Mesoscale modeling: solving complex flows in biology and biotechnology
Tài liệu tham khảo
Frenkel, 2002
Groot, 1997, Dissipative particle dynamics: bridging the gap between atomistic and mesoscopic simulation, J. Chem. Phys., 107, 4423, 10.1063/1.474784
Succi, 2001
Gompper, 2009, Multi-particle collision dynamics: a particle-based mesoscale simulation approach to the hydrodynamics of complex fluids, Adv. Polym. Sci., 221, 1
Koumoutsakos, 2005, Multiscale flow simulations using particles, Annu. Rev. Fluid Mech., 37, 457, 10.1146/annurev.fluid.37.061903.175753
Pan, 2008, Hydrodynamic interactions for single dissipative-particle-dynamics particles and their clusters and filaments, Phys. Rev. E, 78, 046706, 10.1103/PhysRevE.78.046706
Fellermann, 2007, Life cycle of a minimal protocell – a dissipative particle dynamics study, Artif. Life, 13, 319, 10.1162/artl.2007.13.4.319
Groot, 2003, Electrostatic interactions in dissipative particle dynamics-simulation of polyelectrolytes and anionic surfactants, J. Chem. Phys., 118, 11265, 10.1063/1.1574800
Spenley, 2000, Scaling laws for polymers in dissipative particle dynamics, Europhys. Lett., 49, 534, 10.1209/epl/i2000-00183-2
Sirk, 2012, An enhanced entangled polymer model for dissipative particle dynamics, J. Chem. Phys., 136, 134903, 10.1063/1.3698476
Amati, 1997, Massively parallel lattice-Boltzmann simulation of turbulent channel flow, Int. J. Mod. Phys. C, 8, 869, 10.1142/S0129183197000746
Good, 2004, Effect of hydrodynamic interactions on the evolution of chemically reactive ternary mixtures, J. Chem. Phys., 121, 6052, 10.1063/1.1783872
Swift, 1996, Lattice Boltzmann simulations of liquid-gas and binary fluid systems, Phys. Rev. E, 54, 5041, 10.1103/PhysRevE.54.5041
Mills, 2012, Beating synthetic cilia enhance heat transport in microfluidic channels, Soft Matter, 8, 11508, 10.1039/c2sm26919h
Verberg, 2004, Numerical simulations of binary fluids confined between moving, rough surfaces, Abstr. Pap. Am. Chem. Soc., 227, U860
Verberg, 2006, Modeling the release of nanoparticles from mobile microcapsules, J. Chem. Phys., 125, 224712, 10.1063/1.2404955
Usta, 2005, Lattice-Boltzmann simulations of the dynamics of polymer solutions in periodic and confined geometries, J. Chem. Phys., 122, 094902, 10.1063/1.1854151
Malevanets, 2000, Dynamics of short polymer chains in solution, Europhys. Lett., 52, 231, 10.1209/epl/i2000-00428-0
Ladd, 2001, Lattice-Boltzmann simulations of particle-fluid suspensions, J. Stat. Phys., 104, 1191, 10.1023/A:1010414013942
Aidun, 2010, Lattice-Boltzmann method for complex flows, Annu. Rev. Fluid Mech., 42, 439, 10.1146/annurev-fluid-121108-145519
Chun, 2007, Interpolated boundary condition for lattice Boltzmann simulations of flows in narrow gaps, Phys. Rev. E, 75, 066705, 10.1103/PhysRevE.75.066705
Dunweg, 2009, Lattice Boltzmann simulations of soft matter systems, Adv. Polym. Sci., 221, 89
Li, 2013, Continuum- and particle-based modeling of shapes and dynamics of red blood cells in health and disease, Soft Matter, 9, 28, 10.1039/C2SM26891D
Reasor, 2012, Coupling the lattice-Boltzmann and spectrin-link methods for the direct numerical simulation of cellular blood flow, Int. J. Numer. Methods Fluids, 68, 767, 10.1002/fld.2534
MacMeccan, 2009, Simulating deformable particle suspensions using a coupled lattice-Boltzmann and finite-element method, J. Fluid Mech., 618, 13, 10.1017/S0022112008004011
Bagchi, 2007, Mesoscale simulation of blood flow in small vessels, Biophys. J., 92, 1858, 10.1529/biophysj.106.095042
Zhang, 2011, Effect of suspending viscosity on red blood cell dynamics and blood flows in microvessels, Microcirculation, 18, 562, 10.1111/j.1549-8719.2011.00116.x
Zhang, 2009, Effects of erythrocyte deformability and aggregation on the cell free layer and apparent viscosity of microscopic blood flows, Microvasc. Res., 77, 265, 10.1016/j.mvr.2009.01.010
Ding, 2006, Cluster size distribution and scaling for spherical particles and red blood cells in pressure-driven flows at small Reynolds number, Phys. Rev. Lett., 96, 204502, 10.1103/PhysRevLett.96.204502
Fedosov, 2008, Dissipative particle dynamics simulation of depletion layer and polymer migration in micro- and nanochannels for dilute polymer solutions, J. Chem. Phys., 128, 144903, 10.1063/1.2897761
Xiong, 2012, Two-dimensional lattice Boltzmann study of red blood cell motion through microvascular bifurcation: cell deformability and suspending viscosity effects, Biomech. Model. Mechanobiol., 11, 575, 10.1007/s10237-011-0334-y
Boyd, 2005, Application of the lattice Boltzmann model to simulated stenosis growth in a two-dimensional carotid artery, Phys. Med. Biol., 50, 4783, 10.1088/0031-9155/50/20/003
Voronov, 2010, Computational modeling of flow-induced shear stresses within 3D salt-leached porous scaffolds imaged via micro-CT, J. Biomech., 43, 1279, 10.1016/j.jbiomech.2010.01.007
Sun, 2008, Lattice-Boltzmann simulation of blood flow in digitized vessel networks, Comput. Math. Appl., 55, 1594, 10.1016/j.camwa.2007.08.019
Wu, 2011, Numerical investigation of the effects of channel geometry on platelet activation and blood damage, Ann. Biomed. Eng., 39, 897, 10.1007/s10439-010-0184-2
Yun, 2012, A numerical investigation of blood damage in the hinge area of aortic bileaflet mechanical heart valves during the leakage phase, Ann. Biomed. Eng., 40, 1468, 10.1007/s10439-011-0502-3
Pivkin, 2009, Effect of red blood cells on platelet aggregation, IEEE Eng. Med. Biol. Mag., 28, 32, 10.1109/MEMB.2009.931788
Mao, 2011, Hydrodynamic sorting of microparticles by size in ridged microchannels, Phys. Fluids, 23, 051704, 10.1063/1.3590264
Arata, 2009, Designing microfluidic channel that separates elastic particles upon stiffness, Soft Matter, 5, 2721, 10.1039/b908213a
Kilimnik, 2011, Inertial migration of deformable capsules in channel flow, Phys. Fluids, 23, 123302, 10.1063/1.3664402
Masaeli, 2012, Continuous inertial focusing and separation of particles by shape, Phys. Rev. X, 2, 031017, 10.1103/PhysRevX.2.031017
Alexeev, 2007, Patterned surfaces segregate compliant microcapsules, Langmuir, 23, 983, 10.1021/la062914q
Usta, 2007, Fork in the road: patterned surfaces direct microcapsules to make a decision, Langmuir, 23, 10887, 10.1021/la7018583
Moeendarbary, 2010, Migration of DNA molecules through entropic trap arrays: a dissipative particle dynamics study, Microfluid. Nanofluid., 8, 243, 10.1007/s10404-009-0463-0
Cupelli, 2013, Leukocyte enrichment based on a modified pinched flow fractionation approach, Microfluid. Nanofluid., 14, 551, 10.1007/s10404-012-1073-9
Masoud, 2011, Selective control of surface properties using hydrodynamic interactions, Chem. Commun., 47, 472, 10.1039/C0CC02165B
Lei, 2012, Predicting the morphology of sickle red blood cells using coarse-grained models of intracellular aligned hemoglobin polymers, Soft Matter, 8, 4507, 10.1039/c2sm07294g
Li, 2012, Effect of chain chirality on the self-assembly of sickle hemoglobin, Biophys. J., 103, 1130, 10.1016/j.bpj.2012.08.017
Li, 2012, Blood-plasma separation in Y-shaped bifurcating microfluidic channels: a dissipative particle dynamics simulation study, Phys. Biol., 9, 026010, 10.1088/1478-3975/9/2/026010
Lei, 2012, Quantifying the rheological and hemodynamic characteristics of sickle cell anemia, Biophys. J., 102, 185, 10.1016/j.bpj.2011.12.006
Fedosov, 2011, Wall shear stress-based model for adhesive dynamics of red blood cells in malaria, Biophys. J., 100, 2084, 10.1016/j.bpj.2011.03.027
Fedosov, 2011, Quantifying the biophysical characteristics of Plasmodium-falciparum-parasitized red blood cells in microcirculation, Proc. Natl. Acad. Sci. U.S.A., 108, 35, 10.1073/pnas.1009492108
Chen, 2007, The coordination of protein motors and the kinetic behavior of microtubule – a computational study, Biophys. Chem., 129, 60, 10.1016/j.bpc.2007.05.008
Cristea, 2011, Lattice Boltzmann simulations of the time evolution of living multicellular systems, Biorheology, 48, 185, 10.3233/BIR-2011-0595
Sriyab, 2009, Mesoscale modeling technique for studying the dynamics oscillation of Min protein: pattern formation analysis with lattice Boltzmann method, Comput. Biol. Med., 39, 412, 10.1016/j.compbiomed.2009.02.003
Guo, 2009, Computational studies on self-assembled paclitaxel structures: templates for hierarchical block copolymer assemblies and sustained drug release, Biomaterials, 30, 6556, 10.1016/j.biomaterials.2009.08.022
Posocco, 2010, Morphology prediction of block copolymers for drug delivery by mesoscale simulations, J. Mater. Chem., 20, 7742, 10.1039/c0jm01301c
Djohari, 2009, Kinetics of nanoparticle targeting by dissipative particle dynamics simulations, Biomacromolecules, 10, 3089, 10.1021/bm900785c
Tomasini, 2012, Dissipative particle dynamics simulation of poly(ethylene oxide)-poly(ethyl ethylene) block copolymer properties for enhancement of cell membrane rupture under stress, Chem. Eng. Sci., 71, 400, 10.1016/j.ces.2011.10.061
Patterson, 2011, Adsorption behavior of model proteins on surfaces, Fluid Phase Equilib., 302, 48, 10.1016/j.fluid.2010.08.009
Masoud, 2012, Controlled release of nanoparticles and macromolecules from responsive microgel capsules, ACS Nano, 6, 212, 10.1021/nn2043143
Delcea, 2011, Stimuli-responsive LbL capsules and nanoshells for drug delivery, Adv. Drug Deliv. Rev., 63, 730, 10.1016/j.addr.2011.03.010
Shchepelina, 2010, Anisotropic micro- and nano-capsules, Macromol. Rapid Commun., 31, 2041, 10.1002/marc.201000490
Verberg, 2007, Healing substrates with mobile, particle-filled microcapsules: designing a ‘repair and go’ system, J. R. Soc. Interface, 4, 349, 10.1098/rsif.2006.0165
Usta, 2008, Modeling microcapsules that communicate through nanoparticles to undergo self-propelled motion, ACS Nano, 2, 471, 10.1021/nn700379v
Kolmakov, 2010, Designing communicating colonies of biomimetic microcapsules, Proc. Natl. Acad. Sci. U.S.A., 107, 12417, 10.1073/pnas.1001950107
Nelson, 2010, Microrobots for minimally invasive medicine, Annu. Rev. Biomed. Eng., 12, 55, 10.1146/annurev-bioeng-010510-103409
Peyer, 2013, Bio-inspired magnetic swimming microrobots for biomedical applications, Nanoscale, 5, 1259, 10.1039/C2NR32554C
Masoud, 2012, Designing maneuverable micro-swimmers actuated by responsive gel, Soft Matter, 8, 8944, 10.1039/c2sm25898f
Yang, 2010, Computer simulation of the translocation of nanoparticles with different shapes across a lipid bilayer, Nat. Nanotechnol., 5, 579, 10.1038/nnano.2010.141
Dutt, 2011, Forming transmembrane channels using end-functionalized nanotubes, Nanoscale, 3, 240, 10.1039/C0NR00578A
Li, 2012, Effects of electrostatic interactions on the translocation of polymers through a narrow pore under different solvent conditions: a dissipative particle dynamics simulation study, Macromol. Theor. Simul., 21, 120, 10.1002/mats.201100079
Li, 2012, Surface-structure-regulated penetration of nanoparticles across a cell membrane, Nanoscale, 4, 3768, 10.1039/c2nr30379e
Ding, 2012, Designing nanoparticle translocation through membranes by computer simulations, ACS Nano, 6, 1230, 10.1021/nn2038862
Alexeev, 2008, Harnessing Janus nanoparticles to create controllable pores in membranes, ACS Nano, 2, 1117, 10.1021/nn8000998
Yan, 2011, Complexes comprised of a dendrimer and a vesicle: role of vesicle size and the surface tension of the vesicle membrane, Nanoscale, 3, 3812, 10.1039/c1nr10446b
Grafmuller, 2009, The fusion of membranes and vesicles: pathway and energy barriers from dissipative particle dynamics, Biophys. J., 96, 2658, 10.1016/j.bpj.2008.11.073
Chen, 2012, How the antimicrobial peptides kill bacteria: computational physics insights, Commun. Comput. Phys., 11, 709, 10.4208/cicp.071210.240511a
Ding, 2012, Interactions between Janus particles and membranes, Nanoscale, 4, 1116, 10.1039/C1NR11425E
Smith, 2007, Designing synthetic vesicles that engulf nanoscopic particles, J. Chem. Phys., 127, 084703, 10.1063/1.2766953