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Proto-Plasm: parallel language for adaptive and scalable modelling of biosystems by Chandrajit Bajaj, Antonio DiCarlo, and Alberto Paoluzzi Philosophical Transactions A Volume 366(1878):3045-3065 September 13, 2008 ©2008 by The Royal Society

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Translated cube plus translated cylinder minus two rotated cylinders. Chandrajit Bajaj et al. Phil. Trans. R. Soc. A 2008;366:3045- 3065 ©2008 by The Royal Society

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(a) Progressive geometry and (b) dataflow of the generating expression. Chandrajit Bajaj et al. Phil. Trans. R. Soc. A 2008;366:3045- 3065 ©2008 by The Royal Society

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Pipelined execution: (f ∼ g ∼ h):x=(f ∼ g):(h:x)=f:(g:(h:x)). Chandrajit Bajaj et al. Phil. Trans. R. Soc. A 2008;366:3045- 3065 ©2008 by The Royal Society

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Parallel execution: [f,g,h]:x= 〈 f:x, g:x, h:x 〉. Chandrajit Bajaj et al. Phil. Trans. R. Soc. A 2008;366:3045- 3065 ©2008 by The Royal Society

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The whole scheme holds for d odd; for d even, the last block row should be discarded (ki denotes the cardinality of the k-skeleton, i.e. the number of k-cells). Chandrajit Bajaj et al. Phil. Trans. R. Soc. A 2008;366:3045- 3065 ©2008 by The Royal Society

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A docking pair of molecules M1 and M2: (a) the docked complex M1 ∪ M2, (b) the difference M1\M2, (c) the difference M2\M1, (d) the intersection M1∩M2, (e) zoom in on M1\M2, and (f) zoom in on M2\M1. Chandrajit Bajaj et al. Phil. Trans. R. Soc. A 2008;366:3045- 3065 ©2008 by The Royal Society

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A toy heart model: definition of profile and section curves; transfinite operator profileproduct; interior surface1 and exterior surface2; volume mapping. Chandrajit Bajaj et al. Phil. Trans. R. Soc. A 2008;366:3045- 3065 ©2008 by The Royal Society

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Piecewise approximation of a toy heart model. Chandrajit Bajaj et al. Phil. Trans. R. Soc. A 2008;366:3045- 3065 ©2008 by The Royal Society

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(a–d) The univariate vector mappings profile : 3 and section : 〈 2.5,2 〉 are evaluated here on the intervals [0, 1] and [2π/3, 2π], respectively. Chandrajit Bajaj et al. Phil. Trans. R. Soc. A 2008;366:3045- 3065 ©2008 by The Royal Society

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Spatially realistic finite-element reconstruction of human heart from patient-specific imaging data (Bajaj & Goswami 2008): (a) volume rendering from CT Angio imaging of a human thoracic region, (b) the initial reconstructed heart model extracted from the r... Chandrajit Bajaj et al. Phil. Trans. R. Soc. A 2008;366:3045- 3065 ©2008 by The Royal Society

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A cross-sectional unfolded layout of the interface of a typical frog NMJ, showing the cell membrane parameters to be reconstructed via spatially realistic finite-element modelling using Proto-Plasm. Chandrajit Bajaj et al. Phil. Trans. R. Soc. A 2008;366:3045- 3065 ©2008 by The Royal Society

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One-dimensional manifolds in figure 6a. Chandrajit Bajaj et al. Phil. Trans. R. Soc. A 2008;366:3045- 3065 ©2008 by The Royal Society

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Two-dimensional manifolds in figure 6b. Chandrajit Bajaj et al. Phil. Trans. R. Soc. A 2008;366:3045- 3065 ©2008 by The Royal Society

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Three-dimensional manifold in figure 6c. Chandrajit Bajaj et al. Phil. Trans. R. Soc. A 2008;366:3045- 3065 ©2008 by The Royal Society

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(a) A single slice of a transmission electron micrograph of a NMJ showing the presynaptic axonal end with many spherical vesicles filled with neurotransmitters (pointed to by arrows). Chandrajit Bajaj et al. Phil. Trans. R. Soc. A 2008;366:3045- 3065 ©2008 by The Royal Society

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