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In-situ parallel workflows couple multiple component applications, such as simulation and analysis, via streaming data transfer. in order to avoid data exchange via shared file systems. Such workflows are challenging to configure for…
The molecular self-assembly of various structures such as micelles and vesicles has been the subject of comprehensive studies. Recently, a new approach to design these structures, the frame-guided assembly, has been developed to progress…
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 present a series of results related to mathematical models of self-assembling tiles and the impacts that three diverse properties have on their dynamics. We expand upon a series of prior results which showed that (1) the abstract Tile…
Dynamic sparsity, where the sparsity patterns are unknown until runtime, poses a significant challenge to deep learning. The state-of-the-art sparsity-aware deep learning solutions are restricted to pre-defined, static sparsity patterns due…
Self-assembly in natural and synthetic molecular systems can create complex aggregates or materials whose properties and functionality rises from their internal structure and molecular arrangement. The key microscopic features that control…
We propose a four-component molecular model of bitumen. The model includes realistic chemical constituents and introduces a coarse-graining level that suppresses the highest frequency modes. Molecular dynamics simulations of the model are…
The rise of simulation environments has enabled learning-based approaches for assembly planning, which is otherwise a labor-intensive and daunting task. Assembling furniture is especially interesting since furniture are intricate and pose…
Curved structures in soft matter and biological systems commonly emerge as a result of self-assembly processes where building blocks aggregate in a controlled manner, giving rise to specific system structure and properties. Learning how to…
Colloids that interact via a short-range attraction serve as the primary building blocks for a broad range of self-assembled materials. However, one of the well-known drawbacks to this strategy is that these building blocks rapidly and…
Self-assembly is one of the prevalent strategies used by living systems to fabricate ensembles of precision nanometer-scale structures and devices. The push for analogous approaches to create synthetic nanomaterials has led to the…
Tile assembly systems in the abstract Tile Assembly Model (aTAM) are computationally universal and capable of building complex shapes, but DNA-based implementations encounter formidable error rates that stifle this theoretical potential.…
In liquid-fueled combustion systems, optimization of the fuel atomization process is critical to reducing fuel consumption and lowering pollutant emissions. Accurate and efficient computational modeling of liquid atomization can open the…
Many forms of programmable matter have been proposed for various tasks. We use an abstract model of self-organizing particle systems for programmable matter which could be used for a variety of applications, including smart paint and…
We show here that a model called directed self-assembly at temperature 1 is unable to do complex computations like the ones of a Turing machine. Since this model can be seen as a generalization of finite automata to 2D languages, a logical…
Working in a three-dimensional variant of Winfree's abstract Tile Assembly Model, we show that, for all $N \in \mathbb{N}$, there is a tile set that uniquely self-assembles into an $N \times N$ square shape at temperature 1 with optimal…
Because of consuming energy to drive their motion, systems of active colloids are intrinsically out of equilibrium. In the past decade, a variety of intriguing dynamic patterns have been observed in systems of active colloids, and they…
In the abstract Tile Assembly Model (aTAM) square tiles self-assemble, autonomously binding via glues on their edges, to form structures. Algorithmic aTAM systems can be designed in which the patterns of tile attachments are forced to…
Designing heterogeneous, self-assembling systems is a central challenge in soft matter and biology. We present a framework that uses gradient-based optimization to invert an analytical yield calculation, tuning systems toward target…
The experimental use of micropatterned quasi-1D substrates has emerged as an useful experimental tool to study the nature of cell-cell interactions and gain insight on collective behaviour of cell colonies. Inspired by these experiments, we…