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We design BioScape, a high-level modeling language for the stochastic simulation of biological and biomaterials processes in a reactive environment in 3D space. BioScape is based on the Stochastic Pi-Calculus, and it is motivated by the need for individual-based, continuous motion, and continuous space simulation in modeling complex bacteria-materials interactions. Our models in BioScape will help in identifying biological targets and materials strategies to treat biomaterials associated bacterial infections.

We use BioScape to build a 3D computational model of bifunctional surfaces. The resulting model is able to Simulate varying configurations of surface coatings at a fraction of the time. The output of the model not only plot populations over time, but it also produces 3D-rendered videos of bacteria-surface interactions enhancing the visualization of the system’s behavior.

We extend BioScape with a fully parallel semantics in order to model larger systems and define BioScapeL, an extension of BioScape with abstract locations.

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•  Model interactions/behavior •  Bacteria is killed by Lysozyme. •  Bacteria attaches to PEO. •  Bacteria multiplies.

•  Concurrency, Stochasticity and 3D Space •  Bacteria-biomaterials interactions are highly concurrent. •  Wet lab experiments are stochastic. •  3D space has 3 new attributes: movement space (!), step (") and shape (#).

•  Process algebra •  Send/Receive Handshake (!/?)

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•  Total Number of Bacteria and % Dead Bacteria for varying % of Pluronic-Lysozyme conjugates. ?&'!":$"%=#(%@($A'(:%B?C$8$"%=8D(B%!'D(

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•  A stochastic and parallel language for mobile and spatial interactions. •  Maximally parallel semantics. •  Parallel Movement: Control on spatial overlapping •  Parallel Communications: Control on communication conflicts •  Challenge

!  How do we advance the simulation clock? !  Solution: Timed Configurations

Annotating each product of a reaction with a timer indicating how long that reaction will take.

!  Example: If Cell 30 Cell|Cell means that a Cell takes 30 minutes to split, through mitosis, into two daughter cells, then we will annotate the two daughter cells as {{Cell}}30 and {{Cell}}30. As time lapses, the timer will be reduced, and when reaching {{Cell}}0, both cells will be available for new reactions.

:%=:DC#"%=#("  We define BioScape, a high-level modeling and simulation language for the stochastic simulation of biological and biomaterials processes. "  We visualize biofilm formation. "  We construct and validate the stochastic computational model for antibacterial surfaces. "  We predict optimal surface configuration with minimal number of attached bacteria and maximal proportion of dead bacteria. "  We define BioScape with a fully parallel semantics in order to model larger and more realistic systems (GPU architectures). "  We define BioScapeL, a high level language of entities with programmable abstract locations.

&'@'&'=:'#(1. Adriana Compagnoni, Vishakha Sharma, Matthew Libera, Svetlana Sukhishvili, Philippe Bidinger, Livio Bioglio, Eduardo Bonelli. BioScape: A High-Level Modeling and Simulation Language. Theoretical Computer Science (TCS) 2013. Submitted. 2. Vishakha Sharma, Adriana Compagnoni, Matthew Libera, Agnieszka K. Muszanska, Henk J. Busscher and Henny C. van der Mei. Simulating Anti-adhesive and Antibacterial Bifunctional Polymers for Surface Coating using BioScape. ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, 2013. September 22 – 25, Washington, DC. To appear. 3. Adriana Compagnoni, Paola Giannini, Catherine Kim, Matthew Milideo, Vishakha Sharma A Calculus of Located Entities. 9th International Workshop on Developments in Computational Models (DCM) 2013. To appear. 4. Adriana Compagnoni, Vishakha Sharma, Yifei Bao, Matthew Libera, Svetlana Sukhishvili. Philippe Bidinger, Livio Bioglio and Eduardo Bonelli. BioScape: A Modeling and Simulation Language for Bacteria-Materials Interactions. Electronic Notes in Theoretical Computer Science, 293(0): 35 - 49, 2013. Proceedings of the Third International Workshop on Interactions Between Computer Science and Biology (CS2Bio'12). 5. Adriana Compagnoni, Mariangiola Dezani-Ciancaglini, Paola Giannini, Karin Sauer, Vishakha Sharma, Angelo Troina. Parallel BioScape: A Stochastic and Parallel Language for Mobile and Spatial Interactions. In Proceedings Sixth Workshop on Membrane Computing and Biologically Inspired Process Calculi. 8th September 2012, Newcastle, UK. (MeCBIC 2012). In Electronic Proceedings in Theoretical Computer Science, Volume 100 Issue 7, Pages 101-106, 2012. 6. Jie Li, Vishakha Sharma, Narayan Ganesan, and Adriana Compagnoni. Simulation and Study of Large- Scale Bacteria-Materials Interactions via BioScape Enabled by GPUs. In Proceedings of ACM-BCB 2012, Pages 610-612.

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•  A Stochastic Pi-Calculus in 3D space with abstract locations. •  Builds on BioScape by associating with each entity a position in space, which is the barycentre of its associated shape. •  The position of an entity instance is programmable. •  Motivation: To describe complex structures, like polymers/oligomers/membranes and pre-existing/ reactive environment – video games/antibacterial surfaces. •  Extensions: Random Translation and Scaling

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Bac()@msBac, stepBac, shapeBac(size, color) = !attach.PBac() + mov.Bac()

PBac()@msPBac, stepPBac, shapePBac(size, color) = delay@0.000001.(PBac() | PBac()) + ?kill().DBac()

DBac()@msDBac, stepDBac, shapeDBac(size, color) = delay@0.1

PEO()@msPEO, stepPEO, shapePEO(size, color) = ?attach()

Lyso()@msLyso, stepLyso, shapeLyso(size, color) = !kill()

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Figure 7: Bifunctional Surface with Polymers Brushes and Pluronic-Lysozyme Conjugates.

•  Biomaterials used for implants in the human body often lead to the development of the biofilm formation which are resistant to antibiotics and the immune system.

•  The current state of art lies in the design and composition of the biomaterials with antimicrobial agents.

•  Anti-adhesive and Antibacterial Bifunctional Polymers is one way to prevent biofilm growth.

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•  Our model predicts that between 1 and 10% of conjugation in the initial concentration yields the minimal amount of bacteria with the maximal percentage of dead bacteria.

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•  From Lab Data to Computational Model and Validation

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Figure 9: Control on communication conflicts.

Figure 8: Control on spatial overlapping.

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"  Build a framework based on BioScapeL for the computationally assisted development of antibacterial surfaces. "  Study adenoviral traffic in healthy/cancerous eukaryotic cells.

Planktonic bacterium !  adsorb (A p) !  diffuse !  flow !  killed by AmA (Kp >> Ka) !  reproduce (Rp ! Ra) !  metabolize (Mp ! Ma)

Released AmA !  bind !  diffuse !  flow !  kill !  hydrolyze

Adsorbed bacterium !  desorb !  killed by AmA (Ka << Kp) !  reproduce (Ra ! Rp)

!  metabolize (Ma ! Mp) !  produce ECM

Bound AmA !  stay bound !  pH -release !  contact-release

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