List of Crunch Group Publications on DPD

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.

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.

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.

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. 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.

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.

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, 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.

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.