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The recently introduced Thermodynamic Binding Networks (TBN) model was developed with the purpose of studying self-assembling systems by focusing on their thermodynamically favorable final states, and ignoring the kinetic pathways through…
Cells control fluid flows with a spatial and temporal precision that far exceeds the capabilities of current microfluidic technologies. Cells achieve this superior spatio-temporal control by harnessing dynamic networks of cytoskeleton and…
The applicability of computational and dynamical systems models to organisms is scrutinized, using examples from developmental biology and cognition. Developmental morphogenesis is dependent on the inherent material properties of developing…
The true power of computational research typically can lay in either what it accomplishes or what it enables others to accomplish. In this work, both avenues are simultaneously embraced across several distinct efforts existing at three…
Coordinating functional parts to operate in concert is essential for machinery. In gear trains, meshed gears are compactly interlocked, working together to impose rotation or translation. In photosynthetic systems, a variety of biological…
Winfree's abstract Tile Assembly Model (aTAM) is a model of molecular self-assembly of DNA complexes known as tiles, which float freely in solution and attach one at a time to a growing "seed" assembly based on specific binding sites on…
Structural DNA nanotechnology has advanced to the extent that extremely complex structures can be designed. Much of this advancement has been due to the development of automated DNA design and simulation tools. Typically, the tools (e.g.…
In this paper we define the Dupled abstract Tile Assembly Model (DaTAM), which is a slight extension to the abstract Tile Assembly Model (aTAM) that allows for not only the standard square tiles, but also "duple" tiles which are rectangles…
In this paper, we investigate the abilities of systems of self-assembling tiles which can each pass a constant number of signals to their immediate neighbors to create replicas of input shapes. Namely, we work within the Signal-passing Tile…
Both biological and artificial self-assembly processes can take place by a range of different schemes, from the successive addition of identical building blocks, to hierarchical sequences of intermediates, all the way to the fully…
We need much better understanding of information processing and computation as its primary form. Future progress of new computational devices capable of dealing with problems of big data, internet of things, semantic web, cognitive robotics…
The promise of chemical computation lies in controlling systems incompatible with traditional electronic micro-controllers, with applications in synthetic biology and nano-scale manufacturing. Computation is typically embedded in…
One of the defining features of living systems is their adaptability to changing environmental conditions. This requires organisms to extract temporal and spatial features of their environment, and use that information to compute the…
As computers get faster, researchers -- not hardware or algorithms -- become the bottleneck in scientific discovery. Computational study of colloidal self-assembly is one area that is keenly affected: even after computers generate massive…
Recent advancements in microbiology have motivated the study of the production of nanostructures with applications such as biomedical computing and molecular robotics. One way to construct these structures is to construct branched DNA…
Synaptic plasticity dynamically shapes the connectivity of neural systems and is key to learning processes in the brain. To what extent the mechanisms of plasticity can be exploited to drive a neural network and make it perform some kind of…
The transport of macromolecules, such as DNA, through the cytoskeleton is critical to wide-ranging cellular processes from cytoplasmic streaming to transcription. The rigidity and steric hindrances imparted by the network of filaments…
The vision of Organic Computing addresses challenges that arise in the design of future information systems that are comprised of numerous, heterogeneous, resource-constrained and error-prone components or devices. Here, the notion organic…
Harnessing the rich nonlinear dynamics of highly-deformable materials has the potential to unlock the next generation of functional smart materials and devices. However, unlocking such potential requires effective strategies to spatially…
In the context of self-assembly, where complex structures can be assembled from smaller units, it is desirable to devise strategies towards disassembly and reassembly processes that reuse the constituent parts. A non-reciprocal multifarious…