title: A Multiple Time Stepping Algorithm for Efficient Multiscale Modeling of Platelets Flowing in Blood Plasma.
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.
authors: Department of Biomedical Engineering, Stony Brook University, NY 11794, United States.
authors: Peng
authors: P
authors: Zhang
authors: Department of Applied Mathematics and Statistics, Stony Brook University, NY 11794, United States.
authors: Na
authors: N
authors: Zhang
authors: Department of Applied Mathematics and Statistics, Stony Brook University, NY 11794, United States ; National Supercomputer Center in Jinan, Shandong 250101, China.
authors: Yuefan
authors: Y
authors: Deng
authors: Department of Biomedical Engineering, Stony Brook University, NY 11794, United States.
authors: Danny
authors: D
authors: Bluestein
keywords: coarse-grained molecular dynamics; multiple time stepping; multiscale modeling
references: Annu Rev Biophys. 2012;41:429-52
references: 22577825
references: Biophys J. 2010 May 19;98(10):2215-25
references: 20483330
references: Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 2000 Dec;62(6 Pt A):R7611-4
references: 11138113
references: Cell Mol Bioeng. 2014 Dec 1;7(4):552-574
references: 25530818
references: J Chem Phys. 2006 Mar 7;124(9):94104
references: 16526842
references: Biophys J. 2005 Feb;88(2):1432-43
references: 15533923
references: J Phys Condens Matter. 2011 Jun 15;23(23):233101
references: 21613700
references: Biomech Model Mechanobiol. 2004 Mar;2(3):157-67
references: 14685822
references: J Heart Valve Dis. 2004 May;13(3):501-8
references: 15222299
references: J Chem Phys. 2007 Sep 28;127(12):124109
references: 17902895
references: J Mol Model. 2002 Jan;8(1):33-43
references: 12111400
references: Artif Organs. 2001 May;25(5):341-7
references: 11403662
references: J Phys Chem B. 2009 Sep 3;113(35):11876-86
references: 19678631
references: J Comput Phys. 2011 May 31;230(10):3765-377
references: 21499548
references: Front Bioeng Biotechnol. 2013 Dec 03;1:18
references: 25022613
references: Ann Biomed Eng. 2012 Nov;40(11):2345-54
references: 22481228
references: Biophys J. 2008 Sep;95(5):2556-74
references: 18515386
references: Ann Biomed Eng. 1998 Mar-Apr;26(2):268-77
references: 9525767
references: Ann Biomed Eng. 2004 Aug;32(8):1058-66
references: 15446502
references: J Comput Chem. 2005 Dec;26(16):1781-802
references: 16222654
references: Ann Biomed Eng. 2010 Mar;38(3):1225-35
references: 20336827
references: Adv Exp Med Biol. 1990;281:287-96
references: 2102619
references: Blood. 1996 Sep 1;88(5):1525-41
references: 8781407
references: Artif Organs. 2007 Sep;31(9):677-88
references: 17725695
references: Ann Biomed Eng. 2013 Nov;41(11):2318-33
references: 23695489
references: J Comput Phys. 2014 Jan 15;257(Pt A):726-736
references: 24910470
references: J Chem Phys. 2009 Oct 21;131(15):154107
references: 20568847
references: Ann Intern Med. 2010 Sep 21;153(6):387-95
references: 20713770
references: Biophys J. 2008 Sep;95(5):2539-55
references: 18515387
references: PLoS One. 2012;7(3):e32463
references: 22396768
references: Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Dec;72(6 Pt 2):066704
references: 16486095
references: J R Soc Interface. 2011 Dec 7;8(65):1760-71
references: 21593027