references.bib

% =============================================================================
% References for VEM biofilm paper
% =============================================================================

% --- Machine learning ---
@inproceedings{Ronneberger2015,
  author    = {Ronneberger, O. and Fischer, P. and Brox, T.},
  title     = {U-Net: Convolutional Networks for Biomedical Image Segmentation},
  booktitle = {Medical Image Computing and Computer-Assisted Intervention (MICCAI)},
  series    = {LNCS},
  volume    = {9351},
  pages     = {234--241},
  year      = {2015},
  doi       = {10.1007/978-3-319-24574-4_28},
}

% --- VEM foundational ---
@article{BeiraodaVeiga2013,
  author  = {Beir{\~a}o da Veiga, L. and Brezzi, F. and Cangiani, A. and
             Manzini, G. and Marini, L. D. and Russo, A.},
  title   = {Basic principles of virtual element methods},
  journal = {Mathematical Models and Methods in Applied Sciences},
  volume  = {23},
  number  = {01},
  pages   = {199--214},
  year    = {2013},
  doi     = {10.1142/S0218202512500492},
}

@article{BeiraodaVeiga2014,
  author  = {Beir{\~a}o da Veiga, L. and Brezzi, F. and Marini, L. D. and Russo, A.},
  title   = {The hitchhiker's guide to the virtual element method},
  journal = {Mathematical Models and Methods in Applied Sciences},
  volume  = {24},
  number  = {08},
  pages   = {1541--1573},
  year    = {2014},
  doi     = {10.1142/S021820251440003X},
}

@article{Sutton2017,
  author  = {Sutton, O. J.},
  title   = {The virtual element method in 50 lines of {MATLAB}},
  journal = {Numerical Algorithms},
  volume  = {75},
  pages   = {1141--1159},
  year    = {2017},
  doi     = {10.1007/s11075-016-0235-3},
}

@article{Gain2014,
  author  = {Gain, A. L. and Talischi, C. and Paulino, G. H.},
  title   = {On the virtual element method for three-dimensional linear
             elasticity problems on arbitrary polyhedral meshes},
  journal = {Computer Methods in Applied Mechanics and Engineering},
  volume  = {282},
  pages   = {132--160},
  year    = {2014},
  doi     = {10.1016/j.cma.2014.05.005},
}

@article{Chi2017,
  author  = {Chi, H. and Beir{\~a}o da Veiga, L. and Paulino, G. H.},
  title   = {Some basic formulations of the virtual element method ({VEM})
             for finite deformations},
  journal = {Computer Methods in Applied Mechanics and Engineering},
  volume  = {318},
  pages   = {148--192},
  year    = {2017},
  doi     = {10.1016/j.cma.2016.12.020},
}

@article{Antonietti2022,
  author  = {Antonietti, P. F. and Manzini, G. and Scacchi, S. and Verani, M.},
  title   = {A review on arbitrarily regular conforming virtual element methods
             for second- and higher-order elliptic partial differential equations},
  journal = {Mathematical Models and Methods in Applied Sciences},
  volume  = {31},
  number  = {14},
  pages   = {2825--2853},
  year    = {2021},
  doi     = {10.1142/S0218202521500627},
}

% --- VEM nonlinear / fracture (IKM Hannover) ---
@article{Wriggers2019,
  author  = {Wriggers, P. and Hudobivnik, B.},
  title   = {A low order virtual element formulation for finite
             elasto-plastic deformations},
  journal = {Computer Methods in Applied Mechanics and Engineering},
  volume  = {327},
  pages   = {459--477},
  year    = {2017},
  doi     = {10.1016/j.cma.2017.08.053},
}

@book{Wriggers2024,
  author    = {Wriggers, P. and Aldakheel, F. and Hudobivnik, B.},
  title     = {Virtual Element Methods in Engineering Sciences},
  publisher = {Springer},
  address   = {Cham},
  year      = {2024},
  doi       = {10.1007/978-3-031-39255-9},
}

@article{Aldakheel2018,
  author  = {Aldakheel, F. and Hudobivnik, B. and Hussein, A. and Wriggers, P.},
  title   = {Phase-field modeling of brittle fracture using an efficient
             virtual element scheme},
  journal = {Computer Methods in Applied Mechanics and Engineering},
  volume  = {341},
  pages   = {443--466},
  year    = {2018},
  doi     = {10.1016/j.cma.2018.07.008},
}

@article{Artioli2017,
  author  = {Artioli, E. and Beir{\~a}o da Veiga, L. and Lovadina, C. and Sacco, E.},
  title   = {Arbitrary order 2{D} virtual elements for polygonal meshes:
             {P}art {II}, inelastic problem},
  journal = {Computational Mechanics},
  volume  = {60},
  pages   = {643--657},
  year    = {2017},
  doi     = {10.1007/s00466-017-1429-9},
}

% --- Viscoelastic mechanics ---
@article{Simo1987,
  author  = {Simo, J. C.},
  title   = {On a fully three-dimensional finite-strain viscoelastic damage
             model: formulation and computational aspects},
  journal = {Computer Methods in Applied Mechanics and Engineering},
  volume  = {60},
  number  = {2},
  pages   = {153--173},
  year    = {1987},
  doi     = {10.1016/0045-7825(87)90107-1},
}

@book{SimoHughes1998,
  author    = {Simo, J. C. and Hughes, T. J. R.},
  title     = {Computational Inelasticity},
  publisher = {Springer},
  address   = {New York},
  year      = {1998},
  doi       = {10.1007/b98904},
}

% --- Phase-field fracture ---
@article{Miehe2010,
  author  = {Miehe, C. and Hofacker, M. and Welschinger, F.},
  title   = {A phase field model for rate-independent crack propagation:
             robust algorithmic implementation based on operator splits},
  journal = {Computer Methods in Applied Mechanics and Engineering},
  volume  = {199},
  number  = {45--48},
  pages   = {2765--2778},
  year    = {2010},
  doi     = {10.1016/j.cma.2010.04.011},
}

@article{Bourdin2000,
  author  = {Bourdin, B. and Francfort, G. A. and Marigo, J.-J.},
  title   = {Numerical experiments in revisited brittle fracture},
  journal = {Journal of the Mechanics and Physics of Solids},
  volume  = {48},
  number  = {4},
  pages   = {797--826},
  year    = {2000},
  doi     = {10.1016/S0022-5096(99)00028-9},
}

% --- Cohesive zone ---
@article{Park2009,
  author  = {Park, K. and Paulino, G. H. and Roesler, J. R.},
  title   = {A unified potential-based cohesive model of mixed-mode fracture},
  journal = {Journal of the Mechanics and Physics of Solids},
  volume  = {57},
  number  = {6},
  pages   = {891--908},
  year    = {2009},
  doi     = {10.1016/j.jmps.2008.10.003},
}

% --- Biofilm mechanics ---
@article{Pattem2018,
  author  = {Pattem, J. and Daood, U. and Yiu, C. K. Y. and Hedge, J. and
             Nazar, A. S. A. and Halib, N. and Ho, T. C. S. and Malik, S. N.},
  title   = {Mechanical and nanomechanical properties of oral biofilms
             developing on clinical and novel dental restorative materials},
  journal = {Scientific Reports},
  volume  = {8},
  pages   = {3638},
  year    = {2018},
  doi     = {10.1038/s41598-018-21318-3},
}

@article{Pattem2021,
  author  = {Pattem, J. and Daood, U. and Yiu, C. K. Y.},
  title   = {Nano-mechanical properties of oral biofilms},
  journal = {Scientific Reports},
  volume  = {11},
  pages   = {17162},
  year    = {2021},
  doi     = {10.1038/s41598-021-96340-3},
}

@article{Peterson2015,
  author  = {Peterson, B. W. and He, Y. and Ren, Y. and Zerdoum, A. and
             Libber, M. R. and Sharma, P. K. and van Winkelhoff, A. J. and
             Rinastiti, M. and Aarnisalo, A. A. and Luo, T. J. M. and
             Zuo, F. and Zhang, L. and Fang, C. and van der Mei, H. C. and
             Busscher, H. J.},
  title   = {Viscoelasticity of biofilms and their recalcitrance to
             mechanical and chemical challenges},
  journal = {FEMS Microbiology Reviews},
  volume  = {39},
  number  = {2},
  pages   = {234--245},
  year    = {2015},
  doi     = {10.1093/femsre/fuu008},
}

@article{Flemming2010,
  author  = {Flemming, H.-C. and Wingender, J.},
  title   = {The biofilm matrix},
  journal = {Nature Reviews Microbiology},
  volume  = {8},
  pages   = {623--633},
  year    = {2010},
  doi     = {10.1038/nrmicro2415},
}

@article{Gloag2020a,
  author  = {Gloag, E. S. and Fabbri, S. and Wozniak, D. J. and Stoodley, P.},
  title   = {Biofilm mechanics: implications in infection and survival},
  journal = {Biofilm},
  volume  = {2},
  pages   = {100017},
  year    = {2020},
  doi     = {10.1016/j.bioflm.2019.100017},
}

@article{Gloag2020b,
  author  = {Gloag, E. S. and Wozniak, D. J. and Stoodley, P. and
             Hall-Stoodley, L.},
  title   = {A micro-rheological perspective of biofilm mechanics},
  journal = {Journal of Bacteriology},
  volume  = {202},
  number  = {17},
  pages   = {e00764-19},
  year    = {2020},
  doi     = {10.1128/JB.00764-19},
}

@article{Stoodley1999,
  author  = {Stoodley, P. and Lewandowski, Z. and Boyle, J. D. and Lappin-Scott, H. M.},
  title   = {Structural deformation of bacterial biofilms caused by
             short-term fluctuations in fluid shear: an in situ investigation
             of biofilm rheology},
  journal = {Biotechnology and Bioengineering},
  volume  = {65},
  number  = {1},
  pages   = {83--92},
  year    = {1999},
  doi     = {10.1002/(SICI)1097-0290(19991005)65:1<83::AID-BIT10>3.0.CO;2-B},
}

@article{Klempt2024,
  author  = {Klempt, C. and Soleimani, M. and Wriggers, P. and Junker, P.},
  title   = {A {H}amilton principle-based model for diffusion-driven
             biofilm growth},
  journal = {Biomechanics and Modeling in Mechanobiology},
  volume  = {23},
  pages   = {2091--2113},
  year    = {2024},
  doi     = {10.1007/s10237-024-01883-x},
}

@article{Heine2025,
  author  = {Heine, N. and Bittroff, K. and Szafra{\'n}ski, S. P. and
             Duitscher, M. and Behrens, W. and Vollmer, C. and
             Mikolai, C. and Kommerein, N. and Debener, N. and
             Frings, K. and Heisterkamp, A. and Scheper, T. and
             Torres-Mapa, M. L. and Bahnemann, J. and Stiesch, M. and
             Doll-Nikutta, K.},
  title   = {Influence of species composition and cultivation condition
             on peri-implant biofilm dysbiosis in vitro},
  journal = {Frontiers in Oral Health},
  volume  = {6},
  pages   = {1649419},
  year    = {2025},
  doi     = {10.3389/froh.2025.1649419},
}

@article{Laspidou2014,
  author  = {Laspidou, C. S. and Aravas, N.},
  title   = {Variation in the mechanical properties of a porous multi-phase
             biofilm under compression due to void closure},
  journal = {Water Science and Technology},
  volume  = {69},
  number  = {7},
  pages   = {1504--1512},
  year    = {2014},
  doi     = {10.2166/wst.2014.054},
}

@article{Ohashi2009,
  author  = {Ohashi, A. and Harada, H.},
  title   = {Adhesion strength of biofilm developed in an attached-growth reactor},
  journal = {Water Science and Technology},
  volume  = {36},
  number  = {1},
  pages   = {17--23},
  year    = {1997},
  doi     = {10.1016/S0273-1223(97)00325-9},
}

% --- Percolation theory ---
@book{Sahimi1994,
  author    = {Sahimi, M.},
  title     = {Applications of Percolation Theory},
  publisher = {Taylor \& Francis},
  address   = {London},
  year      = {1994},
}

@article{Arbabi1993,
  author  = {Arbabi, S. and Sahimi, M.},
  title   = {Mechanics of disordered solids. {I}. {P}ercolation on elastic
             networks with central forces},
  journal = {Physical Review B},
  volume  = {47},
  number  = {2},
  pages   = {695--702},
  year    = {1993},
  doi     = {10.1103/PhysRevB.47.695},
}

% --- Real confocal datasets ---
@article{MorilloLopez2022,
  author  = {Morillo-Lopez, V. and Strber, A. and Hedlund, T. and
             Drescher, K. and Mark Welch, J. L.},
  title   = {Corncob structures in dental plaque reveal microhabitat
             taxon specificity},
  journal = {Microbiome},
  volume  = {10},
  pages   = {187},
  year    = {2022},
  doi     = {10.1186/s40168-022-01323-x},
}

@article{Shi2020,
  author  = {Shi, H. and Shi, Q. and Grodner, B. and Lenz, J. S. and
             Lai, W. K. and Shortridge, M. D. and Vaiana, C. A. and
             Mohanty, S. and Behura, S. K. and Marks, D. S. and
             DeLisa, M. P. and De Vlaminck, I.},
  title   = {Highly multiplexed spatial mapping of microbial
             communities},
  journal = {Nature},
  volume  = {588},
  pages   = {676--681},
  year    = {2020},
  doi     = {10.1038/s41586-020-2983-4},
}

@article{NguyenThanh2018,
  author  = {Nguyen-Thanh, V. M. and Zhuang, X. and Nguyen-Xuan, H. and
             Rabczuk, T. and Wriggers, P.},
  title   = {A virtual element method for {2D} linear elastic fracture analysis},
  journal = {Computer Methods in Applied Mechanics and Engineering},
  volume  = {340},
  pages   = {366--395},
  year    = {2018},
  doi     = {10.1016/j.cma.2018.05.021},
}