, L.; Gao, Y.; Deng, Y.; and Bluestein, D.\n\n\n \n \n \n \n \n Scalability Test of Multiscale Fluid-Platelet Model for Three Top Supercomputers.\n \n \n \n \n\n\n \n\n\n\n
Comput. Phys. Commun, 204: 132-140. 2016.\n
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@article{z4,\r\n author = {Zhang, P. and Zhang, N. and Gao, C. and Zhang, L. and Gao, Y. and Deng, Y. and Bluestein, D.},\r\n year = {2016},\r\n title = {Scalability Test of Multiscale Fluid-Platelet Model for Three Top Supercomputers},\r\n journal = {Comput. Phys. Commun},\r\n volume = {204},\r\n pages = {132-140},\r\n url_Link = {https://doi.org/10.1016/j.cpc.2016.03.019},\r\n abstract = {We have tested the scalability of three supercomputers: the Tianhe-2, Stampede and CS-Storm with multiscale fluid–platelet simulations, in which a highly-resolved and efficient numerical model for nanoscale biophysics of platelets in microscale viscous biofluids is considered. Three experiments involving varying problem sizes were performed: Exp-S: 680,718-particle single-platelet; Exp-M: 2,722,872-particle 4-platelet; and Exp-L: 10,891,488-particle 16-platelet. Our implementations of multiple time-stepping (MTS) algorithm improved the performance of single time-stepping (STS) in all experiments. Using MTS, our model achieved the following simulation rates: 12.5, 25.0, 35.5 μs/day for Exp-S and 9.09, 6.25, 14.29 μs/day for Exp-M on Tianhe-2, CS-Storm 16-K80 and Stampede K20. The best rate for Exp-L was 6.25 μs/day for Stampede. Utilizing current advanced HPC resources, the simulation rates achieved by our algorithms bring within reach performing complex multiscale simulations for solving vexing problems at the interface of biology and engineering, such as thrombosis in blood flow which combines millisecond-scale hematology with microscale blood flow at resolutions of micro-to-nanoscale cellular components of platelets. This study of testing the performance characteristics of supercomputers with advanced computational algorithms that offer optimal trade-off to achieve enhanced computational performance serves to demonstrate that such simulations are feasible with currently available HPC resources.},\r\n project = {Multiscale},\r\n type = {1. Peer-Reviewed Journal Papers}\r\n}\r\n\r\n\n
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\n We have tested the scalability of three supercomputers: the Tianhe-2, Stampede and CS-Storm with multiscale fluid–platelet simulations, in which a highly-resolved and efficient numerical model for nanoscale biophysics of platelets in microscale viscous biofluids is considered. Three experiments involving varying problem sizes were performed: Exp-S: 680,718-particle single-platelet; Exp-M: 2,722,872-particle 4-platelet; and Exp-L: 10,891,488-particle 16-platelet. Our implementations of multiple time-stepping (MTS) algorithm improved the performance of single time-stepping (STS) in all experiments. Using MTS, our model achieved the following simulation rates: 12.5, 25.0, 35.5 μs/day for Exp-S and 9.09, 6.25, 14.29 μs/day for Exp-M on Tianhe-2, CS-Storm 16-K80 and Stampede K20. The best rate for Exp-L was 6.25 μs/day for Stampede. Utilizing current advanced HPC resources, the simulation rates achieved by our algorithms bring within reach performing complex multiscale simulations for solving vexing problems at the interface of biology and engineering, such as thrombosis in blood flow which combines millisecond-scale hematology with microscale blood flow at resolutions of micro-to-nanoscale cellular components of platelets. This study of testing the performance characteristics of supercomputers with advanced computational algorithms that offer optimal trade-off to achieve enhanced computational performance serves to demonstrate that such simulations are feasible with currently available HPC resources.\n
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\n\n \n \n Zhang, P.; Zhang, N.; Deng, Y.; and Bluestein, D.\n\n\n \n \n \n \n \n A Multiple Time Stepping Algorithm for Efficient Multiscale Modeling of Platelets Flowing in Blood Plasma.\n \n \n \n \n\n\n \n\n\n\n
J. Comput. Phys, 284: 668-686. 2015.\n
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@article{z15,\r\n author = {Zhang, P. and Zhang, N. and Deng, Y. and Bluestein, D.},\r\n year = {2015},\r\n title = {A Multiple Time Stepping Algorithm for Efficient Multiscale Modeling of Platelets Flowing in Blood Plasma},\r\n journal = {J. Comput. Phys},\r\n volume = {284},\r\n pages = {668-686},\r\n url_Link = {https://doi.org/10.1016/j.jcp.2015.01.004},\r\n abstract = {We developed a multiple time-stepping (MTS) algorithm for multiscale modeling of the dynamics of platelets flowing in viscous blood plasma. This MTS algorithm improves considerably the computational efficiency without significant loss of accuracy. This study of the dynamic properties of flowing platelets employs a combination of the dissipative particle dynamics (DPD) and the coarse-grained molecular dynamics (CGMD) methods to describe the dynamic microstructures of deformable platelets in response to extracellular flow-induced stresses. The disparate spatial scales between the two methods are handled by a hybrid force field interface. However, the disparity in temporal scales between the DPD and CGMD that requires time stepping at microseconds and nanoseconds respectively, represents a computational challenge that may become prohibitive. Classical MTS algorithms manage to improve computing efficiency by multi-stepping within DPD or CGMD for up to one order of magnitude of scale differential. In order to handle 3-4 orders of magnitude disparity in the temporal scales between DPD and CGMD, we introduce a new MTS scheme hybridizing DPD and CGMD by utilizing four different time stepping sizes. We advance the fluid system at the largest time step, the fluid-platelet interface at a middle timestep size, and the nonbonded and bonded potentials of the platelet structural system at two smallest timestep sizes. Additionally, we introduce parameters to study the relationship of accuracy versus computational complexities. The numerical experiments demonstrated 3000x reduction in computing time over standard MTS methods for solving the multiscale model. This MTS algorithm establishes a computationally feasible approach for solving a particle-based system at multiple scales for performing efficient multiscale simulations.},\r\n project = {Multiscale},\r\n type = {1. Peer-Reviewed Journal Papers}\r\n}\r\n\r\n\n
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\n We developed a multiple time-stepping (MTS) algorithm for multiscale modeling of the dynamics of platelets flowing in viscous blood plasma. This MTS algorithm improves considerably the computational efficiency without significant loss of accuracy. This study of the dynamic properties of flowing platelets employs a combination of the dissipative particle dynamics (DPD) and the coarse-grained molecular dynamics (CGMD) methods to describe the dynamic microstructures of deformable platelets in response to extracellular flow-induced stresses. The disparate spatial scales between the two methods are handled by a hybrid force field interface. However, the disparity in temporal scales between the DPD and CGMD that requires time stepping at microseconds and nanoseconds respectively, represents a computational challenge that may become prohibitive. Classical MTS algorithms manage to improve computing efficiency by multi-stepping within DPD or CGMD for up to one order of magnitude of scale differential. In order to handle 3-4 orders of magnitude disparity in the temporal scales between DPD and CGMD, we introduce a new MTS scheme hybridizing DPD and CGMD by utilizing four different time stepping sizes. We advance the fluid system at the largest time step, the fluid-platelet interface at a middle timestep size, and the nonbonded and bonded potentials of the platelet structural system at two smallest timestep sizes. Additionally, we introduce parameters to study the relationship of accuracy versus computational complexities. The numerical experiments demonstrated 3000x reduction in computing time over standard MTS methods for solving the multiscale model. This MTS algorithm establishes a computationally feasible approach for solving a particle-based system at multiple scales for performing efficient multiscale simulations.\n
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\n\n \n \n Pothapragada, S.; Zhang, P.; Sheriff, J.; Livelli, M.; Slepian, M. J.; Deng, Y.; and Bluestein, D.\n\n\n \n \n \n \n \n A Phenomenological Particle-Based Platelet Model for Simulating Filopodia Formation During Early Activation.\n \n \n \n \n\n\n \n\n\n\n
Int. J. Numer. Meth. Biomed. Engng, 2015: e02702. 2015.\n
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@article{z18,\r\n author = {Pothapragada, S. and Zhang, P. and Sheriff, J. and Livelli, M. and Slepian, M. J. and Deng, Y. and Bluestein, D.},\r\n year = {2015},\r\n title = {A Phenomenological Particle-Based Platelet Model for Simulating Filopodia Formation During Early Activation},\r\n journal = {Int. J. Numer. Meth. Biomed. Engng},\r\n volume = {2015},\r\n pages = {e02702},\r\n url_Link = {https://doi.org/10.1002/cnm.2702},\r\n abstract = {We developed a phenomenological three-dimensional platelet model to characterize the filopodia formation observed during early stage platelet activation. Departing from continuum mechanics based approaches, this coarse-grained molecular dynamics (CGMD) particle-based model can deform to emulate the complex shape change and filopodia formation that platelets undergo during activation. The platelet peripheral zone is modeled with a two-layer homogeneous elastic structure represented by spring-connected particles. The structural zone is represented by a cytoskeletal assembly comprising of a filamentous core and filament bundles supporting the platelet's discoid shape, also modeled by spring-connected particles. The interior organelle zone is modeled by homogeneous cytoplasm particles that facilitate the platelet deformation. Nonbonded interactions among the discrete particles of the membrane, the cytoskeletal assembly, and the cytoplasm are described using the Lennard-Jones potential with empirical constants. By exploring the parameter space of this CGMD model, we have successfully simulated the dynamics of varied filopodia formations. Comparative analyses of length and thickness of filopodia show that our numerical simulations are in agreement with experimental measurements of flow-induced activated platelets.},\r\n project = {Multiscale},\r\n type = {1. Peer-Reviewed Journal Papers}\r\n}\r\n\r\n\n
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\n We developed a phenomenological three-dimensional platelet model to characterize the filopodia formation observed during early stage platelet activation. Departing from continuum mechanics based approaches, this coarse-grained molecular dynamics (CGMD) particle-based model can deform to emulate the complex shape change and filopodia formation that platelets undergo during activation. The platelet peripheral zone is modeled with a two-layer homogeneous elastic structure represented by spring-connected particles. The structural zone is represented by a cytoskeletal assembly comprising of a filamentous core and filament bundles supporting the platelet's discoid shape, also modeled by spring-connected particles. The interior organelle zone is modeled by homogeneous cytoplasm particles that facilitate the platelet deformation. Nonbonded interactions among the discrete particles of the membrane, the cytoskeletal assembly, and the cytoplasm are described using the Lennard-Jones potential with empirical constants. By exploring the parameter space of this CGMD model, we have successfully simulated the dynamics of varied filopodia formations. Comparative analyses of length and thickness of filopodia show that our numerical simulations are in agreement with experimental measurements of flow-induced activated platelets.\n
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\n\n \n \n Zhang, P.; Gao, C.; Zhang, N.; Slepian, M. J.; Deng, Y.; and Bluestein, D.\n\n\n \n \n \n \n \n Multiscale Particle-Based Modeling of Flowing Platelets in Blood Plasma Using Dissipative Particle Dynamics and Coarse Grained Molecular Dynamics.\n \n \n \n \n\n\n \n\n\n\n
Cell. Mol. Bioeng, 7: 552-574. 2014.\n
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@article{z20,\r\n author = {Zhang, P. and Gao, C. and Zhang, N. and Slepian, M. J. and Deng, Y. and Bluestein, D.},\r\n year = {2014},\r\n title = {Multiscale Particle-Based Modeling of Flowing Platelets in Blood Plasma Using Dissipative Particle Dynamics and Coarse Grained Molecular Dynamics},\r\n journal = {Cell. Mol. Bioeng},\r\n volume = {7},\r\n issue = {4},\r\n pages = {552-574},\r\n url_Link = {https://doi.org/10.1007/s12195-014-0356-5},\r\n abstract = {We developed a multiscale particle-based model of platelets, to study the transport dynamics of shear stresses between the surrounding fluid and the platelet membrane. This model facilitates a more accurate prediction of the activation potential of platelets by viscous shear stresses - one of the major mechanisms leading to thrombus formation in cardiovascular diseases and in prosthetic cardiovascular devices. The interface of the model couples coarse-grained molecular dynamics (CGMD) with dissipative particle dynamics (DPD). The CGMD handles individual platelets while the DPD models the macroscopic transport of blood plasma in vessels. A hybrid force field is formulated for establishing a functional interface between the platelet membrane and the surrounding fluid, in which the microstructural changes of platelets may respond to the extracellular viscous shear stresses transferred to them. The interaction between the two systems preserves dynamic properties of the flowing platelets, such as the flipping motion. Using this multiscale particle-based approach, we have further studied the effects of the platelet elastic modulus by comparing the action of the flow-induced shear stresses on rigid and deformable platelet models. The results indicate that neglecting the platelet deformability may overestimate the stress on the platelet membrane, which in turn may lead to erroneous predictions of the platelet activation under viscous shear flow conditions. This particle-based fluid-structure interaction multiscale model offers for the first time a computationally feasible approach for simulating deformable platelets interacting with viscous blood flow, aimed at predicting flow induced platelet activation by using a highly resolved mapping of the stress distribution on the platelet membrane under dynamic flow conditions.},\r\n project = {Multiscale},\r\n type = {1. Peer-Reviewed Journal Papers}\r\n}\r\n\r\n\n
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\n We developed a multiscale particle-based model of platelets, to study the transport dynamics of shear stresses between the surrounding fluid and the platelet membrane. This model facilitates a more accurate prediction of the activation potential of platelets by viscous shear stresses - one of the major mechanisms leading to thrombus formation in cardiovascular diseases and in prosthetic cardiovascular devices. The interface of the model couples coarse-grained molecular dynamics (CGMD) with dissipative particle dynamics (DPD). The CGMD handles individual platelets while the DPD models the macroscopic transport of blood plasma in vessels. A hybrid force field is formulated for establishing a functional interface between the platelet membrane and the surrounding fluid, in which the microstructural changes of platelets may respond to the extracellular viscous shear stresses transferred to them. The interaction between the two systems preserves dynamic properties of the flowing platelets, such as the flipping motion. Using this multiscale particle-based approach, we have further studied the effects of the platelet elastic modulus by comparing the action of the flow-induced shear stresses on rigid and deformable platelet models. The results indicate that neglecting the platelet deformability may overestimate the stress on the platelet membrane, which in turn may lead to erroneous predictions of the platelet activation under viscous shear flow conditions. This particle-based fluid-structure interaction multiscale model offers for the first time a computationally feasible approach for simulating deformable platelets interacting with viscous blood flow, aimed at predicting flow induced platelet activation by using a highly resolved mapping of the stress distribution on the platelet membrane under dynamic flow conditions.\n
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\n\n \n \n Zhang, N.; Zhang, P.; Kang, W.; Bluestein, D.; and Deng, Y.\n\n\n \n \n \n \n \n Parameterizing the Morse potential for coarse-grained modeling of blood plasma.\n \n \n \n \n\n\n \n\n\n\n
J. Comp. Phys, 257: 726-736. 2014.\n
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\n\n \n \n ![\"Parameterizing](\"//bibbase.org/img/filetypes/pdf.svg\"\n\t "\\"")
paper\n \n \n \n link\n \n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n
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@article{z24,\r\n author = {Zhang, N. and Zhang, P. and Kang, W. and Bluestein, D. and Deng, Y.},\r\n year = {2014},\r\n title = {Parameterizing the Morse potential for coarse-grained modeling of blood plasma},\r\n journal = {J. Comp. Phys},\r\n volume = {257},\r\n pages = {726-736},\r\n url_Paper={/labs/dbluestein/PDF/Zhang_2014_morse_potential_plasma.pdf},\r\n url_Link = {https://doi.org/10.1016/j.jcp.2013.09.040},\r\n abstract = {Multiscale simulations of fluids such as blood represent a major computational challenge of coupling the disparate spatiotemporal scales between molecular and macroscopic transport phenomena characterizing such complex fluids. In this paper, a coarse-grained (CG) particle model is developed for simulating blood flow by modifying the Morse potential, traditionally used in Molecular Dynamics for modeling vibrating structures. The modified Morse potential is parameterized with effective mass scales for reproducing blood viscous flow properties, including density, pressure, viscosity, compressibility and characteristic flow dynamics of human blood plasma fluid. The parameterization follows a standard inverse-problem approach in which the optimal micro parameters are systematically searched, by gradually decoupling loosely correlated parameter spaces, to match the macro physical quantities of viscous blood flow. The predictions of this particle based multiscale model compare favorably to classic viscous flow solutions such as Counter-Poiseuille and Couette flows. It demonstrates that such coarse grained particle model can be applied to replicate the dynamics of viscous blood flow, with the advantage of bridging the gap between macroscopic flow scales and the cellular scales characterizing blood flow that continuum based models fail to handle adequately.},\r\n project = {Multiscale},\r\n type = {1. Peer-Reviewed Journal Papers}\r\n}\r\n\r\n\n
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\n Multiscale simulations of fluids such as blood represent a major computational challenge of coupling the disparate spatiotemporal scales between molecular and macroscopic transport phenomena characterizing such complex fluids. In this paper, a coarse-grained (CG) particle model is developed for simulating blood flow by modifying the Morse potential, traditionally used in Molecular Dynamics for modeling vibrating structures. The modified Morse potential is parameterized with effective mass scales for reproducing blood viscous flow properties, including density, pressure, viscosity, compressibility and characteristic flow dynamics of human blood plasma fluid. The parameterization follows a standard inverse-problem approach in which the optimal micro parameters are systematically searched, by gradually decoupling loosely correlated parameter spaces, to match the macro physical quantities of viscous blood flow. The predictions of this particle based multiscale model compare favorably to classic viscous flow solutions such as Counter-Poiseuille and Couette flows. It demonstrates that such coarse grained particle model can be applied to replicate the dynamics of viscous blood flow, with the advantage of bridging the gap between macroscopic flow scales and the cellular scales characterizing blood flow that continuum based models fail to handle adequately.\n
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\n\n \n \n Soares, J. S.; Gao, C.; Alemu, Y.; Slepian, M. J.; and Bluestein, D.\n\n\n \n \n \n \n \n Simulation of Platelets Suspension Flowing Through a Stenosis Model Using a Dissipative Particle Dynamics Approach.\n \n \n \n \n\n\n \n\n\n\n
Ann. Biomed. Eng, 41: 2318-2333. 2013.\n
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@article{z28,\r\n author = {Soares, J. S. and Gao, C. and Alemu, Y. and Slepian, M. J. and Bluestein, D.},\r\n year = {2013},\r\n title = {Simulation of Platelets Suspension Flowing Through a Stenosis Model Using a Dissipative Particle Dynamics Approach},\r\n journal = {Ann. Biomed. Eng},\r\n volume = {41},\r\n issue = {11},\r\n pages = {2318-2333},\r\n url_Paper={/labs/dbluestein/PDF/Soares_2013_platelet_stenosis_DPD.pdf},\r\n url_Link = {https://doi.org/10.1007/s10439-013-0829-z},\r\n abstract = {Stresses on blood cellular constituents induced by blood flow can be represented by a continuum approach down to the mum 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.},\r\n project = {Multiscale},\r\n type = {1. Peer-Reviewed Journal Papers}\r\n}\r\n\r\n\n
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\n Stresses on blood cellular constituents induced by blood flow can be represented by a continuum approach down to the mum 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.\n
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\n\n \n \n Feng, R.; Xenos, M.; Girdhar, G.; Kang, W.; Davenport, J. W.; Deng, Y.; and Bluestein, D.\n\n\n \n \n \n \n \n Viscous Flow Simulation in a Stenosis Model Using Discrete Particle Dynamics: A Comparison between DPD and CFD.\n \n \n \n \n\n\n \n\n\n\n
Biomech. Model. Mechan, 11: 119-129. 2011.\n
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@article{z39,\r\n author = {Feng, R. and Xenos, M. and Girdhar, G. and Kang, W. and Davenport, J. W. and Deng, Y. and Bluestein, D.},\r\n year = {2011},\r\n title = {Viscous Flow Simulation in a Stenosis Model Using Discrete Particle Dynamics: A Comparison between DPD and CFD},\r\n journal = {Biomech. Model. Mechan},\r\n volume = {11},\r\n issue = {1-2},\r\n pages = {119-129},\r\n url_Paper={/labs/dbluestein/PDF/Feng_2011_DPD.pdf},\r\n url_Link = {https://doi.org/10.1007/s10237-011-0297-z},\r\n abstract = {Flow and stresses induced by blood flow acting on the blood cellular constituents can be represented to a certain extent by a continuum mechanics approach down to the order of the mum level. However, the molecular effects of, e.g., adhesion/aggregation bonds of blood clotting can be on the order of nm. The coupling of the disparate length and timescales between such molecular levels and macroscopic transport represents a major computational challenge. To address this challenge, a multiscale numerical approach based on discrete particle dynamics (DPD) methodology derived from molecular dynamics (MD) principles is proposed. The feasibility of the approach was firstly tested for its ability to simulate viscous flow conditions. Simulations were conducted in low Reynolds numbers flows (Re = 25-33) through constricted tubes representing blood vessels with various degrees of stenosis. Multiple discrete particles interacting with each other were simulated, with 1.24-1.36 million particles representing the flow domain and 0.4 million particles representing the vessel wall. The computation was carried out on the massive parallel supercomputer NY BlueGene/L employing NAMD-a parallel MD package for high performance computing (HPC). Typical recirculation zones were formed distal to the stenoses. The velocity profiles and recirculation zones were in excellent agreement with computational fluid dynamics (CFD) 3D Navier-Stokes viscous fluid flow simulations and with classic numerical and experimental results by YC Fung in constricted tubes. This feasibility analysis demonstrates the potential of a methodology that widely departs from a continuum approach to simulate multiscale phenomena such as flow induced blood clotting.},\r\n project = {Multiscale},\r\n type = {1. Peer-Reviewed Journal Papers}\r\n}\r\n\r\n\n
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\n Flow and stresses induced by blood flow acting on the blood cellular constituents can be represented to a certain extent by a continuum mechanics approach down to the order of the mum level. However, the molecular effects of, e.g., adhesion/aggregation bonds of blood clotting can be on the order of nm. The coupling of the disparate length and timescales between such molecular levels and macroscopic transport represents a major computational challenge. To address this challenge, a multiscale numerical approach based on discrete particle dynamics (DPD) methodology derived from molecular dynamics (MD) principles is proposed. The feasibility of the approach was firstly tested for its ability to simulate viscous flow conditions. Simulations were conducted in low Reynolds numbers flows (Re = 25-33) through constricted tubes representing blood vessels with various degrees of stenosis. Multiple discrete particles interacting with each other were simulated, with 1.24-1.36 million particles representing the flow domain and 0.4 million particles representing the vessel wall. The computation was carried out on the massive parallel supercomputer NY BlueGene/L employing NAMD-a parallel MD package for high performance computing (HPC). Typical recirculation zones were formed distal to the stenoses. The velocity profiles and recirculation zones were in excellent agreement with computational fluid dynamics (CFD) 3D Navier-Stokes viscous fluid flow simulations and with classic numerical and experimental results by YC Fung in constricted tubes. This feasibility analysis demonstrates the potential of a methodology that widely departs from a continuum approach to simulate multiscale phenomena such as flow induced blood clotting.\n
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\n\n \n \n Yamaguchi, T.; Ishikawa, T.; Imai, Y.; Matsuki, N.; Xenos, M.; Deng, Y.; and Bluestein, D.\n\n\n \n \n \n \n \n Particle-Based Methods for Multiscale Modeling of Blood Flow in the Circulation and in Devices: Challenges and Future Directions.\n \n \n \n \n\n\n \n\n\n\n
Ann Biomed Eng, 38: 1225-1235. 2010.\n
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@article{z46,\r\n author = {Yamaguchi, T. and Ishikawa, T. and Imai, Y. and Matsuki, N. and Xenos, M. and Deng, Y. and Bluestein, D.},\r\n year = {2010},\r\n title = {Particle-Based Methods for Multiscale Modeling of Blood Flow in the Circulation and in Devices: Challenges and Future Directions},\r\n journal = {Ann Biomed Eng},\r\n volume = {38},\r\n issue = {3},\r\n pages = {1225-1235},\r\n url_Paper={/labs/dbluestein/PDF/Yamaguchi_2010_multiscale_modeling_blood.pdf},\r\n url_Link = {10.1007/s10439-010-9904-x},\r\n abstract = {A major computational challenge for a multiscale modeling is the coupling of disparate length and timescales between molecular mechanics and macroscopic transport, spanning the spatial and temporal scales characterizing the complex processes taking place in flow-induced blood clotting. Flow and pressure effects on a cell-like platelet can be well represented by a continuum mechanics model down to the order of the micrometer level. However, the molecular effects of adhesion/aggregation bonds are on the order of nanometer. A successful multiscale model of platelet response to flow stresses in devices and the ensuing clotting responses should be able to characterize the clotting reactions and their interactions with the flow. This paper attempts to describe a few of the computational methods that were developed in recent years and became available to researchers in the field. They differ from traditional approaches that dominate the field by expanding on prevailing continuum-based approaches, or by completely departing from them, yielding an expanding toolkit that may facilitate further elucidation of the underlying mechanisms of blood flow and the cellular response to it. We offer a paradigm shift by adopting a multidisciplinary approach with fluid dynamics simulations coupled to biophysical and biochemical transport.},\r\n project = {Multiscale},\r\n type = {1. Peer-Reviewed Journal Papers}\r\n}\r\n\r\n\n
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\n A major computational challenge for a multiscale modeling is the coupling of disparate length and timescales between molecular mechanics and macroscopic transport, spanning the spatial and temporal scales characterizing the complex processes taking place in flow-induced blood clotting. Flow and pressure effects on a cell-like platelet can be well represented by a continuum mechanics model down to the order of the micrometer level. However, the molecular effects of adhesion/aggregation bonds are on the order of nanometer. A successful multiscale model of platelet response to flow stresses in devices and the ensuing clotting responses should be able to characterize the clotting reactions and their interactions with the flow. This paper attempts to describe a few of the computational methods that were developed in recent years and became available to researchers in the field. They differ from traditional approaches that dominate the field by expanding on prevailing continuum-based approaches, or by completely departing from them, yielding an expanding toolkit that may facilitate further elucidation of the underlying mechanisms of blood flow and the cellular response to it. We offer a paradigm shift by adopting a multidisciplinary approach with fluid dynamics simulations coupled to biophysical and biochemical transport.\n
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