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−Table of Contents
List of Crunch Group Publications on DPD
Biomedical/Multiscale/Microfluidic Modeling
- 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.
- 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.
- 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.
- 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.
- 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.
- Z. L. Peng, X. J. Li, I. V. Pivkin, M. Dao, G. E. Karniadakis and S. Suresh. Lipid-bilayer and cytoskeletal interactions in a red blood cell. Proc. Natl. Acad. Sci. USA, 2013, 110, 13356-13361.
- 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.
- 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.
- 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, B. Caswell and G.E. Karniadakis. Wall shear stress-based model for adhesive dynamics of red blood cells in malaria. Biophysical Journal, 2011, 100, 2084-2093.
- D.J. Quinn, I. Pivkin, S.Y. Wong, K-H. Chiam, M. Dao, G.E. Karniadakis and S. Suresh. Combined simulation and experimental study of large deformation of red blood cells in microfluidic systems. Annls Biomed. Eng., 2011, 39, 041-1050.
- D.A. Fedosov, B. Caswell, S. Suresh and G.E. Karniadakis. Quantifying the biophysical characteristics of Plasmodium-falciparum-parasitized red blood cells in microcirculation. Proc. Natl. Acad. Sci. USA, 2011, 108, 35-39.
- D.A. Fedosov, B. Caswell, A. Popel and G.E. Karniadakis. Blood flow and cell-free layer in microvessels. Microcirculation, 2010, 17, 615-628.
- D. Fedosov, B. Caswell and G.E. Karniadakis. Systematic coarse-graining of spectrin-level red blood cell models. Comput. Meth. Appl. Mech. Eng., 2010, 199, 1937-1948.
- W. Pan, B. Caswell and G.E. Karniadakis. A low-dimensional model for the red blood cell. Soft Matter, 2010, 6, 4366-4376.
- D. Fedosov, B. Caswell and G.E. Karniadakis. A multiscale red blood cell model with accurate mechanics, rheology and dynamics. Biophys. J., 2010, 98, 2215-2225.
- I.V. Pivkin, P. Richardson and G.E. Karniadakis. Effect of red blood cells on platelet aggregation. IEEE Engineering in Medicine and Biology Magazine, 2009, 28, 32-32.
- 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.
MUI
- 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, 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.
DPD + X
- M. Deng, W. Pan, and G. E. Karniadakis. Anisotropic single-particle dissipative particle dynamics model. J. Comput. Phys., 2017, 336: 481-491.
- 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.
- - 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.
- 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.
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.