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list_of_the_crunch_group_publications_on_dpd [2017/05/24 16:45]
xl24 [DPD + X]
list_of_the_crunch_group_publications_on_dpd [2017/05/24 17:13] (current)
xl24 [Biomedical/Multiscale/Microfluidic Modeling]
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 ===== Biomedical/​Multiscale/​Microfluidic Modeling ===== ===== 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. +   - 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. 
-   - 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. 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. 
-   - A. Yazdani, X. Li, and G. E. Karniadakis. Dynamic and rheological properties of soft biological cell suspensions. Rheol. Acta 2016, 55, 433-449.  +   - 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. 
-   - 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.+   - 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.    - 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.
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 ===== DPD + X ===== ===== DPD + X =====
   - M. Deng, W. Pan, and G. E. Karniadakis. Anisotropic single-particle dissipative particle dynamics model. //J. Comput. Phys.//, ​ 2017, 336: 481-491.   - 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.   - 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.   - 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.
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   - 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.   - 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.   - 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.

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