Related papers: Two-dimensional tile displacement can simulate cel…
Aims To propose and analyze a general, dynamic, process-oriented theory of the area of distribution. Methods The area of distribution is modelled by combining (by multiplication) three matrices: one matrix represents movements, another…
Cellular automata are often used to model systems in physics, social sciences, biology that are inherently asynchronous. Over the past 20 years, studies have demonstrated that the behavior of cellular automata drastically changed under…
Recent advances in imaging technology now provide us with 3D images of developing organs. These can be used to extract 3D geometries for simulations of organ development. To solve models on growing domains, the displacement fields between…
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…
Rotary motors play key roles in energy transduction, from macroscale windmills to nanoscale turbines such as ATP synthase in cells. Despite our capabilities to construct engines at many scales, developing functional synthetic turbines at…
Invertible cellular automata are useful as models of physical systems with microscopically revesible dyanmics. There are several well-understood ways to construct them: partitioning rules, second-order rules, and alternating-grid rules. We…
Branched junction molecule assembly of DNA nanostructures, pioneered by Seeman's laboratory in the 1980s, has become increasingly sophisticated, as have the assembly targets. A critical design step is finding minimal sets of branched…
Object manipulation is a fundamental challenge in robotics, where systems must balance trade-offs among manipulation capabilities, system complexity, and throughput. Distributed manipulator systems (DMS) use the coordinated motion of…
We seek to characterize the motility of mouse fibroblasts on 2D substrates. Utilizing automated tracking techniques, we find that cell trajectories are super-diffusive, where displacements scale faster than t^(1/2) in all directions. Two…
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…
In areas as diverse as contemporary art, play structures, climbing equipment, and modular construction toys, we see the presence of building block-like polyhedral complexes, which are generalizations of the pieces in the game Tetris. We…
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 fixed point construction is a method for designing tile sets and cellular automata with highly nontrivial dynamical and computational properties. It produces an infinite hierarchy of systems where each layer simulates the next one. The…
We perform a spatially resolved simulation study of an AND gate based on DNA strand displacement using several lengths of the toehold and the adjacent domains. DNA strands are modelled using a coarse-grained dynamic bonding model {[}C.…
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
The two strands of a DNA molecule with a repetitive sequence can pair into many different basepairing patterns. For perfectly periodic sequences, early bulk experiments of Poerschke indicate the existence of a sliding process, permitting…
The mechanism and driving forces of chromosome segregation in the bacterial cell cycle of E. coli is one of the least understood events in its life cycle. Using principles of entropic repulsion between polymer loops confined in a cylinder,…
Distributed Manipulator Systems, composed of arrays of robotic actuators necessitate dense actuator arrays to effectively manipulate small objects. This paper presents a system composed of modular 3-DoF robotic tiles interconnected by a…
A tiling is a cover of R^d by tiles such as polygons that overlap only on their borders. A patch is a configuration consisting of finitely many tiles that appears in tilings. From a tiling, we can construct a dynamical system which encodes…
We present herein an introduction to implementing 2-color cellular automata on quantum annealing systems, such as the D-Wave quantum computer. We show that implementing nearest-neighbor cellular automata is possible. We present an…