Publications


peer-reviewed articles | book chapters | patents | conference proceedings | theses


 

Peer-reviewed articles


2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2005-2009

     

      2015

     
  1. H. Turlier, D. A. Fedosov, B. Audoly, T. Auth, N. S. Gov, C. Sykes, J.-F. Joanny, G. Gompper, and T. Betz, "Equilibrium physics breakdown reveals the active nature of red blood cell membrane fluctuations", Nature Physics, in press, 2015.
  2.  
  3. Z. Zhang, E. Henry, G. Gompper, and D. A. Fedosov, "Behavior of rigid and deformable particles in deterministic lateral displacement devices with different post shapes", Journal of Chemical Physics, in press, 2015.
  4.  
  5. G. Gompper and D. A. Fedosov, "Modeling microcirculatory blood flow: current state and future perspectives", WIREs Systems Biology and Medicine, in press, 2015.
  6.  
  7. K. Müller, D. A. Fedosov, and G. Gompper, "Understanding particle margination in blood flow - A step toward optimized drug delivery systems", Medical Engineering and Physics, in press, 2015.  [PDF]
  8.  
  9. D. A. Fedosov, A. Sengupta, and G. Gompper, "Effect of fluid–colloid interactions on the mobility of a thermophoretic microswimmer in non-ideal fluids", Soft Matter, 11, 6703-6715, 2015.  [PDF]
  10.  
  11. D. A. Fedosov, "In silico modeling of malaria and sickle-cell disease", Drug Discovery Today: Disease Models, in press, 2015.  [PDF]
  12.  
  13. D. Katanov, G. Gompper, and D. A. Fedosov, "Microvascular blood flow resistance: role of red blood cell migration and dispersion", Microvascular Research, 99, 57-66, 2015.  [PDF]
  14.  
  15. F. Römer and D. A. Fedosov, "Dense brushes of stiff polymers or filaments in fluid flow", Europhysics Letters, 109, 68001, 2015.  [PDF]
  16.  
  17. K. Müller, D. A. Fedosov, and G. Gompper, "Smoothed dissipative particle dynamics with angular momentum conservation", Journal of Computational Physics, 281, 301-315, 2015.  [PDF]
  18.  

      2014

     
  19. R. G. Winkler, D. A. Fedosov, and G. Gompper, "Dynamical and rheological properties of soft colloid suspensions", Current Opinion in Colloid and Interface Science, 19, 594-610, 2014.  [PDF]
  20.  
  21. K. Müller, D. A. Fedosov, and G. Gompper, "Margination of micro- and nano-particles in blood flow and its effect on drug delivery", Scientific Reports, 4, 4871, 2014.  [PDF]
  22.  
  23. D. A. Fedosov, M. Peltomäki, and G. Gompper, "Deformation and dynamics of red blood cells in flow through cylindrical microchannels", Soft Matter, 10, 4258-4267, 2014.  [PDF]
  24.  
  25. D. A. Fedosov and G. Gompper, "White blood cell margination in microcirculation", Soft Matter, 10, 2961-2970, 2014.  [PDF]
  26.  
  27. D. A. Fedosov, M. Dao, G. E. Karniadakis, and S. Suresh, "Computational biorheology of human blood flow in health and disease", Annals of Biomedical Engineering, 42, 368-387, 2014.  [PDF]
  28.  
  29. D. A. Fedosov, H. Noguchi, and G. Gompper, "Multiscale modeling of blood flow: from single cells to blood rheology", Biomechanics and Modeling in Mechanobiology, 13, 239-258, 2014.  [PDF]
  30.  

      2013

     
  31. R. G. Winkler, S. P. Singh, C.-C. Huang, D. A. Fedosov, K. Mussawisade, A. Chatterji, M. Ripoll, and G. Gompper, "Mesoscale hydrodynamics simulations of particle suspensions under shear flow: From hard to ultrasoft colloids", European Physical Journal-Special Topics, 222, 2773-2786, 2013.  [PDF]
  32.  
  33. X. Shi, G. Lin, J.-F. Zou, and D. A. Fedosov, "A lattice Boltzmann fictitious domain method for modeling red blood cell deformation and multiple-cell hydrodynamic interactions in flow", International Journal for Numerical Methods in Fluids, 72, 895-911, 2013.
  34.  
  35. L. Grinberg, D. A. Fedosov, and G. E. Karniadakis, "Parallel multiscale simulations of a brain aneurysm", Journal of Computational Physics, 244, 131-147, 2013.  [PDF]
  36.  
  37. H. Lei, D. A. Fedosov, B. Caswell, and G. E. Karniadakis, "Blood flow in small tubes: quantifying the transition to the non-continuum regime", Journal of Fluid Mechanics, 722, 214-239, 2013.  [PDF]
  38.  

      2012

     
  39. L. Grinberg, J. A. Insley, D. A. Fedosov, V. Morozov, M. E. Papka, and G. E. Karniadakis, "Tightly coupled atomistic-continuum simulations of brain blood flow on petaflop supercomputers", Computing in Science and Engineering , 14, 58-67, 2012.
  40.  
  41. S. P. Singh, D. A. Fedosov, A. Chatterji, R. G. Winkler, and G. Gompper, "Conformational and dynamical properties of ultra-soft colloids in semi-dilute solutions under shear flow", Journal of Physics: Condensed Matter, 24, 464103, 2012.  [PDF]
  42.  
  43. D. A. Fedosov, S. P. Singh, A. Chatterji, R. G. Winkler, and G. Gompper, "Semidilute solutions of ultra-soft colloids under shear flow", Soft matter, 8, 4109-4120, 2012.  [PDF]
  44.  
  45. D. A. Fedosov, J. Fornleitner, and G. Gompper, "Margination of white blood cells in microcapillary flow", Physical Review Letters, 108, 028104, 2012.  [PDF]
  46.  

      2011

     
  47. L. Grinberg, V. Morozov, D. A. Fedosov, J. A. Insley, M. E. Papka, K. Kumaran, and G. E. Karniadakis, "A new computational paradigm in multiscale simulations: Application to brain blood flow", refereed article in Proceedings of the 2011 ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis, SC’11, accepted as a finalist for the Gordon Bell award, 2011.  [PDF]
  48.  
  49. D. A. Fedosov, H. Lei, B. Caswell, S. Suresh, and G. E. Karniadakis, "Multiscale modeling of red blood cell mechanics and blood flow in malaria", PLoS Computational Biology, 7, e1002270, 2011.  [PDF]
  50.  
  51. D. A. Fedosov, W. Pan, B. Caswell, G. Gompper, and G. E. Karniadakis, "Predicting human blood viscosity in silico", Proceedings of the National Academy of Sciences USA, 108, 11772-11777, 2011.  [PDF]
  52.  
  53. D. A. Fedosov, B. Caswell, and G. E. Karniadakis, "A wall-shear-stress based model for adhesive dynamics of red blood cells in malaria", Biophysical Journal, 100, 2084-2093, 2011.  [PDF]
  54.  
  55. W. Pan, D. A. 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", Microvascular Research, 82, 163-170, 2011.  [PDF]
  56.  
  57. H. Lei, D. A. Fedosov, and G. E. Karniadakis, "Time-dependent and outflow boundary conditions for Dissipative Particle Dynamics", Journal of Computational Physics, 230, 3765-3779, 2011.  [PDF]
  58.  
  59. D. A. Fedosov, B. Caswell, S. Suresh, and G. E. Karniadakis, "Quantifying the biophysical characteristics of Plasmodium-falciparum-parasitized red blood cells in microcirculation", Proceedings of the National Academy of Sciences USA, 108, 35-39, 2011.  [PDF]
  60.  

      2010

     
  61. D. A. Fedosov, B. Caswell, A. S. Popel, and G. E. Karniadakis, "Blood flow and cell-free layer in microvessels", Microcirculation, 17, 615-628, 2010.  [PDF]
  62.  
  63. D. A. Fedosov, B. Caswell, and G. E. Karniadakis, "A multiscale red blood cell model with accurate mechanics, rheology, and dynamics", Biophysical Journal, 98, 2215-2225, 2010.  [PDF]
  64.  
  65. D. A. Fedosov, B. Caswell, and G. E. Karniadakis, "Systematic coarse-graining of spectrin-level red blood cell models", Computer Methods in Applied Mechanics and Engineering, 199, 1937-1948, 2010.  [PDF]
  66.  
  67. D. A. Fedosov, B. Caswell, and G. E. Karniadakis, "Steady shear rheometry of dissipative particle dynamics models of polymer fluids in reverse Poiseuille flow", Journal of Chemical Physics, 132, 144103, 2010.  [PDF]
  68.  

      2005-2009

     
  69. D. A. Fedosov and G. E. Karniadakis, "Triple-decker: Interfacing atomistic-mesoscopic-continuum flow regimes", Journal of Computational Physics, 228, 1157-1171, 2009.  [PDF]
  70.  
  71. W. Pan, D. A. Fedosov, B. Caswell, and G. E. Karniadakis, "Hydrodynamic interactions for single dissipative-particle-dynamics particles and their clusters and filaments", Physical Review E, 78, 046706, 2008.  [PDF]
  72.  
  73. D. A. Fedosov, B. Caswell, and G. E. Karniadakis, "Dissipative particle dynamics simulation of depletion layer and polymer migration in micro- and nanochannels for dilute polymer solutions", Journal of Chemical Physics, 128, 144903, 2008.  [PDF]
  74.  
  75. D. A. Fedosov, I. V. Pivkin, and G. E. Karniadakis, "Velocity limit in DPD simulations of wall-bounded flows", Journal of Computational Physics, 227, 2540-2559, 2008.  [PDF]
  76.  
  77. A. A. Alexeenko, D. A. Fedosov, D. A. Levin, S. F. Gimelshein, and R. J. Collins, "Transient heat transfer and gas flow in a MEMS-based thruster", Journal of Microelectromechanical Systems, 15, 181-194, 2006.
  78.  
  79. A. A. Alexeenko, D. A. Fedosov, D. A. Levin, S. F. Gimelshein, and R. J. Collins, "Performance analysis of microthrusters based on coupled thermal-fluid modeling and simulation", Journal of Propulsion and Power, 21, 95-101, 2005.
  80.  
  81. T. Ozawa, D. A. Fedosov, D. A. Levin, and S. F. Gimelshein, "Quasi-classical trajectory modeling of OH production in direct simulation Monte Carlo", Journal of Thermophysics and Heat Transfer, 19, 235-244, 2005.

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Book chapters


  1. D. A. Fedosov, K. Müller, and G. Gompper, "Smoothed dissipative particle dynamics - a mesoscopic particle-based hydrodynamic technique for complex fluids", lecture manuscript of the Jülich School on Computational Trends in Solvation and Transport in Liquids organized by J. Grotendorst, G. Sutmann, G. Gompper, and D. Marx, Jülich, Germany, 2015.  [PDF]
  2.  
  3. D. A. Fedosov, K. Müller, and G. Gompper, "Drug delivery in blood", lecture manuscript of the 46th IFF Spring School on Functional Soft Matter organized by J. K. G. Dhont, G. Gompper, G. Meier, D. Richter, G. Vliegenthart, and R. Zorn, Jülich, Germany, 2015.  [PDF]
  4.  
  5. D. A. Fedosov, "Simulations of blood flow on the cell scale", lecture manuscript of the IAS Winter School - Hierarchical Methods for Dynamics in Complex Molecular Systems organized by J. Grotendorst, G. Sutmann, G. Gompper, and D. Marx, Jülich, Germany, 2012.  [PDF]
  6.  
  7. D. A. Fedosov, I. V. Pivkin, W. Pan, M. Dao, B. Caswell, and G. E. Karniadakis, "Multiscale modeling of hematologic disorders", in Modelling of physiological flows edited by D. Ambrosi, A. Quarteroni, and G. Rozza, Springer, Milan, Italy, 2011.  [PDF]
  8.  
  9. D. A. Fedosov, "Blood cells and blood flow", lecture manuscript of the 42nd IFF Spring School - Macromolecular Systems in Soft and Living Matter organized by J. K. G. Dhont, G. Gompper, P. Lang, D. Richter, M. Ripoll, D. Willbold, and R. Zorn, Jülich, Germany, 2011.  [PDF]
  10.  
  11. D. A. Fedosov, B. Caswell, and G. E. Karniadakis, "Dissipative particle dynamics modeling of red blood cells", in Computational Hydrodynamics of Capsules and Biological Cells edited by C. Pozrikidis, CRC Press, Inc., Boca Raton, FL, 2010.  [PDF]

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Patents


  1. S. Suresh, G. E. Karniadakis, B. Caswell, I. V. Pivkin, D. A. Fedosov, D. J. Quinn, and M. Dao, "Computational methods and compositions", patent numbers: WO2011119492-A2, US2011287948-A1, US2011289043-A1, US2011293558-A1, US2012064505-A1, WO2011119492-A3.
  2.  

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Conference proceedings


  1. K. Müller, D. A. Fedosov, and G. Gompper, "Margination of micro- and nano-particles in blood flow and its effect on drug delivery", Proceedings of the 4th International Conference on Computational and Mathematical Biomedical Engineering (CMBE2015), Paris, France, 2015.
  2.  
  3. D. A. Fedosov, J. Fornleitner, J. L. McWhirter, K. Müller, H. Noguchi, M. Peltomäki, and G. Gompper, "Blood flow in silico: from single cells to blood rheology", Proceedings of the 4th Micro and Nano Flows Conference, London, England, 2014.
  4.  
  5. K. Müller, D. A. Fedosov, and G. Gompper, "The behavior of von Willebrand factor in blood flow", Proceedings of the 4th Micro and Nano Flows Conference, London, England, 2014.
  6.  
  7. K. Müller, D. A. Fedosov, and G. Gompper, "Margination of micro- and nano-particles in blood flow and its effect on the efficiency of drug delivery", Proceedings of the 4th Micro and Nano Flows Conference, London, England, 2014.
  8.  
  9. D. A. Fedosov and G. Gompper, "Simulating blood cells and blood flow", inSIDE: Innovatives Supercomputing in Deutschland, 10, 28-33, 2012.
  10.  
  11. D. A. Fedosov and G. Gompper, "Mesoscale simulations of human blood flow: From red blood cell elasticity and interactions to blood rheology", Proceedings of the 6th NIC Symposium 2012, Jülich, Germany, 2012.
  12.  
  13. D. A. Fedosov, B. Caswell, and G. E. Karniadakis, "Multiscale modeling of blood flow in cerebral malaria", Proceedings of ASME 2010 First Global Congress on NanoEngineering for Medicine and Biology, paper no. NEMB2010-13012, pp. 253-254, 2010.
  14.  
  15. D. A. Fedosov, B. Caswell, and G. E. Karniadakis, "Coarse-grained red blood cell model with accurate mechanical properties, rheology and dynamics", Proceedings of the Engineering in Medicine and Biology Society, EMBC, 2009 Annual International Conference of the IEEE, pp. 4266-4269, 2009.
  16.  
  17. D. A. Fedosov, B. Caswell, and G. E. Karniadakis, "Dissipative particle dynamics simulation of polymer- and cell-wall depletion in micro-channels", Proceedings of the XV International Congress on Rheology: The Society of Rheology 80th Annual Meeting, AIP Conference Proceedings, 1027, 612-614, 2008.
  18.  
  19. D. A. Fedosov, B. Caswell, and G. E. Karniadakis, "Reverse Poiseuille flow: The numerical viscometer", Proceedings of the XV International Congress on Rheology: The Society of Rheology 80th Annual Meeting, AIP Conference Proceedings, 1027, 1432-1434, 2008.
  20.  
  21. D. A. Fedosov, S. V. Rogazinsky, M. I. Zeifman, M. S. Ivanov, A. A. Alexeenko, and D. A. Levin, "Analysis of numerical errors in the DSMC method", Proceedings of the Rarefied Gas Dynamics: 24th International Symposium on Rarefied Gas Dynamics, AIP Conference Proceedings, 762, 589-594, 2005.
  22.  
  23. T. Ozawa, D. A. Fedosov, and D. A. Levin, "Modeling of OH product distributions using QCT-MD and BL models in a bow shock", Proceedings of the Rarefied Gas Dynamics: 24th International Symposium on Rarefied Gas Dynamics, AIP Conference Proceedings, 762, 902-907, 2005.
  24.  
  25. T. Ozawa, D. A. Fedosov, D. A. Levin, and S. F. Gimelshein, "Use of quasi-classical trajectory methods in the modeling of OH production mechanisms in DSMC", AIAA Paper 2004-0336, 42nd AIAA Aerospace Sciences Meeting, 2004.
  26.  
  27. A. A. Alexeenko, D. A. Levin, D. A. Fedosov, S. F. Gimelshein, and R. J. Collins, "Coupled thermal-fluid modeling of micronozzles for performance analysis", AIAA Paper 2003-4717, 39th AIAA/ASME/SAE/ASEE Joint Propulsion Conference and Exhibit, 2003.
  28.  
  29. A. A. Alexeenko, D. A. Levin, D. A. Fedosov, S., F. Gimelshein, and R. J. Collins, "Coupled thermal-fluid analyses of microthruster flows", AIAA Paper 2003-0673, 41st Aerospace Sciences Meeting and Exhibit, 2003.

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Theses


  1. K. Müller, PhD thesis "In Silico Particle Margination in Blood Flow", Department of Physics, University of Cologne, Germany, 2014.
  2.  
  3. M. Katava, Master thesis "Fluctuations of Vesicles and Cells", Department of Chemistry, University of Zagreb, Croatia, 2012.
  4.  
  5. D. A. Fedosov, PhD thesis "Multiscale Modeling of Blood Flow and Soft Matter", Division of Applied Mathematics, Brown University, USA, 2010.  [PDF]
  6.  
  7. D. A. Fedosov, Master thesis "Investigation of Numerical Errors in Direct Simulation Monte Carlo", Department of Aerospace Engineering, Pennsylvania State University, USA, 2004.

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