{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,16]],"date-time":"2026-05-16T23:33:39Z","timestamp":1778974419870,"version":"3.51.4"},"reference-count":49,"publisher":"SAGE Publications","issue":"3-4","license":[{"start":{"date-parts":[[2022,1,7]],"date-time":"2022-01-07T00:00:00Z","timestamp":1641513600000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["ISB"],"published-print":{"date-parts":[[2022,1,7]]},"abstract":"<jats:p>Yeasts exist in communities that expand over space and time to form complex structures and patterns. We developed a lattice-based framework to perform spatial-temporal Monte Carlo simulations of budding yeast colonies exposed to different nutrient and magnetic field conditions. The budding patterns of haploid and diploid yeast cells were incorporated into the framework, as well as the filamentous growth that occurs in yeast colonies under nutrient limiting conditions. Simulation of the framework predicted that magnetic fields decrease colony growth rate, solidity, and roundness. Magnetic field simulations further predicted that colony elongation and boundary fluctuations increase in a nutrient- and ploidy-dependent manner. These in-silico predictions are an important step towards understanding the effects of the physico-chemical environment on microbial colonies and for informing bioelectromagnetic experiments on yeast colony biofilms and fungal pathogens.<\/jats:p>","DOI":"10.3233\/isb-210233","type":"journal-article","created":{"date-parts":[[2021,12,14]],"date-time":"2021-12-14T11:51:01Z","timestamp":1639482661000},"page":"53-69","source":"Crossref","is-referenced-by-count":4,"title":["Lattice-based Monte Carlo simulation of the effects of nutrient concentration and magnetic field exposure on yeast colony growth and morphology"],"prefix":"10.1177","volume":"14","author":[{"given":"Rebekah","family":"Hall","sequence":"first","affiliation":[{"name":"Department of Mathematical and Statistical Sciences, University of Alberta, Edmonton, AB, Canada"}]},{"given":"Daniel A.","family":"Charlebois","sequence":"additional","affiliation":[{"name":"Department of Physics, University of Alberta, Edmonton, AB, Canada"},{"name":"Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada"}]}],"member":"179","reference":[{"key":"10.3233\/ISB-210233_ref1","doi-asserted-by":"crossref","first-page":"806","DOI":"10.1111\/j.1574-6976.2006.00034.x","article-title":"Life within a community:benefit to yeast long-term survival","volume":"30","author":"Palkov\u00e1","year":"2006","journal-title":"FEMS Microbiol Rev"},{"key":"10.3233\/ISB-210233_ref2","doi-asserted-by":"crossref","first-page":"e1003979","DOI":"10.1371\/journal.pcbi.1003979","article-title":"Two-Dimensionality of Yeast Colony Expansion Accompanied by Pattern Formation","volume":"10","author":"Chen","year":"2014","journal-title":"PLoS Comput Biol"},{"key":"10.3233\/ISB-210233_ref3","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1134\/S0026261707020014","article-title":"Biofilm\u2014\u201cCity of Microbes\u201d or an Analogue of Multicellular Organisms?","volume":"76","author":"Nikolaev","year":"2007","journal-title":"Microbiology"},{"issue":"9","key":"10.3233\/ISB-210233_ref4","doi-asserted-by":"crossref","first-page":"881","DOI":"10.3201\/eid0809.020063","article-title":"Biofilms: microbial life on surfaces","volume":"8","author":"Donlan","year":"2002","journal-title":"Emerg Infect Dis"},{"key":"10.3233\/ISB-210233_ref5","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1128\/CMR.17.2.255-267.2004","article-title":"Candida infections of medical devices","volume":"17","author":"Kojic","year":"2004","journal-title":"Clin Microbiol Rev"},{"key":"10.3233\/ISB-210233_ref6","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1128\/EC.4.4.633-638.2005","article-title":"Candida biofilms: an update","volume":"4","author":"Ramage","year":"2005","journal-title":"Eukaryot Cell"},{"key":"10.3233\/ISB-210233_ref7","doi-asserted-by":"crossref","first-page":"012010","DOI":"10.1088\/1742-6596\/105\/1\/012010","article-title":"Biomaterials - where biology, physics, chemistry, engineering and medicine meet","volume":"105","author":"Hing","year":"2008","journal-title":"Journal of Physics Conference Series"},{"key":"10.3233\/ISB-210233_ref8","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1016\/S0302-4598(96)05180-X","article-title":"Effects of 60Hz AC magnetic fields on gene expression following exposure over multiple cell generations using Saccharomyces cerevisiae","volume":"43","author":"Binninger","year":"1997","journal-title":"Bioelectrochem Bioenerg"},{"key":"10.3233\/ISB-210233_ref9","doi-asserted-by":"crossref","first-page":"6724","DOI":"10.1063\/1.1556929","article-title":"Effects of intense magnetic fields on sedimentation pattern and gene expression profile in budding yeast","volume":"93","author":"Ikehata","year":"2005","journal-title":"J Appl Phys"},{"key":"10.3233\/ISB-210233_ref10","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1016\/j.bioelechem.2006.03.029","article-title":"Effects of low-frequency magnetic fields on the viability of yeast Saccharomyces cerevisiae","volume":"70","author":"Novak","year":"2007","journal-title":"Bioelectrochemistry"},{"issue":"1","key":"10.3233\/ISB-210233_ref11","doi-asserted-by":"crossref","first-page":"e0209843","DOI":"10.1371\/journal.pone.0209843","article-title":"Biochemical and biomolecular effects induced by a static magnetic field in Saccharomyces cerevisiae: Evidence for oxidative stress","volume":"14","author":"Kthiri","year":"2019","journal-title":"PLOS ONE"},{"key":"10.3233\/ISB-210233_ref12","doi-asserted-by":"crossref","first-page":"694713","DOI":"10.1155\/2015\/694713","article-title":"Modificationof S. cerevisiae Growth Dynamics Using Low Frequency ElectromagneticFields in the 1-2kHz Range","volume":"2015","author":"Barab\u00e1\u0161","year":"2015","journal-title":"BioMed Res Int"},{"key":"10.3233\/ISB-210233_ref13","doi-asserted-by":"crossref","first-page":"622","DOI":"10.1002\/bem.20599","article-title":"Effect of static magnetic fields on the budding of yeast cells","volume":"31","author":"Egami","year":"2010","journal-title":"Bioelectromagnetics"},{"key":"10.3233\/ISB-210233_ref14","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1007\/s40571-015-0082-3","article-title":"Simulating tissue mechanics with agent-based models: concepts, perspectives and some novel results","volume":"2","author":"Van Liedekerke","year":"2015","journal-title":"Comptutational Particle Mechanics"},{"key":"10.3233\/ISB-210233_ref15","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1007\/BF02980577","article-title":"Beitrag zur Theorie des Ferromagnetismus","volume":"31","author":"Ising","year":"1925","journal-title":"Z Physik"},{"key":"10.3233\/ISB-210233_ref16","doi-asserted-by":"crossref","first-page":"3986","DOI":"10.1021\/ma00200a030","article-title":"A lattice statistical mechanics model of the conformational and sequence spaces of proteins","volume":"22","author":"Lau","year":"1989","journal-title":"Macromolecules"},{"key":"10.3233\/ISB-210233_ref17","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1615\/CritRevBiomedEng.2018026093","article-title":"A review of protein structure prediction using lattice model","volume":"46","author":"Dubey","year":"2018","journal-title":"Crit Rev Biomed Eng"},{"key":"10.3233\/ISB-210233_ref18","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1006\/jtbi.1993.1007","article-title":"Cellular Automata Approaches to Biological Modeling","volume":"160","author":"Ermentrout","year":"1993","journal-title":"J Theor Biol"},{"key":"10.3233\/ISB-210233_ref19","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1016\/S0070-2153(07)81014-3","article-title":"Cellular automata as microscopic models of cell migration in heterogeneous environments","volume":"81","author":"Hatzikirou","year":"2008","journal-title":"Curr Top Dev Biol"},{"key":"10.3233\/ISB-210233_ref20","first-page":"309","article-title":"Random Growth of Fungal Colony Model on Diffusive and Non-Diffusive Media","volume":"15","author":"Matsuura","year":"2000","journal-title":"Froma"},{"key":"10.3233\/ISB-210233_ref21","doi-asserted-by":"crossref","first-page":"5992","DOI":"10.1038\/s41598-018-23649-z","article-title":"Diffusion-limited growth of microbial colonies","volume":"8","author":"Tronnolone","year":"2018","journal-title":"Scientific Reports"},{"key":"10.3233\/ISB-210233_ref22","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1146\/annurev-cellbio-100616-060856","article-title":"Cell Polarity in Yeast","volume":"33","author":"Chiou","year":"2017","journal-title":"Annu Rev Cell Dev Biol"},{"key":"10.3233\/ISB-210233_ref23","doi-asserted-by":"crossref","first-page":"1.6.1","DOI":"10.1002\/0471143030.cb0106s04","article-title":"Media and culture of yeast","volume":"4","author":"Green","year":"1999","journal-title":"Curr Protoc Cell Biol"},{"key":"10.3233\/ISB-210233_ref24","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1016\/0168-9525(94)90036-1","article-title":"Cell polarity in yeast","volume":"10","author":"Chant","year":"1994","journal-title":"Trends Genet"},{"issue":"1","key":"10.3233\/ISB-210233_ref25","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1534\/genetics.111.127456","article-title":"The Regulation of Filamentous Growth in Yeast","volume":"190","author":"Cullen","year":"2012","journal-title":"Genetics"},{"key":"10.3233\/ISB-210233_ref26","doi-asserted-by":"crossref","first-page":"2974","DOI":"10.1101\/gad.8.24.2974","article-title":"Elements of a single MAP kinase cascade in Saccharomyces cerevisiae mediate two developmental programs in the same cell type: mating and invasive growth","volume":"8","author":"Roberts","year":"1994","journal-title":"Genes Dev"},{"key":"10.3233\/ISB-210233_ref27","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1016\/0955-0674(95)80069-7","article-title":"Budding yeast morphogenesis: signalling, cytoskeleton and cell cycle","volume":"7","author":"Kron","year":"1995","journal-title":"Curr Opin Cell Biol"},{"key":"10.3233\/ISB-210233_ref28","doi-asserted-by":"crossref","first-page":"13619","DOI":"10.1073\/pnas.240345197","article-title":"Glucose depletion causes haploid invasive growth in yeast","volume":"97","author":"Cullen","year":"2000","journal-title":"Proc Natl Acad Sci USA"},{"key":"10.3233\/ISB-210233_ref29","first-page":"2100","article-title":"Induction of pseudohyphal growth by overexpression of PHD1, a Saccaromyces cerevisiae gene related to transcriptional regulators of fungal development","volume":"14","author":"Gimeno","year":"1993","journal-title":"Mol Cell Biol"},{"key":"10.3233\/ISB-210233_ref30","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1111\/j.1574-6976.2011.00275.x","article-title":"Choosing the right lifestyle: adhesion and development in Saccharomyces cerevisiae","volume":"36","author":"Br\u00fcckner","year":"2012","journal-title":"FEMS Microbiol Rev"},{"key":"10.3233\/ISB-210233_ref31","doi-asserted-by":"crossref","first-page":"517529","DOI":"10.1155\/2012\/517529","article-title":"Hyphal Growth in Human Fungal Pathogens and Its Role in Virulence","volume":"2012","author":"Brand","year":"2012","journal-title":"International Journal of Microbiology"},{"issue":"8","key":"10.3233\/ISB-210233_ref32","doi-asserted-by":"crossref","first-page":"827","DOI":"10.15252\/msb.20156185","article-title":"Stress-response balance drives the evolution of a network module and its host genome","volume":"11","author":"Gonzalez","year":"2015","journal-title":"Molecular Systems Biology"},{"key":"10.3233\/ISB-210233_ref33","doi-asserted-by":"crossref","first-page":"751","DOI":"10.1083\/jcb.129.3.751","article-title":"Patterns of bud-site selection in the yeast Saccharomyces cerevisiae","volume":"3","author":"Chant","year":"1995","journal-title":"J Cell Biol"},{"issue":"4","key":"10.3233\/ISB-210233_ref34","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1128\/mr.52.4.536-553.1988","article-title":"Life cycle of the budding yeast Saccharomyces cerevisiae","volume":"52","author":"Herskowitz","year":"1988","journal-title":"Microbiology Reviews"},{"issue":"1","key":"10.3233\/ISB-210233_ref35","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1534\/genetics.114.163188","article-title":"Budding Yeast for Budding Geneticists: A Primer on the Saccharomyces cerevisiae model system","volume":"197","author":"Duina","year":"2014","journal-title":"Genetics"},{"issue":"18","key":"10.3233\/ISB-210233_ref36","doi-asserted-by":"crossref","first-page":"3037","DOI":"10.1007\/s00018-012-0974-9","article-title":"How to halve ploidy: lessons from budding yeast meiosis","volume":"69","author":"Kerr","year":"2012","journal-title":"Cellular and Molecular Life Sciences"},{"key":"10.3233\/ISB-210233_ref37","doi-asserted-by":"crossref","first-page":"1505","DOI":"10.1103\/PhysRevLett.56.1505","article-title":"A lattice gas automaton for the Navier-Stokes equations","volume":"56","author":"Frisch","year":"1986","journal-title":"Physical Review Letters"},{"issue":"2","key":"10.3233\/ISB-210233_ref38","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1088\/1478-3975\/3\/2\/001","article-title":"A cellular automaton model for the migration of glioma cells","volume":"3","author":"Aubert","year":"2006","journal-title":"Physical Biology"},{"key":"10.3233\/ISB-210233_ref39","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1007\/BF01023491","article-title":"Local structure theory: Calculation on hexagonal arrays, and interaction of rule and lattice","volume":"54","author":"Gutowitz","year":"1989","journal-title":"Journal of Statistical Physics"},{"issue":"11","key":"10.3233\/ISB-210233_ref40","doi-asserted-by":"crossref","first-page":"e1005843","DOI":"10.1371\/journal.pcbi.1005843","article-title":"A modeling study of budding yeast colony formation and its relationship to budding pattern and aging","volume":"13","author":"Wang","year":"2017","journal-title":"PLOS Comput Biol"},{"issue":"2","key":"10.3233\/ISB-210233_ref41","doi-asserted-by":"crossref","first-page":"346","DOI":"10.1137\/040603255","article-title":"An explicit spatial model of yeast microcolony growth","volume":"3","author":"J\u00f6nsson","year":"2005","journal-title":"Multiscale Model Simul"},{"key":"10.3233\/ISB-210233_ref42","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1016\/j.micres.2012.04.002","article-title":"Magnetotactic bacteria, magnetosomes and their application","volume":"167","author":"Yan","year":"2012","journal-title":"Microbiol Res"},{"issue":"Suppl 4","key":"10.3233\/ISB-210233_ref43","first-page":"67","article-title":"The Importance of Neighborhood Scheme Selection in Agent-based Tumor Growth Modeling","volume":"14","author":"Tzedakis","year":"2015","journal-title":"Cancer Informatics"},{"key":"10.3233\/ISB-210233_ref44","doi-asserted-by":"crossref","first-page":"248101","DOI":"10.1103\/PhysRevLett.99.248101","article-title":"Classifying the expansion kinetics and critical surface dynamics of growing cell populations","volume":"99","author":"Block","year":"2007","journal-title":"Phys Rev Lett"},{"key":"10.3233\/ISB-210233_ref45","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1016\/S0303-2647(99)00089-1","article-title":"Cellular automaton of idealized brain tumor growth dynamics","volume":"55","author":"Kansal","year":"2000","journal-title":"Biosystems"},{"key":"10.3233\/ISB-210233_ref46","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1142\/S0219525905000440","article-title":"Coarse graining in simulated cell populations","volume":"8","author":"Drasdo","year":"2005","journal-title":"Adv Complex Syst"},{"key":"10.3233\/ISB-210233_ref47","doi-asserted-by":"crossref","first-page":"921","DOI":"10.1016\/j.resmic.2005.05.012","article-title":"The morphology of Saccharomycescerevisiae colonies is affected by cell adhesion and the buddingpattern","volume":"156","author":"Vop\u00e1lensk\u00e1","year":"2005","journal-title":"Res Microbiol"},{"key":"10.3233\/ISB-210233_ref48","unstructured":"Nelson P. , Biological Physics: Energy, Information, Life. 2020, Philadelphia, PA USA: Chiliagon Science."},{"key":"10.3233\/ISB-210233_ref49","doi-asserted-by":"crossref","first-page":"5992","DOI":"10.1038\/s41598-018-23649-z","article-title":"Diffusion-limited growth of microbial colonies","volume":"8","author":"Tronnolone","year":"2018","journal-title":"Sci Rep"}],"container-title":["In Silico Biology"],"original-title":[],"link":[{"URL":"https:\/\/content.iospress.com\/download?id=10.3233\/ISB-210233","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T11:49:26Z","timestamp":1777463366000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.sagepub.com\/doi\/full\/10.3233\/ISB-210233"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,1,7]]},"references-count":49,"journal-issue":{"issue":"3-4"},"URL":"https:\/\/doi.org\/10.3233\/isb-210233","relation":{},"ISSN":["1386-6338","1434-3207"],"issn-type":[{"value":"1386-6338","type":"print"},{"value":"1434-3207","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,1,7]]}}}