TY - JOUR AU - Alonso, M. J. PY - 2004 DA - 2004// TI - Nanomedicines for overcoming biological barriers JO - Biomed Pharmacother VL - 58 UR - https://doi.org/10.1016/j.biopha.2004.01.007 DO - 10.1016/j.biopha.2004.01.007 ID - Alonso2004 ER - TY - JOUR AU - Jain, R. K. AU - Stylianopoulos, T. PY - 2010 DA - 2010// TI - Delivering nanomedicine to solid tumors JO - Nat Rev Clin Oncol VL - 7 UR - https://doi.org/10.1038/nrclinonc.2010.139 DO - 10.1038/nrclinonc.2010.139 ID - Jain2010 ER - TY - JOUR AU - Blanco, E. AU - Shen, H. AU - Ferrari, M. PY - 2015 DA - 2015// TI - Principles of nanoparticle design for overcoming biological barriers to drug delivery JO - Nat Biotechnol VL - 33 UR - https://doi.org/10.1038/nbt.3330 DO - 10.1038/nbt.3330 ID - Blanco2015 ER - TY - JOUR AU - Barua, S. AU - Mitragotri, S. PY - 2014 DA - 2014// TI - Challenges associated with penetration of nanoparticles across cell and tissue barriers: a review of current status and future prospects JO - Nano Today VL - 9 UR - https://doi.org/10.1016/j.nantod.2014.04.008 DO - 10.1016/j.nantod.2014.04.008 ID - Barua2014 ER - TY - JOUR AU - Gaumet, M. AU - Vargas, A. AU - Gurny, R. AU - Delie, F. PY - 2008 DA - 2008// TI - Nanoparticles for drug delivery: the need for precision in reporting particle size parameters JO - Eur J Pharm Biopharm VL - 69 UR - https://doi.org/10.1016/j.ejpb.2007.08.001 DO - 10.1016/j.ejpb.2007.08.001 ID - Gaumet2008 ER - TY - JOUR AU - Wong, C. AU - Stylianopoulos, T. AU - Cui, J. AU - Martin, J. AU - Chauhan, V. P. AU - Jiang, W. AU - Popović, Z. AU - Jain, R. K. AU - Bawendi, M. G. AU - Fukumura, D. PY - 2011 DA - 2011// TI - Multistage nanoparticle delivery system for deep penetration into tumor tissue JO - Proc Natl Acad Sci VL - 108 UR - https://doi.org/10.1073/pnas.1018382108 DO - 10.1073/pnas.1018382108 ID - Wong2011 ER - TY - JOUR AU - Tang, L. AU - Gabrielson, N. P. AU - Uckun, F. M. AU - Fan, T. M. AU - Cheng, J. PY - 2013 DA - 2013// TI - Size-dependent tumor penetration and in vivo efficacy of monodisperse drug–silica nanoconjugates JO - Mol Pharm VL - 10 UR - https://doi.org/10.1021/mp300684a DO - 10.1021/mp300684a ID - Tang2013 ER - TY - JOUR AU - Cortez, R. PY - 2001 DA - 2001// TI - The method of regularized stokeslets JO - SIAM J Sci Comput VL - 23 UR - https://doi.org/10.1137/S106482750038146X DO - 10.1137/S106482750038146X ID - Cortez2001 ER - TY - JOUR AU - Rejniak, K. A. AU - Estrella, V. AU - Chen, T. AU - Cohen, A. S. AU - Lloyd, M. C. AU - Morse, D. L. PY - 2013 DA - 2013// TI - The role of tumor tissue architecture in treatment penetration and efficacy: an integrative study JO - Front Oncol VL - 3 ID - Rejniak2013 ER - TY - CHAP AU - Smith, D. J. PY - 2009 DA - 2009// TI - A boundary element regularized stokeslet method applied to cilia-and flagella-driven flow BT - Proceedings of the Royal Society of London A: Mathematical, Physical and Engineering Sciences, vol. 465 PB - The Royal Society Publishing CY - London ID - Smith2009 ER - TY - JOUR AU - Lobaton, E. J. AU - Bayen, A. M. PY - 2009 DA - 2009// TI - Modeling and optimization analysis of a single-flagellum micro-structure through the method of regularized stokeslets JO - IEEE Trans Control Syst Technol VL - 17 UR - https://doi.org/10.1109/TCST.2008.2011889 DO - 10.1109/TCST.2008.2011889 ID - Lobaton2009 ER - TY - JOUR AU - Flores, H. AU - Lobaton, E. AU - Méndez-Diez, S. AU - Tlupova, S. AU - Cortez, R. PY - 2005 DA - 2005// TI - A study of bacterial flagellar bundling JO - Bull Math Biol VL - 67 UR - https://doi.org/10.1016/j.bulm.2004.06.006 DO - 10.1016/j.bulm.2004.06.006 ID - Flores2005 ER - TY - JOUR AU - Cummins, B. AU - Gedeon, T. AU - Klapper, I. AU - Cortez, R. PY - 2007 DA - 2007// TI - Interaction between arthropod filiform hairs in a fluid environment JO - J Theor Biol VL - 247 UR - https://doi.org/10.1016/j.jtbi.2007.02.003 DO - 10.1016/j.jtbi.2007.02.003 ID - Cummins2007 ER - TY - JOUR AU - Nguyen, H. AU - Ortiz, R. AU - Cortez, R. AU - Fauci, L. PY - 2011 DA - 2011// TI - The action of waving cylindrical rings in a viscous fluid JO - J Fluid Mech VL - 671 UR - https://doi.org/10.1017/S0022112010006075 DO - 10.1017/S0022112010006075 ID - Nguyen2011 ER - TY - JOUR AU - Tlupova, S. AU - Cortez, R. PY - 2009 DA - 2009// TI - Boundary integral solutions of coupled stokes and darcy flows JO - J Comput Phys VL - 228 UR - https://doi.org/10.1016/j.jcp.2008.09.011 DO - 10.1016/j.jcp.2008.09.011 ID - Tlupova2009 ER - TY - JOUR AU - Yong, C. W. PY - 2015 DA - 2015// TI - Study of interactions between polymer nanoparticles and cell membranes at atomistic levels JO - Phil Trans R Soc B VL - 370 UR - https://doi.org/10.1098/rstb.2014.0036 DO - 10.1098/rstb.2014.0036 ID - Yong2015 ER - TY - JOUR AU - He, C. AU - Hu, Y. AU - Yin, L. AU - Tang, C. AU - Yin, C. PY - 2010 DA - 2010// TI - Effects of particle size and surface charge on cellular uptake and biodistribution of polymeric nanoparticles JO - Biomaterials VL - 31 UR - https://doi.org/10.1016/j.biomaterials.2010.01.065 DO - 10.1016/j.biomaterials.2010.01.065 ID - He2010 ER - TY - JOUR AU - Sasidharan, A. AU - Riviere, J. E. AU - Monteiro-Riviere, N. A. PY - 2015 DA - 2015// TI - Gold and silver nanoparticle interactions with human proteins: impact and implications in biocorona formation JO - J Mater Chem B VL - 3 UR - https://doi.org/10.1039/C4TB01926A DO - 10.1039/C4TB01926A ID - Sasidharan2015 ER - TY - JOUR AU - Cedervall, T. AU - Lynch, I. AU - Lindman, S. AU - Berggård, T. AU - Thulin, E. AU - Nilsson, H. AU - Dawson, K. A. AU - Linse, S. PY - 2007 DA - 2007// TI - Understanding the nanoparticle–protein corona using methods to quantify exchange rates and affinities of proteins for nanoparticles JO - Proc Natl Acad Sci VL - 104 UR - https://doi.org/10.1073/pnas.0608582104 DO - 10.1073/pnas.0608582104 ID - Cedervall2007 ER - TY - JOUR AU - Lundqvist, M. AU - Stigler, J. AU - Elia, G. AU - Lynch, I. AU - Cedervall, T. AU - Dawson, K. A. PY - 2008 DA - 2008// TI - Nanoparticle size and surface properties determine the protein corona with possible implications for biological impacts JO - Proc Natl Acad Sci VL - 105 UR - https://doi.org/10.1073/pnas.0805135105 DO - 10.1073/pnas.0805135105 ID - Lundqvist2008 ER - TY - JOUR AU - Sahneh, F. D. AU - Scoglio, C. AU - Riviere, J. PY - 2013 DA - 2013// TI - Dynamics of nanoparticle-protein corona complex formation: analytical results from population balance equations JO - PloS one VL - 8 UR - https://doi.org/10.1371/journal.pone.0064690 DO - 10.1371/journal.pone.0064690 ID - Sahneh2013 ER - TY - JOUR AU - Poon, Z. AU - Chen, S. AU - Engler, A. C. AU - Lee, H. -. i. AU - Atas, E. AU - von Maltzahn, G. AU - Bhatia, S. N. AU - Hammond, P. T. PY - 2010 DA - 2010// TI - Ligand-clustered “patchy” nanoparticles for modulated cellular uptake and in vivo tumor targeting JO - Angew Chem Int Ed VL - 49 UR - https://doi.org/10.1002/anie.201003445 DO - 10.1002/anie.201003445 ID - Poon2010 ER - TY - JOUR AU - Yang, P. H. AU - Sun, X. AU - Chiu, J. F. AU - Sun, H. AU - He, Q. Y. PY - 2005 DA - 2005// TI - Transferrin-mediated gold nanoparticle cellular uptake JO - Bioconjug Chem VL - 16 UR - https://doi.org/10.1021/bc049775d DO - 10.1021/bc049775d ID - Yang2005 ER - TY - JOUR AU - Barua, S. AU - Mitragotri, S. PY - 2013 DA - 2013// TI - Synergistic targeting of cell membrane, cytoplasm, and nucleus of cancer cells using rod-shaped nanoparticles JO - ACS Nano VL - 7 UR - https://doi.org/10.1021/nn403913k DO - 10.1021/nn403913k ID - Barua2013 ER - TY - JOUR AU - Petros, R. A. AU - DeSimone, J. M. PY - 2010 DA - 2010// TI - Strategies in the design of nanoparticles for therapeutic applications JO - Nat Rev Drug Discov VL - 9 UR - https://doi.org/10.1038/nrd2591 DO - 10.1038/nrd2591 ID - Petros2010 ER - TY - JOUR AU - Thurber, G. M. AU - Weissleder, R. PY - 2011 DA - 2011// TI - A systems approach for tumor pharmacokinetics JO - PloS One VL - 6 UR - https://doi.org/10.1371/journal.pone.0024696 DO - 10.1371/journal.pone.0024696 ID - Thurber2011 ER - TY - JOUR AU - Monine, M. I. AU - Haugh, J. M. PY - 2005 DA - 2005// TI - Reactions on cell membranes: Comparison of continuum theory and brownian dynamics simulations JO - J Chem Phys VL - 123 UR - https://doi.org/10.1063/1.2000236 DO - 10.1063/1.2000236 ID - Monine2005 ER - TY - JOUR AU - Kudgus, R. A. AU - Walden, C. A. AU - McGovern, R. M. AU - Reid, J. M. AU - Robertson, J. D. AU - Mukherjee, P. PY - 2014 DA - 2014// TI - Tuning pharmacokinetics and biodistribution of a targeted drug delivery system through incorporation of a passive targeting component JO - Sci Rep VL - 4 UR - https://doi.org/10.1038/srep05669 DO - 10.1038/srep05669 ID - Kudgus2014 ER - TY - JOUR AU - Lammers, T. AU - Kiessling, F. AU - Hennink, W. E. AU - Storm, G. PY - 2012 DA - 2012// TI - Drug targeting to tumors: principles, pitfalls and (pre-) clinical progress JO - J Control Release VL - 161 UR - https://doi.org/10.1016/j.jconrel.2011.09.063 DO - 10.1016/j.jconrel.2011.09.063 ID - Lammers2012 ER - TY - CHAP AU - Zaman, R. T. AU - Diagaradjane, P. AU - Krishnan, S. AU - Tunnell, J. W. PY - 2007 DA - 2007// TI - Measuring gold nanoparticle concentrations in tissue using diffuse optical spectroscopy BT - Lasers and Electro-Optics, 2007. CLEO 2007. Conference On PB - IEEE CY - New York ID - Zaman2007 ER - TY - JOUR AU - Sahneh, F. D. AU - Scoglio, C. M. AU - Monteiro-Riviere, N. A. AU - Riviere, J. E. PY - 2015 DA - 2015// TI - Predicting the impact of biocorona formation kinetics on interspecies extrapolations of nanoparticle biodistribution modeling JO - Nanomedicine VL - 10 UR - https://doi.org/10.2217/nnm.14.60 DO - 10.2217/nnm.14.60 ID - Sahneh2015 ER - TY - JOUR AU - Hossain, S. S. AU - Hossainy, S. F. AU - Bazilevs, Y. AU - Calo, V. M. AU - Hughes, T. J. PY - 2012 DA - 2012// TI - Mathematical modeling of coupled drug and drug-encapsulated nanoparticle transport in patient-specific coronary artery walls JO - Comput Mech VL - 49 UR - https://doi.org/10.1007/s00466-011-0633-2 DO - 10.1007/s00466-011-0633-2 ID - Hossain2012 ER - TY - JOUR AU - Wang, Y. AU - Kim, J. H. AU - Baek, J. B. AU - Miller, G. W. AU - Pennell, K. D. PY - 2012 DA - 2012// TI - Transport behavior of functionalized multi-wall carbon nanotubes in water-saturated quartz sand as a function of tube length JO - Water Res VL - 46 UR - https://doi.org/10.1016/j.watres.2012.05.036 DO - 10.1016/j.watres.2012.05.036 ID - Wang2012 ER - TY - JOUR AU - Wang, Y. AU - Li, Y. AU - Fortner, J. D. AU - Hughes, J. B. AU - Abriola, L. M. AU - Pennell, K. D. PY - 2008 DA - 2008// TI - Transport and retention of nanoscale c60 aggregates in water-saturated porous media JO - Environ Sci Technol VL - 42 UR - https://doi.org/10.1021/es800128m DO - 10.1021/es800128m ID - Wang2008 ER - TY - JOUR AU - Goldberg, E. AU - Scheringer, M. AU - Bucheli, T. D. AU - Hungerbuhler, K. PY - 2014 DA - 2014// TI - Critical assessment of models for transport of engineered nanoparticles in saturated porous media JO - Environ Sci Technol VL - 48 UR - https://doi.org/10.1021/es502044k DO - 10.1021/es502044k ID - Goldberg2014 ER - TY - CHAP AU - Faeder, J. R. AU - Blinov, M. L. AU - Hlavacek, W. S. PY - 2009 DA - 2009// TI - Rule-based modeling of biochemical systems with bionetgen BT - Systems Biology PB - Springer CY - New York ID - Faeder2009 ER - TY - CHAP AU - Danos, V. AU - Feret, J. AU - Fontana, W. AU - Harmer, R. AU - Krivine, J. PY - 2007 DA - 2007// TI - Rule-based modelling of cellular signalling BT - CONCUR 2007–Concurrency Theory PB - Springer CY - Berlin Heidelberg ID - Danos2007 ER - TY - JOUR AU - Blinov, M. L. AU - Faeder, J. R. AU - Goldstein, B. AU - Hlavacek, W. S. PY - 2004 DA - 2004// TI - Bionetgen: software for rule-based modeling of signal transduction based on the interactions of molecular domains JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/bth378 DO - 10.1093/bioinformatics/bth378 ID - Blinov2004 ER - TY - JOUR AU - Barua, D. AU - Faeder, J. R. AU - Haugh, J. M. PY - 2007 DA - 2007// TI - Structure-based kinetic models of modular signaling protein function: focus on shp2 JO - Biophys J VL - 92 UR - https://doi.org/10.1529/biophysj.106.093484 DO - 10.1529/biophysj.106.093484 ID - Barua2007 ER - TY - JOUR AU - Barua, D. AU - Hlavacek, W. S. AU - Lipniacki, T. PY - 2012 DA - 2012// TI - A computational model for early events in b cell antigen receptor signaling: analysis of the roles of lyn and fyn JO - J Immunol VL - 189 UR - https://doi.org/10.4049/jimmunol.1102003 DO - 10.4049/jimmunol.1102003 ID - Barua2012 ER - TY - JOUR AU - Sorokina, O. AU - Sorokin, A. AU - Armstrong, J. D. AU - Danos, V. PY - 2013 DA - 2013// TI - A simulator for spatially extended kappa models JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/btt523 DO - 10.1093/bioinformatics/btt523 ID - Sorokina2013 ER - TY - JOUR AU - Meier-Schellersheim, M. AU - Xu, X. AU - Angermann, B. AU - Kunkel, E. J. AU - Jin, T. AU - Germain, R. N. PY - 2006 DA - 2006// TI - Key role of local regulation in chemosensing revealed by a new molecular interaction-based modeling method JO - PLoS Comput Biol VL - 2 UR - https://doi.org/10.1371/journal.pcbi.0020082 DO - 10.1371/journal.pcbi.0020082 ID - Meier-Schellersheim2006 ER - TY - JOUR AU - Andrews, S. S. PY - 2017 DA - 2017// TI - Smoldyn: particle-based simulation with rule-based modeling, improved molecular interaction and a library interface JO - Bioinformatics VL - 33 UR - https://doi.org/10.1093/bioinformatics/btw700 DO - 10.1093/bioinformatics/btw700 ID - Andrews2017 ER - TY - JOUR AU - Perilla, J. R. AU - Goh, B. C. AU - Cassidy, C. K. AU - Liu, B. AU - Bernardi, R. C. AU - Rudack, T. AU - Yu, H. AU - Wu, Z. AU - Schulten, K. PY - 2015 DA - 2015// TI - Molecular dynamics simulations of large macromolecular complexes JO - Curr Opin Struct Biol VL - 31 UR - https://doi.org/10.1016/j.sbi.2015.03.007 DO - 10.1016/j.sbi.2015.03.007 ID - Perilla2015 ER -