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list_of_the_crunch_group_publications_on_dpd [2017/05/24 20:28] xl24 [Extensions of DPD] |
list_of_the_crunch_group_publications_on_dpd [2017/05/24 20:56] xl24 [Biomedical/Multiscale/Microfluidic Modeling] |
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| ====== List of Crunch Group Publications on DPD ====== | ====== List of Crunch Group Publications on DPD ====== | ||
| - | ===== Computational Biology ===== | + | ===== Biomedical/Multiscale/Microfluidic Modeling ===== |
| + | - Y.-H. Tang, L. Lu, H. Li, C. Evangelinos, L. Grinberg, V. Sachdeva, and G. E. Karniadakis. OpenRBC: A fast simulator of red blood cells at protein resolution. //Biophys. J.//, 2017, 112, 2030-2037. | ||
| + | - A. L. Blumers, Y.-H. Tang, Z. Li, X. Li and G. E. Karniadakis. GPU-accelerated red blood cells simulations with transport dissipative particle dynamics. //Comput. Phys. Commun.//, 2017, 217, 171-179. | ||
| + | - X. Li, E. Du, M. Dao, S. Suresh, and G. E. Karniadakis. Patient-specific modeling of individual sickle cell behavior under transient hypoxia. //PLOS Comput. Biol.//, 2017, 13, e1005426. | ||
| + | - A. Yazdani, H. Li, J. D. Humphrey, and G. E. Karniadakis. A general shear-dependent model for thrombus formation. //PLOS Comput. Biol.//, 2017, 13, e1005291. | ||
| - X. Li, M. Dao, G. Lykotrafitis, and G. E. Karniadakis. Biomechanics and biorheology of red blood cells in sickle cell anemia. J. Biomech. 2017, 50, 34-41. | - X. Li, M. Dao, G. Lykotrafitis, and G. E. Karniadakis. Biomechanics and biorheology of red blood cells in sickle cell anemia. J. Biomech. 2017, 50, 34-41. | ||
| - H.-Y. Chang, X. Li, H. Li, and G. E. Karniadakis. MD/DPD multiscale framework for predicting morphology and stresses of red blood cells in health and disease. PLOS Comput. Biol. 2016, 12, e1005173. | - H.-Y. Chang, X. Li, H. Li, and G. E. Karniadakis. MD/DPD multiscale framework for predicting morphology and stresses of red blood cells in health and disease. PLOS Comput. Biol. 2016, 12, e1005173. | ||
| + | - A. Yazdani and G. E. Karniadakis. Sub-cellular modeling of platelet transport in blood flow through microchannels with constriction. //Soft Matter//, 2016, 12, 4339-4351. | ||
| - A. Yazdani, X. Li, and G. E. Karniadakis. Dynamic and rheological properties of soft biological cell suspensions. Rheol. Acta 2016, 55, 433-449. | - A. Yazdani, X. Li, and G. E. Karniadakis. Dynamic and rheological properties of soft biological cell suspensions. Rheol. Acta 2016, 55, 433-449. | ||
| - L. Lu, X. J. Li, P. G. Vekilov, and G. E. Karniadakis. Probing the twisted structure of sickle hemoglobin fibers via particle simulations. Biophys. J. 2016, 110, 2085-2093. | - L. Lu, X. J. Li, P. G. Vekilov, and G. E. Karniadakis. Probing the twisted structure of sickle hemoglobin fibers via particle simulations. Biophys. J. 2016, 110, 2085-2093. | ||
| + | - Y.-H. Tang, Z. Li, X. J. Li, M. G. Deng and G. E. Karniadakis. Non-equilibrium dynamics of vesicles and micelles by self-assembly of block copolymers with double thermoresponsivity. //Macromolecules//, 2016, 49, 2895–2903. | ||
| - K. Lykov, X. J. Li, I. V. Pivkin and G. E. Karniadakis. Inflow/Outflow boundary conditions for particle-based blood flow simulations: Application to arterial bifurcations and trees. //PLOS Comput. Biol.//, 2015, 11, e1004410. | - K. Lykov, X. J. Li, I. V. Pivkin and G. E. Karniadakis. Inflow/Outflow boundary conditions for particle-based blood flow simulations: Application to arterial bifurcations and trees. //PLOS Comput. Biol.//, 2015, 11, e1004410. | ||
| - X. J. Li, Z. L. Peng, H. Lei, M. Dao and G. E. Karniadakis. Probing red blood cell mechanics, rheology and dynamics with a two-component multiscale model. //Phil. Trans. R. Soc. A.// 2014, 372, 20130389. | - X. J. Li, Z. L. Peng, H. Lei, M. Dao and G. E. Karniadakis. Probing red blood cell mechanics, rheology and dynamics with a two-component multiscale model. //Phil. Trans. R. Soc. A.// 2014, 372, 20130389. | ||
| + | - X. J. Li, Y.-H. Tang, H. J. Liang, and G. E. Karniadakis. Large-scale dissipative particle dynamics simulations of self-assembled amphiphilic systems. //Chem. Commun.// 2014, 50, 8306-8308. | ||
| - D.A. Fedosov, M. Dao, G.E. Karniadakis and S.Suresh. Computational biorheology of human blood flow in health and disease. //Ann. Biomed. Eng.//, 2014, 42, 368-387. | - D.A. Fedosov, M. Dao, G.E. Karniadakis and S.Suresh. Computational biorheology of human blood flow in health and disease. //Ann. Biomed. Eng.//, 2014, 42, 368-387. | ||
| - H. Lei and G. E. Karniadakis. Probing vaso-occlusion phenomena in sickle cell anemia via mesoscopic simulations. //Proc. Natl. Acad. Sci. USA//, 2013, 110, 11326-11330. | - H. Lei and G. E. Karniadakis. Probing vaso-occlusion phenomena in sickle cell anemia via mesoscopic simulations. //Proc. Natl. Acad. Sci. USA//, 2013, 110, 11326-11330. | ||
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| - X. J. Li, P. Vlahovska and G.E. Karniadakis. Continuum- and particle-based modeling of shapes and dynamics of red blood cells in health and disease. //Soft Matter//, 2013, 9, 28-37. | - X. J. Li, P. Vlahovska and G.E. Karniadakis. Continuum- and particle-based modeling of shapes and dynamics of red blood cells in health and disease. //Soft Matter//, 2013, 9, 28-37. | ||
| - H. Lei, D. Fedosov, B. Caswell and G. E. Karniadakis. Blood flow in small tubes: Quantifying the transition to the non-Newtonian regime. //J. Fluid Mech.//, 2013, 722, 214-239. | - H. Lei, D. Fedosov, B. Caswell and G. E. Karniadakis. Blood flow in small tubes: Quantifying the transition to the non-Newtonian regime. //J. Fluid Mech.//, 2013, 722, 214-239. | ||
| + | - X. J. Li, B. Caswell, and G. E. Karniadakis. Effect of chain chirality on the self-assembly of sickle hemoglobin. //Biophys. J.// 2012, 103, 1130-1140. | ||
| - W. Pan, D. Fedosov, B. Caswell and G.E. Karniadakis. Predicting dynamics and rheology of blood flow: A comparative study of multiscale and low dimensional models of red blood cells. //Microvas. J.//, 2011, 82, 163-170. | - W. Pan, D. Fedosov, B. Caswell and G.E. Karniadakis. Predicting dynamics and rheology of blood flow: A comparative study of multiscale and low dimensional models of red blood cells. //Microvas. J.//, 2011, 82, 163-170. | ||
| - D.A. Fedosov, W. Pan, B. Caswell, G. Gompper and G.E. Karniadakis. Predicting human blood viscosity in silico. //Proc. Natl. Acad. Sci. USA//, 2011, 108, 11772-11777. | - D.A. Fedosov, W. Pan, B. Caswell, G. Gompper and G.E. Karniadakis. Predicting human blood viscosity in silico. //Proc. Natl. Acad. Sci. USA//, 2011, 108, 11772-11777. | ||
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| - X.J. Li, I.V. Pivkin, H.J. Liang and G.E. Karniadakis. Shape transformation of membrane vesicles from amphiphilic triblock copolymers: A dissipative particle dynamics simulation study. //Macromolecules//, 2009, 42, 3195-3200. | - X.J. Li, I.V. Pivkin, H.J. Liang and G.E. Karniadakis. Shape transformation of membrane vesicles from amphiphilic triblock copolymers: A dissipative particle dynamics simulation study. //Macromolecules//, 2009, 42, 3195-3200. | ||
| - I.V. Pivkin and G.E. Karniadakis. Accurate coarse-grained modeling of red blood cells. //Phys. Rev. Letts.//, 2008, 101, 118105. | - I.V. Pivkin and G.E. Karniadakis. Accurate coarse-grained modeling of red blood cells. //Phys. Rev. Letts.//, 2008, 101, 118105. | ||
| + | |||
| + | |||
| + | ===== DPD + X ===== | ||
| + | - M. Deng, W. Pan, and G. E. Karniadakis. Anisotropic single-particle dissipative particle dynamics model. //J. Comput. Phys.//, 2017, 336: 481-491. | ||
| + | - H. Lei, X. Yang, Z. Li, and G. E. Karniadakis. Systematic parameter inference in stochastic mesoscopic modeling. //J. Comput. Phys.//, 2017, 330, 571-593. | ||
| + | - Z. Li, H.S. Lee, E. Darve, and G. E. Karniadakis. Computing the non-Markovian coarse-grained interactions derived from the Mori–Zwanzig formalism in molecular systems: Application to polymer melts. //J. Chem. Phys.//, 2017, 146: 014104. | ||
| + | - M. Deng, Z. Li, O. Borodin, and G. E. Karniadakis. cDPD: A new dissipative particle dynamics method for modeling electrokinetic phenomena at the mesoscale. //J. Chem. Phys.// 2016, 145: 144109. | ||
| + | - Z. Li, X. Bian, X. Yang and G.E. Karniadakis. A comparative study of coarse-graining methods for polymeric fluids: Mori-Zwanzig vs. iterative Boltzmann inversion vs. stochastic parametric optimization. //J. Chem. Phys.//, 2016, 145: 044102. | ||
| + | - Z. Li, A. Yazdani, A. Tartakovsky and G. E. Karniadakis. Transport dissipative particle dynamics model for mesoscopic advection-diffusion-reaction problems. //J. Chem. Phys.//, 2015, 143: 014101. | ||
| + | - Z. Li, Y.-H. Tang, X. J. Li and G. E. Karniadakis. Mesoscale modeling of phase transition of thermoresponsive polymers. //Chem. Commun.//, 2015, 51: 11038-11040. | ||
| + | - Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G. E. Karniadakis. Energy-conserving dissipative particle dynamics with temperature-dependent properties. //J. Comput. Phys.//, 2014, 265: 113-127. | ||
| + | - M. Arienti, W. Pan, X. Li, G. E. Karniadakis. Many-body dissipative particle dynamics simulation of liquid/vapor and liquid/solid interactions. //J. Chem. Phys.//, 2011, 134: 204114. | ||
| + | - H. Lei, B. Caswell, and G.E. Karniadakis. Direct construction of mesoscopic models from microscopic simulations. //Phys. Rev. E//, 2010, 81, 026704. | ||
| + | - W. Pan, B. Caswell, and G. E. Karniadakis. Rheology, Microstructure and Migration in Brownian Colloidal Suspensions. //Langmuir//, 2010, 26, 133-142. | ||
| + | - D. A. Fedosov and G.E. Karniadakis. Triple-decker: Interfacing atomistic-mesocopic-continuum flow regimes. //J. Comput. Phys.//, 2009, 228, 1157-1171. | ||
| + | - W. Pan, I.V. Pivkin, and G.E. Karniadakis. Single-particle hydrodynamics in DPD: A new formulation. //Europhys. Lett.//, 2008, 84, 10012. | ||
| + | - D. A. Fedosov, I.V. Pivkin, and G.E. Karniadakis. Velocity limit in DPD simulations of wall-bounded flows. //J. Comput. Phys.//, 2008, 227, 2540-2559. | ||
| - I.V. Pivkin and G.E. Karniadakis. Controlling density fluctuations in wall bounded DPD systems. //Phys. Rev. Letts.//, 2006, 96, 206001. | - I.V. Pivkin and G.E. Karniadakis. Controlling density fluctuations in wall bounded DPD systems. //Phys. Rev. Letts.//, 2006, 96, 206001. | ||
| - I.V. Pivkin and G.E. Karniadakis. Coarse-graining limits in open and wall-bounded dissipative particle dynamics systems. //J. Chem. Phys.//, 2006, 124, 184101. | - I.V. Pivkin and G.E. Karniadakis. Coarse-graining limits in open and wall-bounded dissipative particle dynamics systems. //J. Chem. Phys.//, 2006, 124, 184101. | ||
| + | - V. Symeonidis, G.E. Karniadakis, and B. Caswell. Schmidt number effects in simulation of polymer dissipative particle dynamics. //J. Chem. Phys.//, 2006, 125, 184902. | ||
| - V. Symeonidis, G.E. Karniadakis and B. Caswell. Dissipative particle dynamics simulations of polymer chains: Scaling laws and shearing response compared to DNA experiments. //Phys. Rev. Lett.//, 2005, 95, 076001. | - V. Symeonidis, G.E. Karniadakis and B. Caswell. Dissipative particle dynamics simulations of polymer chains: Scaling laws and shearing response compared to DNA experiments. //Phys. Rev. Lett.//, 2005, 95, 076001. | ||
| - I.V. Pivkin and G.E. Karniadakis. A new method to impose no-slip boundary conditions in dissipative particles dynamics. //J. Comp. Phys.//, 2005, 207, 114-128. | - I.V. Pivkin and G.E. Karniadakis. A new method to impose no-slip boundary conditions in dissipative particles dynamics. //J. Comp. Phys.//, 2005, 207, 114-128. | ||
| - | ===== MUI ===== | + | ===== Multiscale Universal Interface (MUI) and its applications ===== |
| - Y.-H. Tang, S. Kudo, X. Bian, Z. Li and G. E. Karniadakis. Multiscale Universal Interface: A Concurrent Framework for Coupling Heterogeneous Solvers. //J. Comput. Phys.//, 2015, 297, 13-31. | - Y.-H. Tang, S. Kudo, X. Bian, Z. Li and G. E. Karniadakis. Multiscale Universal Interface: A Concurrent Framework for Coupling Heterogeneous Solvers. //J. Comput. Phys.//, 2015, 297, 13-31. | ||
| - X. Bian, Z. Li and G. E. Karniadakis. Multi-resolution flow simulations by smoothed particle hydrodynamics via domain decomposition. //J. Comput. Phys.//, 2015, 297, 132-155. | - X. Bian, Z. Li and G. E. Karniadakis. Multi-resolution flow simulations by smoothed particle hydrodynamics via domain decomposition. //J. Comput. Phys.//, 2015, 297, 132-155. | ||
| + | - X. Bian, Z. Li, M. G. Deng, and G. E. Karniadakis. Fluctuating hydrodynamics in periodic domains and heterogeneous adjacent multidomains: Thermal equilibrium. // Phys. Rev. E//, 2015, 92, 053302. | ||
| - X. Bian, M. G. Deng, Y.-H. Tang and G. E. Karniadakis. Analysis of hydrodynamic fluctuations in heterogeneous adjacent multidomains in shear flow. // Phys. Rev. E//, 2016, 93, 033312. | - X. Bian, M. G. Deng, Y.-H. Tang and G. E. Karniadakis. Analysis of hydrodynamic fluctuations in heterogeneous adjacent multidomains in shear flow. // Phys. Rev. E//, 2016, 93, 033312. | ||
| + | - A. Yazdani, M. Deng, B. Caswell, and G. E. Karniadakis. Flow in complex domains simulated by dissipative particle dynamics driven by geometry-specific body-forces. //J. Comput. Phys.//, 2016, 305, 906-920. | ||
| + | - S. Lee, I. G. Kevrekidis, and G. E. Karniadakis. A resilient and efficient CFD framework: Statistical learning tools for multi-fidelity and heterogeneous information fusion. //J. Comput. Phys.//, 2017, 344, 516-533. | ||
| - | ===== Extensions of DPD ===== | ||
| - | - Z Li, HS Lee, E Darve, GE Karniadakis. Computing the non-Markovian coarse-grained interactions derived from the Mori–Zwanzig formalism in molecular systems: Application to polymer melts. //J. Chem. Phys.//, 2017, 146: 014104. | ||
| - | - M. Deng, Z. Li, O. Borodin, and G. E. Karniadakis. cDPD: A new dissipative particle dynamics method for modeling electrokinetic phenomena at the mesoscale. //J. Chem. Phys.// 2016, 145: 144109. | ||
| - | - Z. Li, X. Bian, X. Yang and G.E. Karniadakis. A comparative study of coarse-graining methods for polymeric fluids: Mori-Zwanzig vs. iterative Boltzmann inversion vs. stochastic parametric optimization. //J. Chem. Phys.//, 2016, 145: 044102. | ||
| - | - Z. Li, A. Yazdani, A. Tartakovsky and G. E. Karniadakis. Transport dissipative particle dynamics model for mesoscopic advection-diffusion-reaction problems. J. Chem. Phys., 2015, 143: 014101. | ||
| - | - Z. Li, Y.-H. Tang, X. J. Li and G. E. Karniadakis. Mesoscale modeling of phase transition of thermoresponsive polymers. //Chem. Commun.//, 2015, 51: 11038-11040. | ||
| - | - Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G. E. Karniadakis. Energy-conserving dissipative particle dynamics with temperature-dependent properties. //J. Comput. Phys.//, 2014, 265: 113-127. | ||
| - | - M. Arienti, W. Pan, X. Li, G. E. Karniadakis. Many-body dissipative particle dynamics simulation of liquid/vapor and liquid/solid interactions. J. Chem. Phys., 2011, 134: 204114. | ||
| - | ===== Self Assembly ===== | ||
| - | - Y.-H. Tang, Z. Li, X. J. Li, M. G. Deng and G. E. Karniadakis. Non-equilibrium dynamics of vesicles and micelles by self-assembly of block copolymers with double thermoresponsivity. Macromolecules, 2016, 49, 2895–2903. | ||
| - | - X. J. Li, Y.-H. Tang, H. J. Liang, and G. E. Karniadakis. Large-scale dissipative particle dynamics simulations of self-assembled amphiphilic systems. //Chem. Commun.// 2014, 50, 8306-8308. | ||
| - | - X. J. Li, B. Caswell, and G. E. Karniadakis. Effect of chain chirality on the self-assembly of sickle hemoglobin. //Biophys. J.// 2012, 103, 1130-1140. | ||
