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A review of models in bioengineering developed by the group led by Miloš Kojić in the period 2006-2016
Bioengineering Research and Development Center - BioIRC, Kragujevac + Methodist Hospital Research Institute, Hjuston, SAD

emailmkojic42@gmail.com
Keywords: FE models in bioengineering; tissue; muscles; transport in capillaries and tissue multiscale; underground water flow; FE package PAK
Abstract
A brief summary of results in the period 2006-2016 of the group led by Milos Kojic is given in this report. Three fields are included: general bioengineering problems, models for transport in capillary systems and tissue, and modeling of underground water flow. This research has been published in books, journal papers and conference proceedings. The research has been supported by various grants, national (Ministry of Education, Science and Technological Development of Serbia) and international, and industry. The computational models have been implemented into our software PAK.
References
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Filipovic, N., Haber, S., Kojic, M., Tsuda, A. (2008) Dissipative particle dynamics simulation of flow generated by two rotating concentric cylinders: II. Lateral dissipative and random forces. Journal of Physics D: Applied Physics, 41(3): 035504
Filipovic, N., Isailović, V., Đukić, T., Ferrari, M., Kojic, M. (2012) Multiscale Modeling of Circular and Elliptical Particles in Laminar Shear Flow. IEEE Transactions on Biomedical Engineering, 59(1): 50-53
Filipovic, N. (2009) Computer simulation of flow and mixing at the duodenal stump after gastric resection. World Journal of Gastroenterology, 15(16): 1990
Filipovic, N., Kojic, M., Ferrari, M. (2010) Dissipative particle dynamics simulation of circular and elliptical particles motion in 2D laminar shear flow. Microfluidics and Nanofluidics, 10(5): 1127-1134
Filipovic, N., Kojic, M., Ferrari, M. (2011) Dissipative particle dynamics simulation of circular and elliptical particles motion in 2D laminar shear flow. Microfluidics and Nanofluidics, 10(5): 1127-1134
Filipovic, N., Ivanovic, M., Kojic, M. (2008) A comparative numerical study between dissipative particle dynamics and smoothed particle hydrodynamics when applied to simple unsteady flows in microfluidics. Microfluidics and Nanofluidics, 7(2): 227-235
Filipovic, N.D., Ivanovic, M.R., Krstajic, D., Kojic, M.R. (2011) Hemodynamic Flow Modeling Through an Abdominal Aorta Aneurysm Using Data Mining Tools. IEEE Transactions On Information Technology in Biomedicine, vol. 15, br. 2, str. 189-194
Filipović, N., Jovanović, A., Petrović, D., Obradović, M., Jovanović, S., Balos, D., Kojić, M. (2012) Modelling of self-healing materials using discrete and continuum methods. Surface Coatings International, Vol. 95; No. 2; pp. 74-79; 1754-0925
Filipović, N., Petrović, D., Isailović, V., Jovanović, A., Kojić, M. (2010) Modeling of self-healing process in new nanocoating of surfaces by material with containers filled with healing agents. Contemporary Materials, 1(2): 129-132
Filipović, N., Petrović, D., Jovanović, A., Jovanović, S., Balos, D., Kojić, M. (2008) DPD simulation of self-healing process of nanocoating. Journal of Serbian Society for Computational Mechanics, vol. 2, br. 2, str. 42-50
Filipović, N., Petrović, D., Obradović, M., Jovanović, A., Jovanović, S., Baloš, D., Kojić, M. (2011) Modeling of self-healing materials using nanocontainers. Contemporary Materials, 2(1): 18-26
Filipović, N., Radović, M., Isailović, V., Milošević, Z., Nikolić, D., Saveljić, I., Milošević, M., Petrović, D., Obradović, M., Krsmanović, D., Themis, E., Sakellarios, A., Siogkas, P., Marraccini, P., Vozzi, F., Meunier, N., Teng, Z., Fotiadis, D., Parodi, O., Kojić, M. (2012) Plaque formation and stent deployment with heating thermal effects in arteries. JSSCM, Vol. 6(1), pp. 11-28, Special Issue
Filipović, N., Kojić, M., Tsuda, A. (2008) Modeling of thrombosis using dissipative particle method. Phylosoph. Trans. Roy. Soc. London, A 366(1879)
Filipović, N., Rosić, M., Isailović, V., Milošević, Ž., Nikolić, D., Milašinović, D., Radović, M., Stojanović, B., Ivanović, M., Tanasković, I., Saveljić, I., Milošević, M., Petrović, D., Obradović, M., Themis, E. (2011) ARTREAT project: Computer, experimental and clinical analysis of threedimensional plaque formation and progression in arteries. Journal of Serbian Society for Computational Mechanics, vol. 5, br. 2, str. 129-146
Fine, D., Grattoni, A., Hosali, S., Ziemys, A., de Rosa, E., Gill, J., Medema, R., Hudson, L., Kojic, M., Milosevic, M., III, L.B., Goodall, R., Ferrari, M., Liu, X. (2010) A robust nanofluidic membrane with tunable zero-order release for implantable dose specific drug delivery. Lab on a Chip, 10(22): 3074
Isailović, V. (2012) Numerical modeling of motion of cells, micro and nano particles in blood vessels. Belgrade: Metropolitan University, Ph. D. Thesis
Isailović, V., Kojić, M., Milošević, M., Filipović, N., Kojić, N., Ziemys, A., Ferrari, M. (2014) A computational study of trajectories of micro- and nano-particles with different shapes in flow through small channels. Journal of Serbian Society for Computational Mechanics, vol. 8, br. 2, str. 14-28
Kojic, M., Butler, J.P., Vlastelica, I., Stojanovic, B., Rankovic, V., Tsuda, A. (2011) Geometric Hysteresis of Alveolated Ductal Architecture. Journal of Biomechanical Engineering, 133(11): 111005
Kojic, M., Milosevic, M., Kojic, N., Koay, E.J., Fleming, J.B., Ferrari, M., Ziemys, A. (2016) Mass release curves as the constitutive curves for modeling diffusive transport within biological tissue. Computers in Biology and Medicine
Kojic, M., Milosevic, M., Kojic, N., Kim, K., Ferrari, M., Ziemys, A. (2014) A multiscale MD–FE model of diffusion in composite media with internal surface interaction based on numerical homogenization procedure. Computer Methods in Applied Mechanics and Engineering, 269: 123-138
Kojic, M., Milosevic, M., Kojic, N., Starosolski, Z., Ghaghada, K., Serda, R., Annapragada, A., Ferrari, M., Ziemys, A. (2015) A multi-scale FE model for convective–diffusive drug transport within tumor and large vascular networks. Computer Methods in Applied Mechanics and Engineering, 294: 100-122
Kojic, M., Vlastelica, I., Decuzzi, P., Granik, V.T., Ferrari, M. (2011) A finite element formulation for the doublet mechanics modeling of microstructural materials. Computer Methods in Applied Mechanics and Engineering, 200(13-16): 1446-1454
Kojic, M., Vlastelica, I., Stojanovic, B., Rankovic, V., Tsuda, A. (2006) Stress integration procedures for a biaxial isotropic material model of biological membranes and for hysteretic models of muscle fibres and surfactant. International Journal for Numerical Methods in Engineering, 68(8): 893-909
Kojic, M., Milosevic, M., Kojic, N., Isailovic, V., Petrovic, D., Filipovic, N., Ferrari, M., Ziemys, A. (2014) Transport Phenomena: Computational Models for Convective and Diffusive Transport in Capillaries and Tissue. in: Suvranu De, Wonmuk Hwang, Ellen Kuhl [ed.] Multiscale Modeling in Biomechanics and Mechanobiology, str. 131-156
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Kojić, M., Milošević, M., Simić, V., Ferrari, M. (2014) A 1D pipe finite element with rigid and deformable walls. Journal of Serbian Society for Computational Mechanics, vol. 8, br. 2, str. 38-53
Kojić, M., Milošević, M., Wu, S., Blanco, E., Ferrari, M., Ziemys, A. (2015) Mass partitioning effects in diffusion transport. Physical Chemistry Chemical Physics
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Kojić, M., Isailović, V., Stojanović, B., Filipović, N. (2007) Modeling of cell mechanical response by biphasic models with activation. Journal of Serbian Society for Computational Mechanics, vol. 1, br. 1, str. 135-143
Kojić, M., Milošević, M., Kojić, N., Ferrari, M., Ziemys, A. (2011) On diffusion in nanospace. Journal of Serbian Society for Computational Mechanics, vol. 5, br. 1, str. 89-103
Kojić, M., Milošević, M., Kojić, N., Ferrari, M., Ziemys, A. (2013) Numerical modeling of diffusion in complex media with surface interaction effects. Contemporary Materials, 2(3)
Kojić, M., Filipović, N., Stojanović, B., Ranković, V., Krstić, M., Otašević, L., Ivanović, M., Nedeljković, M., Dimkić, M., Tričković, M., Pušić, M., Boreli-Zdravković, Đ., Đurić, D. (2007) Finite element modeling of underground water flow with Ranney wells. Water Science & Technology: Water Supply, 7(3): 41
Kojić, M., Filipović, N. (2013) Computational mechanics in science, applications and teaching. Theoretical and Applied Mechanics, vol. 40, br. 1, str. 147-162
Kojić, M. (2015) Mixed formulation for incompressible solid in the finite element method, with application to motion of solid within fluid: Reports of the Department of Technical Sciences of the Serbian Academy of Sciences and Arts
Kojić, M. (2010) On the stress integration for nonlinear material models within the finite element method. Bulletin CXLII de l'Académie serbe des sciences et des arts Classe des sciences techniques, 47-82; 32
Kojić, M. (2013) Simple concepts in computational mechanics: Do they really work?. Journal of Serbian Society for Computational Mechanics, vol. 7, br. 1, str. 1-16
Kojić, M., Filipović, N., Stojanović, B., Kojić, N. (2008) Computer Modeling in Bioengineering: Theoretical background, examples and software. Chichester: John Wiley & Sons
Kojić, M., Ziemys, A., Milošević, M., Isailović, V., Kojić, N., Rosić, M., Filipović, N., Ferrari, M. (2011) Transport in biological systems. Journal of Serbian Society for Computational Mechanics, vol. 5, br. 2, str. 101-128
Kojić, N., Huang, A., Chung, E., Ivanović, M., Filipović, N., Kojić, M., Tschumperlin, D.J. (2010) A 3-D Model of Ligand Transport in a Deforming Extracellular Space. Biophysical Journal, 99(11): 3517-3525
Kojić, N., Milošević, M., Petrović, D., Isailović, V., Sarioglu, A. F., Haber, D.A., Kojić, M., Toner, M. (2015) A computational study of circulating large tumor cells traversing microvessels. Computers in Biology and Medicine, 63: 187-195
Mahadevan, T., Kojic, M., Ferrari, M., Ziemys, A. (2013) Mechanisms of reduced solute diffusivity at nanoconfined solid–liquid interface. Chemical Physics, 421: 15-21
Mahadevan, T.S., Milosevic, M., Kojic, M., Hussain, F., Kojic, N., Serda, R., Ferrari, M., Ziemys, A. (2013) Diffusion transport of nanoparticles at nanochannel boundaries. Journal of Nanoparticle Research, 15(3): 1477-1487
Martinez, J.O., Chiappini, C., Ziemys, A., Faust, A.M., Kojic, M., Liu, X., Ferrari, M., Tasciotti, E. (2013) Engineering multi-stage nanovectors for controlled degradation and tunable release kinetics. Biomaterials, 34(33): 8469-8477
Mijailovich, S.M., Kojic, M., Tsuda, A. (2010) Particle-induced indentation of the alveolar epithelium caused by surface tension forces. Journal of Applied Physiology, 109(4): 1179-94
Mijailovich, S.M., Stojanovic, B., Kojic, M., Liang, A., Wedeen, van J., Gilbert, R.J. (2010) Derivation of a finite-element model of lingual deformation during swallowing from the mechanics of mesoscale myofiber tracts obtained by MRI. Journal of Applied Physiology, 109(5): 1500-14
Miljković, O., Ivanović, M., Filipović, N., Kojić, M. (2008) Ai models of the hemodynamic simulation. Journal of Serbian Society for Computational Mechanics, vol. 2, br. 2, str. 59-72
Norvaisas, P., Kojić, M., Milošević, M., Ziemys, A. (2015) Prediction and Analysis of Drug Delivery Systems: From Drug-Vector Compatibility to Release Kinetics. CRS_Newsletter, 09, 30,14-15
Rakić, D., Živković, M., Slavković, R., Kojić, M. (2008) Stress integration for the Drucker-Prager material model without hardening using the incremental plasticity theory. Journal of Serbian Society for Computational Mechanics, vol. 2, br. 1, str. 80-89
Ranković, V., Ristić, B., Kojić, M. (2007) Internal fixation of femoral bone comminuted fracture: FE analysis. Journal of Serbian Society for Computational Mechanics, vol. 1, br. 1, str. 120-128
Rosic, M.A., Pantovic, S.B., Rankovic, V., Obradovic, Z., Filipovic, N.D., Kojic, M.R. (2008) Evaluation of dynamic response and biomechanical properties of isolated blood vessels. Journal of biochemical and biophysical methods, vol. 70, br. 6, str. 966-972
Ruiz-Esparza, G.U., Wu, S., Segura-Ibarra, V., Cara, F.E., Evans, K.W., Milosevic, M., Ziemys, A., Kojic, M., Meric-Bernstam, F., Ferrari, M., Blanco, E. (2014) Polymer Nanoparticles Encased in a Cyclodextrin Complex Shell for Potential Site- and Sequence-Specific Drug Release. Advanced Functional Materials, 24(30): 4753-4761
Stamenović, D., Kojić, M., Stojanović, B., Hunter, D. (2009) Pneumatic Osteoarthritis Knee Brace. Journal of Biomechanical Engineering, 131(4): 045001
Stamenović, D., Kojić, M., Stojanović, B., Hunter, D. (2008) A finite element analysis of an osteoarthritis knee brace. Journal of Serbian Society for Computational Mechanics, vol. 2, br. 2, str. 29-41
Stojanović, B., Kojić, M. (2007) Modeling of musculoskeletal systems using finite element method. Journal of Serbian Society for Computational Mechanics, vol. 1, br. 1, str. 110-119
Stojanović, B., Kojić, M., Rosić, M., Tsui, C.P., Tang, C.Y. (2007) An extension of Hill's three-component model to include different fibre types in finite element modelling of muscle. International Journal for Numerical Methods in Engineering, 71(7): 801
Tang, C.Y., Tsui, C.P., Stojanovic, B., Kojic, M. (2007) Finite element modelling of skeletal muscles coupled with fatigue. International Journal of Mechanical Sciences, 49(10): 1179-1191
Veljković, D., Ranković, V., Pantović, S., Rosić, M., Kojić, M. (2014) Hyperelastic behavior of porcine aorta segment under extension-inflation tests fitted with various phenomenological models. Acta of Bioengineering and Biomechanics, Vol. 16, No. 3, pp. 37-45
Veljković, D., Kojić, M. (2010) Prediction of planar uniaxial and constrained biaxial state of deformation by commonly used anisotropic constitutive models in arterial mechanics. Journal of Serbian Society for Computational Mechanics, vol. 4, br. 2, str. 54-74
Veljković, D., Filipović, N., Kojić, M. (2012) The effect of asymmetry and axial prestraining on the amplitude of mechanical stresses in abdominal aortic aneurysm. Journal of Mechanics in Medicine and Biology, 12(05): 1250089
Vlastelica, I., Isailović, V., Đukić, T., Filipović, N., Kojić, M. (2008) On accuracy of the Element-free Galerkin (EFG) method in modeling incompressible fluid flow. Journal of Serbian Society for Computational Mechanics, vol. 2, br. 1, str. 90-99
Vlastelica, I., Veljković, D., Ranković, V., Stojanović, B., Rosić, M., Kojić, M. (2007) Modeling of urinary bladder deformation within passive and active regimes. Journal of Serbian Society for Computational Mechanics, vol. 1, br. 1, str. 129-134
Wilson, T.A. (1982) Surface Tension: Surface Area Curves Calculated from Pressure: Volume Loops. J. Appl. Physiol. Respir. Environ. Exercise. Physiol, 53(6), pp. 1512-1520
Yazdi, I.K., Ziemys, A., Evangelopoulos, M., Martinez, J.O., Kojic, M., Tasciotti, E. (2015) Physicochemical properties affect the synthesis, controlled delivery, degradation and pharmacokinetics of inorganic nanoporous materials. Nanomedicine, 10(19): 3057-3075
Yokoi, K., Kojic, M., Milosevic, M., Tanei, T., Ferrari, M., Ziemys, A. (2014) Capillary-Wall Collagen as a Biophysical Marker of Nanotherapeutic Permeability into the Tumor Microenvironment. Cancer Research, 74(16): 4239-4246
Yokoi, K., Chan, D., Kojic, M., Milosevic, M., Engler, D., Matsunami, R., Tanei, T., Saito, Y., Ferrari, M., Ziemys, A. (2015) Liposomal doxorubicin extravasation controlled by phenotype-specific transport properties of tumor microenvironment and vascular barrier. Journal of Controlled Release, 217: 293-299
Ziemys, A., Filipovic, N., Ferrari, M., Kojic, M. (2013) Transport in Nanoconfinement and Within Blood Vessel Wall. in: M. Garbey, B. Lee Bass, S. Berceli, C. Collet, and P. Cerveri [ed.] Computational Surgery and Dual Training, str. 273-288
Ziemys, A., Klemm, S., Milosevic, M., Yokoi, K., Ferrari, M., Kojic, M. (2015) Computational analysis of drug transport in tumor microenvironment as a critical compartment for nanotherapeutic pharmacokinetics. Drug Delivery, DOI: O.3109/10717544.2015.1022837
Ziemys, A., Kojic, M., Milosevic, M., Ferrari, M. (2012) Interfacial Effects on Nanoconfined Diffusive Mass Transport Regimes. Physical Review Letters, 108(23)
Ziemys, A., Kojic, M., Milošević, M., Kojić, N., Hussain, F., Ferrari, M., Grattoni, A. (2011) Hierarchical modeling of diffusive transport through nanochannels by coupling molecular dynamics with finite element method. Journal of Computational Physics, 230(14): 5722-5731
Ziemys, A., Kojic, M., Ferrari, M. (2015) Physics-based multiscale mass transport model in drug delivery and tumor microenvironment. in: Handbook of Mathematical Methods in Cancer Biology, NCI
 

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article language: English
document type: unclassified
DOI: 10.5937/jsscm1601005K
published in SCIndeks: 25/03/2017

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