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Zohravi E, Moreno N, Ellero M. Computational mesoscale framework for biological clustering and fractal aggregation. SOFT MATTER 2023; 19:7399-7411. [PMID: 37743687 DOI: 10.1039/d3sm01090b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Hierarchical clustering due to diffusion and reaction is a widespread occurrence in natural phenomena, displaying fractal behavior with non-integer size scaling. The study of this phenomenon has garnered interest in both biological systems such as morphogenesis and blood clotting, and synthetic systems such as colloids and polymers. The modeling of biological clustering can be difficult, as it can occur on a variety of scales and involve multiple mechanisms, necessitating the use of various methods to capture its behavior. Here, we propose a novel framework, the generalized-mesoscale-clustering (GMC), for the study of complex hierarchical clustering phenomena in biological systems. The GMC framework incorporates the effects of hydrodynamic interactions, bonding, and surface tension, and allows for the analysis of both static and dynamic states of cluster development. The framework is applied to a range of biological clustering mechanisms, with a focus on blood-related clustering from fibrin network formation to platelet aggregation. Our study highlights the importance of a comprehensive characterization of the structural properties of the cluster, including fractal dimension, pore-scale diffusion, initiation time, and consolidation time, in fully understanding the behavior of biological clustering systems. The GMC framework also provides the potential to investigate the temporal evolution and mechanical properties of the clusters by tracking bond density and including hydrodynamic interactions.
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Affiliation(s)
- Elnaz Zohravi
- Basque Center for Applied Mathematics (BCAM), Alameda de Mazarredo 14, Bilbao 48009, Spain.
| | - Nicolas Moreno
- Basque Center for Applied Mathematics (BCAM), Alameda de Mazarredo 14, Bilbao 48009, Spain.
| | - Marco Ellero
- Basque Center for Applied Mathematics (BCAM), Alameda de Mazarredo 14, Bilbao 48009, Spain.
- IKERBASQUE, Basque Foundation for Science, Calle de Maria Diaz de Haro 3, 48013, Bilbao, Spain
- Zienkiewicz Center for Computational Engineering (ZCCE), Swansea University, Bay Campus, Swansea SA1 8EN, UK
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Jacob B, Drawert B, Yi TM, Petzold L. An arbitrary Lagrangian Eulerian smoothed particle hydrodynamics (ALE-SPH) method with a boundary volume fraction formulation for fluid-structure interaction. ENGINEERING ANALYSIS WITH BOUNDARY ELEMENTS 2021; 128:274-289. [PMID: 34040286 PMCID: PMC8143034 DOI: 10.1016/j.enganabound.2021.04.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We present a new weakly-compressible smoothed particle hydrodynamics (SPH) method capable of modeling non-slip fixed and moving wall boundary conditions. The formulation combines a boundary volume fraction (BVF) wall approach with the transport-velocity SPH method. The resulting method, named SPH-BVF, offers detection of arbitrarily shaped solid walls on-the-fly, with small computational overhead due to its local formulation. This simple framework is capable of solving problems that are difficult or infeasible for standard SPH, namely flows subject to large shear stresses or at moderate Reynolds numbers, and mass transfer in deformable boundaries. In addition, the method extends the transport-velocity formulation to reaction-diffusion transport of mass in Newtonian fluids and linear elastic solids, which is common in biological structures. Taken together, the SPH-BVF method provides a good balance of simplicity and versatility, while avoiding some of the standard obstacles associated with SPH: particle penetration at the boundaries, tension instabilities and anisotropic particle alignments, that hamper SPH from being applied to complex problems such as fluid-structure interaction in a biological system.
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Affiliation(s)
- Bruno Jacob
- Department of Mechanical Engineering, University of California-Santa Barbara, Santa Barbara, California, 93106, USA
| | - Brian Drawert
- Department of Computer Science, University of North Carolina at Asheville, Asheville, North Carolina, 28804, USA
| | - Tau-Mu Yi
- Department of Molecular, Cellular, and Developmental Biology, University of California-Santa Barbara, Santa Barbara, California 93106, USA
| | - Linda Petzold
- Department of Mechanical Engineering, University of California-Santa Barbara, Santa Barbara, California, 93106, USA
- Department of Computer Science, University of California-Santa Barbara, Santa Barbara, California, 93106, USA
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Feng YH, Zhang XP, Zhao ZQ, Guo XD. Dissipative Particle Dynamics Aided Design of Drug Delivery Systems: A Review. Mol Pharm 2020; 17:1778-1799. [DOI: 10.1021/acs.molpharmaceut.0c00175] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Yun Hao Feng
- Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P.R. China
- Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology), Ministry of Education, Beijing 100029, China
| | - Xiao Peng Zhang
- Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P.R. China
- Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology), Ministry of Education, Beijing 100029, China
| | - Ze Qiang Zhao
- Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P.R. China
- Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology), Ministry of Education, Beijing 100029, China
| | - Xin Dong Guo
- Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P.R. China
- Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology), Ministry of Education, Beijing 100029, China
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Yi Y, Tamagawa M. Development of a novel hybrid method combining finite difference method and dissipative particle dynamics to simulate thrombus formation on orifice flow. Comput Methods Biomech Biomed Engin 2020; 23:611-626. [PMID: 32310682 DOI: 10.1080/10255842.2020.1755274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
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.
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Affiliation(s)
- Y Yi
- Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
| | - M Tamagawa
- Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
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Yesudasan S, Averett RD. Recent advances in computational modeling of fibrin clot formation: A review. Comput Biol Chem 2019; 83:107148. [PMID: 31751883 DOI: 10.1016/j.compbiolchem.2019.107148] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/17/2019] [Accepted: 10/15/2019] [Indexed: 12/12/2022]
Abstract
The field of thrombosis and hemostasis is crucial for understanding and developing new therapies for pathologies such as deep vein thrombosis, diabetes related strokes, pulmonary embolisms, and hemorrhaging related diseases. In the last two decades, an exponential growth in studies related to fibrin clot formation using computational tools has been observed. Despite this growth, the complete mechanism behind thrombus formation and hemostasis has been long and rife with obstacles; however, significant progress has been made in the present century. The computational models and methods used in this context are diversified into different spatiotemporal scales, yet there is no single model which can predict both physiological and mechanical properties of fibrin clots. In this review, we list the major strategies employed by researchers in modeling fibrin clot formation using recent and existing computational techniques. This review organizes the computational strategies into continuum level, system level, discrete particle (DPD), and multi-scale methods. We also discuss strengths and weaknesses of various methods and future directions in which computational modeling of fibrin clots can advance.
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Affiliation(s)
- Sumith Yesudasan
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, 597 D.W. Brooks Drive, Athens, GA 30602
| | - Rodney D Averett
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, 597 D.W. Brooks Drive, Athens, GA 30602.
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Petsev ND, Leal LG, Shell MS. Coupling discrete and continuum concentration particle models for multiscale and hybrid molecular-continuum simulations. J Chem Phys 2017; 147:234112. [DOI: 10.1063/1.5001703] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Nikolai D. Petsev
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - L. Gary Leal
- Department of Chemical Engineering, University of California at Santa Barbara, Santa Barbara, California 93106-5080, USA
| | - M. Scott Shell
- Department of Chemical Engineering, University of California at Santa Barbara, Santa Barbara, California 93106-5080, USA
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Affiliation(s)
- Pep Español
- Dept. Física Fundamental, Universidad Nacional de Educación a Distancia, Aptdo. 60141, E-28080 Madrid, Spain
| | - Patrick B. Warren
- Unilever R&D Port Sunlight, Quarry Road East, Bebington, Wirral CH63 3JW, United Kingdom
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Petsev ND, Leal LG, Shell MS. Multiscale simulation of ideal mixtures using smoothed dissipative particle dynamics. J Chem Phys 2016; 144:084115. [PMID: 26931689 DOI: 10.1063/1.4942499] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Smoothed dissipative particle dynamics (SDPD) [P. Español and M. Revenga, Phys. Rev. E 67, 026705 (2003)] is a thermodynamically consistent particle-based continuum hydrodynamics solver that features scale-dependent thermal fluctuations. We obtain a new formulation of this stochastic method for ideal two-component mixtures through a discretization of the advection-diffusion equation with thermal noise in the concentration field. The resulting multicomponent approach is consistent with the interpretation of the SDPD particles as moving volumes of fluid and reproduces the correct fluctuations and diffusion dynamics. Subsequently, we provide a general multiscale multicomponent SDPD framework for simulations of molecularly miscible systems spanning length scales from nanometers to the non-fluctuating continuum limit. This approach reproduces appropriate equilibrium properties and is validated with simulation of simple one-dimensional diffusion across multiple length scales.
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Affiliation(s)
- Nikolai D Petsev
- Department of Chemical Engineering, University of California at Santa Barbara, Santa Barbara, California 93106-5080, USA
| | - L Gary Leal
- Department of Chemical Engineering, University of California at Santa Barbara, Santa Barbara, California 93106-5080, USA
| | - M Scott Shell
- Department of Chemical Engineering, University of California at Santa Barbara, Santa Barbara, California 93106-5080, USA
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Faure G, Maillet JB, Roussel J, Stoltz G. Size consistency in smoothed dissipative particle dynamics. Phys Rev E 2016; 94:043305. [PMID: 27841494 DOI: 10.1103/physreve.94.043305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Indexed: 06/06/2023]
Abstract
Smoothed dissipative particle dynamics (SDPD) is a mesoscopic method that allows one to select the level of resolution at which a fluid is simulated. In this work, we study the consistency of the resulting thermodynamic properties as a function of the size of the mesoparticles, both at equilibrium and out of equilibrium. We also propose a reformulation of the SDPD equations in terms of energy variables. This increases the similarities with dissipative particle dynamics with energy conservation and opens the way for a coupling between the two methods. Finally, we present a numerical scheme for SDPD that ensures the conservation of the invariants of the dynamics. Numerical simulations illustrate this approach.
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Affiliation(s)
| | | | - Julien Roussel
- Université Paris-Est, CERMICS (ENPC), INRIA, F-77455 Marne-la-Vallée, France
| | - Gabriel Stoltz
- Université Paris-Est, CERMICS (ENPC), INRIA, F-77455 Marne-la-Vallée, France
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Petsev ND, Leal LG, Shell MS. Hybrid molecular-continuum simulations using smoothed dissipative particle dynamics. J Chem Phys 2015; 142:044101. [PMID: 25637963 PMCID: PMC5848718 DOI: 10.1063/1.4905720] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 12/26/2014] [Indexed: 11/14/2022] Open
Abstract
We present a new multiscale simulation methodology for coupling a region with atomistic detail simulated via molecular dynamics (MD) to a numerical solution of the fluctuating Navier-Stokes equations obtained from smoothed dissipative particle dynamics (SDPD). In this approach, chemical potential gradients emerge due to differences in resolution within the total system and are reduced by introducing a pairwise thermodynamic force inside the buffer region between the two domains where particles change from MD to SDPD types. When combined with a multi-resolution SDPD approach, such as the one proposed by Kulkarni et al. [J. Chem. Phys. 138, 234105 (2013)], this method makes it possible to systematically couple atomistic models to arbitrarily coarse continuum domains modeled as SDPD fluids with varying resolution. We test this technique by showing that it correctly reproduces thermodynamic properties across the entire simulation domain for a simple Lennard-Jones fluid. Furthermore, we demonstrate that this approach is also suitable for non-equilibrium problems by applying it to simulations of the start up of shear flow. The robustness of the method is illustrated with two different flow scenarios in which shear forces act in directions parallel and perpendicular to the interface separating the continuum and atomistic domains. In both cases, we obtain the correct transient velocity profile. We also perform a triple-scale shear flow simulation where we include two SDPD regions with different resolutions in addition to a MD domain, illustrating the feasibility of a three-scale coupling.
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Affiliation(s)
- Nikolai D Petsev
- Department of Chemical Engineering, University of California at Santa Barbara, Santa Barbara, California 93106-5080, USA
| | - L Gary Leal
- Department of Chemical Engineering, University of California at Santa Barbara, Santa Barbara, California 93106-5080, USA
| | - M Scott Shell
- Department of Chemical Engineering, University of California at Santa Barbara, Santa Barbara, California 93106-5080, USA
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Optimized Simulation and Validation of Particle Advection in Asymmetric Staggered Herringbone Type Micromixers. MICROMACHINES 2014. [DOI: 10.3390/mi6010136] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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A clinically oriented introduction and review on finite element models of the human cochlea. BIOMED RESEARCH INTERNATIONAL 2014; 2014:975070. [PMID: 25530973 PMCID: PMC4235757 DOI: 10.1155/2014/975070] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 08/29/2014] [Accepted: 09/03/2014] [Indexed: 12/30/2022]
Abstract
Due to the inaccessibility of the inner ear, direct in vivo information on cochlear mechanics is difficult to obtain. Mathematical modelling is a promising way to provide insight into the physiology and pathology of the cochlea. Finite element method (FEM) is one of the most popular discrete mathematical modelling techniques, mainly used in engineering that has been increasingly used to model the cochlea and its elements. The aim of this overview is to provide a brief introduction to the use of FEM in modelling and predicting the behavior of the cochlea in normal and pathological conditions. It will focus on methodological issues, modelling assumptions, simulation of clinical scenarios, and pathologies.
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