bioﬁlm-inspired formation of artiﬁcial adaptive...

Biofilm-inspired Formation of Artificial AdaptiveStructures

Mohammad Hassan Saleh Tabari1, Saleh Kalantari2, Nooshin Ahmadi31Pars University, Iran 2Washington State University 3University of [email protected] [email protected] [email protected]

Todays design researchers are beginning to develop a process-based approach tobiomimicry. Instead of merely looking at static natural structures for inspiration,we are learning to draw from the underlying organic processes that lead to thecreation of those structures. This paradigm shift points us in the direction ofadaptive fabrication systems that can grow through processes of self-assemblyand can reconfigure themselves to meet the contours of local environments. Inthis study we examined the structural growth patterns of bacterial biofilms as abasis for a new kind of artificial, self-assembling module. This demonstration ofbio-inspired design shows how contemporary technology allows us to harness thelessons of evolution in new and innovative ways. By exploring the dynamicassembly of complex structural formations in nature, we are able to derive newresource-efficient approaches to adaptable designs that are suited to changingenvironments. Ultimately we aspire to produce fully synthetic analogues thatfollow similar patterns of self-assembly to those found in bacterial biofilmcolonies. Designers have only just begun to explore the tremendous wealth ofnatural form-creation processes that can now be replicated with computer-aideddesign and fabrication; this project shows just one example of what the futuremight hold.

Keywords: Biofilm, Adaptive Structure, Formation, Quorum Sensing,Parametric Condition

CONTEXT AND RESEARCH GOALSToday’s technology has allowed architects to drawinspiration from the natural world in new and inno-vative ways. Recent work has begun to explore thepossibilities of using biological systems either as amodel for design algorithms (Duro-Royo et al., 2015;Kalantari & Saleh Tabari, 2017) or as an actual com-ponent in fabrication processes (Araya, Zolotovsky,

& Gidekel, 2012). Evolution has produced brilliantarrangements that are ideally suited to the naturaland physical environment, and if we attend to theirlessons these natural systems can teach us how tocreate strong, durable, adaptable, and flexible struc-tures with a minimum of waste (Discher, Janmey, &Wang, 2005; Philp & Stoddart, 1996; Vincent, 2012).Our own efforts in the field of architecture have not

MATERIAL STUDIES 1 - Volume 2 - eCAADe 35 | 303

yetbegun toapproach the level of sophistication thatis seen in the natural world (Benyus, 1997; Oxman etal., 2012; Vincent, 2012), and there is a tremendousamount of potential still to be found in improvingour designs through lessons learned from nature. Inthis project, the researchers analyzed bacterial cel-lular growth as a basis for new human-created ar-chitectural processes. We examined various patternsof bacterial growth, including their use of respon-sivemembranes and scaffolding structures, and thencombined this knowledge with the exciting new po-tential of digital fabrication technology to investigatenew architectural assembly methods. The creationof self-assembling structures modeled on bacterialgrowth has the potential to replicate the tremendousstructural advantages and resource-efficiency of thisorganic process.

BACKGROUND: BIO-INSPIRED STRUC-TURES“Morphogenesis” is a term used in the natural sci-ences to describe how structures develop in geo-logical formations and biological organisms. Archi-tectural designers have become increasingly inter-ested in studying morphogenesis as a way to in-form human-created structures, particularly as tech-nological advancements have opened new frontiersfor replicating these natural processes. For exam-ple, Kreig and colleagues (2012) drew from biome-chanical studies of the sea urchins to develop a newtype of jointed structural system. Ortega-Sanchezand colleagues (2000) used the model of organic tis-sues to develop newmaterials that are “self-healing”and tolerant of structural faults. Using advancesin “soft” robotics and nano-engineering, some re-searchershavebegun todevelopaprocess-basedap-proach to biomimicry. In other words, we are nolonger simply looking to the static design-solutionsof the natural world, but are now taking lessons fromthe organic processes throughwhich those solutionsare created. This approach focuses on how natu-ral processes achieve effective designs to fit the con-tours of a specific local environment and its structural

requirements (Tibbits, 2012; Raviv et al., 2014)Bacterial cellulose structures are a fascinating

model for this cutting-edge biomimetic design re-search. The small scale and rapid duration of bac-terial growth patterns makes them relatively easy tostudy, and the use of bacterial cellulose in indus-trial, scientific, and medical applications has led toa burgeoning amount of data on the topic (Fernan-dez et al. 2013; Mohite et al. 2014). Previous stud-ies have focused on analyzing and manipulating thegrowth patterns of bacteria. For example, founda-tional workwas carried out by Araya, Zolotovsky, andGidekel (2012), who demonstrated that digital toolsand technologies could be combinedwith living bac-teria systems in a controlled environment to inducespecific biological functions leading to desired struc-tural patterns. Derme, Mitterberger, and Di Tanna(2016) similarly developed bio-fabrication and scaf-folding techniques to control the development ofbacterial cellulose, with the ultimate goal of enhanc-ing bio-materials science.

In the current research, we weremore interestedin reviewing the data on bacterial growth as a modelfor new types of artificial self-assembling structures.The concept of self-assembly refers to a process bywhich small building-blocks, on the basis of their lo-cal interactions, come together to produce elegantand effective structures tailored to the contours ofthe environment. This type of assembly is extremelywidespread innature (Widesides&Grzybowski, 2002;Pelesko, 2007). In recent years a variety of researchershave made strides in theorizing the components ofself-assembly, taking lessons from observed featuresin the natural world. The most common model ac-knowledges four defining features that affect self-assembly-the building blocks (cells, molecules, com-ponent structures, etc.), the forces that connect theblocks together (chemical bonds, connective tissue,electromagnetic interactions), the features of the sur-rounding environment, and the driving force that en-ergizes the assembly process and prompts it to oc-cur (Pelesko, 2007; Tibbits, 2012). Some researchersdistinguishbetween self-assemblyprocesses that ap-

304 | eCAADe 35 - MATERIAL STUDIES 1 - Volume 2

proach a static equilibrium in their environment vs.those that remain in a state of perpetual dynamicgrowth and energy exchange in relation to their sur-roundings (Whitesides & Grzybowski, 2002).

The use of self-assembly approaches in artificialarchitectural fabrication is an extremely new field,but investigations in this area have yielded excitingresults. Schoessler and colleagues (2015), for exam-ple, demonstrated a system that allowed for con-structive assembly, disassembly, and reassembly us-ing passive building blocks. Mairopoulos (2015) sim-ilarly developed a component-based system that al-lowed for a highly autonomous local assembly to fitthe contours of the environment. The current re-search contributes to this innovative direction in ar-chitectural assembly by analyzing lessons from bac-terial growth. By learning more about the morpho-genesis of bacterial structures, designers can even-tually produce fully synthetic analogues that fol-low similar patterns of adaptation and development,thereby harnessing the lessons of countless years ofevolution.

BIOFILMS AS AN INSPIRATION FORSTRUCTURAL FORMATIONBiofilms are arrangements of cells ormicroorganismsthat stick together, typically along an external sur-face. The cellular arrangement of biofilms is knownto confer specialized functions and properties thatare not otherwise demonstrated by the individualcomponents of the film (for example, by free-floatingforms of the samemicroorganisms in a fluidmedium)(Flemming & Wingender, 2010). Organisms embed-ded within a biofilm matrix gain specific advantagesto nutrient flow and architectural integrity (Oliveira& Cunha, 2008; Tolker-Nielsen & Molin, 2000; Suther-land, 2001). Biofilm formation is typically amulti-stepprocess, beginning when individual cells adhere to asurfaceusingelectromagneticor chemical bonds. Af-ter this initial attachment, three-dimensional growthbegins to occur, leading to complex microcoloniesthat may be comprised of multiple types of organ-isms. Once the biofilmmatures and its structural ma-trix is established, it typically begins to release indi-vidual cells, which regain a free-floating planktoniclifestyle and may eventually colonize other surfaces(Flemming & Wingender, 2010; Rendueles & Ghigo,2012) (Figure 1).

Figure 1Stages of biofilmformation.


In this study, we examined the natural formationof E. Coli bacterial biofilms as an inspiration for devel-oping an artificial, self-assembling system. The fea-tures of bacteria cells were studied as amodel for de-signing architectural units (or “bricks”), and the at-tachment processes between the cells in bacterialbiofilms were studied as a model for developing asmart adaptation system to combine and recombinethe individual units together. The selection of E. Colibiofilms as amodel for this architectural researchwasmade on the basis of the extensive, pre-existing em-pirical knowledge that we have about their forma-tion, as well as the complexity of the biofilm struc-tures, their demonstrated environmental fitness, andthe relevance of that knowledge to potential designapplications.

We reviewed the scientific literature to discoverhow biofilm structures are formed. One conceptthat we quickly learned is that cell-surface polysac-charides play a crucial role in mediating the at-tachment process among individual units. In ad-dition to serving as a barrier between the cell walland the external environment, these polysaccharidemolecules providemuch of the structural connectivetissue of biofilms. The way in which the connect-ing polysaccharides are produced by the cells dur-

ing biofilm formation is mediated by a process calledquorumsensing (QS). This is a kindof cell-to-cell com-munication, mediated by an exchange of signalingmolecules, that affects the way genetic instructionsare expressed in individual cells. QS allows the indi-vidual cells to receive feedback about thedensity andrelative positioning of other nearby bacteria cells.Based on this information a variety of processmay beadjusted or initiated within each individual cell, ulti-mately leading to the formationof effective structuralattachments to specific neighboring units (Federle &Bassler, 2003; Vasudevan, 2014; Walters and Speran-dio, 2006; Miller and Bassler, 2001; Whitehead et al.,2001) (Figure 2).

Considering the QS system as a form of commu-nication, we investigated what type of information isexchanged among neighboring cells to allow for theeffective biofilm formation. Using contemporary ar-chitectural language QS can be understood as a kindof distributed “smart system” that adapts to local en-vironmental conditions. The units that are activatedby QS can be involved in:

• Processes inwhich individual units request as-sistance and communicate their needs, suchas the initiation of a larger solid structure.

• Processes that require individual responsive-

Figure 2Quorum sensing asa communicationmechanism.


ness to environmental variables, such as pro-duction of optimized light for each unit.

• Processes that favor the colonization of newterritory and the development of expanded,complex communities after local structuresare stabilized.

To identify potential configurations among thebuild-ingunits, weanalyzed the topologyof the connectivematrix, in particular the O-antigen repeating units ofcell-surface lipopolysaccharide. This typology variesdepending on the number and positioning of sugarresidues that are present in each O-antigen, varyingfrom two to seven nodes (Brade et al., 1999; Stenutzet al., 2006) (Figure 3).

Figure 3Topology ofconnectivepolysaccharides inE. Coli biofilms.

RESULTSThe assembly models that were developed in thisstudy are based on the features of biofilm forma-tion and the QS communication system as describedabove. The result is a smart, self-assembling structurethat is adaptable in its shape depending on the lo-

cal environment. The basic cell or building-bock ofthe structure is a truncated tetrahedron. It has fourhexagonal faces which can link to other units, plusfour additional triangular faces that do not form links.The structure allows for two basic types of compactcolonies consisting of five or six units each (Figure 4).

Once cells create a basic colony in one of thesetwo shapes, they begin to engage in QS communica-tion with other nearby colonies. As a result of this in-formation exchange, the individual colonies may ad-just their shapes and link up with each other. Basedon the needs of the environment and the availabletopologies, eachof the two colonies can assumea va-riety of shapes (Figures 5 and 6).

In a manner similar to bacterial polysaccharidebranching systems, adjacent cell colonies can link upinto different arrangements. Some of these connec-tions will be structurally stronger than others. Thestronger connections will generally be favored bythe colonies, depending on the environmental pa-rameters and the overall structural goal of the units,which are defined by QS inputs. By specifying theavailable cell colonies, the possible assembly typolo-gies, and the environmental needs, a unique struc-tural arrangement is formed. (Figures 7 and 8). Whenneeded, this final structure can be easily disassem-bled into its component colonies and/or reconfig-ured into a different overall shape.

CONCLUSIONS AND FUTUREWORKThis project studied E. Coli biofilm formation as a po-tential basis for computer-mediated “smart” architec-tural assemblies. The resulting simulations demon-strate how the morphogenesis of biofilms can beused as inspiration for developing new types of envi-ronmentally responsive structures. This demonstra-tion is intended to inspire designers to make use ofbiofilm formation concepts in their work, and to pro-vide practical tools for this purpose. The 3D modelsproduced in the research provide concrete examplesof how biofilm logic can be used in the design of in-novative and adaptive forms (Figure 9). Ultimately,the ultimate goal of abstracting biological formation


Figure 4Compact coloniesconsisting of five orsix cells.

Figure 5Each colony canassume a variety ofshapes.


Figure 6Cell colony rotationand formationbased on E. Colitopologies.

Figure 7Colonies linktogether to formlarger structures.The “Alpha Joint”identified here willbe a stronger linkthat the “Beta Joint”and will thus bepreferred duringthe self-assemblyprocess.


Figure 8Formation of largerstructures based onQS communicationamong colonies.


Figure 9An example of acomplex structuralformation based onenvironmentalparameters and QScommunicationamong individualcell colonies.

procedure into code-driven models and tools is togain new insights into hownature dealswith physicaldynamics, environmental parameters, and feedbackwithin cell and tissue structures. The potential appli-cations includenovel designs for responsive surfaces,new fabrication processes, and unique spatial struc-tures.

While this study presents a first step toward sim-ulating biofilm formation in computer-aided design,there remains a tremendous amount of opportunityfor analyzing various organic assemblages. By link-ing the biological sciences to the computational de-sign process we can open significant new horizonsfor organically inspired design. The next step in thisproject is to fabricate these cells as “robotic bricks”with embedded sensors. By creating physical exam-ples of this adaptive structure we can further exploreits potential applications and verify the effectivenessof our approach. Future work may seek to combinebio-inspired formation directly with established soft-ware algorithms, leading to newdesign tools in para-metric modeling.

REFERENCESAraya, S, Zolotovsky, E and Gidekel, M 2012 ’Living archi-

tecture: Micro performances of bio fabrication’, Pro-ceedings of eCAADe 2012, Prague, p. 447–457

Benyus, JM 1997, Biomimicry: Innovation Inspired by Na-ture, Quill, New York

Derme, T, Mitterberger, D and Di Tanna, U 2016 ’Growth-based fabrication techniques for bacterial cellulose:Three-dimensional grownmembranes and scaffold-ing design for biological polymers’, Proceedings ofACADIA 2016, Ann Arbor, MI, p. 488–495

Discher, DE, Janmey, P and Wang, YL 2005, ’Tissue cellsfeel and respond to the stiffness of their substrate’,Science, 310(5751), p. 1139–1143

Duro-Royo, J, Zolotovsky, K, Mogas-Soldevila, L, Varsh-ney, S, Oxman, N, Boyce, MC and Ortiz, C 2015,’MetaMesh: A hierarchical computational model fordesign and fabrication of biomimetic armored sur-faces’, Computer-Aided Design, 60, p. 14–27

Federle, MJ and Bassler, BL 2003, ’Interspecies commu-nication in bacteria’, Journal of Clinical Investigation,112(9), p. 1291–1299

Fernandez, JG and Donald, EI 2013, ’Bioinspired chiti-nous material solutions for environmental sustain-ability andmedicine’, Advanced FunctionalMaterials,23(36), p. 4454–4466

Flemming, HC and Wingender, J 2010, ’The biofilm ma-trix’,Natural ReviewofMicrobiololgy, 8(9), p. 623–633

Kalantari, S and Saleh Tabari, M 2017 ’GrowMorph: Bac-teria Growth Algorithm and Design’, Proceedings ofthe 22nd CAADRIA Conference, Suzhou, China, pp.479-487

Mairopoulos, D 2015,M-Cell assembly, Ph.D. Thesis, Mas-sachusetts Institute of Technology

Mohite, BV and Satish, VP 2014, ’A novel bio-material:Bacterial cellulose and its new-era applications’,Biotechnology and Applied Biochemistry, 61(2), p.101–110

Oliveira, A and Cunha, MLRS 2008, ’Bacterial biofilmswith emphasis on coagulase-negative Staphylo-


cocci’, Journal ofVenomousAnimalsandToxins, 14(4),p. 572–596

Ortega-Sanchez, C, Mange, D, Smith, S and Tyrrell, A2000, ’Embryonics: A bio-inspired cellular architec-ture with fault-tolerant properties’, Genetic Program-ming and Evolvable Machines, 1(3), p. 187–215

Oxman, N 2011, ’Variable property rapid prototyping’,Virtual and Physical Prototyping, 6(1), p. 3–31

Philp, D and Stoddart, JF 1996, ’Self-assembly in naturalandunnatural systems’,AngewandteChemie Interna-tional Edition in English, 35(11), p. 1154–1196

Raviv, D, Zhao, W, McKnelly, C, Papadopoulou, A,Kadambi, A, Shi, B, Hirsch, S, Dikovsky, D, Zyracki, M,Olguin, C and Raskar, R 2014, ’Active printed materi-als for complex self-evolvingdeformations’, ScientificReports, 4, pp. 1-18

Rendueles, O and Ghigo, JM 2012, ’Multi-speciesbiofilms: How to avoid unfriendly neighbors’, FEMSMicrobiology Review, 36(5), p. 972–989

Schoessler, P, Windham, D, Leithinger, D, Follmer, S andIshii, H 2015 ’Kinetic blocks: Actuated constructiveassembly for interaction and display’, Proceedings ofthe 28th Annual ACM Symposium on User InterfaceSoftware & Technology, Charlotte, NC, pp. 341-349

Stenutz, R, Weintraub, A and Widmalm, G 2006, ’Thestructures of Escherichia coli O-polysaccharide anti-gens’, FEMSmicrobiology reviews, 30(3), pp. 382-403

Sutherland, I 2001, ’Biofilmexopolysaccharides: A strongand sticky framework’,Microbiology, 147(1), pp. 3-9

Tibbits, S 2012, ’Design to Self-Assembly’, ArchitecturalDesign, 82(2), pp. 68-73

Tolker-Nielsen, T andMolin, S 2000, ’Spatial organizationof microbial biofilm communities’, Microbe Ecology,40(2), pp. 75-84

Vasudevan, R 2014, ’Biofilms: Microbial cities of scientificsignificance’, Journal of Microbiology, 1(3), pp. 1-16

Vincent, J 2012, Structuralbiomaterials, PrincetonUniver-sity Press, Princeton

Whitesides, GM and Grzybowski, B 2002, ’Self-assemblyat all scales’, Science, 295(5564), p. 2418–2421


bioﬁlm-inspired formation of artiﬁcial adaptive...

Documents