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list_of_the_crunch_group_publications_on_dpd [2017/05/24 16:29]
xl24 [Extensions of DPD]
list_of_the_crunch_group_publications_on_dpd [2017/05/24 17:13] (current)
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 ​===== 
-   - 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.
   - 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.
-  - 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. 
  
-===== 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. 
  
-===== Extensions of DPD =====+===== 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.   - 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.
-===== Self Assembly ​===== +  - H. Lei, B. Caswell, and G.E. Karniadakis. Direct construction of mesoscopic models from microscopic simulations. //Phys. Rev. E//, 2010, 81, 026704. 
-  - 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 thermoresponsivityMacromolecules2016492895–2903+  - W. Pan, B. Caswell, and G. E. Karniadakis. Rheology, Microstructure and Migration in Brownian Colloidal Suspensions. //​Langmuir//,​ 2010, 26, 133-142. 
-  - X. JLi, Y.-H. Tang, HJLiang, and G. E. Karniadakis. ​Large-scale ​dissipative particle dynamics ​simulations of self-assembled amphiphilic systems. //ChemCommun.// 2014508306-8308+  - D. A. Fedosov and G.E. Karniadakis. Triple-decker:​ Interfacing atomistic-mesocopic-continuum flow regimes. //J. Comput. Phys.//, 2009, 228, 1157-1171. 
-  - XJ. LiBCaswell, and G. E. Karniadakis. ​Effect of chain chirality on the self-assembly of sickle hemoglobin. //Biophys. ​J.// 20121031130-1140.+  - 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. 
 + 
 +===== 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. 
 +  - 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. Dengand G. E. Karniadakis. ​Fluctuating hydrodynamics in periodic domains ​and heterogeneous adjacent multidomains:​ Thermal equilibrium// Phys. Rev. E//201592053302
 +  - X. Bian, MG. 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. 
 +  - AYazdani, M. Deng, B. Caswell, and G. E. Karniadakis. ​Flow in complex domains simulated by dissipative particle dynamics ​driven by geometry-specific body-forces. //JComput. Phys.//, 2016, 305906-920
 +  - SLeeIG. Kevrekidis, and G. E. Karniadakis. ​A resilient and efficient CFD framework: Statistical learning tools for multi-fidelity and heterogeneous information fusion. //J. Comput. Phys.//, 2017344, 516-533. 

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